Protein Structure Flashcards
What is the pK1 of an amino acid?
pKa of carboxyl group
pH < pK1, prevalent form = mostly protonated
pH > pk1, prevalent form = mostly deprotonated
What is the pK2 of an amino acid?
pKa of amino group
What is the pKr of an amino acid?
pKa of side chain, determines whether the side chain of an AA will carry a charge at biological pH
What is a weak acid or base? How do they act as buffers—what does this mean?
Weak acids can act as buffers in pH range near pKa, little change in ionization state within buffering range
pI
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 = -
How are these physical properties related to amino acid chemistry? How are they related to protein structure and function?
pKas tell us likely state of AAs at biological pH
AAs are metabolic intermediates - changes charge of structure, leads to overall chemical structure changes
What is the amino acid sequence in the peptide PHKLISTHMDERTFWAGNY? What amino acid is not present in this peptide?
Pro-His-Lys-Leu-Ile-Ser-Thr-His-Met-Asp-Glu-Arg-Thr-Phe-Trp-Ala-Gly-Asn-Tyr
Valine, Glutamine, Cysteine are missing
Can you spell your name or initials in amino acids?
Ser-/-Met-Met-Ala-Tyr-Ala-His
Ser-Glu-Ala
Is any fraction of acidic amino acids protonated at pH=7.4? Any basic amino acid?
No acidic AAs, basic AAs - lysine, arginine, histidine
What pH range would you expect all of the groups on all amino acids to be protonated? All deprotonated?
Below 2.2 (acidic conditions) - protonated
Above 9.7 (basic conditions) - deprotonated
What would be the net charge of the peptide KTMNGRDDHDEFFW at pH 7.4?
Use method for finding pI of AA w/ ionizable group
Why is a peptide bond planar?
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
What limits the possible angles around the other bonds—phi and psi?
Steric hindrance from R groups
What bonds contribute to the phi and psi angles?
Covalent bonds
Primary protein structure
AA sequence
Secondary protein structure
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
Tertiary protein structure
Geometric arrangement of all atoms in a protein, sum of all secondary structures
Quaternary protein structure
Polypeptide formed via interactions of individual tertiary structures
What contributes to an alpha helix?
R-groups influence ability to form alpha helix through potential steric hindrance or other chem properties
What is a hydropathy plot? What information does it show? How can it help to predict a membrane protein’s organization?
Hydropathy index - influences whether an AA within a peptide is likely to be exposed to aqueous envr
What contributes to an alpha helix?
R-groups influence ability to form alpha helix through potential steric hindrance or other chem properties
H-bonding
Globular protein
Assemble into final structure on own, final structure determined by energy states of AA sequences
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?
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
What is a beta turn? What isoform of proline is likely to be involved?
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)
Why are proline and glycines prevalent in collagen helices?
Glycine is small and doesn’t cause steric hindrance in the tighter collagen helix structure
Proline stabilizes helix by structuring sharp left beta turns
Is the structure in collagen an alpha helix? Why or why not—what’s the difference, if any?
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)
Prion
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)
Amyloid
Insoluble buildup of proteins that spontaneously form inside cells
Caused by misfolding proteins that promote misfolding in other molecules of the same protein
What might you predict about any difference in amino acid composition between intrinsically unstructured protein and globular protein?
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)
Post-translational modification
Modification that occurs to AAs after a protein has been translated
How can PTM affect amino acid chemistry and protein structure/function?
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)
How can PTM affect protein: ligand, enzyme:substrate, and/or protein:protein interactions?
Changes in protein shape can disrupt ability for enzyme:substrate and protein:protein interactions; disruption of specificity
Are PTMs permanent? Would it make sense to have them permanent? Why or why not?
NOT permanent - reversible!
There needs to be the ability to change based on envr changes (internal and external conditions)
How do energetics contribute to protein structure? Protein folding?
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
What determines the preferred structure of a protein?
Most favorable protein structure = less energy
Why does heat lead to denaturation of a protein?
Heat incr kinetic energy, causing incr entropy and native states to unfold
What would a sudden rise in temperature, or heat-shock, do to proteins?
Cause them to denature, heat-shock proteins created to help lessen impact and rebuild native state
Why are almost all AAs in nature L-stereoisomers?
Need to match enzymes for specificity; if not in L conformation, AAs and enzymes wouldn’t be able to work together
