LESSON 1: AMINO ACIDS & PROTEINS Flashcards
(96 cards)
1
Q
What are proteins made of?
A
Chains of amino acids called polypeptides.
2
Q
What determines a protein’s function?
A
Its 3D structure, which is determined by the amino acid sequence and folding.
3
Q
Are all proteins the same?
A
No, proteins vary widely in size, shape, and function.
4
Q
What is the role of enzymes?
A
Catalyze biochemical reactions by lowering activation energy.
5
Q
What do peptide hormones do?
A
Act as long-distance chemical messengers (e.g., insulin).
5
Q
Example of a digestive enzyme?
A
Salivary amylase (breaks starch into sugars).
6
Q
Example of a transport protein?
A
Hemoglobin (carries oxygen in blood).
7
Q
Example of a structural protein?
A
Actin, tubulin, keratin.
8
Q
Example of a defense protein?
A
Antibodies (immune response).
9
Q
What is myosin’s function?
A
Muscle contraction.
10
Q
What do storage proteins do?
A
Store nutrients for embryos/seeds (e.g., albumin).
11
Q
What are the two main shapes of proteins?
A
Globular (e.g., hemoglobin) and fibrous (e.g., collagen).
12
Q
What is denaturation?
A
Loss of protein function due to shape disruption (caused by pH, temperature, chemicals).
13
Q
What is the basic structure of an amino acid?
A
Central α-carbon bonded to an amino group, carboxyl group, hydrogen, and R group.
14
Q
What gives each amino acid its unique identity?
A
Its R group (side chain).
15
Q
How many amino acids are commonly found in proteins?
A
20
16
Q
What charge does an amino acid have at physiological pH (7.2–7.4)?
A
Amino group = +, Carboxyl group = –
17
Q
What type of side chains do valine and leucine have?
A
Nonpolar, hydrophobic.
18
Q
What type of side chains do serine and glutamine have?
A
Polar, hydrophilic.
19
Q
Which amino acids are basic?
A
Lysine, arginine (sometimes histidine).
20
Q
Which amino acids are acidic?
A
Aspartate, glutamate.
21
Q
What is unique about proline?
A
Has a ring structure; causes bends/kinks in chains.
22
Q
What is special about cysteine?
A
Has –SH group; forms disulfide bonds.
23
Q
What type of reaction forms a peptide bond?
A
Dehydration synthesis (condensation).
24
What kind of bond is a peptide bond?
Covalent bond between amino group and carboxyl group of adjacent amino acids.
25
What is the directionality of a polypeptide chain?
N-terminus (amino) → C-terminus (carboxyl)
26
What are amino acids the building blocks of?
Proteins.
27
What functional groups do all amino acids share?
Amino group (–NH₂), carboxyl group (–COOH), R group, and central α-carbon.
28
What makes glycine unique?
It’s the only achiral amino acid (R = H).
29
Why is the α-carbon important?
It is where the amino, carboxyl, hydrogen, and variable R group are attached.
30
What are the abbreviation formats for amino acids?
One-letter and three-letter codes (e.g., Gly, G).
31
Why are abbreviations useful?
They make biochemical communication efficient.
32
What is a key trait of nonpolar amino acids?
Hydrophobic; found in protein cores.
33
Glycine (G)
Smallest; flexible
34
Alanine (A)
Methyl side chain
35
Valine (V), Leucine (L), Isoleucine (I)
Branched alkyl chains
36
Methionine (M)
Sulfur-containing; starts protein synthesis
37
Proline (P)
Cyclic; causes kinks in chains
38
What’s a shared property of aromatic amino acids?
Contain aromatic rings; absorb UV light (~280 nm)
39
Phenylalanine (F)
Nonpolar benzyl group
40
Tyrosine (Y)
Polar OH group on benzyl ring
41
Tryptophan (W)
Largest; double-ring (indole) with N
42
What do polar uncharged amino acids do well?
Form hydrogen bonds; hydrophilic
43
Serine (S), Threonine (T)
Have OH groups; can be phosphorylated
44
Cysteine (C)
Thiol (–SH); forms disulfide bonds
45
Asparagine (N), Glutamine (Q)
Contain amide groups; H-bonding
45
How are charged amino acids categorized?
Acidic (– charge) vs Basic (+ charge)
46
Aspartic Acid (D), Glutamic Acid (E)
Have –COO⁻ side chains; often in enzyme active sites
47
Lysine (K)
Has terminal amino group; can be acetylated
48
Arginine (R)
Guanidinium group; strongly basic
49
Histidine (H)
Imidazole ring; proton donor/acceptor, pKa ~6
50
What are essential amino acids?
Must be obtained from the diet.
51
Name 3 essential amino acids.
Valine, Leucine, Tryptophan (others: H, I, L, K, M, F, T)
52
What are non-essential amino acids?
Can be synthesized by the body.
53
Name 3 non-essential amino acids.
Glutamine, Alanine, Glycine (others: A, N, D, E, S, R, C, Q, P, Y)
54
What is phosphorylation and where does it occur?
Addition of phosphate; often on Ser, Thr, or Tyr.
55
What does glycosylation do?
Adds sugars; helps in folding, stability, cell recognition.
56
What is ubiquitination’s function?
Tags proteins (at lysine) for degradation.
57
Acetylation & methylation affect what?
Gene expression & protein function, often on lysine.
58
Why do egg whites turn white when cooked?
Heat denatures albumin proteins, exposing hydrophobic residues that clump and form a solid white network.
59
What is primary protein structure?
Linear sequence of amino acids in a polypeptide.
60
What determines primary structure?
The gene’s DNA sequence.
60
What disease results from a single amino acid change in hemoglobin?
Sickle cell anemia (Glu → Val at position 6 of β chain).
61
What causes secondary structure formation?
Hydrogen bonds between backbone atoms (not R groups).
62
What are two common secondary structures?
α-Helices and β-Pleated Sheets.
63
What amino acid is a "helix breaker"?
Proline (rigid ring disrupts helix).
64
Where are bulky aromatics (Trp, Tyr, Phe) often found?
β-Pleated sheets (spacious structure fits bulky side chains).
65
What interactions contribute to tertiary structure?
R-group interactions: hydrogen bonds, ionic bonds, Van der Waals, hydrophobic effects, and disulfide bridges.
66
What are disulfide bridges?
Covalent bonds between cysteine residues (–SH groups); stabilize structure.
67
What drives hydrophobic amino acids into the protein interior?
Avoidance of water (hydrophobic effect).
68
What is quaternary structure?
The assembly of multiple polypeptide chains (subunits) into one functional protein.
69
Example of a protein with quaternary structure?
Hemoglobin (4 subunits: 2α, 2β).
70
What holds subunits together in quaternary structure?
Same forces as tertiary structure (mostly weak interactions).
71
What is protein denaturation?
Loss of higher-order structure (secondary, tertiary, quaternary) due to heat, pH, or chemicals.
72
Does denaturation affect primary structure?
No — the amino acid sequence remains intact.
73
Is denaturation reversible?
Sometimes — if the environment is restored and the protein can refold.
74
Example of irreversible denaturation?
Cooking an egg (albumin permanently changes).
75
What are chaperone proteins (chaperonins)?
Proteins that assist in proper protein folding, especially under stress or in crowded cell environments.
76
Can some proteins fold without help?
Yes — some fold spontaneously based on their primary sequence.
77
Why are chaperones important in cells?
Prevent misfolding and aggregation, especially during stress (e.g., heat shock).
78
What drives the folding of a protein into its functional 3D shape?
The hydrophobic effect — nonpolar residues cluster to avoid water, increasing solvent entropy.
79
What is the major entropic driving force in protein folding?
Release of ordered water molecules surrounding hydrophobic residues → increases solvent entropy.
80
What are the five main forces stabilizing tertiary protein structure?
1. Hydrophobic interactions (entropy-driven clustering)
2. Hydrogen bonds (between polar side chains or backbone)
3. Ionic bonds (salt bridges) (acidic-basic R groups)
4. Disulfide bonds (covalent –SH links between cysteines)
5. Van der Waals forces (weak but numerous interactions)
81
What is a disulfide bond and where is it commonly found?
A covalent bond between two cysteine side chains; stabilizes extracellular proteins.
82
How does entropy contribute to protein folding?
1. Conformational entropy ↓ (protein becomes more ordered)
2. Solvent entropy ↑ (water released from hydrophobic regions)
83
What stabilizes protein quaternary structure?
- Same as tertiary:
1. Hydrophobic interactions (subunit interfaces)
2. Hydrogen bonds
3. Ionic bonds
4. Disulfide bonds (between subunits)
84
Give an example of a protein with quaternary structure.
Hemoglobin (2α + 2β subunits)
85
What are molecular chaperones?
Proteins that assist folding and prevent aggregation of new or misfolded polypeptides.
86
Example of a molecular chaperone?
HSP70 — binds hydrophobic regions to prevent misfolding.
87
What are chaperonins?
Large protein complexes (e.g., GroEL/GroES) that provide an isolated environment for proper folding.
88
What is protein denaturation?
Disruption of secondary, tertiary, or quaternary structure, usually irreversible.
89
What interactions are disrupted during denaturation?
Hydrogen bonds, ionic bonds, hydrophobic interactions, and Van der Waals forces — but primary structure stays intact.
90
How does temperature cause denaturation?
Increased kinetic energy breaks non-covalent bonds (e.g., cooking an egg).
91
How does pH lead to denaturation?
Alters charge states of side chains → disrupts ionic & hydrogen bonds (e.g., protein digestion in stomach).
92
What are some common chemical denaturants?
Urea and guanidine hydrochloride (disrupt hydrogen bonding and hydrophobic forces).
93
What’s the difference between reversible and irreversible denaturation?
a. Reversible: Protein can refold once conditions return to normal.
b. Irreversible: Protein cannot refold (e.g., heat-cooked egg).
