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Amino acids and proteins study guide, Study Guides, Projects, Research of Biochemistry

Virginia State University (VSU)Biochemistry

Amino acids and proteins study guide

Typology: Study Guides, Projects, Research

2025/2026

Available from 09/02/2025

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Amino acids and proteins study guide
1.What are amino acids?: - Organic compounds that contain both an amine group
(R-NH2) and a carboxylic acid group (R-COOH)
-R is a variable side chain
2.Asparagine: - First amino acid discovered (1806)
-Initially found in asparagus juice
3.Glycine: - Simplest amino acid
-R group is single hydrogen atom
4.Zwitterions: - Amino acids are zwitterions
-Zwitterion: dipolar ion
-At physiologic pH (~7.4), amino acids have both a positive and negative charge
on the same molecule
-R side chain my also have a charge (+ or -)
5.Acid-base properties of amino acids: - All amino acids have at least two pKa
values: one for the COOH proton and one for the NH3+ proton
-Some amino acids have ionizable R groups (and have a third pKa values)
-Amino acids (and some R groups) can act as buffers
6.Chirality: - Most amino acids are chiral
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Amino acids and proteins study guide

1. What are amino acids?: - Organic compounds that contain both an amine group

(R-NH2) and a carboxylic acid group (R-COOH)

  • R is a variable side chain

2. Asparagine: - First amino acid discovered (1806)

  • Initially found in asparagus juice

3. Glycine: - Simplest amino acid

  • R group is single hydrogen atom

4. Zwitterions: - Amino acids are zwitterions

  • Zwitterion: dipolar ion
  • At physiologic pH (~7.4), amino acids have both a positive and negative charge on the same molecule
  • R side chain my also have a charge (+ or - )

5. Acid-base properties of amino acids: - All amino acids have at least two pKa

values: one for the COOH proton and one for the NH3+ proton

  • Some amino acids have ionizable R groups (and have a third pKa values)
  • Amino acids (and some R groups) can act as buffers

6. Chirality: - Most amino acids are chiral

  • Chirality is a property of asymmetry
  • The alpha carbon can form four bonds
  • Swapping bonds forms a mirror image molecule (chiral) D (right) and L (left) (in glycine, the R "group" is an H, so no D or L form)
  • Only L-amino acids are used as building blocks for animal proteins
  • D-amino acids are found in bacterial cell walls and in some antibiotics produced by microorganisms

7. Classification of amino acids: - Protein vs. nonprotein amino acids

  • Essential vs. nonessential amino acids
  • Catabolism (ketogenic vs. glucogenic)
  • Based on structure or charge of R group

8. Canonical (standard) amino acids: - These are amino acids that are genetically

encoded and incorporated into proteins

  • There are twenty canonical amino acids (also called standard or common amino acids)

9. Nonprotein amino acids: - Amino acids that are not incorporated into proteins

  • Ornithine and citrulline: intermediates in the urea cycle
  • GABA ( ³ a- minobutyric acid): neurotransmitter formed in the brain through decar- boxylation of glutamate
  • Taurine: essential for cats, synthesized from cystine
  • Essential amino acids must be obtained from the diet
  • Biosynthetic enzyme pathways for the essential amino acids are lacking or exist at inadequate levels

11. What are the essential amino acids?: - Arginine

  • Histidine
  • Isoleucine
  • Leucine
  • Lysine
  • Methionine
  • Phenylalanine
  • Threonine
  • Tryptophan
  • Valine

12. What are the "other" essential amino acids?: - Taurine is essential for cats

  • Growing chickens cannot synthesize all of the glycine and proline that they need

13. Taurine:

14. Amino acid catabolism: - Glucogenic

  • Ketogenic
  • Some amino acids are both glucogenic and ketogenic

15. Glucogenic: - Catabolism yields pyruvate or intermediates in the TCA cycle

  • Arginine, histidine, glutamate, glutamine, proline, valine, cysteine, methionine, aspartame, asparagine, alanine, serine, glycine

16. Ketogenic: - Catabolism yields either acetoacetate or one of its precursors

(acetylene CoA or acetoacetyl CoA)

  • Lysine, leucine

17. Which amino acids are both glucogenic and ketogenic?: Tryptophan, thre- onine,

phenylalanine, tyrosine, isoleucine

18. R group classifications: - Nonpolar amino acids

  • Polar amino acids
  • Positively charged amino acids
  • Negatively charged amino acids
  • Aromatic amino acids (R groups contains aromatic ring)

19. Nonpolar (hydrophobic) amino acids: - Most have hydrocarbon R groups

  • Tend to cluster inside protein structures and interact via hydrophobic interactions
  • Crucial for protein folding and three-dimensional structure

20. What are the nonpolar amino acids?: Alanine, glycine, isoleucine, leucine,

methionine, tryptophan, phenylalanine, proline, valine

  • Polar charged
  • Found on the external surface of proteins

22. What are the polar amino acids?: Cysteine, serine, threonine, tyrosine, as-

paragine, glutamine

23. What are the polar basic (positively charged) amino acids?: Histidine, ly- sine,

arginine

24. What are the polar acidic (negatively charged) amino acids?: Aspartate,

glutamate

25. Proteins: primary structure: - Polymers of the twenty standard amino acids

  • a-Carboxyl group of one amino acids reacts with the a-amino group of another to form peptide bonds

26. Directionality of proteins: - Amino acid at one end which contains a free amino

group is the amino terminal end (N-terminus)

  • Amino acid at the other end which contains a free carboxyl group is the carboxyl terminal end (C-terminus)
  • Numbering of amino acids in proteins starts at the N-terminus

27. Amino acid modifications in proteins: - Hydroxyproline and hydroxylysine

  • Desmosine and isodesmosine
  • Phosphotyrosine, phosphoserine, phosphothreonine
  • a-Carboxyglutamate

28. Hydroxyproline and hydroxylysine: - Hydroxylation of proline and lysine in

collagen is important for proper collagen structure and function

  • Hydroxylation of proline requires ascorbic acid (vitamin C)
  • Deficiency of vitamin C leads to decreased collagen and signs of scurvy
  • Ascorbic acid is required in the diet of primates, guinea pigs, bats

29. Desmosine and isodesmosine: - Formed from lysine residues in proteins

  • Prevalent in elastin (smooth muscle)

30. Phosphotyrosine, phosphoserine, phosphothreonine: - Phosphorylation of

proteins is a key regulator of protein activity

  • Important in cell signaling
  • a-Carboxyglutamate

31. a-Carboxyglutamate: - Activation of proteins by carboxylation of glutamic acid

residues

  • Involved in the clotting cascade
  • Chelation of calcium ions important for coagulation

32. Protein structure: - Primary

  • Secondary
  • Initial folding is guided by chaperones - proteins that help other proteins fold properly
  • Misfolding of proteins can cause pathologies

42. Intramolecular interactions: - Noncovalent interactions

  • Covalent bonding

43. Noncovalent interactions: - Hydrogen bonding

  • Ionic bonding
  • Hydrophobic interactions or effects

44. Hydrogen bonding: Between amino acids with polar R groups

45. Ionic bonding: Between amino acids with charged R groups

46. Hydrophobic interactions or effects: Between amino acids with nonpolar R

groups

47. Covalent bonding: - Disulfide bonds between cysteines

  • Can be between cysteine residues in the same protein chains or between different chains

48. Quaternary structure: - Association of several protein chains or subunits into a

closely packed arrangement (e.g., hemoglobin)

  • Stabilized by the same types of interactions that generate tertiary structure

49. Disorders of protein folding/accumulation: - Amyloid: term for a protein that

misfolds and aggregates

  • Accumulation of insoluble amyloid in various organs
  • Clinical diseases

50. Clinical diseases of protein folding/accumulation: - Prion diseases

  • Amyloidosis/serum amyloid A (SAA)

51. Prion diseases: - Caused by misfolded prion proteins (PrP) (e.g., scrapie prion

protein is rich in pleated sheets, while normal prion is rich in helix structures)

  • Once inside a cell, they cause normal prion proteins to become misfolded
  • "Chain reaction" propagation occurs
  • Abnormal proteins aggregate inside cells and cause cell death (long incubation periods before diseases manifest)
  • Transmissible, progressive, and fatal

52. Prion diseases examples: - Scrapie (sheep, goats)

  • Bovine spongiform encephalopathy (BSE, "mad cow disease")
  • Chronic wasting disease (CWD) (deer, elk, moose, bison, antelope, squirrels)
  • Creutzfeldt-Jakob disease (humans)

53. Scrapie: - Sheep, goats

  • First described in 1732
  • Behavioral changes, tremor, pruritus, locomotor in coordination

amyloidosis)

58. What organ systems does amyloidosis affect?: - Kidney is most common —

glomerular disease

  • Genetic component in Chinese Shar Pei, beagle, English foxhound