Week 2

Question 1

What makes up an amino acid?

Answer 1

alpha carbon
amino group
carboxyl group
R group

Question 2

What kind of bond is formed between two amino acids? How?

Answer 2

covalent peptide bond
condensation reaction between OH on carboxyl and H from amino group of 2 amino acids

Question 3

How often is H bonding repeated? Between which atoms?

Answer 3

3.6 aa/turn
carbonyl O and amide H 4 aa’s later

Question 4

overall protein structure

Answer 4

primary (sequence) –> secondary (local folding) –> tertiary (long-range folding) –> quaternary (multimeric organization) –> multiprotein complexes

Question 5

primary

Answer 5

amino acid sequence
Amino group, Hydrogen, and carboxyl all attached to alpha carbon

Question 6

What does the R group determine?

Answer 6

acid/base, uncharged polar, nonpolar
OVERALL CHARACTERISTICS
type of aa

Question 7

What determines the amino acid used?

Answer 7

3 RNA letter sequence

Question 8

What trend does the amino acid chart unintentionally adhere to and why?

Answer 8

grouped somewhat by polarity because helps cells withstand some mutations / major mutation
if only one letter is messed up and changes the amino acid used, it will still have similar properties as the intended amino acid

Question 9

What bond can 2 cysteine amino acids form?

Answer 9

disulphide bonds

Question 10

What amino acid forms disulphide bonds?

Answer 10

cysteine
R group = H2C-SH —> S-S

Question 11

How are disulphide bonds between 2 cysteine amino acids formed?

Answer 11

in OXIDATION conditions, 2 S’s form a covalent bond

Question 12

What are the 2 types of cysteine disulphide bonds?

Answer 12

1. INTERchain: b/w 2 different proteins/polypeptides
2. INTRAchain: w/i same polypeptide/protein

Question 13

What is the function of disulphide bonds?

Answer 13

braces, stabalises protein structure

Question 14

Under what conditions and where in the cell do disulphide bonds form?

Answer 14

cytosol - REDUCTION environment so no bonds
endoplasmic reticulum - OXIDATION environment so bonds form

Question 15

What organelle aids in linking 2 amino acids? How?

Answer 15

RIBOSOME takes OH from carboxyl and H from amino
note: never from side R chain

Question 16

What is the carbon in the peptide bond called?

Answer 16

carbonyl (from carboxyl carbon)

Question 17

What is the nitrogen in the peptide bond called?

Answer 17

amide (from amino nitrogen)

Question 18

Quick way to find peptide bond?

Answer 18

look for O=C-N

Question 19

What is the backbone of a polypeptide comprised of? What is the pattern? How do you distinguish the 2 ends?

Answer 19

residues (peptide bonded amino acids)
N-C-C
amino end - N terminus
carboxyl end - C terminus

Question 20

How do you order/number residues? What is important not to change?

Answer 20

Left N terminus to right C terminus (unless told otherwise)
don’t change order of individual ends or direction of residues

Question 21

True or false: Amino acid side chains help to stabilize alpha-helix and beta-sheet secondary structures.

Answer 21

false

Question 22

Compare DNA and an alpha helix (3 main things)

Answer 22

1. side chain direction
   alpha - R groups face outwards
   DNA - bases faces inwards
2. strands
   alpha - 1
   DNA - 2
3. ordering/ends
   alpha - N and C terminus
   DNA - 5’ and 3’ ends

Question 23

Do side chains stabilize the helix?

Answer 23

no