1.7 Protein structure and self-assembly

Question 1

polypeptide

Answer 1

long chain of amino acids

Question 2

protein

Answer 2

filed chains of amino acids

Question 3

peptide

Answer 3

short chain of <50 amino acids

Question 4

amino acyl residues (don’t need to know but good to be familiar to avoid confusion

Answer 4

in a peptide = amino acids with either OH (from Carboxyl group) or H (from the amino group) removed in the process of peptide bond formation

equivalents of one H2O removed per peptide bond

Question 5

directionality of proteins

Answer 5

always in the N -> C direction (amino -> carboxyl end)
amino acyl residues are number 1 to “n” in this direction

Question 6

what is the backbone of the polypeptide chain

Answer 6

everything BUT the R group

Question 7

hydrophobic Amino acids

Answer 7

have NON-POLAR side chains

Question 8

Hydrophilic Amino Acids

Answer 8

CHARGED and POLAR side chains

Question 9

acidic amino acids

Answer 9

NEGATIVELY charged

Question 10

basic amino acids

Answer 10

POSITIVELY charged

Question 11

important of sequence and structure in proteins

Answer 11

sequence determines structure
structure determines function

Question 12

Primary structure

Answer 12

sequence of amino acids in a protein

the makeup of R-groups in a polypeptide chain determines the structure of a protein since the backbone is the same and AA are differentiated only by the different groups!

sequence determines the protein’s 3D structure

Question 13

secondary structure

Answer 13

results from interactions of nearby amino acids

alpha helices and beta sheets

both structures are stabilized by H-bonds as they form between the backbone of a folding polypeptide chain

Question 14

backbone interactions (secondary structure

Answer 14

carbonyl group in one peptide bond and an amide group in another form repetitive H-bonds

Question 15

beta sheet

Answer 15

it a flat wobbly thing

adjacent strands can run in the same direction (parallel) or in opposite directions (antiparallel)

antiparallel is more stable

Question 16

tertiary structure

Answer 16

3D shape of a protein

Question 17

what interactions are tertiary structures stabilized by

Answer 17

side-chain interactions
- non-covalent and disulphide bonds
annnnnd interactions between side chains and backbone atoms

Question 18

quaternary structure

Answer 18

multiple folded polypeptide chains!
multiple subunits
form, interact, and are stabilized by non-covalent interactions

Question 19

properly folded proteins will be…

Answer 19

energetically favourable for the whole system

Question 20

denaturation

Answer 20

• protein unfolding
• due to disruption of non-covalent interactions
• can happen by changing pH, temperature, etc. (basically a change in surroundings)
• not all proteins can denature and then regain function

STRONG interactions between side chains = more difficult to denature
WEAK interactions between side chains = easy to denature
basically…
STRONG interaction = more STABLE protein

Question 21

integral membrane proteins

Answer 21

aka transmembrane proteins
cross THROUGH the lipid bilayer

Question 22

peripheral membrane proteins

Answer 22

are associated with the lipid bilayer on either side
NOT EMBEDDED in the lipid bilayer

Question 23

why are easily broken bonds within folded polypeptide chains important?

Answer 23

more dynamic!!
stronger does NOT equal better
folded polypeptide chains have lots of non-covalent interactions

Question 24

other factors that affect interactions

Answer 24

size of side chain
- can potentially increase the number of interactions
- small to big v.s. big to small (“fit”)

hydrophobic (ID-ID) interactions?
- lots of interactions make them very strong!

location in the protein
- interior vs exterior – charged and polar side chains tend to interact with water vs non polar side chains

Question 25

how to approach substitution questions

Answer 25

1. what is the interaction between the existing side chains? (R groups?)
2. does the interaction increase, decrease, or No change if one A.A. is subsituted
3. could this change the stability of the protein? what substitution results in the greatest change?

Question 26

active site

Answer 26

protein folding brings specific amino acids close to each other to form the active site

Question 27

conformation change

Answer 27

shape change
happened when substrates bind in the active site of enzymes

Question 28

competitive inhibition

Answer 28

inhibitor binds to the active site of the enzyme, competing with the substrate and reducing the rate of the reaction

Question 29

non-competitive inhibition

Answer 29

i.e. allosteric regulators

inhibitor binds to a site other than the active site, changing the shape of the enzyme and reducing the rate of the reaction

Question 30

Amino acid residues

Answer 30

amino acids that are incorporated into a protein

Question 31

what determines tertiary structure

Answer 31

determined by the spatial distribution of hydrophilic and hydrophobic R groups along the molecules
◊ As well!! As by different types of chemical bonds and interactions that form between various R grouops
○ Ionic
○ Hydrogen
○ Van der Waals

Question 32

higher-order quaternary structure

Answer 32

many other proteins composed of two or more polypeptide chains or subunits with a tertiary structure that come together
* Polypeptide subunits may be either identical or different
○ Can influence each other in subtle ways and influence their function