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Questions and Answers
Questions and Answers
Which amino acid is a precursor for both heme and creatine?
Which amino acid is a precursor for both heme and creatine?
- Tyrosine
- Tryptophan
- Histidine
- Glycine (correct)
What role do tyrosine derivatives primarily play in the body?
What role do tyrosine derivatives primarily play in the body?
- They act as neurotransmitters.
- They produce hormones and skin pigment. (correct)
- They serve as precursors for blood clotting factors.
- They contribute to muscle endurance.
Which uncommon amino acid is involved in blood clotting proteins?
Which uncommon amino acid is involved in blood clotting proteins?
- N-methylarginine
- γ-Carboxyglutamic acid (correct)
- Selenocysteine
- Desmosine
Which neurotransmitter is synthesized from the decarboxylation of glutamic acid?
Which neurotransmitter is synthesized from the decarboxylation of glutamic acid?
What function does selenocysteine primarily serve in the body?
What function does selenocysteine primarily serve in the body?
Which amino acid is specifically mentioned as being converted to histamine?
Which amino acid is specifically mentioned as being converted to histamine?
Which of the following amino acids is NOT typically found in proteins?
Which of the following amino acids is NOT typically found in proteins?
What is the primary role of methylated amino acids like methylhistidine and N-methyllysine?
What is the primary role of methylated amino acids like methylhistidine and N-methyllysine?
Which type of protein is primarily responsible for regulating other proteins?
Which type of protein is primarily responsible for regulating other proteins?
Which of the following examples is not classified as a structural protein?
Which of the following examples is not classified as a structural protein?
Which amino acid is classified as hydrophilic and possesses a cyclic structure?
Which amino acid is classified as hydrophilic and possesses a cyclic structure?
What type of protein is responsible for the contraction of muscle tissues?
What type of protein is responsible for the contraction of muscle tissues?
What is the pKa value of histidine, indicating its behavior in enzymatic reactions?
What is the pKa value of histidine, indicating its behavior in enzymatic reactions?
What is the primary role of transport proteins?
What is the primary role of transport proteins?
Which of the following is a characteristic of cysteine?
Which of the following is a characteristic of cysteine?
Which amino acid is not considered essential or indispensable for humans?
Which amino acid is not considered essential or indispensable for humans?
Which of the following is a shared characteristic of proteins with quaternary structure?
Which of the following is a shared characteristic of proteins with quaternary structure?
Which amino acid contains two chiral carbons?
Which amino acid contains two chiral carbons?
Which example correctly illustrates a transport protein?
Which example correctly illustrates a transport protein?
Which of the following proteins primarily serves in the storage of minerals?
Which of the following proteins primarily serves in the storage of minerals?
Which group of amino acids is classified as having acidic side chains?
Which group of amino acids is classified as having acidic side chains?
What type of bonds can tyrosine form due to its functional groups?
What type of bonds can tyrosine form due to its functional groups?
Which of the following is not considered a functional class of proteins?
Which of the following is not considered a functional class of proteins?
Which statement about essential amino acids is true?
Which statement about essential amino acids is true?
Which type of protein plays an active role in cell defense and protection?
Which type of protein plays an active role in cell defense and protection?
What distinguishes complete proteins from incomplete proteins?
What distinguishes complete proteins from incomplete proteins?
Which of the following is an example of a conjugated protein?
Which of the following is an example of a conjugated protein?
What is the primary function of lipoproteins?
What is the primary function of lipoproteins?
Which classification of proteins contains only amino acids?
Which classification of proteins contains only amino acids?
What do metalloproteins primarily function as?
What do metalloproteins primarily function as?
Phosphoproteins are characterized by the presence of what?
Phosphoproteins are characterized by the presence of what?
Which of these proteins is NOT classified as a conjugated protein?
Which of these proteins is NOT classified as a conjugated protein?
Which amino acid is most frequently found in the Gly-x-y motif of collagen?
Which amino acid is most frequently found in the Gly-x-y motif of collagen?
What is the primary significance of the 40-nm gaps between adjacent collagen molecules?
What is the primary significance of the 40-nm gaps between adjacent collagen molecules?
Which type of collagen is primarily found in cartilage?
Which type of collagen is primarily found in cartilage?
What essential vitamin is required for the hydroxylation process of collagen synthesis?
What essential vitamin is required for the hydroxylation process of collagen synthesis?
Which of the following statements about collagen triple helices is accurate?
Which of the following statements about collagen triple helices is accurate?
Which structural feature distinguishes fibrous proteins from globular proteins?
Which structural feature distinguishes fibrous proteins from globular proteins?
What is the primary function of collagen in the body?
What is the primary function of collagen in the body?
How does the structure of alpha-keratin contribute to its function in hair and nails?
How does the structure of alpha-keratin contribute to its function in hair and nails?
Which statement accurately describes membrane proteins?
Which statement accurately describes membrane proteins?
What characteristic of collagen gives it high tensile strength?
What characteristic of collagen gives it high tensile strength?
Which of the following proteins is a major component of skin and connective tissues?
Which of the following proteins is a major component of skin and connective tissues?
Which of the following best describes fibrous proteins?
Which of the following best describes fibrous proteins?
What type of bonding stabilizes the alpha-helix structure in alpha-keratin?
What type of bonding stabilizes the alpha-helix structure in alpha-keratin?
Questions and Answers
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Flashcards
Flashcards
Insulin's Function
Insulin's Function
Insulin regulates blood glucose levels.
Protein Structure Levels
Protein Structure Levels
Protein structure progresses from amino acid sequence (primary) to interactions among different parts of the protein (quarternary).
Protein Function: Enzymes
Protein Function: Enzymes
Enzymes speed up biochemical reactions in the body.
Transport Proteins
Transport Proteins
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Storage Proteins
Storage Proteins
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Amino Acid Classification: pKa of Histidine
Amino Acid Classification: pKa of Histidine
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Essential Amino Acids
Essential Amino Acids
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Contractile Proteins
Contractile Proteins
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Tyrosine and its Properties
Tyrosine and its Properties
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Structural Proteins
Structural Proteins
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Disulfide Bond Formation
Disulfide Bond Formation
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Protein Classification
Protein Classification
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Acidic Side Chains
Acidic Side Chains
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Basic Side Chains
Basic Side Chains
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Amino Acid Classification by Nutritional Value
Amino Acid Classification by Nutritional Value
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Hydrophobic Amino Acids (List)
Hydrophobic Amino Acids (List)
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Amino acid precursors for heme
Amino acid precursors for heme
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Amino acid precursors for hormones
Amino acid precursors for hormones
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Tryptophan's derivatives
Tryptophan's derivatives
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Histidine's conversion
Histidine's conversion
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Hydroxylysine and hydroxyproline function
Hydroxylysine and hydroxyproline function
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Selenocysteine role
Selenocysteine role
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Amino acids not in proteins
Amino acids not in proteins
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Ornithine and Citrulline's role
Ornithine and Citrulline's role
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Complete Proteins
Complete Proteins
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Incomplete Proteins
Incomplete Proteins
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Simple Proteins
Simple Proteins
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Conjugated Proteins
Conjugated Proteins
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Glycoproteins
Glycoproteins
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Lipoproteins
Lipoproteins
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Nucleoproteins
Nucleoproteins
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Protective Proteins
Protective Proteins
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Collagen Types
Collagen Types
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Tropocollagen: Structure
Tropocollagen: Structure
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Glycine's Role in Collagen
Glycine's Role in Collagen
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Hydroxylation in Collagen
Hydroxylation in Collagen
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Collagen Fibril Gaps
Collagen Fibril Gaps
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Fibrous Proteins
Fibrous Proteins
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Globular Proteins
Globular Proteins
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Membrane Proteins
Membrane Proteins
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-Keratin
-Keratin
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Collagen's Structure
Collagen's Structure
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Collagen: Function
Collagen: Function
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Collagen: Benefits
Collagen: Benefits
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Protein Classification: Shape
Protein Classification: Shape
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Flashcards
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Study Notes
Study Notes
Chemistry of Amino Acids and Proteins - I
- The topic will cover general structure of amino acids, classification of amino acids, function of amino acids, acid-base properties of amino acids, peptide bond structure and functional peptides, protein structure, biological functions of proteins, and protein classification.
Objectives
- Students will be able to describe the general structure of amino acids.
- Students will be able to list the biochemical functions of amino acids.
- Students will be able to categorize amino acids by different classification bases.
- Students will be able to explain the acid-base properties of amino acids.
- Students will be able to explain the peptide bond and its characteristics.
- Students will be able to mention functional peptides.
- Students will be able to detail protein structure.
- Students will be able to explain the biological functions of proteins.
- Students will be able to classify proteins.
What are Proteins?
- Unbranched polymers of amino acids, linked head-to-tail.
- Major constituents of most cells.
- Form multi-molecular complexes.
- Folded into specific conformations.
- Conformation and functional-group chemistry control function.
- Responsible for most of an organism's phenotype (defining what it looks like, how it behaves, etc.).
- Made from almost 20 different types of standard amino acids.
- Selenocysteine is incorporated during co-translation in humans.
Amino Acids
- Structure:
- Central carbon.
- Amino group.
- Carboxyl group.
- Side chain (R group) - a variable group. The R group confers unique chemical functionality.
- Chiral/Optically Active:
- Acid-base properties.
- Capacity to polymerize.
Classification of Amino Acids
- Based on:
- Side chain character (e.g., nonpolar, aliphatic, aromatic).
- Nutritional value (essential, non-essential, conditionally essential).
- Metabolic fate (ketogenic, glucogenic, mixed).
- Presence/absence in proteins.
Amino Acid Classification by Side Chain Character
- Hydrophobic side chain: stabilize protein structure by hydrophobic interactions.
- Tyrosine can form hydrogen bonds.
Classification...
- Polar, uncharged R groups: Includes Serine, Threonine, Cysteine, Asparagine, and Glutamine.
- Reversible formation of a disulfide bond by the oxidation of two molecules of Cysteine.
Classification...
- Acidic side chain: H+ (proton) donor.
- Examples: Aspartate, Glutamate.
Classification...
- Amino Acids with Basic Side Chains:
- Basic side chains: serve as H+ acceptors.
- Examples: Lysine (Lys, K), Arginine (Arg, R), and Histidine (His, H).
- Histidine side chain: pKa=6.0, 10% protonated at pH=7. Serving as a proton donor/acceptor in many enzymatic reactions.
- Identification of carbon atoms in amino acids: a, b, y, d etc
Names and Codes of Amino Acids
- Provides a list of amino acids, their single-letter and three-letter codes, and their R-group properties (e.g., hydrophobic, hydrophilic, reactive).
Amino Acid Classification Based on Nutritional Value
- Essential amino acids: Nine amino acids not synthesizable in the body in adequate amounts (Val, Ile, Thr, Trp, Leu, Lys, Met, Phe, and His).
- Dispensable/non-essential amino acids: Can be synthesized in the body from essential ones.
- Conditionally essential amino acids: Required during illness or stress. (Tyrosine, cysteine, arginine, glutamine, glycine, proline, and serine).
Classification Based on Metabolic Fate
- Ketogenic: Catabolically yield intermediates convertible to Acetyl-CoA or Acetoacetyl-CoA. (e.g., Leucine, Lysine, Isoleucine, Phenylalanine , Tyrosine, Tryptophan, etc.)
- Glucogenic: Yield intermediates of glycolysis or Kreb's cycle. (e.g., Alanine, Arginine, Asparagine, Aspartate, Glutamate, Glutamine, Glycine, Histidine, Methionine, Proline, Serine, Threonine, Valine, etc).
- Mixed Ketogenic/Glucogenic: Yield both intermediates for glycolysis or Kreb's cycle and those convertible to Acetyl-CoA. (e.g., Phenylalanine, Tyrosine, Tryptophan, etc).
Some Common Biological Functions of Amino Acids
- Formation of peptides and proteins.
- Stabilizing the 3D structure of proteins.
- Vital for enzyme catalysis at active sites.
- Source of glucose.
- Sources of sulfur (S) for Fe-S center formation (Cysteine & Methionine).
- For nucleic acid synthesis.
- Roles in detoxification mechanisms (e.g., Glycine & Methionine).
- Methyl group donors in methylation reactions (e.g., Methionine).
Amino Acids as Precursors of Biologically Important Derivatives
- Glycine: Precursor for heme and creatine.
- Tyrosine: Precursor for hormones (thyroxine, triiodothyronine, epinephrine, norepinephrine), and skin pigment melanin.
- Tryptophan: Precursor of niacin and serotonin.
- Histidine: Precursor to histamine.
Uncommon Amino Acids – Found in proteins
- Hydroxylysine and hydroxyproline (mainly in collagen).
- Tyrosine and Triiodothyronine (hormones).
- N-methylarginine and N-acetyllysine (in histone proteins).
- Methylhistidine, -N-methyllysine and N,N,N-trimethyllysine (methylated amino acids in myosin).
- Y-Carboxyglutamic acid(for blood clotting proteins & Ca2+ containing proteins).
- Desmosine (in fibrous protein elastin).
- Selenocysteine (derived from serine, introduced during protein synthesis, key role in antioxidant activity e.g. Glutathione peroxidase active site).
Amino Acids not found in proteins
- GABA (a potent neurotransmitter).
- Histamine (smooth muscle contraction).
- Serotonin (neurotransmitter).
- ß-Alanine.
- Epinephrine (adrenaline).
- Ornithine & Citrulline (in urea cycle).
- Dopa (precursor of melanin).
- S-adenosylmethionine (SAM) (methyl donor in transmethylation reactions).
Acid-Base Properties of Amino Acids
- At low pH, the amino acid exists as the ammonium form.
- At neutral pH, the amino acid exists as a zwitterion (dipolar ion).
- At high pH, the amino acid exists as the carboxylate form.
- The pI is the average of pKa1 and pKa2, representing the specific pH at which the molecule is electrically neutral.
pI of Neutral Amino Acids
- Calculating the pI: the average of pKa1 (ionization of carboxyl group) and pKa2 (ionization of amine group).
pI of Amino Acids
- The pI of alanine.
Amino Acids with Ionizable Side Chains.
- pI of Lysine (shows the process).
pI of Amino Acids
- Show pIs for acidic, neutral and basic amino acids.
Peptide Bond & Functional Peptides
- Peptide bonds (amide bonds): Condensation reactions.
- Forming dipeptides, tripeptides, etc.
- N-terminal and C-terminal.
- Predicting acid-base behavior (free -amino and -carboxyl groups).
- Characteristic pI.
- pKa value for ionizable group changes in peptides.
- Examples: Serylglycyltyrosylalanylleucine, or Ser-Gly-Tyr-Ala-Leu.
Planar Peptide Groups in a Polypeptide Chain
- Amide nitrogens are non-basic.
- Rotation around C-N bond is restricted.
- Peptide groups are planar.
Biologically Active Peptides
- Glutathione: Formed from y-glutamic acid, cysteine, and glycine. Protects cell membranes. A good example.
- Slightly larger peptides/oligopeptides:
- Insulin (two polypeptide chains).
- Corticotropin (hormone).
Commercial Peptide: Example
- Aspartame (dipeptide).
Structure and Classification of Proteins
- A summary of protein structure levels and types.
Protein Structure
- The 3-D structure depends on amino acid types, number, and sequence.
- Folding, twisting, and coiling create a unique shape.
- The structure determines the protein's function.
- Native structure depends on: interactions with solvent molecules, pH and ionic composition of the solvent, sequence of amino acids.
Primary Structure of Proteins
- Describes the sequence and number of amino acids in a protein chain.
- Determined by gene sequence.
- Contains the information necessary to fold into its native structure.
- Amino acid sequence example for Lysozyme.
Does Amino Acid Sequence Determine Protein Function?
- Example: Oxytocin (uterine contractions, milk release).
- Example: Vasopressin (regulates water balance).
- Change in amino acid sequence can cause problems: Hemoglobin (sickle-cell anemia).
Secondary Structure of Proteins
- Formed by hydrogen bonds.
- Describes the folding pattern.
- Common types: alpha helix, beta pleated sheet, turns/bends.
- The development of regular hydrogen-bond patterns creates distinct folding patterns.
Secondary Structure: Examples
- Alpha helix: peptide carbonyl H-bonded to peptide N-H group.
- Beta pleated sheet: each strip of paper as a single peptide strand.
Secondary Structure: Examples
- Three-ten helix.
- 27 ribbon.
Secondary Structure: Examples
- Beta bulge.
Super Secondary Structures
- Helix-loop-helix.
- Coiled coils.
- Helix bundles.
- Beta-alpha-beta units.
- Hairpins.
- Beta meander.
- Greek key.
- Beta-sandwich.
- Zinc finger.
- Leucine zipper.
Tertiary Structure of Proteins
- Shows the overall 3-D folding pattern of a polypeptide.
- Determined by interactions between R groups.
- Bonds involved in tertiary structure:
- Hydrogen bonds.
- Hydrophobic interactions.
- Disulfide bridges.
- Ionic bonds.
- Van der Waals forces.
Examples of Some Domains
- β-barrel.
- Bundle.
- Saddle.
Quaternary Structure of Proteins
- Formed by more than one polypeptide chain.
- Organized by the same types of bonds as tertiary structures.
- Intracellular enzymes are oligomers (examples).
- Advantages of quaternary association:
- Stability.
- Genetic economy and efficiency (less DNA needed for monomer).
- Bringing catalytic sites together to regulate catalytic activity.
Advantages of Quaternary Association
- Stability
- Genetic economy and efficiency
- Bringing catalytic sites together
Examples of Proteins with Quaternary Structure
- Listing specific examples of proteins and their subunit numbers.
Protein Classification Based on Nutritional Value
- Complete or high-quality proteins
- Incomplete or low-quality proteins
Protein Classification Based on Composition
- Simple proteins
- Conjugated proteins
Types of Conjugated Proteins
- Glycoproteins
- Lipoproteins
- Nucleoproteins
- Phosphoproteins
- Metalloproteins
- Hemoproteins
- Flavoproteins
Protein Classification Based on Shape (Architecture)
- Fibrous proteins: long and thin, insoluble
- Examples: Collagen (triple helix), α-keratin.
- Globular proteins: roughly spherical, soluble
- Examples: Insulin, Hemoglobin, Enzymes
Membrane Proteins
- Hydrophobic side chains for membrane interaction.
- Insoluble in aqueous but soluble in detergents.
- Have fewer hydrophilic amino acids compared to cytosolic proteins.
Common Fibrous and Globular Proteins: Occurrence & Use
- Tabular presentation of fibrous and globular proteins, their occurrence, and use.
Example of Fibrous Proteins: α-Keratin
- Major components of hair and nails.
- α-helix strands wound into "superhelix" structure.
- Stabilized by H-bonds.
Your Hair
- Image of a cross-section of hair showing the different components.
Examples of Fibrous Proteins: Collagen
- Constituent of connective tissues.
- Triple helix structure.
- Rigid, high tensile strength.
- Important for running, jumping.
- Types of collagen: I, II, III.
Examples of Fibrous Proteins: Collagen
- Tropocollagen (basic structural unit of collagen).
- Composed of three polypeptide chains, each longer than 1000 amino acids.
- Sequence repeats (Gly-x-y motif): x and y are often proline or hydroxyproline.
- Crucial role in intermolecular and intramolecular cross-links.
- Hydroxylation requires ascorbic acid (vitamin C).
Examples of Fibrous Proteins: Collagen
- Collagen triple helices are 300 nm long, with 40-nm gaps between adjacent collagen molecules in a row.
- Pattern repeats every five rows (5 x 68 nm = 340 nm).
- The hole regions are for sugar attachment, organizing fibril assembly, and bone formation.
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