Amino Acids Structure and Stereochemistry
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Questions and Answers

What happens to the zwitterion form of an amino acid when the pH of the solution increases?

  • It becomes a non-zwitterion form.
  • It stays unchanged.
  • It gains an additional proton.
  • It loses a proton. (correct)

    • Which of the following amino acids does not have a chiral α-carbon atom?

  • Isoleucine
  • Threonine
  • Glycine (correct)
  • Alanine

    • What term is used for compounds that have the same molecular formula but differ in the arrangement of atoms in space?

  • Isomers
  • Chiral compounds
  • Stereoisomers (correct)
  • Enantiomers

    • Which classification describes amino acids with a positive side chain due to the presence of two amino groups and one carboxyl group?

    <p>Polar basic side chain</p> Signup and view all the answers

    In terms of hydropathy, what does a larger hydropathy value indicate?

    <p>Greater tendency to prefer a hydrophobic environment.</p> Signup and view all the answers

    What classification of amino acids yields ketone bodies upon metabolism?

    <p>Ketogenic amino acids</p> Signup and view all the answers

    Which of the following amino acids can exist in mirror image pairs designated as L and D?

    <p>Only chiral amino acids</p> Signup and view all the answers

    What characterizes an amino acid with a polar neutral side chain?

    <p>It contains uncharged hydrocarbon groups.</p> Signup and view all the answers

    Which amino acids are classified as purely ketogenic?

    <p>Leucine and Lysine</p> Signup and view all the answers

    Which of the following amino acids can yield both ketone bodies and glucose?

    <p>Isoleucine</p> Signup and view all the answers

    What characterizes glucogenic amino acids?

    <p>They yield products that enter into glycogen and glucose formation.</p> Signup and view all the answers

    What distinguishes proteins from peptides based on the number of amino acids?

    <p>Peptides contain less than 50 amino acids.</p> Signup and view all the answers

    Which of the following is a rare amino acid found in collagen?

    <p>4-Hydroxyproline</p> Signup and view all the answers

    What is the primary cause of the formation of Lewy bodies in Parkinson's disease?

    <p>Misfolding of the alpha-synuclein protein</p> Signup and view all the answers

    What effect does cooking have on protein structure?

    <p>It denatures proteins making them easier to digest</p> Signup and view all the answers

    Which factor is NOT listed as affecting protein denaturation?

    <p>Radioactivity</p> Signup and view all the answers

    What happens to proteins when a person experiences a high fever (above 104 ºF)?

    <p>Proteins begin to denature and may lead to fatalities</p> Signup and view all the answers

    What is the consequence of protein denaturation?

    <p>Proteins lose their natural shape and cannot function properly</p> Signup and view all the answers

    What is the primary cause of Scurvy?

    <p>Vitamin C deficiency</p> Signup and view all the answers

    What is Osteogenesis Imperfecta primarily associated with?

    <p>Collagen type I mutations</p> Signup and view all the answers

    Which protein is primarily affected in emphysema due to α1-antitrypsin deficiency?

    <p>Elastin</p> Signup and view all the answers

    Which of the following describes the structure of elastin?

    <p>Similar to collagen with 33% glycine</p> Signup and view all the answers

    What is a characteristic feature of glycoproteins?

    <p>Involved in blood group determination</p> Signup and view all the answers

    How do lipoproteins function in the body?

    <p>Facilitate lipid transport in blood</p> Signup and view all the answers

    Which type of protein is casein classified as?

    <p>Phosphoprotein</p> Signup and view all the answers

    What is a primary role of α1-antitrypsin in the lungs?

    <p>Inhibit elastase activity</p> Signup and view all the answers

    What is the primary structural characteristic of collagen?

    <p>It forms a fibrous trimeric structure</p> Signup and view all the answers

    Which type of protein is insulin classified as?

    <p>Globular protein</p> Signup and view all the answers

    Which of the following proteins is classified as an α-globulin?

    <p>Antitrypsin</p> Signup and view all the answers

    What is the main function of γ-globulins?

    <p>Mediating immune responses</p> Signup and view all the answers

    What occurs when collagen is heat-treated or mixed with dilute hydrochloric acid?

    <p>It transforms into gelatin</p> Signup and view all the answers

    What distinguishes scleroproteins from other types of proteins?

    <p>They are structural proteins that are not easily digested</p> Signup and view all the answers

    What percentage of total body proteins do collagens constitute in mammals?

    <p>30%</p> Signup and view all the answers

    What is the key feature of globins (Histones)?

    <p>They combine with DNA and heme</p> Signup and view all the answers

    What is the primary function of amino acids in proteins?

    <p>To determine the structure and function of proteins</p> Signup and view all the answers

    Which statement accurately reflects the synthesis of amino acids?

    <p>Plants can synthesize all essential amino acids.</p> Signup and view all the answers

    What bond links amino acids together in a protein?

    <p>Peptide bond</p> Signup and view all the answers

    How do protein structures differ among organisms?

    <p>Proteins are species-specific and organ-specific.</p> Signup and view all the answers

    How many different amino acids are used to make proteins?

    <p>20</p> Signup and view all the answers

    What property distinguishes polar neutral amino acids from polar acidic amino acids?

    <p>They contain uncharged hydrocarbon groups.</p> Signup and view all the answers

    Which of the following classifications of amino acids is characterized by having a side chain that is hydrophobic?

    <p>Nonpolar</p> Signup and view all the answers

    What is the typical location of hydrophobic side chains in protein structures?

    <p>In the interior of the protein</p> Signup and view all the answers

    Which statement is true regarding amino acids and their chiral nature?

    <p>Nineteen of the twenty common amino acids are chiral.</p> Signup and view all the answers

    What is the function of essential amino acids in the human body?

    <p>They must be obtained from dietary sources.</p> Signup and view all the answers

    Which amino acid classification denotes those that have a net negative charge?

    <p>Polar acidic</p> Signup and view all the answers

    How do L-amino acids differ from D-amino acids in their stereochemistry?

    <p>L-amino acids and D-amino acids are enantiomers.</p> Signup and view all the answers

    What is the major characteristic of polar basic amino acids?

    <p>They contain two amino groups and one carboxyl group.</p> Signup and view all the answers

    What is a characteristic feature of enkephalins among neurotransmitters?

    <p>They help reduce pain and are pentapeptides.</p> Signup and view all the answers

    Which small peptide is considered a powerful antioxidant present in high levels within most cells?

    <p>Glutathione</p> Signup and view all the answers

    Which statement about isometric peptides is accurate?

    <p>They have the same amino acids arranged differently.</p> Signup and view all the answers

    What distinguishes the primary structure of a protein?

    <p>It is defined by the unique sequence of amino acids.</p> Signup and view all the answers

    Which of the following peptides is classified as an artificial sweetener?

    <p>Aspartame</p> Signup and view all the answers

    What role do hydrogen bonds play in protein structure?

    <p>They stabilize tertiary and quaternary structures.</p> Signup and view all the answers

    Which of the following best describes the tertiary structure of a protein?

    <p>The overall three-dimensional shape of a single polypeptide chain.</p> Signup and view all the answers

    Which of the following is an example of a quaternary structure in proteins?

    <p>Hemoglobin, consisting of four polypeptide subunits.</p> Signup and view all the answers

    Which classification describes proteins composed of multiple polypeptide chains?

    <p>Oligomeric proteins.</p> Signup and view all the answers

    What is a key function of amino acid side chains in proteins?

    <p>They influence protein solubility and interactions.</p> Signup and view all the answers

    Which property of amino acids is important in forming ionic bonds within protein structures?

    <p>The charge of the side chain.</p> Signup and view all the answers

    In proteins, what is the primary factor that allows different structures to form?

    <p>The sequence and nature of amino acids.</p> Signup and view all the answers

    Which type of interaction primarily stabilizes the secondary structure of proteins?

    <p>Hydrogen bonds.</p> Signup and view all the answers

    How does denaturation affect protein structure?

    <p>It disrupts secondary and tertiary structures without breaking peptide bonds.</p> Signup and view all the answers

    Which factor is NOT a major determinant of protein structure?

    <p>Presence of zwitterions.</p> Signup and view all the answers

    What type of bonding results in the formation of secondary structures in proteins?

    <p>Hydrogen bonds</p> Signup and view all the answers

    Which of the following best describes the tertiary structure of a protein?

    <p>The overall three-dimensional shape of a single polypeptide chain</p> Signup and view all the answers

    What characterizes mixed ketogenic and glucogenic amino acids?

    <p>They can produce ketone bodies and glucose.</p> Signup and view all the answers

    What characterizes quaternary structure in proteins?

    <p>Interaction between multiple polypeptide chains</p> Signup and view all the answers

    Which amino acids are classified as purely ketogenic?

    <p>Lysine and Leucine</p> Signup and view all the answers

    What defines a dipeptide?

    <p>A chain containing only two amino acids.</p> Signup and view all the answers

    Which classification describes globular proteins?

    <p>Soluble in water and have diverse functions</p> Signup and view all the answers

    What role do amino acid side chains (R groups) play in protein structure?

    <p>They influence the protein's 3D shape and interactions</p> Signup and view all the answers

    What role does hydroxyproline play in protein structure?

    <p>It enhances the stability of collagen.</p> Signup and view all the answers

    How are amino acids linked together in proteins?

    <p>Using peptide bonds.</p> Signup and view all the answers

    In beta-pleated sheets, what kind of hydrogen bonding is primarily involved?

    <p>Both intra-chain and inter-chain hydrogen bonds</p> Signup and view all the answers

    Which secondary structure is characterized by R-groups being located outside the helix?

    <p>Alpha-helix</p> Signup and view all the answers

    What distinguishes proteins from peptides in terms of structure?

    <p>Proteins contain more than 50 amino acids.</p> Signup and view all the answers

    Which of the following describes the role of side chains in amino acids?

    <p>They affect the amino acid's polarity and reactivity.</p> Signup and view all the answers

    What stabilizes the tertiary structure of proteins?

    <p>Hydrophobic interactions, ionic bonds, and hydrogen bonds</p> Signup and view all the answers

    Which type of amino acids produce glucose upon metabolism?

    <p>Glucogenic amino acids</p> Signup and view all the answers

    What is a characteristic of antiparallel beta-pleated sheets?

    <p>More stable due to fully collinear hydrogen bonds</p> Signup and view all the answers

    What is a unique feature of rare amino acids like β-alanine?

    <p>They serve as intermediates in amino acid metabolism.</p> Signup and view all the answers

    What is the significance of the N-terminal end in peptides?

    <p>It is the start point of the peptide structure representation.</p> Signup and view all the answers

    What role do chaperones play in protein structure?

    <p>They prevent proteins from folding incorrectly.</p> Signup and view all the answers

    Which disease is primarily associated with the misfolding of amyloid-beta proteins?

    <p>Alzheimer's disease</p> Signup and view all the answers

    What is the consequence of protein misfolding in cells?

    <p>Degradation of misfolded proteins by quality-control mechanisms.</p> Signup and view all the answers

    Which of the following best describes prions?

    <p>Infectious proteins causing neurodegenerative diseases.</p> Signup and view all the answers

    What is a common feature of amyloid diseases?

    <p>Diminished neuronal plasticity due to protein aggregation.</p> Signup and view all the answers

    What defines the isoelectric point of an amino acid?

    <p>It is the pH at which amino acids become zwitterions.</p> Signup and view all the answers

    Which group does NOT form part of the general structure of all amino acids?

    <p>Sulfhydryl group (SH)</p> Signup and view all the answers

    What percentage of a cell's overall mass do proteins typically account for?

    <p>15%</p> Signup and view all the answers

    Which statement regarding the hierarchy of protein structure is accurate?

    <p>Quaternary structure involves multiple polypeptide chains.</p> Signup and view all the answers

    Which of the following is a consequence of amino acid misfolding?

    <p>Aggregation leading to disease.</p> Signup and view all the answers

    What role does the side chain (R) group have in amino acids?

    <p>It determines the amino acid's charge at physiological pH.</p> Signup and view all the answers

    How many amino acids are primarily used in protein synthesis in living organisms?

    <p>20</p> Signup and view all the answers

    How does the hydropathy index relate to amino acids?

    <p>It reflects the amino acid's hydrophobic or hydrophilic nature.</p> Signup and view all the answers

    What defining characteristic distinguishes isometric peptides from one another?

    <p>They have the same amino acids but in different orders.</p> Signup and view all the answers

    Which of the following peptides is known for its role in pain reduction?

    <p>Met-enkephalin</p> Signup and view all the answers

    What is the primary function of glutathione within the cell?

    <p>As a regulator of oxidation-reduction reactions</p> Signup and view all the answers

    Which of the following statements about enkephalins is accurate?

    <p>They include Met-enkephalin and Leu-enkephalin as best-known examples.</p> Signup and view all the answers

    Which peptide is categorized as a dipeptide and known for its sweetness?

    <p>Aspartame</p> Signup and view all the answers

    What structural feature is essential for distinguishing the primary structure of a protein?

    <p>The specific arrangement of amino acids in the polypeptide chain</p> Signup and view all the answers

    What is the primary structural characteristic of collagen?

    <p>Trimeric structure forming a triplet-helix</p> Signup and view all the answers

    Which biologically significant small peptide functions primarily as an antioxidant?

    <p>Glutathione</p> Signup and view all the answers

    What role do enkephalins serve in the human body?

    <p>They reduce the perception of pain</p> Signup and view all the answers

    Which of the following conditions results primarily from a deficiency in vitamin C?

    <p>Scurvy</p> Signup and view all the answers

    What is the main function of elastin in the body?

    <p>Giving elasticity to various tissues including lungs and blood vessels</p> Signup and view all the answers

    Which of the following pairs identify the best-known enkephalins?

    <p>Tyr–Gly–Gly–Phe–Met and Tyr–Gly–Gly–Phe–Leu</p> Signup and view all the answers

    How is collagen converted into gelatin?

    <p>By heating it with water or dilute hydrochloric acid</p> Signup and view all the answers

    In what manner do the properties of peptides differ?

    <p>Due to variations in their amino acid sequences</p> Signup and view all the answers

    Which type of collagen is the most abundant in mammals?

    <p>Collagen type I</p> Signup and view all the answers

    What type of protein is α-keratin primarily classified as?

    <p>Structural scleroprotein that is water insoluble</p> Signup and view all the answers

    What is one primary function of fibrous proteins?

    <p>Provide structural strength</p> Signup and view all the answers

    Which of the following is true regarding the structure of elastin?

    <p>Consists of 4 polypeptide chains arranged in a tetramer</p> Signup and view all the answers

    Which medical condition is associated with a genetic mutation affecting collagen type I?

    <p>Osteogenesis Imperfecta</p> Signup and view all the answers

    Which type of bond is critical for the stabilization of tertiary protein structure through disulfide bridges?

    <p>Covalent bonds</p> Signup and view all the answers

    What characterizes the quaternary structure of a protein?

    <p>Aggregation of multiple polypeptide subunits</p> Signup and view all the answers

    What role does α1-antitrypsin play in relation to emphysema?

    <p>It inhibits elastin degradation</p> Signup and view all the answers

    Which of the following is an example of a simple protein?

    <p>Albumin</p> Signup and view all the answers

    What percentage of total body proteins do collagens constitute?

    <p>30%</p> Signup and view all the answers

    What is the role of γ-globulins in the body?

    <p>Facilitate immune responses</p> Signup and view all the answers

    What type of interactions holds together the polypeptide subunits in quaternary structure?

    <p>All types of weak interactions</p> Signup and view all the answers

    What distinguishes globular proteins from fibrous proteins?

    <p>Globular proteins are soluble and often function in transport and regulation</p> Signup and view all the answers

    What is a common feature of proteins classified as α-globulins?

    <p>Binding hemoglobin to prevent excretion</p> Signup and view all the answers

    Which characteristic is NOT true about collagen?

    <p>It is a dimeric protein with two chains</p> Signup and view all the answers

    What is a primary feature of proteins known as histones?

    <p>Basic proteins that bind DNA</p> Signup and view all the answers

    Which amino acid classification is characterized by side chains containing uncharged hydrocarbon groups or benzene rings?

    <p>Polar neutral amino acids</p> Signup and view all the answers

    Which statement regarding chiral amino acids is accurate?

    <p>Threonine and Isoleucine each have two chiral centers.</p> Signup and view all the answers

    What role do hydrophobic side chains play in protein folding?

    <p>They tend to avoid exposure to water and remain inside proteins.</p> Signup and view all the answers

    Which classification of amino acids must be obtained from dietary sources?

    <p>Essential amino acids</p> Signup and view all the answers

    Which of the following statements about zwitterions is correct?

    <p>They are formed at the isoelectric point.</p> Signup and view all the answers

    What defines an amino acid as having a polar basic side chain?

    <p>Presence of two amino groups and one carboxyl group.</p> Signup and view all the answers

    Which condition indicates the transition of an amino acid to a zwitterionic form?

    <p>Increase in pH</p> Signup and view all the answers

    Which type of side chain is likely to participate in hydrogen bonding due to having a net negative charge?

    <p>Polar acidic side chain</p> Signup and view all the answers

    What is the primary function of chaperones in protein folding?

    <p>To help proteins achieve their native configuration</p> Signup and view all the answers

    What type of protein aggregates are characteristic of Alzheimer's disease?

    <p>Toxic aggregates formed by amyloid-beta and tau</p> Signup and view all the answers

    What type of enzyme is pepsin classified as?

    <p>Endopeptidase</p> Signup and view all the answers

    Which of the following correctly describes the consequence of misfolded proteins in neurodegenerative diseases?

    <p>They lead to the formation of aggregates that impair cellular functions</p> Signup and view all the answers

    What is a notable characteristic of prions in relation to neurodegenerative diseases?

    <p>They are infectious proteins that cause transmissible spongiform encephalopathies</p> Signup and view all the answers

    What is the primary interaction responsible for the formation of secondary structures in proteins?

    <p>Hydrogen bonds</p> Signup and view all the answers

    Which type of secondary structure is characterized by intramolecular hydrogen bonding?

    <p>Alpha-helices</p> Signup and view all the answers

    Which of the following best describes the role of excess amino acids in the body?

    <p>They are converted into different forms of energy or stored as fat</p> Signup and view all the answers

    In which way do antiparallel beta-pleated sheets differ from parallel beta-pleated sheets?

    <p>The chains run in opposite directions.</p> Signup and view all the answers

    What does the tertiary structure of a protein primarily depend on?

    <p>Hydrophobic interactions between side chains</p> Signup and view all the answers

    Which amino acid does trypsin specifically cleave at its carboxyl end?

    <p>Arginine</p> Signup and view all the answers

    What structure does an alpha-helix resemble?

    <p>A coiled spring</p> Signup and view all the answers

    What indicates that a protein is more stable in beta-pleated sheet conformation?

    <p>Fully collinear hydrogen bonds</p> Signup and view all the answers

    Which statement is true regarding endopeptidases?

    <p>They cleave peptide bonds within the protein chain.</p> Signup and view all the answers

    What role do hydrogen bonds play in beta-pleated sheets?

    <p>They hold adjacent strands together.</p> Signup and view all the answers

    What distinguishes fibrous proteins from globular proteins in terms of solubility?

    <p>Fibrous proteins provide structural strength, while globular proteins are involved in transport.</p> Signup and view all the answers

    Which type of bond is primarily responsible for the stabilization of protein tertiary structure?

    <p>Disulfide bridges</p> Signup and view all the answers

    What is the structural characteristic of collagen in terms of its assembly?

    <p>It consists of a triad of polypeptide chains that twist into a supercoiled formation.</p> Signup and view all the answers

    Which of the following best represents the quaternary structure of hemoglobin?

    <p>It consists of four polypeptide chains, forming a tetrameric structure.</p> Signup and view all the answers

    Which type of globulin is specifically known for transporting iron in the blood?

    <p>β-globulin</p> Signup and view all the answers

    What type of proteins are histones predominantly characterized as?

    <p>Basic proteins that are rich in histidine.</p> Signup and view all the answers

    Which of the following statements accurately describes simple proteins?

    <p>Simple proteins, upon hydrolysis, yield only amino acids.</p> Signup and view all the answers

    What role does α1-antitrypsin play in the human body?

    <p>It inhibits proteases to protect tissues from damage.</p> Signup and view all the answers

    In which context are γ-globulins categorized, and what is their primary function?

    <p>They are involved in immunity and act as antibodies.</p> Signup and view all the answers

    Which classification can be used to describe proteins that are extracted from blood and are of high biological value?

    <p>Globulins, including albumin and transferrin.</p> Signup and view all the answers

    What type of conjugated protein is casein classified as?

    <p>Phosphoprotein</p> Signup and view all the answers

    Which function is NOT associated with lipoproteins?

    <p>Provide structural support to collagen</p> Signup and view all the answers

    Which component is typically found in metalloproteins?

    <p>Metals like iron or copper</p> Signup and view all the answers

    What is the primary role of elastase in the lung?

    <p>To degrade elastin</p> Signup and view all the answers

    What term describes proteins conjugated with nucleic acids?

    <p>Nucleoproteins</p> Signup and view all the answers

    Which enzyme is responsible for initiating protein digestion in the stomach?

    <p>Pepsin</p> Signup and view all the answers

    What type of structure do fibrous proteins primarily provide?

    <p>Structural support</p> Signup and view all the answers

    Which of the following is an example of a glycoprotein?

    <p>Mucin</p> Signup and view all the answers

    What is a characteristic feature of lipoproteins?

    <p>Facilitate lipid transport in blood</p> Signup and view all the answers

    Which conjugated protein is specifically associated with iron storage?

    <p>Ferritin</p> Signup and view all the answers

    What is the primary function of proteins in biological systems?

    <p>To act as structural components and enzymes</p> Signup and view all the answers

    Which group of the amino acid is attached to the α-carbon?

    <p>Amino, Carboxyl, Hydrogen, and R group</p> Signup and view all the answers

    What is true about zwitterions in amino acids?

    <p>They are molecules that have no net charge</p> Signup and view all the answers

    What percentage of a cell's overall mass do proteins typically account for?

    <p>15%</p> Signup and view all the answers

    Why is the modification of amino acids significant?

    <p>It changes the functional properties of proteins</p> Signup and view all the answers

    Which term describes the lowest pH at which an amino acid exists as a zwitterion?

    <p>Isoelectric point</p> Signup and view all the answers

    What makes proteins distinct from peptides?

    <p>Proteins are usually larger and have more complex structures</p> Signup and view all the answers

    Which structural feature do all amino acids share?

    <p>Central carbon atom attached to four different groups</p> Signup and view all the answers

    What role do chaperones play in protein folding?

    <p>They assist proteins in achieving their native configuration.</p> Signup and view all the answers

    What is a consequence of protein misfolding in neurodegenerative diseases?

    <p>Formation of toxic aggregates.</p> Signup and view all the answers

    Which of the following diseases is associated with the misfolding of the tau protein?

    <p>Alzheimer's disease.</p> Signup and view all the answers

    What happens to misfolded proteins when they are detected by quality-control mechanisms in the cell?

    <p>They are marked for degradation.</p> Signup and view all the answers

    What is the primary function of misfolded proteins in the context of prion diseases?

    <p>They lead to transmissible spongiform encephalopathies.</p> Signup and view all the answers

    Which of the following is a primary function of elastin in the body?

    <p>Allows tissues to return to their original shape after stretching</p> Signup and view all the answers

    What is the main consequence of collagen deficiency in the human body?

    <p>Abnormal bone development and bleeding gums</p> Signup and view all the answers

    What characteristic mainly distinguishes collagen type I from other types of collagen?

    <p>It constitutes about 90% of cell collagens</p> Signup and view all the answers

    Which of the following statements about keratin is true?

    <p>It contains a high proportion of hydrophobic amino acids</p> Signup and view all the answers

    What is the main structural feature of collagens?

    <p>Trimeric structure with three helical chains</p> Signup and view all the answers

    What happens to collagen when it is heated with water or dilute HCl?

    <p>It transforms into gelatin</p> Signup and view all the answers

    What disease is primarily associated with vitamin C deficiency and its impact on collagen synthesis?

    <p>Scurvy</p> Signup and view all the answers

    Which amino acid plays a critical role in the conversion process necessary for collagen synthesis?

    <p>Proline</p> Signup and view all the answers

    What is a significant characteristic of α-keratin in relation to its solubility?

    <p>It is a water-insoluble protein</p> Signup and view all the answers

    What role does α1-antitrypsin play in relation to elastin in the lungs?

    <p>Inhibits elastin degradation</p> Signup and view all the answers

    What is the primary role of elastase in the lungs?

    <p>To cause destruction of lung elastin</p> Signup and view all the answers

    Which type of conjugated protein is primarily associated with transporting lipids in the blood?

    <p>Lipoproteins</p> Signup and view all the answers

    What specific group do proteins classified as glycoproteins contain?

    <p>Carbohydrates</p> Signup and view all the answers

    Which of the following examples represents a nucleoprotein?

    <p>Histones</p> Signup and view all the answers

    What type of proteins are categorized as metalloproteins?

    <p>Proteins that contain metal ions</p> Signup and view all the answers

    What initiates the process of protein digestion in the stomach?

    <p>Pepsin</p> Signup and view all the answers

    Which of the following correctly describes a function of lipoproteins?

    <p>Facilitate lipid transport</p> Signup and view all the answers

    What is the structural characteristic of globular proteins?

    <p>They are spherical or roughly spherical</p> Signup and view all the answers

    Which substance is primarily stored in ferritin?

    <p>Iron</p> Signup and view all the answers

    Which of the following proteins is linked to the respiratory system and is affected in conditions like emphysema?

    <p>Elastase</p> Signup and view all the answers

    Which amino acids are classified as purely ketogenic?

    <p>Lysine and Leucine</p> Signup and view all the answers

    Which of the following describes the classification of mixed ketogenic and glucogenic amino acids?

    <p>Amino acids that can generate both ketone bodies and glucose</p> Signup and view all the answers

    What defines a peptide bond between amino acids?

    <p>It links the carboxyl group of one amino acid to the amino group of another.</p> Signup and view all the answers

    Which statement correctly defines the length of peptides and proteins?

    <p>Peptides are chains with fewer than 50 amino acids.</p> Signup and view all the answers

    Which of the following amino acids is identified as a rare amino acid in collagen?

    <p>4-Hydroxyproline</p> Signup and view all the answers

    What occurs when a chain of amino acids exceeds 20 in number?

    <p>It becomes a polypeptide.</p> Signup and view all the answers

    Which measurement method is not typically used for classifying amino acids into their metabolic categories?

    <p>Analyzing the type of bond in the amino acid</p> Signup and view all the answers

    What is a common metabolic role of glucogenic amino acids?

    <p>Yield glucose through catabolism</p> Signup and view all the answers

    Which of the following correctly describes the structural representation of peptides?

    <p>Represented beginning with the N-terminal end</p> Signup and view all the answers

    What characterizes β-alanine in the context of amino acids?

    <p>A component of pantothenic acid (vitamin B5)</p> Signup and view all the answers

    What is the function of lipoproteins in the human body?

    <p>They help transport lipids in the blood.</p> Signup and view all the answers

    Which of the following is an example of a glycoprotein?

    <p>Mucin</p> Signup and view all the answers

    What type of protein is classified as metalloproteins?

    <p>Proteins that hold metal ions.</p> Signup and view all the answers

    What initiates the digestion of proteins in the stomach?

    <p>Pepsin, activated by stomach acid.</p> Signup and view all the answers

    Which type of conjugated protein is primarily found in chromosomes?

    <p>Nucleoproteins.</p> Signup and view all the answers

    What is the primary structural unit of proteins?

    <p>Amino acids</p> Signup and view all the answers

    Which groups are attached to the α-carbon of an amino acid?

    <p>Amine group, COOH group, hydrogen atom, and side chain</p> Signup and view all the answers

    What is a zwitterion?

    <p>A dipolar ion in a neutral charge state</p> Signup and view all the answers

    Why are proteins considered the most abundant molecules in cells after water?

    <p>They account for about 15% of a cell’s mass</p> Signup and view all the answers

    What determines the isoelectric point of an amino acid?

    <p>The pH at which the amino acid has no net charge</p> Signup and view all the answers

    What is the relationship between proteins and amino acids?

    <p>Proteins are polymers made up of amino acids linked by peptide bonds</p> Signup and view all the answers

    How many amino acids naturally occur in living organisms?

    <p>700</p> Signup and view all the answers

    What is the importance of amino acid modification?

    <p>It can affect protein function and stability</p> Signup and view all the answers

    Which peptide is known for its role in pain reduction and is produced by the brain?

    <p>Met-enkephalin</p> Signup and view all the answers

    What is the primary structure of a protein based on?

    <p>Unique sequence of amino acids</p> Signup and view all the answers

    Which of the following small peptides is recognized as an antioxidant found in high levels in cells?

    <p>Glutathione</p> Signup and view all the answers

    What differentiates isometric peptides from each other?

    <p>Order of amino acids</p> Signup and view all the answers

    Which of the following best describes the composition of aspartame?

    <p>Dipeptide made from Aspartic acid and Phenylalanine</p> Signup and view all the answers

    Which of the following small peptides is classified as a neurotransmitter?

    <p>Met-enkephalin</p> Signup and view all the answers

    What is the amino acid sequence of the best-known enkephalin, Met-enkephalin?

    <p>Tyr–Gly–Gly–Phe–Met</p> Signup and view all the answers

    How does the structure of Lysozyme differ from small peptides?

    <p>It consists of a polypeptide chain of 129 amino acids.</p> Signup and view all the answers

    Which of the following is a function of fibrous proteins?

    <p>Mechanical strength</p> Signup and view all the answers

    What type of protein is hemoglobin classified as?

    <p>Globular protein</p> Signup and view all the answers

    Which statement regarding glutathione is true?

    <p>It regulates oxidation–reduction reactions.</p> Signup and view all the answers

    Which of the following interactions contributes to the tertiary structure of proteins?

    <p>Hydrophobic interactions</p> Signup and view all the answers

    What is the result of the aggregation of two or more polypeptide subunits in proteins?

    <p>Quaternary structure</p> Signup and view all the answers

    Which of the following best describes simple proteins?

    <p>Proteins that yield only amino acids upon hydrolysis</p> Signup and view all the answers

    What role does α1-antitrypsin serve in the human body?

    <p>Preventing lung tissue damage</p> Signup and view all the answers

    Which of the following is a type of globulin responsible for immunity?

    <p>Immunoglobulins</p> Signup and view all the answers

    What type of interactions stabilize the quaternary structure of proteins?

    <p>Non-covalent interactions</p> Signup and view all the answers

    Why are globins, such as hemoglobin, considered basic proteins?

    <p>They have a high histidine content</p> Signup and view all the answers

    What is the main function of transferrin in the body?

    <p>Transporting iron</p> Signup and view all the answers

    What is the defining characteristic of a peptide bond?

    <p>It links amino acids through a secondary amide bond.</p> Signup and view all the answers

    Which of the following pairs of amino acids are classified as purely ketogenic?

    <p>Lysine and Leucine</p> Signup and view all the answers

    How are glucogenic amino acids characterized?

    <p>They yield glucose through catabolism.</p> Signup and view all the answers

    Which statement correctly describes rare amino acids?

    <p>They serve specific roles in select proteins.</p> Signup and view all the answers

    What distinguishes proteins from peptides based on their amino acid chain length?

    <p>Peptides have less than 50 amino acids.</p> Signup and view all the answers

    Which amino acids fall into the category of mixed ketogenic and glucogenic amino acids?

    <p>Isoleucine and Tyrosine</p> Signup and view all the answers

    What characterizes the structure of peptides in nomenclature?

    <p>They are conventionally represented starting with the N-terminal end.</p> Signup and view all the answers

    Which of the following amino acids is NOT considered nonessential?

    <p>Leucine</p> Signup and view all the answers

    What is a primary role of β-alanine in the body?

    <p>It's a precursor to coenzyme A.</p> Signup and view all the answers

    What role do chaperones play in protein folding?

    <p>They prevent proteins from folding incorrectly.</p> Signup and view all the answers

    Which protein misfolding condition is associated with the development of Lewy bodies?

    <p>Parkinson's disease</p> Signup and view all the answers

    What is the consequence of protein misfolding in neurodegenerative diseases?

    <p>Formation of toxic aggregates in neural tissues.</p> Signup and view all the answers

    What type of disease is caused by prions, which are infectious proteins?

    <p>Transmissible spongiform encephalopathies</p> Signup and view all the answers

    How does the body utilize excess amino acids?

    <p>They are transformed into fatty acids for storage.</p> Signup and view all the answers

    What is the primary structural unit of proteins?

    <p>Amino acids</p> Signup and view all the answers

    What characterizes the zwitterion form of amino acids?

    <p>They have no net charge.</p> Signup and view all the answers

    Which of the following groups is NOT attached to the α-carbon of an amino acid?

    <p>Peptide group</p> Signup and view all the answers

    What is the significance of the isoelectric point in amino acids?

    <p>It is the pH where the amino acid has no net charge.</p> Signup and view all the answers

    How many amino acids are predominantly incorporated into proteins?

    <p>20</p> Signup and view all the answers

    Which statement about proteins' abundance in cells is accurate?

    <p>They constitute approximately 15% of a cell's overall mass.</p> Signup and view all the answers

    Which group is NOT correctly associated with the four groups attached to an amino acid's α-carbon?

    <p>Sulfonyl group</p> Signup and view all the answers

    What role do proteins serve in biological systems?

    <p>They perform a variety of functions including catalysis and transport.</p> Signup and view all the answers

    What defines fibrous proteins in terms of their properties and functions?

    <p>They are insoluble and provide mechanical strength.</p> Signup and view all the answers

    Which types of interactions are responsible for determining the tertiary structure of proteins?

    <p>Interactions among R groups and the polypeptide backbone.</p> Signup and view all the answers

    What characterizes the quaternary structure of proteins?

    <p>Association of multiple polypeptide subunits through non-covalent interactions.</p> Signup and view all the answers

    Which of the following is an example of a simple protein?

    <p>Albumin</p> Signup and view all the answers

    What role do α2 globulins, like haptoglobin, serve in the body?

    <p>Bind hemoglobin to prevent its excretion by the kidneys.</p> Signup and view all the answers

    What defines the composition of globins (Histones)?

    <p>Basic proteins rich in histidine.</p> Signup and view all the answers

    Which term describes a fibrous protein like collagen in terms of its structural arrangement?

    <p>Trimeric structure.</p> Signup and view all the answers

    What is a primary function of immunoglobulins (γ-globulins)?

    <p>Facilitate immune responses.</p> Signup and view all the answers

    What is the primary role of transport proteins like transferrin in the body?

    <p>Transporting iron in the bloodstream.</p> Signup and view all the answers

    Which feature distinguishes globular proteins from fibrous proteins?

    <p>Globular proteins are typically enzymes and regulatory molecules.</p> Signup and view all the answers

    What effect does lowering the pH of a solution have on the structure of a zwitterion?

    <p>It causes the zwitterion to gain a proton.</p> Signup and view all the answers

    Which amino acid classification is characterized by a side chain that contains uncharged hydrocarbon groups or benzene rings?

    <p>Nonpolar</p> Signup and view all the answers

    How many possible stereoisomers can threonine have due to its two chiral carbons?

    <p>4</p> Signup and view all the answers

    What is the primary reason for the hydrophobicity of certain amino acid side chains?

    <p>They possess long hydrocarbon chains.</p> Signup and view all the answers

    Which characteristic defines essential amino acids?

    <p>They must be obtained from dietary sources.</p> Signup and view all the answers

    Which of the following best describes enantiomers of amino acids?

    <p>They are designated as L and D forms.</p> Signup and view all the answers

    What role do hydrophilic residues play in protein structure?

    <p>They are typically found on the protein surface.</p> Signup and view all the answers

    What type of amino acids primarily present in proteins ensures the chirality of their structure?

    <p>L-amino acids</p> Signup and view all the answers

    What characteristic is shared by polar basic amino acids?

    <p>They have two amino groups and one carboxyl group.</p> Signup and view all the answers

    Which classification of amino acids describes those that have a side chain with a net positive charge?

    <p>Polar basic</p> Signup and view all the answers

    What defines isometric peptides?

    <p>Peptides that contain the same amino acids but arranged in different sequences</p> Signup and view all the answers

    Which peptide is known as an antioxidant that protects cellular contents?

    <p>Glutathione</p> Signup and view all the answers

    What is the primary function of enkephalins in the brain?

    <p>To help reduce pain</p> Signup and view all the answers

    Which of the following peptides is classified as a dipeptide and is known for its sweetness?

    <p>Aspartame</p> Signup and view all the answers

    Which amino acid sequence accurately represents Met-enkephalin?

    <p>Tyr–Gly–Gly–Phe–Met</p> Signup and view all the answers

    What is considered the primary structure of a protein?

    <p>The unique sequence of amino acids in a polypeptide chain</p> Signup and view all the answers

    What type of reaction is glutathione important in regulating within cells?

    <p>Oxidation-reduction reactions</p> Signup and view all the answers

    Which of the following statements describes the role of lysozyme?

    <p>It attacks bacteria and is composed of 129 amino acids</p> Signup and view all the answers

    Which small peptide is produced by the brain and aids in reducing pain?

    <p>Enkephalins</p> Signup and view all the answers

    Which sequence identifies Leu-enkephalin?

    <p>Tyr–Gly–Gly–Phe–Leu</p> Signup and view all the answers

    Which of the following accurately describes a characteristic of polar neutral amino acids?

    <p>They can participate in hydrogen bonding.</p> Signup and view all the answers

    What is the primary role of essential amino acids in the human body?

    <p>They must be obtained from dietary sources.</p> Signup and view all the answers

    Which statement correctly distinguishes between L- and D-amino acids?

    <p>L-amino acids are exclusively found in proteins.</p> Signup and view all the answers

    What is a defining feature of stereoisomers in amino acids?

    <p>They can have different biological activities.</p> Signup and view all the answers

    Which group of amino acids is characterized by having side chains that do not readily donate or accept protons?

    <p>Polar neutral amino acids</p> Signup and view all the answers

    How do hydrophobic side chains typically influence protein structure?

    <p>They contribute to protein folding by residing in the hydrophobic interior.</p> Signup and view all the answers

    Which type of amino acid classification includes those with a net negative charge due to their two carboxyl groups?

    <p>Polar acidic</p> Signup and view all the answers

    What impact does increasing the pH have on the zwitterion form of amino acids?

    <p>It results in the loss of a proton, leading to a net negative charge.</p> Signup and view all the answers

    What is the primary function of enkephalins in the brain?

    <p>Reducing pain</p> Signup and view all the answers

    Which peptide is known for its high antioxidant properties and is found in most cells?

    <p>Glutathione</p> Signup and view all the answers

    What are isometric peptides?

    <p>Peptides containing the same amino acids in different orders</p> Signup and view all the answers

    What chemical structure characterizes the primary structure of proteins?

    <p>The unique sequence of amino acids</p> Signup and view all the answers

    What is the general sweetness comparison of aspartame to sucrose?

    <p>180 times sweeter</p> Signup and view all the answers

    Which of the following best describes the composition of Met-enkephalin?

    <p>Tyr–Gly–Gly–Phe–Met</p> Signup and view all the answers

    Which dipeptide is used as an artificial sweetener and sold under trade names Equal and Nutrasweet?

    <p>Aspartame</p> Signup and view all the answers

    What role does glutathione play in cellular processes?

    <p>Regulates oxidation-reduction reactions</p> Signup and view all the answers

    Which of the following is NOT considered a biochemical function of small peptides?

    <p>Structural support</p> Signup and view all the answers

    What is the primary function of metalloproteins in biological systems?

    <p>They conjugate with metals to perform specific enzymatic functions.</p> Signup and view all the answers

    Which type of protein is specifically conjugated with carbohydrates?

    <p>Glycoproteins</p> Signup and view all the answers

    In protein digestion, which enzyme is responsible for initiating the breakdown of proteins in the stomach?

    <p>Pepsin</p> Signup and view all the answers

    Which of the following best describes the structural classification of collagen?

    <p>Fibrous protein</p> Signup and view all the answers

    Which type of conjugated protein aids in the transport of lipids in the bloodstream?

    <p>Lipoproteins</p> Signup and view all the answers

    Which statement accurately describes ketogenic amino acids?

    <p>They can be directly metabolized to acetyl CoA.</p> Signup and view all the answers

    What type of amino acid yields products that enter both glycogen and glucose formation?

    <p>Mixed ketogenic and glucogenic amino acids</p> Signup and view all the answers

    Which amino acid is not classified as purely ketogenic?

    <p>Isoleucine</p> Signup and view all the answers

    What distinguishes a peptide from a protein?

    <p>Peptides consist of fewer than 50 amino acids.</p> Signup and view all the answers

    What describes the formation of a peptide bond?

    <p>Condensation of an amino group with a carboxyl group.</p> Signup and view all the answers

    Which of the following is not a rare amino acid found in collagen?

    <p>β-alanine</p> Signup and view all the answers

    Which of the following classifications includes both ketone bodies and glucose producers?

    <p>Mixed ketogenic and glucogenic amino acids</p> Signup and view all the answers

    Which term refers to a linkage between two amino acids?

    <p>Peptide bond</p> Signup and view all the answers

    In which way are amino acids typically represented within a peptide?

    <p>Starting with the amino acid whose amino group is free.</p> Signup and view all the answers

    What is the primary metabolic product derived from glucogenic amino acids?

    <p>Glucose</p> Signup and view all the answers

    What structural characteristic distinguishes collagen from elastin?

    <p>Collagen contains a high amount of hydroxyproline, while elastin has low hydroxyproline content.</p> Signup and view all the answers

    Which of the following diseases is directly related to collagen synthesis abnormalities?

    <p>Both B and C</p> Signup and view all the answers

    What is the primary function of elastin within the body?

    <p>To enable the stretching and recoiling of tissues.</p> Signup and view all the answers

    How is collagen converted into a soluble form for dietary use?

    <p>By heating with water or dilute hydrochloric acid.</p> Signup and view all the answers

    What defines the composition of α-keratin as a structural protein?

    <p>Rich in cysteine and hydrophobic amino acids, leading to water insolubility.</p> Signup and view all the answers

    Which type of collagen is the most prevalent in mammalian tissues?

    <p>Collagen type I</p> Signup and view all the answers

    What is a major determinant of the physical properties of elastin?

    <p>The percentage of glycine and other amino acids in its structure.</p> Signup and view all the answers

    Which factor is crucial for the synthesis of collagen from proline?

    <p>Vitamin C.</p> Signup and view all the answers

    What aspect of collagen significantly impacts its solubility?

    <p>The degree of hydrogen bonding between chains.</p> Signup and view all the answers

    What role does α1-antitrypsin play in the context of lung health?

    <p>It inhibits elastase to protect lung tissue.</p> Signup and view all the answers

    Which of the following is a characteristic of glucogenic amino acids?

    <p>They are involved in glucose formation through catabolism.</p> Signup and view all the answers

    What distinguishes dipeptides from oligopeptides?

    <p>Dipeptides consist of exactly 2 amino acids.</p> Signup and view all the answers

    What contributes to the formation of a peptide bond?

    <p>Condensation of the α-carboxyl of one amino acid and the α-amino of another.</p> Signup and view all the answers

    Which amino acids are classified as purely ketogenic?

    <p>Leucine and Lysine.</p> Signup and view all the answers

    Which of the following is true regarding 4-Hydroxyproline?

    <p>It is primarily found in collagen.</p> Signup and view all the answers

    What defines a peptide bond in terms of its structure?

    <p>It is a covalent bond formed through losing water.</p> Signup and view all the answers

    Which classification of amino acids is capable of yielding both glucose and ketone bodies?

    <p>Mixed ketogenic and glucogenic amino acids.</p> Signup and view all the answers

    What is the maximum number of amino acids that distinguishes a protein from peptides?

    <p>More than 50 amino acids.</p> Signup and view all the answers

    What role do chaperones play in protein folding?

    <p>They help proteins achieve their native configuration.</p> Signup and view all the answers

    Which protein misfolding condition is characterized by the accumulation of amyloid-beta and tau proteins in the brain?

    <p>Alzheimer's disease</p> Signup and view all the answers

    Which of the following statements about prions is accurate?

    <p>They are infectious proteins that cause neurodegenerative diseases.</p> Signup and view all the answers

    What is a consequence of protein misfolding in the context of neurodegenerative diseases?

    <p>Formation of toxic aggregates like Lewy bodies</p> Signup and view all the answers

    What effect do quality-control mechanisms in cells have on misfolded proteins?

    <p>Tag them for degradation in the cytoplasm</p> Signup and view all the answers

    What is the primary role of exopeptidases during enzymatic hydrolysis?

    <p>Cleaving external peptide bonds</p> Signup and view all the answers

    Which statement correctly describes the alpha-helix structure of proteins?

    <p>The structure resembles a tightly coiled spring.</p> Signup and view all the answers

    Which enzyme is specifically known for cleaving peptide bonds following the amino acids Arg and Lys?

    <p>Trypsin</p> Signup and view all the answers

    What feature distinguishes anti-parallel beta-pleated sheets from parallel beta-pleated sheets?

    <p>Chains run in opposite directions.</p> Signup and view all the answers

    What characterizes the tertiary structure of a protein?

    <p>Overall three-dimensional shape from R group interactions</p> Signup and view all the answers

    Which of the following best describes the cleaving action of chymotrypsin?

    <p>It cleaves near aromatic amino acids like Phe, Tyr, and Trp.</p> Signup and view all the answers

    What type of bonding is primarily responsible for maintaining the secondary structure of proteins?

    <p>Hydrogen bonding</p> Signup and view all the answers

    Which statement is true regarding the space within an alpha-helix structure?

    <p>It does not allow solvent molecules to enter.</p> Signup and view all the answers

    What is true about isometric peptides?

    <p>They contain the same amino acids arranged in different sequences.</p> Signup and view all the answers

    Which of the following peptides is known for its role in pain reduction?

    <p>Leu-enkephalin</p> Signup and view all the answers

    What distinguishes exopeptidases from endopeptidases?

    <p>Exopeptidases cleave peptide bonds at the ends of chains.</p> Signup and view all the answers

    What distinguishes glutathione from other small peptides?

    <p>It is a tripeptide and acts as an antioxidant.</p> Signup and view all the answers

    What is the primary structural feature of enkephalins?

    <p>They are pentapeptides with aromatic amino acids.</p> Signup and view all the answers

    Which peptide is considered an artificial sweetener?

    <p>Aspartame</p> Signup and view all the answers

    Which sequence represents the primary structure of Met-enkephalin?

    <p>Tyr–Gly–Gly–Phe–Met</p> Signup and view all the answers

    What role does glutathione serve in cells?

    <p>It regulates oxidation-reduction reactions.</p> Signup and view all the answers

    How does the primary structure of a protein influence its properties?

    <p>It determines the function and stability through amino acid sequence.</p> Signup and view all the answers

    Which of the following statements is true regarding small peptides?

    <p>They can be produced by the body and have various functions.</p> Signup and view all the answers

    What characteristic is unique to dipeptides compared to tripeptides and larger peptides?

    <p>Dipeptides consist of only two amino acids linked together.</p> Signup and view all the answers

    What is a primary role of fibrous proteins in biological systems?

    <p>Mechanical strength and structural support</p> Signup and view all the answers

    Which type of interaction is primarily responsible for the stabilization of tertiary protein structure?

    <p>Disulfide bridges between cysteine residues</p> Signup and view all the answers

    Which protein is specifically known for having a quaternary structure composed of four polypeptide chains?

    <p>Hemoglobin</p> Signup and view all the answers

    What type of protein classification do immunoglobulins belong to?

    <p>Globins</p> Signup and view all the answers

    How do α-globulins primarily function in the body?

    <p>Binding hemoglobin and preventing its excretion</p> Signup and view all the answers

    What distinguishes collagen from other types of proteins?

    <p>It forms a trimeric structure with mechanical strength</p> Signup and view all the answers

    Which classification describes proteins that yield only amino acids upon hydrolysis?

    <p>Simple proteins</p> Signup and view all the answers

    What is the main feature distinguishing globins from other protein types?

    <p>Basic proteins rich in histidine amino acid</p> Signup and view all the answers

    Which of the following proteins is primarily responsible for transporting iron in the body?

    <p>Transferrin</p> Signup and view all the answers

    What role do hydrogen bonds play in protein structure?

    <p>They facilitate the folding of proteins into specific shapes</p> Signup and view all the answers

    Study Notes

    Amino Acid Structure

    • The structure of an amino acid depends on the pH
    • Lower pH leads to zwitterion picking up a proton
    • Higher pH leads to zwitterion losing a proton

    Chirality of Amino Acids

    • 19 out of 20 common amino acids have a chiral α-carbon atom.
    • Glycine does not have a chiral carbon atom.
    • Chiral carbons have four different groups attached.
    • Threonine and isoleucine have two chiral carbons each, leading to four possible stereoisomers.
    • Stereoisomers are compounds with the same molecular formula but different spatial arrangements of atoms.

    Stereochemistry of Amino Acids

    • Mirror image pairs of amino acids are designated as L (levo) and D (dextro) and are called enantiomers.
    • Proteins are built from L-amino acids.
    • Some D-amino acids occur in nature.

    Classifications of Amino Acids

    • Side Chain:

      • Non-polar: Contains uncharged hydrocarbon groups or benzene rings. Hydrophobic and insoluble in water.
      • Polar neutral: Contains side chains with positive or negative charge. Hydrophilic and soluble in water.
      • Polar acidic: Contains one amino group and two carboxyl groups. Side chain is negative, referred to as "-ic acid."
      • Polar basic: Contains two amino groups and one carboxyl group. Side chain is positive.

    • Hydrophobicity:

      • Hydropathy: the relative hydrophobicity of each amino acid.
      • Higher hydropathy indicates a greater tendency to prefer hydrophobic environments.
      • Hydropathy affects protein folding, with hydrophobic residues tending to be in the interior and hydrophilic residues on the surface.

    • Nutrition: Essential amino acids cannot be synthesized by the body and must be obtained from the diet. Non-essential amino acids can be synthesized by the body.

    • Metabolic Products:

      • Ketogenic: Metabolized into ketone bodies. Lysine and Leucine are the only pure ketogenic amino acids.
      • Glucogenic: Metabolized into glucose.
      • Mixed Ketogenic and Glucogenic: Can produce both ketone bodies and glucose.

    Rare Amino Acids

    • 4-Hydroxyproline: Found in plant cell wall proteins (extensins) and collagen.
    • 4-Hydroxylysine: Found in collagen.
    • β-alanine: Component of pantothenic acid (vitamin B5).
    • Homocysteine: Intermediate in amino acid metabolism.
    • Homoserine: Intermediate in amino acid metabolism.

    Protein Structure

    • Peptides: Chains containing less than 50 amino acids.
    • Proteins: Chains containing more than 50 amino acids.

    Classification of Proteins

    • Simple Proteins: Yield only amino acids upon hydrolysis.

      • Albumin and globulins: Present in egg, milk, and blood.
      • Globins (Histones): Basic proteins rich in histidine. Found combined with DNA and heme (hemoglobin).
      • Gliadines: Proteins found in cereals.
      • Scleroproteins: Structural proteins, not digested.
        • α-Keratin: Found in hair, nails, teeth enamel, and skin. α-helical polypeptide chain, rich in cysteine.
        • Collagens: Found in connective tissues. Most common type is collagen I. Composed of three helical polypeptide chains (trimeric).
        • Elastin: Found in blood vessels, lungs, ligaments, and skin. Composed of four polypeptide chains (tetrameric).

    • Conjugated Proteins: Yield protein and non-protein components upon hydrolysis.

      • Phosphoproteins: Contain phosphate groups attached to serine or threonine. (e.g. casein in milk, vitellin in yolk)
      • Lipoproteins: Contain lipids. Assist in lipid transport and cell membrane structure.
      • Glycoproteins: Contain carbohydrates. Found in mucin, some hormones, and cell membranes.
      • Nucleoproteins: Contain nucleic acids. (e.g. histones)

    Protein Denaturation

    • Partial or complete disruption of protein's tertiary structure.
    • Cooking denatures proteins, making them easier to digest and killing microorganisms.
    • Coagulation: Precipitation (denaturation) of proteins, such as in egg white.

    Factors Affecting Protein Denaturation

    • Heat
    • pH
    • Organic solvents
    • Chaotropic agents
    • Heavy metals
    • Scurvy: Deficiency of vitamin C.
    • Osteogenesis Imperfecta (OI): Inherited disease due to genetic deficiency or mutation in collagen type I synthesis.
    • Emphysema: Chronic obstructive lung disease caused by elastase (an enzyme that breaks down elastin) destruction of lung elastin.
    • Parkinson's Disease: Misfolding of α-synuclein protein leads to Lewy body formation.
    • Huntington's Disease: A genetic mutation causes huntingtin protein misfolding and aggregation.

    Protein Structure and Function

    • Proteins are essential macronutrients found in all living organisms.
    • Proteins play a crucial role in various metabolic pathways within the body.
    • Each organism possesses unique proteins, making them species-specific.
    • Proteins are also organ-specific, meaning the composition of proteins in the brain differs from those in the muscles.
    • Proteins are composed of 20 different amino acids.
    • The properties of a protein molecule are determined by the specific amino acids present.
    • Plants can synthesize all necessary amino acids to produce proteins, while animals cannot.
    • Amino acids in proteins are linked together by peptide bonds.
    • Peptide bonds form between the NH group of one amino acid and the COOH group of another amino acid.

    Amino Acid Structure

    • Amino acids are the building blocks of proteins.
    • Twenty amino acids are commonly found in proteins.
    • Each amino acid has a central carbon atom (alpha carbon) bound to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (-H), and a side chain (R group).
    • The R group varies between amino acids, determining their unique chemical properties.

    Zwitterions

    • At physiological pH, amino acids exist as zwitterions, which are dipolar ions with both positive and negative charges.

    Isoelectric Point (pI)

    • pI is the pH at which an amino acid carries no net charge due to the balance of positive and negative charges.

    Chirality of Amino Acids

    • Most amino acids have a chiral alpha carbon, meaning they have four different groups attached to it.
    • Nineteen out of twenty amino acids have a chiral alpha carbon, except glycine.
    • Chirality leads to stereoisomers, which are molecules with the same chemical formula but different 3D arrangements.
    • Proteins predominantly use L-amino acids.

    Classification of Amino Acids

    • Amino acids can be classified based on their side chains:
      • Nonpolar side chains: Contain uncharged, hydrophobic groups, making them oily or lipid-like.
      • Polar neutral side chains: Have side chains with either a net positive or a net negative charge, making them hydrophilic and soluble in water.
      • Polar acidic side chains: Contain one amino group and two carboxyl groups, resulting in a negative charge.
      • Polar basic side chains: Contain two amino groups and one carboxyl group, resulting in a positive charge.

    Classification of Amino Acids (cont.)

    • Amino acids can also be classified based on their nutritional requirements:
      • Essential amino acids: Cannot be synthesized by the body and must be obtained from the diet.
      • Nonessential amino acids: Can be synthesized by the body.

    Peptide Bonds

    • Peptide bonds are covalent bonds that link amino acids together to form peptides and proteins.
    • A peptide bond is formed by condensation between the carboxyl group of one amino acid and the amino group of another, releasing a water molecule.
    • Peptides are chains of fewer than 50 amino acids.
    • Proteins are chains of 50 or more amino acids.

    Protein Structure

    • Primary structure: The linear sequence of amino acids in a polypeptide chain.
    • Secondary structure: The local folding patterns of the polypeptide chain, stabilized by hydrogen bonds. Common secondary structures include:
      • Alpha-helix: A coiled structure stabilized by hydrogen bonds between amino acids within the same chain.
      • Beta-pleated sheet: A flat, sheet-like structure stabilized by hydrogen bonds between amino acids in adjacent chains.
    • Tertiary structure: The overall three-dimensional shape of a single polypeptide chain, resulting from interactions between side chains (R groups).
    • Quaternary structure: The arrangement of multiple polypeptide chains (subunits) in a protein complex.

    Protein Function

    • Proteins perform a wide range of vital roles in the body, including structural support, catalysis, transport, defense, and communication.

    Importance of Protein Structure

    • The primary structure of a protein determines its higher-order structure, which in turn determines the protein’s function.
    • Slight changes in amino acid sequence can drastically alter protein function.

    Protein Hydrolysis

    • Enzymes called peptidases break peptide bonds through hydrolysis, adding a water molecule to cleave the bond.
    • Exopeptidases: Cleave peptide bonds at the ends of polypeptide chains.
      • Aminopeptidases: Cleave from the N-terminus.
      • Carboxypeptidases: Cleave from the C-terminus.
    • Endopeptidases: Cleave peptide bonds within the polypeptide chain.
      • Trypsin: Cleaves after arginine or lysine.
      • Chymotrypsin: Cleaves after phenylalanine, tyrosine, or tryptophan.
      • Pepsin: Cleaves after phenylalanine, tyrosine, or tryptophan.

    Important Small Peptides

    • Enkephalins are pentapeptides that act as neurotransmitters, reducing pain.
    • Glutathione is a tripeptide that acts as an antioxidant, protecting cells from oxidative damage.
    • Aspartame is a dipeptide that is a popular artificial sweetener.

    Protein Modification

    • Proteins can be modified after translation, affecting their function and stability:
      • Phosphorylation
      • Glycosylation
      • Acetylation
      • Ubiquitination
    • These modifications regulate protein activity, localization, and degradation.

    Misfolding

    • Misfolded proteins can lead to a variety of diseases, including Alzheimer's disease and Parkinson's disease.
    • Chaperone proteins assist in protein folding and prevent misfolding.

    Rare Amino Acids

    • Some amino acids, such as hydroxyproline and hydroxylysine, are not directly encoded in DNA but are synthesized after protein translation.
    • These modifications often contribute to specialized protein functions.

    Isoelectric Point

    • The structure of an amino acid can change with the pH of the solution.
    • Lowering the pH of the solution causes the zwitterion to pick up a proton.
    • Increasing the pH of the solution causes the zwitterion to lose a proton.

    Chirality of Amino Acids

    • Nineteen out of twenty common amino acids have a chiral α-carbon atom.
    • Glycine does not have a chiral α-carbon atom.
    • Chiral carbons have four different groups attached.
    • Threonine and isoleucine have two chiral carbons each.
    • Stereoisomers are compounds that have the same molecular formula but differ in the arrangement of atoms in space.

    Stereochemistry of Amino Acids

    • Mirror image pairs of amino acids are designated L (levo) and D (dextro) and are called enantiomers.
    • Proteins are assembled from L-amino acids (a few D-amino acids occur in nature).

    Classification of Amino Acids

    • Side Chain:
      • Nonpolar side chain: Contains uncharged hydrocarbon groups or benzene rings. Does not gain or lose protons or participate in hydrogen or ionic bonds. Hydrophobic.
      • Polar neutral side chain: Have side chains with either a net positive or a net negative charge. Hydrophilic and soluble in water.
      • Polar acidic side chain: Contains one amino group and two carboxyl groups. Side chain is negative and is –ic acid.
      • Polar basic side chain: Contains two amino groups and one carboxyl group. Side chain is positive.
    • Nutrition:
      • Essential Amino Acid: A standard amino acid needed for protein synthesis that must be obtained from dietary sources (cannot be synthesized in the human body).

    Importance of Primary Structure

    • Determines the amino acid sequence of a protein.
    • Determines the biological activity of the protein.

    Enzymatic Hydrolysis

    • Exopeptidases: Cleaves external peptide bonds.
      • Aminopeptidase: Cleaves peptide bonds beginning at the N-terminal end.
      • Carboxypeptidase: Cleaves peptide bonds beginning at the C-terminal end.
    • Endopeptidases: Cleaves internal peptide bonds.
      • Trypsin: Cleaves peptide bonds at the carboxyl end of two strongly basic amino acids: Arg & Lys.
      • Chymotrypsin: Cleaves peptide bonds at the carboxyl end of the three aromatic amino acids: Phe, Tyr, & Trp; and Leu.
      • Pepsin: Cleaves peptide bonds at the amino end of the three aromatic amino acids: Phe, Tyr, & Trp; and Ileu.

    Secondary Structure

    • Results from hydrogen bond formation between the hydrogen of the –NH group of the peptide bond and the carbonyl oxygen of another peptide bond.
    • There are two main forms of secondary structure: Alpha-Helix and Beta-Pleated Sheet.

    Alpha-Helix

    • Single protein chain shaped like a coiled spring.
    • H-bonding between amino acids within the same chain (intramolecular H-bonding).
    • R-groups stay outside the helix.
    • Space in the center of the helix is too small for solvent molecules to enter.

    Beta-Pleated Sheet

    • Completely extended protein chain segments in the same or different molecules governed by intermolecular or intramolecular H-bonding.
    • H-bonding between different parts of a single chain (intramolecular H-bonding).
    • Side chains below or above the axis.
    • U-turn structure.
    • Parallel: Chains run in the same direction.
    • Antiparallel: Chains run in opposite direction; More stable because of fully collinear H-bonds.

    Tertiary Structure

    • Overall three-dimensional shape of a protein.
    • Results from interactions between amino acid side chains (R groups).
    • These interactions are widely separated from each other.
    • Defines the biological function of proteins.
    • Two main forms of tertiary structure:
      • Fibrous proteins (insoluble): Mechanical strength, structural components, movement.
      • Globular proteins (soluble): Transport, regulatory, enzymes.
    • Determined by a variety of interactions including:
      • Disulfide Bridges: Strong covalent bonds that form between the sulfhydryl groups (SH) of cysteine monomers.
      • Electrostatic Interactions (ionic interaction, salt linkages): Salt bridge between charged side chains of acidic and basic amino acids.
      • H-Bonding: Between polar, acidic, and/or basic R groups.

    Quaternary Structure

    • Results from the aggregation (combination) of two or more polypeptide subunits held together by non-covalent interactions (including H-bonds, ionic or hydrophobic interactions).
    • Examples of proteins with quaternary structure:
      • Collagen: Fibrous protein of three polypeptides (trimeric) that are supercoiled like a rope.
      • Hemoglobin: Globular protein with four polypeptide chains (tetrameric).
      • Insulin: Two polypeptide chains (dimeric).

    Protein Digestion

    • The process of breaking down proteins into smaller peptides and amino acids.
    • Begins in the stomach: Pepsin, an enzyme activated by stomach acid, initiates protein digestion.
    • Continues in the small intestine: Pancreatic enzymes like trypsin, chymotrypsin, and carboxypeptidase further break down proteins.
    • Absorption: Amino acids are absorbed through the intestinal walls into the bloodstream.
    • Utilization: Amino acids are used by the body for various functions.
    • Excess: Excess amino acids are converted to glucose or fat.

    Protein Misfolding

    • A biological phenomenon where a protein adopts an abnormal three-dimensional structure, deviating from its native conformation.
    • Protein misfolding can have several consequences:
      • Loss of function
      • Aggregation and formation of amyloid deposits
      • Diseases like Alzheimer's, Parkinson's, and Huntington's disease

    Chaperones

    • Proteins that help other proteins fold properly.
    • Assist proteins that have problems achieving their native configuration.
    • Prevent proteins from folding incorrectly.

    Prions

    • Infectious proteins responsible for transmissible spongiform encephalopathies (TSEs).
    • Examples of prion diseases:
      • Bovine spongiform encephalopathy (mad cow disease)
      • Creutzfeldt-Jakob disease
      • Kuru

    Misfolded Proteins and Neurodegenerative Diseases

    • Amyloid diseases are characterized by the accumulation of misfolded proteins.
      • Alzheimer's Disease: Misfolding of proteins, such as amyloid-beta and tau, leads to the formation of toxic aggregates in the brain.
      • Parkinson's Disease: Misfolding of the alpha-synuclein protein leads to the formation of Lewy bodies, which are pathological protein aggregates found in the brains of Parkinson's disease patients.
      • Huntington's Disease: A genetic mutation causes the huntingtin protein to misfold and form aggregates, which leads to the progressive degeneration of brain cells.

    Protein Classification

    • Simple Proteins: On hydrolysis, give only amino acids.
      • Albumins and globulins: Present in egg, milk, and blood.
      • Globins (histones): Basic proteins rich in histidine, present in combination with DNA or heme.
      • Gliadines: Proteins present in cereals.
    • Conjugated Proteins: On hydrolysis, give protein part and non-protein part.
      • Phosphoproteins: Proteins conjugated with a phosphate group.
      • Lipoproteins: Proteins conjugated with lipids.
      • Glycoproteins: Proteins conjugated with sugar (carbohydrate).
      • Nucleoproteins: Basic proteins conjugated with nucleic acid (DNA or RNA).
      • Metalloproteins: Proteins conjugated with metal ions.

    Protein Classification Based on Shape

    • Globular proteins: Spherical or roughly spherical. Examples: Enzymes, antibodies, hormones.
    • Fibrous proteins: Long, fibrous. Examples: Structural support, mechanical strength.

    Amino Acids

    • The basic building blocks of proteins
    • Approximately 700 amino acids exist in nature, but only 20 are commonly found in proteins
    • Each amino acid has a central carbon atom (alpha carbon) attached to four groups:
      • An amino group (-NH2)
      • A carboxyl group (-COOH)
      • A hydrogen atom (-H)
      • A side chain (R group), which varies between different amino acids

    Zwitterions

    • Amino acids exist as zwitterions (dipolar ions) under normal cellular conditions
    • Zwitterions have both a positive and negative charge
    • The charge depends on the pH of the solution

    Isoelectric Point

    • Isoelectric point (pI) is the pH at which an amino acid has no net charge
    • At the pI, the number of positive and negative charges are equal

    Nonessential Amino Acids

    • Can be synthesized by the human body

    Metabolic Classification

    • Ketogenic amino acids: Metabolized to ketone bodies (e.g., lysine, leucine).
    • Mixed ketogenic and glucogenic amino acids: Metabolized to both ketone bodies and glucose (e.g., isoleucine, phenylalanine, tyrosine, tryptophan)
    • Glucogenic amino acids: Metabolized to glucose (majority of amino acids)

    Rare Amino Acids

    • Found in specific proteins or pathways
    • Examples:
      • 4-Hydroxyproline: Found in collagen and plant cell wall proteins 
      • 4-Hydroxylysine: Found in collagen
      • β-alanine: Component of pantothenic acid (vitamin B5)
      • Homocysteine: Intermediate in amino acid metabolism
      • Homoserine: Intermediate in amino acid metabolism

    Proteins

    • Unbranched polymers of amino acids linked by peptide bonds
    • Most abundant molecules in cells after water (15% of cell mass)

    Peptides vs Proteins

    • Peptides: Chains of fewer than 50 amino acids.
    • Proteins: Chains of more than 50 amino acids.

    Peptide Bonds

    • The linkage between amino acids
    • Formed by condensation reaction between the carboxyl group of one amino acid and the amino group of another
    • Involves the loss of a water molecule

    Hydrolytic Reactions

    • Break peptide bonds
    • Water molecule is added back to the peptide bond

    Protein Structure

    • Primary structure: The linear sequence of amino acids in a polypeptide chain
    • Secondary structure: Local folding patterns of the polypeptide chain, such as alpha-helices and beta-sheets, stabilized by hydrogen bonds.
    • Tertiary structure: Three-dimensional shape of a single polypeptide chain, stabilized by various interactions (e.g., hydrophobic interactions, ionic bonds, disulfide bonds).
    • Quaternary structure: Arrangement of multiple polypeptide chains (subunits) into a functional protein complex

    Scleroproteins

    • Structural proteins, not digested by the body
    • Examples:
      • Keratin: Found in hair, nails, skin. Alpha-helical structure rich in cysteine and hydrophobic amino acids, making it water-insoluble.
      • Collagen: Found in connective tissues (e.g., skin, bones, tendons). Triple helix structure, rich in glycine, proline, and hydroxylysine.
      • Elastin: Found in blood vessel walls, lungs, and elastic ligaments. Composed of four polypeptide chains, rich in glycine and proline but low in hydroxyproline and lacks hydroxylysine.

    Medical Applications

    • Collagen*
    • Scurvy: Deficiency of vitamin C, which is a coenzyme in the synthesis of hydroxyproline and hydroxylysine affecting collagen production.
    • Osteogenesis Imperfecta (OI): Inherited disorder caused by genetic defects in collagen genes.
    • Elastin*
    • Emphysema: Chronic lung disease characterized by damage to elastin in lung tissue.

    Conjugated Proteins

    • Proteins combined with a non-protein component
    • Phosphoproteins: Proteins conjugated with phosphate groups. Examples: Casein (milk), vitellin (yolk)
    • Lipoproteins: Proteins conjugated with lipids. Functions: Transport lipids in blood, part of cell membranes.
    • Glycoproteins: Proteins conjugated with sugar (carbohydrate). Examples: Mucin, some hormones (e.g., erythropoietin), blood group antigens.
    • Nucleoproteins: Proteins conjugated with nucleic acids (DNA or RNA). Examples: Chromosomes (DNA), Ribosomes (RNA).
    • Metalloproteins: Proteins conjugated with metals. Examples: Hemoglobin (iron), Cytochromes (iron), Ferritin (iron), Transferrin (iron).

    Protein Classification Based on Shape

    • Globular proteins: Spherical or roughly spherical shape. Function: Enzymes, antibodies, hormones. Examples: Insulin, hemoglobin.
    • Fibrous proteins: Long, fibrous shape, Function: Structural support, mechanical strength. Examples: Collagen, keratin.

    Protein Digestion

    • Breakdown of proteins into smaller peptides and amino acids.
    • Begins in the stomach with pepsin (activated by stomach acid).
    • Continues in the small intestine with pancreatic enzymes (trypsin, chymotrypsin, carboxypeptidase).
    • Absorption: Amino acids are absorbed into the bloodstream.
    • Utilization: Body uses amino acids for various functions.
    • Excess amino acids are converted to energy (glucose) or stored as fat.

    Protein Misfolding

    • Refers to a protein adopting an abnormal three-dimensional structure, deviating from its native conformation.
    • Can lead to protein dysfunction and toxicity through aggregation.
    • Chaperones: Proteins that help other proteins fold correctly.
    • Misfolded proteins can be detected and degraded by cellular quality control mechanisms.

    Prions

    • Infectious proteins responsible for transmissible spongiform encephalopathies (TSEs), such as mad cow disease (Bovine Spongiform Encephalopathy), Creutzfeldt-Jakob disease, and kuru.

    Misfolded Proteins and Neurodegenerative Diseases

    • Amyloid diseases: Accumulation of misfolded proteins in the brain
    • Alzheimer's disease: Misfolding of amyloid-beta and tau proteins leads to toxic aggregates.
    • Parkinson's disease: Misfolding of alpha-synuclein protein forms Lewy bodies.
    • Huntington's disease: Misfolding of huntingtin protein results from genetic mutation

    Amino Acids

    • Building blocks of proteins
    • Around 700 amino acids exist naturally, 20 are commonly found in proteins
    • Have a general structure: an α-carbon atom bonded to an amino group, carboxyl group, hydrogen atom, and a side chain (R group)
    • Exist as zwitterions under normal cellular conditions: possess both positive and negative charges

    Amino Acids: The Alphabet

    • Nonessential Amino Acids: Can be synthesized by the body
    • Essential Amino Acids: Must be obtained from diet

    Protein Structure

    • Primary Structure: the linear sequence of amino acids in a polypeptide chain.
    • Secondary Structure: Local folding patterns within the polypeptide chain, including α-helices and β-sheets, resulting from hydrogen bonds between backbone atoms.
    • Tertiary Structure: The 3-dimensional shape of a single polypeptide chain, determined by interactions between R groups. Interactions include:
      • Disulfide Bridges: Strong covalent bonds between sulfur atoms of cysteine residues
      • Electrostatic Interactions (Ionic Bonds, Salt Bridges): Occur between charged side chains of acidic and basic amino acids.
      • Hydrogen Bonding: Forms between polar, acidic, and/or basic R groups.
    • Quaternary Structure: The arrangement of multiple polypeptide chains in a protein, held together by non-covalent interactions.

    Protein Example

    • Collagen: Fibrous protein consisting of three polypeptide chains intertwined like a rope, crucial for connective tissue strength.

    Protein Classification

    Simple Proteins

    • Yield only amino acids upon hydrolysis.
    • Albumins & Globulins: Found in egg, milk, and blood.
      • α1 Globulin: e.g., antitrypsin
      • α2 Globulin: e.g., haptoglobin
      • β-Globulin: e.g., transferrin
      • γ-Globulins (Immunoglobulins): Responsible for immunity.
    • Globins (Histones): Basic proteins rich in histidine, found in DNA and hemoglobin.
    • Gliadines: Proteins found in cereals.

    Conjugated Proteins

    • Yield amino acids and a non-protein component upon hydrolysis.
    • Phosphoproteins: Proteins conjugated with phosphate groups (e.g., casein in milk, vitellin in egg yolk)
    • Lipoproteins: Proteins bound to lipids; aid in lipid transport in blood and cell membrane structure.
    • Glycoproteins: Proteins linked to carbohydrates (e.g., mucin, some hormones, cell membrane components, blood groups).
    • Nucleoproteins: Basic proteins (e.g., histones) combined with nucleic acids (DNA or RNA) (e.g., chromosomes, ribosomes).
    • Metalloproteins: Proteins that contain metal ions (e.g., iron, copper, zinc).

    Protein Digestion

    • Begins in the stomach with pepsin, an enzyme activated by stomach acid.

    Peptides vs. Proteins

    • Peptides: Chains of less than 50 amino acids.
    • Proteins: Chains of more than 50 amino acids.
    • Peptide Bond: The covalent bond that connects amino acids to form polypeptides, formed through a condensation reaction involving the carboxyl group of one amino acid and the amino group of another.

    Biochemically Important Small Peptides

    • Hormones
    • Neurotransmitters
    • Antioxidants
    • Enkephalins: Pentapeptide neurotransmitters that bind receptors in the brain, reducing pain.
    • Glutathione: (Glu–Cys–Gly): A tripeptide found in high levels in cells, acting as an antioxidant.
    • Aspartame: (Asp-Phe): A dipeptide artificial sweetener.

    Amino Acids

    • Amino acids are the building blocks of proteins.
    • There are 700 amino acids in nature, but only 20 are used in proteins.
    • Each amino acid has four groups attached to its alpha carbon: an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group).
    • The R group differentiates one amino acid from another, determining its properties.
    • Under normal cellular conditions, amino acids exist as zwitterions, which are dipolar ions with both a positive and negative charge.
    • The pH at which an amino acid solution has no net charge is called the isoelectric point.
    • The structure of an amino acid can change with the pH of the solution.
    • Lowering the pH causes the zwitterion to pick up a proton.
    • Increasing the pH causes the zwitterion to lose a proton.
    • 19 of the 20 common amino acids have a chiral alpha carbon, meaning they have four different groups attached, making them optically active.
    • Glycine does not have a chiral alpha carbon.
    • Some amino acids, like threonine and isoleucine, have two chiral carbons, resulting in four possible stereoisomers.
    • Stereoisomers are compounds that have the same molecular formula but differ in the arrangement of atoms in space.
    • Proteins are assembled from L-amino acids.
    • A few D-amino acids occur naturally.
    • Amino acids are abbreviated using one or three letters.
    • Some commonly used abbreviations include:
      • Ala (Alanine)
      • Arg (Arginine)
      • Asn (Asparagine)
      • Asp (Aspartic acid)
      • Cys (Cysteine)
      • Gln (Glutamine)
      • Glu (Glutamic acid)
      • Gly (Glycine)
      • His (Histidine)
      • Ile (Isoleucine)
      • Leu (Leucine)
      • Lys (Lysine)
      • Met (Methionine)
      • Phe (Phenylalanine)
      • Pro (Proline)
      • Ser (Serine)
      • Thr (Threonine)
      • Trp (Tryptophan)
      • Tyr (Tyrosine)
      • Val (Valine)

    Classification of Amino Acids

    • Amino acids can be classified based on the chemical composition of their side chains (R groups), their nutritional requirements, and their catabolism.
    • Based on their side chain, they are categorized as:
      • Nonpolar (hydrophobic): Contains mainly uncharged hydrocarbon groups or benzene rings. These are relatively insoluble in water and tend to be found on the interior of proteins. Examples include: Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan, and Methionine.
      • Polar (hydrophilic): Have side chains with either a net positive or negative charge. They are soluble in water and tend to be found on the surface of proteins.
        • Polar neutral: Side chains do not gain or lose protons or participate in hydrogen or ionic bonds. Examples include: Serine, Threonine, Tyrosine, Asparagine, and Glutamine.
        • Polar acidic: Contains one amino group and two carboxyl groups. The side chain is negative. Examples include: Aspartic acid and Glutamic acid.
        • Polar basic: Contains two amino groups and one carboxyl group. The side chain is positive. Examples include: Lysine, Arginine, and Histidine.

    Hydropathy Scale

    • This determines how hydrophobic or hydrophilic an amino acid is, impacting protein folding.
    • Hydrophobic side chains tend to be in the interior of proteins, while hydrophilic residues tend to be on the surface.

    Essential Amino Acids

    • These are amino acids necessary for protein synthesis that cannot be synthesized in the human body and must be obtained from the diet.
    • Examples include: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, and Valine.

    Isomeric Peptides

    • Peptides containing the same amino acids in a different order, leading to different properties.
    • For example, the amino acids Glu-Cys-Met-Gly, Asp-Val-Ser, and Gly-His-Lys are all isomers.

    Biochemically Important Small Peptides

    • Hormones: Insulin, glucagon
    • Neurotransmitters: Enkephalins, endorphins, substance P
    • Antioxidant: Glutathione
    • Artificial sweeteners: Aspartame

    Peptide Bond Formation

    • Amino acids are linked together by peptide bonds, which form between the carboxyl group of one amino acid and the amino group of another.
    • The formation of a peptide bond releases a water molecule.
    • The end of a peptide chain with a free amino group is the N-terminal end.
    • The other end contains a free carboxyl group and is the C-terminal end.

    Protein Structure

    Primary Structure

    • The linear sequence of amino acids in a polypeptide chain.
    • The primary structure is determined by genetic information.
    • Determines the biological function of proteins.

    Secondary Structure

    • Refers to the local folding of the polypeptide chain into regular structures.
    • Two common secondary structures are:
      • Alpha-helix: A right-handed spiral structure stabilized by hydrogen bonds between carbonyl and amino groups of the polypeptide backbone.
      • Beta-sheet: A flat sheet-like structure formed by hydrogen bonding between adjacent polypeptide chains.
    • Both structures are stabilized by hydrogen bonds.

    Tertiary Structure

    • The overall three-dimensional shape of a protein.
    • Determined by various interactions, including:
      • Disulfide bonds: Form between cysteine residues and can stabilize the structure.
      • Electrostatic interactions (ionic interactions, salt linkages): Occur between charged side chains of acidic and basic amino acids.
      • Hydrogen bonds: Form between polar, acidic, and/or basic R groups.
      • Hydrophobic interactions: Nonpolar side chains tend to cluster together in the interior of the protein.

    Quaternary Structure

    • The arrangement of multiple polypeptide chains (subunits) in a protein.
    • Subunits are held together by non-covalent interactions, such as hydrogen bonds, ionic bonds, and hydrophobic interactions.
    • Examples of proteins with quaternary structure include:
      • Collagen: A fibrous protein with three polypeptide chains (trimeric) that are supercoiled like a rope for structural strength.
      • Hemoglobin: A globular protein with four polypeptide chains (tetrameric).
      • Insulin: Has two polypeptide chains (dimeric).

    Protein Classification

    • Simple proteins: Composed only of amino acids. Examples include:
      • Albumins and globulins: Found in egg, milk, and blood. They are high in biological value, meaning they contain all essential amino acids and are easily digested.
      • Globins (histones): Basic proteins present in: - Combination with DNA - Combination with heme to form hemoglobin.
      • Gliadines: Proteins found in cereals.

    Protein Misfolding

    • Occurs when a protein adopts an abnormal three-dimensional structure, deviating from its native conformation.
    • Can result in:
      • Loss of protein function: The misfolded protein may be unable to perform its intended function.
      • Aggregation: Misfolded proteins may clump together, forming aggregates that can interfere with cell function.
      • Disease: Protein misfolding is associated with various neurodegenerative diseases.

    Chaperones

    • Proteins that help other proteins fold correctly.
    • Prevent incorrect folding.
    • Assist proteins that have difficulty achieving their native configuration.

    Prions

    • Infectious proteins responsible for transmissible spongiform encephalopathies (TSEs).
    • Examples include:
      • Bovine spongiform encephalopathy (mad cow disease)
      • Creutzfeldt-Jakob disease
      • Kuru

    Misfolded Proteins and Neurodegenerative Diseases

    • Amyloid diseases are caused by the accumulation of misfolded proteins.
    • Examples include:
      • Alzheimer's disease: Misfolding of amyloid-beta and tau proteins contribute to the formation of toxic aggregates in the brain.
      • Parkinson's disease: Misfolding of the alpha-synuclein protein leads to the formation of Lewy bodies.
      • Huntington's disease: A genetic mutation causes the huntingtin protein to misfold and form aggregates.

    Isoelectric Point

    • The structure of an amino acid is dependent on the pH of the solution
    • A low pH causes a zwitterion to pick up a proton
    • A high pH causes a zwitterion to lose a proton

    Chirality of Amino Acids

    • 19 out of 20 common amino acids are chiral and have a chiral α-carbon atom
    • Glycine (Gly) is the only amino acid that is not chiral
    • A chiral carbon has four different groups attached

    General Structure of Amino Acids

    • Threonine and isoleucine have two chiral carbons each
    • Each amino acid with two chiral carbons has four possible stereoisomers
    • Stereoisomers have the same formulas but differ in the spatial arrangement of atoms

    Stereochemistry of Amino Acids

    • Enantiomers are mirror images of amino acids
    • They are designated as L (levo) and D (dextro)
    • Proteins are assembled from L-amino acids
    • D-amino acids are rare and may be found in some proteins

    Abbreviations of Amino Acids

    • Each amino acid has a three-letter and one-letter abbreviation
    • For example, Alanine is abbreviated as Ala or A

    Classification of Amino Acids

    • Amino acids can be classified by the properties of their side chains
    • The side chain is the R-group

    Classification of Amino Acids by Side Chain

    • Nonpolar side chains
      • Contain uncharged, hydrocarbon groups or benzene rings
      • Do not participate in hydrogen or ionic bonds
      • They are hydrophobic and lipid-like
    • Polar neutral side chains
      • Have a net positive or a net negative charge
      • They are hydrophilic and soluble in water
    • Polar acidic side chains
      • Contain one amino group and two carboxyl groups
      • The side chain is negatively charged and ends in -ic acid
    • Polar basic side chains
      • Contain two amino groups and one carboxyl group
      • The side chain is positively charged

    Classification of Amino Acids by Nutrition

    • Essential amino acids
      • They must be obtained from dietary sources
      • The human body cannot synthesize them in adequate amounts
    • Nonessential amino acids
      • The body can synthesize them

    Classification of Amino Acids by Metabolism

    • Ketogenic Amino Acids
      • Produce ketone bodies
      • Lysine and leucine are the only completely ketogenic amino acids
    • Mixed Ketogenic and Glucogenic Amino Acids
      • Produce both ketone bodies and glucose
      • Isoleucine, phenylalanine, tyrosine, and tryptophan
    • Glucogenic Amino Acids
      • Produce glucose
      • All other amino acids

    Rare Amino Acids of Proteins

    • 4-Hydroxyproline
      • Found in plant cell wall proteins and collagen
    • 4-Hydroxylysine
      • Found in collagen
    • β-alanine
      • Component of pantothenic acid (vitamin B5)
    • Homocysteine
      • An intermediate in amino acid metabolism
    • Homoserine
      • An intermediate in amino acid metabolism

    What is the Difference between Peptides and Proteins?

    • Peptides are chains containing less than 50 amino acids
    • Proteins are chains containing more than 50 amino acids

    What is a Peptide Bond?

    • A peptide bond is a secondary amide bond
    • It is formed by condensation of the α-carboxyl group of one amino acid with the α-amino group of another amino acid
    • Results in the loss of a water molecule

    Hydrolytic Reaction

    • Breaks peptide bonds
    • Requires water

    Nature of the Peptide Bond

    • By convention, the N-terminal end is on the left and the C-terminal end is on the right
    • The N-terminal end is the free amino group
    • The C-terminal end is the free carboxyl group

    Isomeric Peptides

    • Peptides that contain the same amino acids but in different orders
    • Display different properties

    Biochemically Important Small Peptides

    • Hormones: Peptides that act as chemical messengers in the body
    • Neurotransmitters: Peptides that transmit signals between neurons
    • Antioxidants: Peptides that protect cells from damage caused by free radicals
    • Artificial Sweeteners: Peptides that are used as sugar substitutes

    Enkephalins

    • Pentapeptide neurotransmitters produced by the brain
    • Bind to receptors in the brain
    • Help reduce pain
    • Met-enkephalin: Tyr-Gly-Gly-Phe-Met
    • Leu-enkephalin: Tyr-Gly-Gly-Phe-Leu

    Glutathione

    • A tripeptide present in high levels in most cells
    • A key regulator of oxidation-reduction reactions
    • A powerful antioxidant that protects cells from damage

    Aspartame

    • Asp-Phe
    • A dipeptide sold as Equal and Nutrasweet
    • ~180 times as sweet as sucrose

    Primary Structure of a Protein

    • The amino acid sequence of a protein
    • Dictated by genetic information
    • Determines the protein's structure and function

    Protein Classification Based on Shape

    • Globular proteins: Have a spherical or roughly spherical shape
    • Fibrous proteins: Have a long, fibrous shape

    Globular Proteins

    • Examples: Enzymes, antibodies, hormones
    • Functions: Catalyze reactions, defend against pathogens, regulate biological processes

    Fibrous Proteins

    • Examples: Collagen, keratin, elastin
    • Functions: Provide structural support and mechanical strength

    Protein Digestion

    • Breaks down proteins into smaller peptides and amino acids
    • Begins in the stomach through the action of pepsin

    4 types of Scleroproteins

    • Scleroproteins are structural proteins that are not digested
    • Keratin: Found in skin, hair, and nails
    • Collagen: Found in bones, cartilage, tendons, and skin
    • Elastin: Found in blood vessels, lungs, skin, and ligaments

    Collagen

    • The most abundant protein in mammals
    • Present in a gel form in the extracellular matrix
    • Contains three helical polypeptide chains that form a triplet-helix molecule
    • Important for bone, skin, and cartilage structure
    • Insoluble in water
    • Heated with water or dilute hydrochloric acid to produce gelatin

    Medical Applications of Collagen

    • Scurvy: Vitamin C deficiency causes problems in collagen synthesis leading to abnormal bone development and other symptoms
    • Osteogenesis Imperfecta (OI): Inherited disorder caused by a mutation in the gene that makes collagen type I. Causes fragile bones, bone deformities, and possible death

    Elastin

    • Found in blood vessel walls and elastic ligaments
    • Provides elasticity
    • Consists of four polypeptide chains (tetramer)
    • Rich in proline and glycine
    • Low in hydroxyproline and hydroxylysine

    Emphysema

    • Chronic obstructive lung disease
    • Caused by elastase-mediated breakdown of elastin
    • Common in smokers due to the deficiency of α1-antitrypsin, an enzyme that inhibits elastase

    Conjugated Proteins

    • Proteins that are bound to a non-protein component
    • The non-protein component is called a prosthetic group

    Types of Conjugated Proteins

    • Phosphoproteins: Have a phosphate group as the prosthetic group
      • Examples: Casein (milk) and vitellin (egg yolk)
    • Lipoproteins: Have a lipid as the prosthetic group
      • Functions: Transport lipids in blood, form cell membranes
      • Examples: Chylomicrons, very-low-density lipoproteins (VLDL), low-density lipoproteins (LDL), high-density lipoproteins (HDL)
    • Glycoproteins: Have a sugar as the prosthetic group
      • Examples: Mucin, erythropoietin (hormone), blood group antigens
    • Nucleoproteins: Have a nucleic acid as the prosthetic group
      • Examples: Chromosomes (DNA + proteins), ribosomes (RNA + proteins)
    • Metalloproteins: Have a metal ion as the prosthetic group
      • Examples: Hemoglobin, myoglobin, catalase, peroxidases, ferritin, hemosiderin, transferrin

    Amino Acid Synthesis

    • Amino acids can be synthesized by the body
    • Lysine and leucine are ketogenic only, meaning they are metabolized through acetyl CoA and can be converted to ketone bodies
    • Isoleucine, phenylalanine, tyrosine, and tryptophan are both ketogenic and glucogenic, meaning they can be converted to both ketone bodies and glucose
    • All other amino acids are glucogenic, meaning they can be converted to glucose
    • The remaining amino acids can yield products that contribute to glycogen and glucose formation

    Rare Amino Acids of Proteins

    • 4-Hydroxyproline is found in plant cell wall proteins (extensins) and collagen
    • 4-Hydroxylysine is found in collagen
    • β-alanine is a component of pantothenic acid (vitamin B5)
    • Homocysteine and homoserine are intermediates in amino acid metabolism

    Peptides and Proteins

    • Chains containing less than 50 amino acids are called "peptides", while those with more than 50 are called "proteins"
    • Amino acids are linked by peptide bonds
    • A "dipeptide" consists of 2 amino acids linked together
    • A "tripeptide" consists of 3 amino acids linked together
    • An "oligopeptide" consists of 10-20 amino acids linked together
    • A "polypeptide" consists of a long chain of amino acids linked together

    Peptide Bonds

    • A peptide bond is a secondary amide bond
    • It is formed by the condensation of the α-carboxyl group of one amino acid with the α-amino group of another amino acid, resulting in the loss of a water molecule

    Isomeric Peptides

    • Peptides with the same amino acids in different orders have different properties

    Biochemically Important Small Peptides

    • Hormones, neurotransmitters, antioxidants and artificial sweeteners are examples of small peptides
    • Enkephalins are pentapeptide neurotransmitters produced by the brain that bind receptors in the brain and help reduce pain
    • Met-enkephalin: Tyr-Gly-Gly-Phe-Met
    • Leu-enkephalin: Tyr-Gly-Gly-Phe-Leu
    • Glutathione (Glu-Cys-Gly) is a tripeptide present in high levels in most cells, and is a regulator of oxidation-reduction reactions, acting as an antioxidant that protects cells from oxidizing agents like peroxides and superoxides
    • Aspartame (Asp-Phe) is a dipeptide sold under the trade names Equal and Nutrasweet, and is approximately 180 times sweeter than sucrose

    Protein Structure

    • Primary structure: The unique sequence of amino acids in a protein. The differences in the chemical and physiologic properties of peptides result from differences in their amino acid sequences

    • Secondary structure: The shape of a polypeptide chain due to hydrogen bonds between the hydrogen of the -NH group of one peptide bond and the carbonyl oxygen of another peptide bond.

      • Alpha helix: A coiled spring-like shape formed by hydrogen bonds between amino acids within the same chain. R-groups are outside the helix.
      • Beta-pleated sheets: A sheet-like structure formed by hydrogen bonds between different parts of a single chain or between different chains. R-groups are above or below the axis.
        • Parallel: Chains run in the same direction
        • Antiparallel: Chains run in opposite directions, which is more stable due to fully collinear hydrogen bonds.

    • Tertiary structure: The overall three-dimensional shape of a protein, which is determined by interactions between amino acid side chains (R-groups) that are widely separated from each other.

      • Fibrous proteins: Insoluble, provide mechanical strength, and are often found in structural components and for movement.
      • Globular proteins: Soluble, and are involved in a wide range of functions including transport, regulation, and enzymatic activity.

    • Quaternary structure: Results from the aggregation of two or more polypeptide subunits held together by non-covalent interactions like hydrogen bonds, ionic interactions, or hydrophobic interactions.

    Protein Function and Classification

    • Simple proteins: Hydrolyze into only amino acids
      • Albumin and globulins: Found in egg, milk, and blood. They are high in biological value, contain all essential amino acids, and are easily digested.
        • α1 globulin: e.g. antitrypsin
        • α2 globulin: e.g. haptoglobin, a protein that binds hemoglobin to prevent its excretion by the kidney
        • β-globulin: e.g. transferrin, a protein that transports iron
        • γ-globulins: Immunoglobulins (antibodies), responsible for immunity,
      • Globins (Histones): Basic proteins rich in histidine, found:
        • Combined with DNA
        • Combined with heme to form hemoglobin of RBCs.
      • Gliadins: Proteins found in cereals
    • Protein digestion: Begins in the stomach with pepsin and ends in the small intestine with the action of pancreatic enzymes (trypsin, chymotrypsin and carboxypeptidase)
    • Protein absorption: Amino acids are absorbed from the small intestine into the bloodstream
    • Protein utilization: Amino acids are used by the body for various functions, including building new proteins, producing hormones and enzymes, and providing energy.
    • Excess protein: Excess amino acids are converted to glucose, fat, or urea, then excreted.

    Protein Misfolding

    • Protein misfolding is a phenomenon where a protein adopts an abnormal three-dimensional structure, deviating from its native conformation.
      • This affects protein function
    • Chaperones are proteins that help proteins fold properly
    • Misfolded proteins can be detected by cellular quality control mechanisms, tagged, and then sent to the cytoplasm for degradation.

    Prions

    • Prions are infectious proteins responsible for transmissible spongiform encephalopathies (TSEs), such as:
      • Bovine spongiform encephalopathy (mad cow disease)
      • Creutzfeldt-Jakob disease
      • Kuru

    Misfolded Proteins and Neurodegenerative Diseases

    • Amyloid diseases are a group of neurodegenerative diseases associated with the accumulation of misfolded proteins.
      • Alzheimer's disease: The misfolding of amyloid-beta and tau proteins leads to the formation of toxic aggregates in the brain.
      • Parkinson's disease: Misfolding of the alpha-synuclein protein leads to the formation of Lewy bodies, pathological protein aggregates found in the brains of Parkinson's disease patients.
      • Huntington's disease: A genetic mutation causes the huntingtin protein to misfold and form aggregates, leading to progressive degeneration of brain cells.

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    Week 5 - Amino Acid and Proteins PDF

    Description

    This quiz explores the intricate structures and classifications of amino acids, focusing on their chirality and stereochemistry. Learn about the effects of pH on amino acid structure and the significance of enantiomers in protein composition. Dive into the world of polar and non-polar side chains and understand their properties.

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