Protein Structure Function and Biomolecular Interactions

Question 1

What types of molecules can freely pass through a biological membrane?

Answer 1

Cell membranes are semipermeable; therefore, only small hydrophobic and small uncharged polar compounds are able to freely pass.

Question 2

Charged polar amino acids

Answer 2

Glutamic acid, aspartic acid - both acidic with negatively charged carboxyl groups
Arginine,lysine and histidine - all basic and positively charged amino groups
Hydrophilic

Question 3

Neutral polar amino acids

Answer 3

Glutamine, asparagine - amine derivatives of acid forms
Threonine, tyrosine and serine - hydroxyl groups
Cysteine - sulfhydryl group

Question 4

Nonpolar amino acids

Answer 4

Strong:
Valine, leucine, isoleucine, methionine (VILM)
Aromatic: tryptophan, phenylalanine
Proline- in chain, missing amide proton in chain
Weak:
Glycine, alanine

Question 5

Change in free energy equation and meaning

Answer 5

Delta g = delta h - t delta s
Negative = spontaneous
+=non spontaneous
Eg bond formation is negative enthalpy…favorable
Burying hydrophobic residues = increase in entropy…favorable

Question 6

Chemical properties of a peptide bond

Answer 6

Between alpha carboxyl group and alpha amino group of two peptides
Results in loss of water molecule
Some partial double bond nature imparts some rigidity
Directional, polypeptide sequence named n to c terminus

Question 7

Four noncovalent interactions underlying all bio molecular interactions

Answer 7

Hydrogen bonds
Salt bridges (electrostatic interactions)
Van dear Vaals
Hydrophobic interactions

Determines much of protein structure and imparts stability and specificity

Question 8

Hydrogen bonding

Answer 8

Between two electronegative atoms, one a proton donor and one a proton acceptor (orbital with free electrons)
Occur between side chains, diff parts of polypeptide backbone and Side chains with backbone
Most often with polar charged side chains as well as asparagine and glutamine
Important characteristics: fixed distance, all atoms must be colinear (think alpha helix),
Can form with water making unfavorable to bury polar side chains unless they can hbond internally with other side chains

Question 9

Electrostatic Interactions

Answer 9

Aka salt bridges
Between oppositely charged groups
Can also have repulsion between same charged groups
Distance is only geometric constraint
Water can shield charge so charged side groups often on outside of protein
Most commonly aspartic acid, glutamic acid, lysine, arginine, (histidine less positive so less common)

Question 10

Van der waals

Answer 10

Between any two adjacent atoms that don’t actively repel one another… it’s energetically favorable for molecules to clump together

Question 11

Hydrophobic interactions

Answer 11

Hydrophobic molecules interact with one another in hydrophobic environment because it increases the entropy of the water molecules forming a solvent cage around them..higher entropy meanS more negative delta g free energy means more favorable interaction
Think large nonpolar side chains

Question 12

Properties of aa side chains changed by PTMs

Answer 12

Predominantly charged polar or neutral polar side chains

May allow side chains to interact more strongly with one another

Question 13

Post translational modifications (ptms)

Answer 13

Covalent modifications to aa side chains
Reversible
Catalyzed by enzymes (Rapid) in forward and backward directions
Formation of disulfide bonds with cysteine is only spontaneous
Can regulate fxn by turning interactions On or Off

Question 14

Phosphorylation

Answer 14

Type of PTM
Confers a -2 charge on a previously neutral side chain PO4(-2)
Kinases

Question 15

Acetylation

Answer 15

Changes a +1 side chain (basic) to 0
Predominantly Lysine (like ubiquitination!)
COCH3 group added
Often histones
More hydrophobic interactions as a result

Question 16

pKa

Answer 16

The pH at which 50% of a weak acid or weak base is protonated
When pH < pKa protonated
When pH > pKa deprotonated

Question 17

How pH affects charge of amino acid side chains

Answer 17

Histidine can be 0 or +
Lysine
Arginine
Cysteine can be 0 sh or - S-
Tyrosine can be 0 OH or - O-
Aspartate 
Glutamate
extent of charge depends on ph according to Henderson hasselbach equation

Question 18

How do the chemical properties of amino acids and primary sequence govern the formation of higher types of structure?

Answer 18

Steric constraints (covalent bonds fixed distance, peptide bond rigidity)
THE MOST ENERGETICALLY FAVORABLE CONFIGURATION FOR A POLYPEPTIDE WILL DETERMINE ITS STRUCTURE
 Formation of low energy secondary structures
Tertiary and quaternary structure made possible by noncovalent interactions, primarily hydrophobic effect
Same chemistry makes Ligand bonding!

Question 19

Alpha helix

Answer 19

Made possible by hydrogen bonding between carboxyl group of n and amino group of n+4
Side groups point out and those directly on top of one another often interact favorable or at least don’t repel(both polar or nonpolar) or else electrostatic stretch
Proline will also disrupt bc bend in chain and lacking amino proton for hbond with previous carboxyl group
Often amphipathic with one side facing polar solution and one side facing hydrophobic interior
Right handed with 3.6 aa per turn

Question 20

Beta pleated sheet

Answer 20

Made up of beta strands that can be close or distant
Stabilized by hbonds between amino and carboxyl groups on different strands
Strands Can be parallel or anti parallel
Side groups point up and down, polar and hydrophobic, when both on each side called amphipathic
Covalent bonds in peptide backbone create bending/twisting

Question 21

Calcium signaling

Answer 21

Influx of calcium ions bind to acidic residues, cause calmodulin (CaM) to take on a rigid shape due to formation of new alpha helix
The new alpha helix binds Cam kinase 1 and activates it by removing the Cam Kinase peptide from its active site where it had been blocking the kinase activity
Therefore, ca2+ is an allosteric effector of calmodulin and the ca2+ bound form of calmodulin is an allosteric effector of Cam kinase 1

Question 22

Isoelectric point

Answer 22

pI is the ph at which there is no net charge on a protein
If the pI > pH…positively charged
If the pI < pH…negatively charged

Question 23

RTK Signalling

Answer 23

Ligand (eg growth factor) binds receptor, receptor dimerizes and autophosphorylates trans, activates GEF guanine nucleotide exchange factor. GEF involved in small gtpase switch with Ras, causing inactive Ras to become active by releasing GDP and binding GTP.
Active Ras activates raf/Mek
Ultimately activating MAPKinase which phosphorylates in the nucleus leading to a txnal response

Question 24

Small GTPase switch

Answer 24

Inactive Ras bound to gdp. Activated GEF guanine nucleotide exchange factor (eg Sos) binds, causing inactive Ras to become active by releasing GDP and binding GTP. The binding of gtp changes ras conformation and it releases gef.
Ras has natural ability to hydrolyze gtp, but this is aided by gap gtpase activating protein. When gtp hydrolyzed to gdp, adding a P to another molecule (eg Raf or Mek) ras changes conformation releasing the gap and returning to its inactive form.

Question 25

GPCR Signaling

Answer 25

Signaling molecule binds gpcr receptor, inside membrane receptor binds galpha subunit (type s or type q)
Changes conformation of alpha subunit, binds gtp, releases beta and gamma subunits
Gtp bound alpha is active and activates second messenger pathway
Eg binds to ac (adenyl clyclase)
Or binds to PLC which cleaves PIP2 into DAG and IP3
DAG activates PKC
IP3 activates CaM Kinase 1

Question 26

Sds page

Answer 26

Separates based on size (molecular weight or more accurately length)
Uses sds detergent to denature (hydrophobic tail accomplishes this) and polar head of sds gives negative charge so it migrates towards positive node

Question 27

Urea page

Answer 27

Separates based on size and charge
Urea denatures but does not affect charge so preserves native charge
Protein applied in middle and can migrate toward anode or cathode