1. Principles of biomolecular structures

Question 1

Define primary, secondary, tertiary, and quaternary structures

Answer 1

Primary: The sequence of amino acids Secondary: backbone conformation (a helices/b sheets) Tertiary: 3D conformation “fold” of secondary elements Quaternary: association of multiple tertiary structures

Question 2

What is the most common sereoisomer of an amino acid?

Answer 2

The L-stereoisomer

Question 3

Name the 5 + 1 aliphatic amino acids (1 letter, 3 letter, full name)

Answer 3

Glycine, (Gly, G) H Alanine (Ala, A) CH3 Proline (Pro, P) Loop Valine (Val, V) V Leucine (Leu, L) Y Isoleucine (Ile, I) L

Question 4

Name the 3 + 1 hydrophobic amino acids (1 letter, 3 letter, full name)

Answer 4

Methionine (Met, M) CH3-S-CH2-CH2 Tryptophan (Trp, W) B Phenylalanine (Phe, F) phe-CH2 Isoleucine (Ile, I) L

Question 5

Name the 6 Polar amino acids (1 letter, 3 letter, full name)

Answer 5

Serine (Ser, S) OH-CH2 Threonine (Thr, T) V-OH Tyrosine (Tyr, Y) OH-phe Asparagine (Asn, N) H2N-C=O Glutamine (Gln, Q) (H2N-C=O)-CH2 Cysteine (Cys, C) SH-CH2

Question 6

Name the 3 basic* and 2 acidic* amino acids *at neutral pH

Answer 6

Lysine (Lys, K) NH3+-(CH2)*4 Arginine (Arg, R) 3(NH2)-C+ - (CH2)3 Histidine (His, H) imidazole-CH2 Aspartate (Asp, D) O-C-O - CH2 Glutamate (Glu, E) O-C-O - CH2 - CH2

Question 7

What are the 2 acidic ionizable groups in proteins?

Answer 7

Terminal alpha carboxyls (Aspartic/Glutamic acid) Histidine

Question 8

What are the 5 basic ionizable groups in proteins?

Answer 8

Terminal alpha amino groups Cysteine Tyrosine Lysine Arginine

Question 9

What are the two resonance forms of a peptide bond? What is a consequence of this dipole on the atoms involved? What does that mean for the mobility of the amino acid as a whole?

Answer 9

N-C=O <-> +N=C-O-

Atoms involved are locked in a panar state

The aa has two rotatable bonds because of this on either side of the R group

Question 10

What are the two confromations of a peptide bond?

Which one is more favored? When is that not the case?

Answer 10

Cis or trans

Trans is more favored (cis has too much steric hindrance)

X-Pro bonds have steric hindrance in either conformation and thus are found in equal populations

Question 11

What are the phi and psi angles in a peptide? How can they be plotted? Why are there only so many combinations of angles?

Answer 11

R-C-C=O = Psi

R-C-C-N = Phi

Can be plotted via a Ramachandran plot, shows sterically possible conformations

Question 12

What are the signs of the phi and psi torsion angles in an alpha helix?

What is the “handedness” of an alpha helix formed by L-amino acids?

How are alpha helices stabilized?

How does the alpha helix present its dipole?

Answer 12

Both negative torsion angles

L-amino acids form a right-handed helix

Stabilized between carbonyl O of residue i and amide group of i + 4

Strong dipole along the axis of the helix

Question 13

Name a protein secondary structure that is not an alpha helix or a beta strand, and specify how it is stabilized

Answer 13

Turn

Most common is the reverse or beta turn

Stabilized by Hbonds between residues i and i + 3

Question 14

What are the signs of the torsion angles in a beta strand?

Can this strand stand on its own? How is it stabilized?

Answer 14

Negative phi and positive psi torsion angles

Cannot stand on its own, stabilized by cross-strand H bonds (can be both parallel and anti-parallel)

Question 15

When folding the secondary structure (forming the tertiary structure) what happens to the protein in order to stabilize interactions?

How do proteins begin folding?

Answer 15

A hydrophobic core is formed

Very tightly efficient, few empty cavities

Usually spontaneous process

Formation of intermediates, secondary structure forms very early on

Question 16

Name and describethe 4 interactions that stabilize protein folding

Which one is less seen in the cytosol?

Answer 16

Hydrogen Bonding:

Between an electronegative X-H and a free electron pair Y: (don’t stabilize per se, unfavorable to produce)

Salt bridging:

hydrogen bond between two groups of full opposite charge

Van der Waals forces:

Maintains tight packing, relevant at close range

Disulfide bonding (less seen intracellularly due to reducing environment of cytosol):
involves two cysteine side-chains

Question 17

Describe the hydration shell.

Is the shell important?

Why can some water molecules detectable in crystal structures, whereas some aren’t?

Answer 17

A layer of bound water molecules on the surface of a protein

Integral part of structure, stabilized by hydrogen bonds

Some have unique positions (can be observed) while some are mobile and exhange rapidly

Question 18

Why are aliphatic/aromatic side chains found inside protein folds whereas polar/charged side chains tend to face out of the protein?

Answer 18

To form H bonds with water molecules outside, compensating for the loss of entropy caused by ordered water molecules

Not the same as VdW forces

Question 19

What are examples of non-protein stabilizers when a protein folds?

Answer 19

Metals (Zn finger motifs) and co-factors (heme)

Question 20

What does the sum of all stabilizing interactions determine?

What can shift it?

What is a chaotropic agent and how does it affect it?

Answer 20

Range of stability: The map of pressure/Temperature combinations that the protein can withstand before denaturing

mutations in proteins can shift this range

Chaotropic agents (urea/guanidium hydrochloride) decrease the entropy of water and also denature the protein

Question 21

What are chaperones and what are their two functions regarding protein synthesis?

What happens if these chaperones do not exist, or if hydrophobic side-chains are exposed?

Answer 21

Proteins that assist the folding of a protein by either allowing the protein to escape a trapped intermediate state (local minimum) or preventing the nascent protein from aggregating

Aggregation can occur from misfolded proteins

Question 22

What are post translational modifications and their purposes?

Answer 22

Protease cleavage (activation/structural changes)

Ser, Thr, and Tyr phosphorylations which activates/inactivates proteins, induces new interactions, causes relocalizations or secretions

Lys or N-terminal ubiquitination, which can signal degradation or relocalization

Ser or Asn Glycosylation, which can induce secretion/refolding

Lys methylation/hydroxylation, N-terminal acetylation, acylation, lipidation, etc

Question 23

What is the difference between an integral and peripheral protein?

What secondary strucutre is more prevalent in these membrane proteins?

What is another structure that is observed?

Answer 23

Integral - inside membrane

Peripheral - on surface

Alpha helices (with hydrophobic side chains interacting withnon-polar lipid chains) more common

Also Beta Barrels

Question 24

What is the difference between orthologs and paralogs?

Answer 24

Orthologs: homologs that evolved from a common gene (eg pyruvate kinase in humans and E. coli)

Paralogs: evolved by gene duplication within the same genome (human Src and Abl kinases)

Question 25

What is a protein motif?

What is Convergent evolution?

Answer 25

Specific topology/arrangement of secondary structure elements

Sequence motifs typically give rise to the same structural motif, however the same structural motif can arise from unrelated sequences

Question 26

What is the difference between molecular/accessible surface area and buried surface area?

What is correlated with a larger BSA?

Answer 26

Molecular/accessible is the VdW surface contact plus the reentrant surface generated with a molecular probe (eg water)

Buried surface area (BSA) is the difference between the sum of the individual subunits’ surface and that of the complex

Larger BSA correlated with stronger interactions

Question 27

What does the order parameter S² characterise?

Answer 27

The degree to which a specific orientation is maintained in a dynamics context