Biology: Proteins and Amino Acids
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Questions and Answers

What is the term for the linear sequence of amino acids in a protein?

  • Secondary structure
  • Quaternary structure
  • Tertiary structure
  • Primary structure (correct)

    • Which structures are formed by the interaction of secondary structures in a protein?

  • Tertiary structure (correct)
  • Quaternary structure
  • Primary structure
  • Linear structure

    • What are the main functional groups present in amino acids?

  • Carbonyl and methyl groups
  • Carboxyl, amino, and variable R group (correct)
  • Thiol and ether groups
  • Hydroxyl and phosphate groups

    • Which statement regarding protein conformation is correct?

    <p>Conformational change alters protein functionality.</p> Signup and view all the answers

    What is the purpose of X-ray diffraction in protein study?

    <p>To determine the 3-dimensional structure of proteins</p> Signup and view all the answers

    Why are L-amino acids predominantly used in all life forms on Earth?

    <p>The basis for their preference is unknown due to evolutionary history.</p> Signup and view all the answers

    What type of biological interactions do proteins participate in?

    <p>With nucleic acids, lipids, and polysaccharides</p> Signup and view all the answers

    How many standard amino acids are used by all organisms on Earth?

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

    What are enantiomers known to affect?

    <p>Rotation of polarized light</p> Signup and view all the answers

    What characterizes a racemic mixture?

    <p>It does not rotate polarized light</p> Signup and view all the answers

    What is a zwitterion?

    <p>A dipolar ion having both positive and negative charges</p> Signup and view all the answers

    What happens to amino acids outside of the physiological pH range?

    <p>Non-dipolar forms predominate</p> Signup and view all the answers

    Which amino acids can lead to ambiguity in peptide sequences due to their side chain differences?

    <p>Aspartic and Glutamic acid</p> Signup and view all the answers

    Who first used the term chirality?

    <p>Lord Kelvin</p> Signup and view all the answers

    What might be a future goal related to chirality in synthetic biology?

    <p>To create mirror image lifeforms</p> Signup and view all the answers

    In which conditions do amino acids exist mostly as zwitterions?

    <p>In neutral pH solutions</p> Signup and view all the answers

    Which amino acid is considered essential for cats but not for humans?

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

    What is the primary function of the mTORC1 complex that leucine modulates?

    <p>Cell growth and division</p> Signup and view all the answers

    What unusual effect does exercise have on appetite as suggested by phenylalanine?

    <p>It can reduce appetite despite energy expenditure.</p> Signup and view all the answers

    Which neurotransmitter is primarily excitatory in the mammalian nervous system?

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

    What role does SOD1 play in the cell?

    <p>It helps control free radical build-up.</p> Signup and view all the answers

    What implication does the presence of some single amino acid mutations have in ALS?

    <p>They can lead to varying penetrance and disease progression.</p> Signup and view all the answers

    How does leucine negatively impact mTOR and affect cell processes?

    <p>By promoting energy conservation through autophagy.</p> Signup and view all the answers

    What can glutamate be modified into in the nervous system?

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

    What does the SEQUENCE of a protein primarily determine?

    <p>The STRUCTURE of the protein</p> Signup and view all the answers

    What important process in protein synthesis begins with the codon ATG?

    <p>Initiation of protein synthesis</p> Signup and view all the answers

    Which amino acid is unique for connecting back to the amino group to form a pyrrolidine ring?

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

    Which of the following amino acids is the first in a protein chain synthesized according to the genetic code?

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

    Why is glycine often noted as not being chiral?

    <p>It has two identical hydrogen atoms attached to the alpha carbon.</p> Signup and view all the answers

    How do polar amino acids generally interact with water compared to hydrophobic amino acids?

    <p>They attract water molecules.</p> Signup and view all the answers

    Which statement correctly describes cysteine's role in protein structure?

    <p>It can form disulfide bridges for stabilization.</p> Signup and view all the answers

    What defines the hydrophobic characteristics of most amino acids?

    <p>Presence of alkane chains in their R groups</p> Signup and view all the answers

    What characterizes the imidazole group of histidine at physiological pH?

    <p>It readily gains and loses H+ ions.</p> Signup and view all the answers

    Which of the following amino acids is considered hydrophilic?

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

    At physiological pH, which form do the side chains of aspartate and glutamate predominantly take?

    <p>Negatively charged.</p> Signup and view all the answers

    Which amino acid is also an ionizable and positively charged amino acid?

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

    What is the pKa value of the carboxyl group in amino acids generally?

    <p>3.1</p> Signup and view all the answers

    Which amino acid is known to contribute to the umami flavor in certain foods?

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

    What can the subtle changes in a single amino acid lead to in proteins?

    <p>Substantial effects on the organism.</p> Signup and view all the answers

    Which classification of amino acids includes phenylalanine, tryptophan, and isoleucine?

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

    Study Notes

    Proteins and Their Importance

    • Proteins are essential for various biological processes like replication, homeostasis, structural support, cell signaling, and development.
    • The linear sequence of amino acids in a protein is called the primary structure.
    • This linear sequence folds into secondary structures like alpha helices and beta sheets.
    • Interactions between secondary structures create the tertiary structure - the final folded form of the polypeptide.
    • Multiple proteins can interact to form larger structures, called quaternary structures, like homodimers, heterodimers, or tetramers.
    • These structures can be determined using techniques like X-ray diffraction.
    • Protein structure determines function, and the specific chemical properties of amino acid R groups contribute to protein-driven catalysis.

    Amino Acids: the Building Blocks of Proteins

    • There are 20 standard amino acids used to build proteins.
    • Each amino acid is defined by its R group, which is attached to the alpha carbon.
    • Amino acids exist as L or D isomers, but life on Earth exclusively uses L-amino acids.
    • Amino acids in aqueous solution exist as zwitterions, with an equal number of positive and negative charges.
    • The non-dipolar forms of amino acids start to predominate outside of physiological pH range: protonated sides at low pH (acidic) and deprotonated sides at high pH (basic).
    • The linear sequence of amino acids dictates the protein's structure and function: Sequence -> Structure -> Function.

    Amino Acid Categories

    • Hydrophobic Amino Acids: Have alkane chains in their R groups, which are repelled by water molecules.
    • Polar Amino Acids: Contain R groups with uneven electron distribution, resulting in a partial charge. These groups are hydrophilic and attract water molecules.
    • Positively Charged Amino Acids: R groups typically contain positively charged functional groups.
    • Negatively Charged Amino Acids: R groups usually contain negatively charged functional groups.
    • Ionizable Amino Acids: R groups have a pKa associated with gaining or losing a proton (H+ ion), and their charge can vary depending on the pH.

    Important Notes

    • The 'Asx' and 'Glx' abbreviations can be ambiguous in protein sequences because they represent Asp/Asn and Glu/Gln, respectively. There is a risk of deamidation, a reaction that can remove an amide group from the side chain.
    • Selenocysteine is a non-standard 21st amino acid encoded by the UGA stop codon.
    • Single amino acid changes in proteins, caused by DNA mutations, can significantly impact the function and phenotype of an organism.
    • Amino acids like Leucine and Phenylalanine can act as signaling molecules and neurotransmitters, playing roles in cell growth regulation and appetite modulation.

    Clinical Significance

    • Single amino acid substitutions in proteins due to mutations can lead to severe diseases, such as ALS (Amyotrophic Lateral Sclerosis/Motor Neuron Disease).
    • These mutations can vary in their penetrance, progression, and impact on individual patients.
    • Understanding the relationship between genetics and disease phenotypes is complex and requires further research.

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    Biochem Exam 2 Lecture 1 PDF

    Description

    Explore the vital role of proteins in biological processes, including their structure and function. Dive into the significance of amino acids as the building blocks of proteins, learning about primary, secondary, tertiary, and quaternary structures. Understand how these structures influence protein functions and interactions.

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