Protein Structure

Question 1

What is the pK1 of an amino acid?

Answer 1

pKa of carboxyl group

pH < pK1, prevalent form = mostly protonated
pH > pk1, prevalent form = mostly deprotonated

Question 2

What is the pK2 of an amino acid?

Answer 2

pKa of amino group

Question 3

What is the pKr of an amino acid?

Answer 3

pKa of side chain, determines whether the side chain of an AA will carry a charge at biological pH

Question 4

What is a weak acid or base? How do they act as buffers—what does this mean?

Answer 4

Weak acids can act as buffers in pH range near pKa, little change in ionization state within buffering range

Question 5

pI

Answer 5

Isoelectric point - pH where neutral form (0 net charge) is prevalent

W/o ionizable side chain
pI = (pKa1+pKa2)/2

W/ ionizable side chain
(pH where charge goes from +1 to 0 - pH where charge goes from 0 to -1)/2

pI > pH, AA net charge = +
pI < pH, AA net charge = -

Question 6

How are these physical properties related to amino acid chemistry? How are they related to protein structure and function?

Answer 6

pKas tell us likely state of AAs at biological pH
AAs are metabolic intermediates - changes charge of structure, leads to overall chemical structure changes

Question 7

What is the amino acid sequence in the peptide PHKLISTHMDERTFWAGNY? What amino acid is not present in this peptide?

Answer 7

Pro-His-Lys-Leu-Ile-Ser-Thr-His-Met-Asp-Glu-Arg-Thr-Phe-Trp-Ala-Gly-Asn-Tyr

Valine, Glutamine, Cysteine are missing

Question 8

Can you spell your name or initials in amino acids?

Answer 8

Ser-/-Met-Met-Ala-Tyr-Ala-His
Ser-Glu-Ala

Question 9

Is any fraction of acidic amino acids protonated at pH=7.4? Any basic amino acid?

Answer 9

No acidic AAs, basic AAs - lysine, arginine, histidine

Question 10

What pH range would you expect all of the groups on all amino acids to be protonated? All deprotonated?

Answer 10

Below 2.2 (acidic conditions) - protonated
Above 9.7 (basic conditions) - deprotonated

Question 11

What would be the net charge of the peptide KTMNGRDDHDEFFW at pH 7.4?

Answer 11

Use method for finding pI of AA w/ ionizable group

Question 12

Why is a peptide bond planar?

Answer 12

Resonance caused by partial sharing of e- between C1 and the N gives peptide bond partial double-bonded character, makes peptide bond rigid (little rotation possible) and flat/planar

Question 13

What limits the possible angles around the other bonds—phi and psi?

Answer 13

Steric hindrance from R groups

Question 14

What bonds contribute to the phi and psi angles?

Answer 14

Covalent bonds

Question 15

Primary protein structure

Answer 15

AA sequence

Question 16

Secondary protein structure

Answer 16

Alpha-helix: planar peptide bond, limited rotation around other bonds, intramolecular H-bonding make helical conformation energetically favored

Beta-strands/beta-sheets: stretches of AAs in extended conformations interacting horizontally through H-bonds that drive association of parallel or anti-parallel AA sequences

Question 17

Tertiary protein structure

Answer 17

Geometric arrangement of all atoms in a protein, sum of all secondary structures

Question 18

Quaternary protein structure

Answer 18

Polypeptide formed via interactions of individual tertiary structures

Question 19

What contributes to an alpha helix?

Answer 19

R-groups influence ability to form alpha helix through potential steric hindrance or other chem properties

Question 20

What is a hydropathy plot? What information does it show? How can it help to predict a membrane protein’s organization?

Answer 20

Hydropathy index - influences whether an AA within a peptide is likely to be exposed to aqueous envr

Question 21

What contributes to an alpha helix?

Answer 21

R-groups influence ability to form alpha helix through potential steric hindrance or other chem properties

H-bonding

Question 22

Globular protein

Answer 22

Assemble into final structure on own, final structure determined by energy states of AA sequences

Question 23

What contributes to an amino acid’s likelihood of being in an alpha-helix? Why is this property less of a concern with beta sheets?

Answer 23

Bulkiness and charges of R groups - adjacent charges branching (steric hindrance), rigid rings (unable to move) destabilize alpha-helices b/c of coiled structure

Greater ΔΔG = harder for AA to be in alpha helix (propensity residue table)

Not a problem for beta sheets b/c beta sheets are horizontal (parallel/anti-parallel) and R groups stick out

Question 24

What is a beta turn? What isoform of proline is likely to be involved?

Answer 24

Secondary structure that causes a change in direction of peptide backbone, connects secondary structures

Trans-proline and cis-proline both can be involved b/c either is energetically favorable (no steric hindrance)

Question 25

Why are proline and glycines prevalent in collagen helices?

Answer 25

Glycine is small and doesn’t cause steric hindrance in the tighter collagen helix structure

Proline stabilizes helix by structuring sharp left beta turns

Question 26

Is the structure in collagen an alpha helix? Why or why not—what’s the difference, if any?

Answer 26

Collagen is NOT an alpha helix
- left-handed (alpha-helix is right-handed)
- abundance of proline and glycines (glycine doesn’t have R group, proline’s ring is bulky)

Question 27

Prion

Answer 27

Misfolded protein that creates amyloids

Dangerous b/c infectious and cause diseases w/ long latency (time btw exposure and infection), fatal and transmissible neurodegenerative diseases (ex: Alzheimer’s, Mad Cow Disease, Kuru)

Question 28

Amyloid

Answer 28

Insoluble buildup of proteins that spontaneously form inside cells

Caused by misfolding proteins that promote misfolding in other molecules of the same protein

Question 29

What might you predict about any difference in amino acid composition between intrinsically unstructured protein and globular protein?

Answer 29

IUPs - more charged and polar (hydrophilic) AAs, on surface, less densely packed
Globular - more hydrophobic AAs, buried and closely packed in interior

Glycine - exception b/c of small size (hydrophobic nature)

Question 30

Post-translational modification

Answer 30

Modification that occurs to AAs after a protein has been translated

Question 31

How can PTM affect amino acid chemistry and protein structure/function?

Answer 31

Addition of chemical groups to AAs

Can affect protein behavior - enzyme function and assembly, protein lifespan, protein-protein interactions, protein folding (changes shape and function)

Question 32

How can PTM affect protein: ligand, enzyme:substrate, and/or protein:protein interactions?

Answer 32

Changes in protein shape can disrupt ability for enzyme:substrate and protein:protein interactions; disruption of specificity

Question 33

Are PTMs permanent? Would it make sense to have them permanent? Why or why not?

Answer 33

NOT permanent - reversible!
There needs to be the ability to change based on envr changes (internal and external conditions)

Question 34

How do energetics contribute to protein structure? Protein folding?

Answer 34

Protein folding = entropy driven, spontaneous (-ΔG)
Final tertiary structure = least energetic, most stable
Unfolded state = most entropic but least stable b/c proteins minimize exposure of hydrophobic AAs to aqueous solvent by folding

Question 35

What determines the preferred structure of a protein?

Answer 35

Most favorable protein structure = less energy

Question 36

Why does heat lead to denaturation of a protein?

Answer 36

Heat incr kinetic energy, causing incr entropy and native states to unfold

Question 37

What would a sudden rise in temperature, or heat-shock, do to proteins?

Answer 37

Cause them to denature, heat-shock proteins created to help lessen impact and rebuild native state

Question 38

Why are almost all AAs in nature L-stereoisomers?

Answer 38

Need to match enzymes for specificity; if not in L conformation, AAs and enzymes wouldn’t be able to work together