Lecture 3 - Proteins

Question 1

levels of protein organization

Answer 1

primary - amino acid sequence
secondary - alpha helix and beta sheets, hydrogen bonds
tertiary - polypeptide chain
quaternary - assembled structure

Question 2

what do all amino acids have

Answer 2

• carboxyl group
• amino group
• single carbon atom (alpha carbon)
• unique side chain (R group)

Question 3

all amino acids except one have an asymmetric alpha carbon which one doesnt

Answer 3

glycine

Question 4

amino acids used in the synthesis of a protein are always?

Answer 4

L-amino acids

Question 5

which amino acids are non-polar and what are their characteristics

Answer 5

ala - A
val- V
leu - L
ile - I
met - M
phe - F
trp - W
pro - p
- hydrophobic side chains
- hydrophobic interactions and van der waals forces
- form inner core of soluble proteins away from aqueous medium
- associate with lipid bilayer

Question 6

which amino acids are polar and uncharged and what are their characteristics

Answer 6

ser - s
thr - t
gln - q
asn - n
tyr - y
cys - c
- hydrophilic side chains that have partial + or - charge
- form h bonds and associate with water
- S,T,Y -> OH groups that can be phosphorylated

Question 7

which amino acids are polar and charged and what are their characteristics

Answer 7

asp - D (-)
glu - E (-)
lys - K
arg - R
his - H
- hydrophilic side chains act as acids or bases
- side chains from ionic bonds

Question 8

Which amino acids have side chains with special properties

Answer 8

• glycine : flexible and can tightly pack, side chain only has hydrogen and can fit into either hydrophobic or hydrophilic
• cysteine : disulfide bond formation
• proline : breaks secondary structure

Question 9

explain peptide bond formation

Answer 9

• stepwise addition of each new amino acid occurs via condensation (dehydration)
• process of elongating a chain of amino acids = protein synthesis
• peptide bond forms between carbonyl carbon and amide group nitrogen

Question 9

describe the secondary structure folding of the peptide backbone

Answer 9

• turns and loops common
• hydrogen bonds among amino acids

Question 10

What will determine whether the alpha helix is hydrophobic or hydrophilic

Answer 10

• depends on the R group whether it is hydrophobic or hydrophilic

Question 11

What are the 5 different constraints that affect the formation/stability of an alpha helix

Answer 11

1. electrostatic repulsion or attraction between successive amino acid residues with charged R groups
2. bulkiness of adjacent R groups
3. interactions between R groups spaced 3 or 4 residues apart
4. helix forming amino acids include: L, M, E
5. helix breakers include P and G residues

Question 12

what do the constraints mean for alpha helix

Answer 12

• tendency of a given segment of a polypeptide chain to fold up as an alpha helix depends on the identity and sequence of amino acid residues within the segment = primary sequence determines structure

Question 13

beta-sheet

Answer 13

• hydrogen bonding
• may involve different polypeptides or different regions of a single polypeptide
• include - I, V, F

Question 14

What are motifs

Answer 14

• units of secondary structure that consist of short stretches of alpha helices and beta sheets connected by loops or turns

Question 15

What common functions can structural motifs perform

Answer 15

• dna binding
• EF hand
• protein protein interaction

Question 16

What stabilizes tertiary structure

Answer 16

1. h bonds
2. ionic bonds
3. van der waals
4. hydrophobic interactions
5. disulfide bridges
   - covalent and noncovalent bonds between the side chains of the protein
   - weak nature of stabilizing forces allows protein to undergo changes in shape
   - unlimited number of conformations

Question 17

what are some experimental methods to determine tertiary structures

Answer 17

• x-ray crystallography
• NMR spectroscopy

Question 18

example of proteins with similar structure and function

Answer 18

• actin and MreB = no similarity at primary level but similarity at tertiary level

Question 19

What is a domain

Answer 19

• locally folded unit of the overall tertiary structure
• 50-350 amino acids long
• proteins with multiple functions have separate domain for each function

Question 20

are proteins static

Answer 20

• no they are capable of internal movements
• every activity in which a protein takes part in is accompanied by conformational changes within the molecule

Question 21

homodimer and heterodimer

Answer 21

• part of quaternary structure
• homodimer = protein composed of 2 identical subunits
• heterodimer = protein composed of 2 non identical subunits

Question 22

Fibrous proteins

Answer 22

• have extensive regions of secondary structure
• highly ordered and repetitive structure
• most common in structural material that resides outside of the cell
  ex. fibroin proteins
  keratin proteins
  collagen
  elastin

Question 23

globular proteins

Answer 23

• different segments of polypeptide chain fold back on each other = compact structure
• mainly in alpha helical, beta sheet or both
  ex. enzymes
  chaperones
  transport proteins
  immunoglobulins

Question 24

what is denaturation and how does it occur

Answer 24

- unfolding of a protein - detergents, organic solvents, radiation, heat, urea

Question 25

explain protein folding using ribonuclease

Answer 25

- denatured ribonuclease can re from form the unfolded protein in vitro - refolded molecules were indistinguishable both structurally and functionally from the correctly folded

Question 26

what path do proteins take when folding

Answer 26

- fast - funnel down to most energetically favorable state

Question 27

what are molecular chaperones

Answer 27

- assist in protein folding - bind to short stretches of hydrophobic amino acids that are exposed in non native proteins to facilitate proper folding - proteins can be released from the chaperones to spontaneously fold into their native state - can be repeatedly bound and released until they are fully folded - larger proteins are transferred to chaperonins

Question 28

what happens if the wrong amino acid is incorporated

Answer 28

- mutations (mad cow, scrapie, creutzfeldt-jacob disease) - sickle cell (E substituted by V)