lecture 3- proteins

Question 1

proteins are…

Answer 1

polypeptides made of amino acids attached to each other via peptide bonds

Question 2

___ are the building blocks of proteins and have these 4 groups

Answer 2

amino acids
amino (NH3), carboxyl (COO-), hydrogen, R group

Question 3

name the nonpolar, alipathic amino acids

Answer 3

glycine
alanine
proline
valine
leucine
isoleucine
methionine

Question 4

name the 3 nonpolar, aromatic amino acids

Answer 4

tyrosine
phenylalanine
tryptophan

Question 5

name the polar, uncharged amino acids

Answer 5

serine
threonine
cysteine
asparagine
glutamine

Question 6

name the polar, positively charged amino acids

Answer 6

lysine
histidine
arginine

Question 7

name the polar, negatively charged amino acids

Answer 7

aspartate
glutamate

Question 8

R groups of the amino acids next to each other face opposite direction- ___ conformation most common

Answer 8

trans

Question 9

list the structures getting to a protein

Answer 9

primary structure (linear sequence of aa’s) — secondary structure — tertiary (protein) — quaternary

Question 10

describe secondary structure

Answer 10

regular repeats resulting from hydrogen bonds involving the backbone

1- alpha helix (coil, 10-15 aa long)
2- beta pleated sheet (a fold, 3-10 aa long)

Question 11

What sequences of amino acids form alpha helices?

Answer 11

• no consecutive bulky or long R groups
• no consecutive like-charged R groups
• few with polar R groups, especially: Serine, threonine, asparagine, aspartate (these destabilize the helix)
• infrequent glycine (very flexible) or proline (not flexible)

Question 12

describe beta sheets

Answer 12

parallel (n terminuses on same side and C terminuses on same side)
or antiparallel
- beta sheets consist of at least two beta strands

Question 13

name three supersecondary structural elements involving alpha helices

Answer 13

1- helix-turn-helix
2- coiled-coil
3- four-helix bundle

Question 14

describe helix-turn-helix

Answer 14

in proteins, the HTH is a major structural motif capable of binding DNA
- C terminal binds to major groove, N terminal helps to position the complex

Question 15

name three supersecondary structural elements involving beta sheets

Answer 15

1- beta hairpin
2- antiparallel B sheet
3- B barrel

Question 16

supersecondary structural elements can also be ___, and combine several superseoncary elements, including both alpha helices and beta sheets

Answer 16

mixed

Question 17

tertiary structure is determined by…

Answer 17

primary and secondary structures combined with interactions between R groups and the environment (most important interaction is hydrophobic exclusion***)

• others are van der Waals, hydrogen bonding, disulfide, ionic

Question 18

proteins composed of multiple polypeptide chains = ___
name the 2

Answer 18

oligomers

homooligomers- identical subunits
heterooligomers- nonidentical subunits

Question 19

proteins may be ________…. 1/3 of all proteins in higher eukaryotes may lack fixed tertiary structure entirely or at least contain unstructured sections or regions- diversity in binding

Answer 19

intrinsically unstructured

Question 20

name one homooligomer and one heterooligomer

Answer 20

E. coli B clamp (homodimer)

hemoglobin

Question 21

due to a toxin called ___ produced by streptococcus auerus, beta barrel can form pores in the ___ and kill the cell

Answer 21

hemolysin
cell membrane

Question 22

in a nucleotide- the nitrogenous base is linked to the ___’ carbon or ribose/deoxyribose and the phosphate group is linked to the ___’ carbon

Answer 22

1’
5’

Question 23

is the transfer of information into RNA irreversible?

Answer 23

no

Question 24

the double helix of DNA under physiological conditions is in what form?

Answer 24

B form

Question 25

What is more stable, G-C or A-T, why?

Answer 25

G-C (3 hydrogen bonds, not 2)

Question 26

T or F:

all nucleic acids with complementary sequences can form duplexes

Answer 26

true

Question 27

deoxiribose differs from ribose by having

Answer 27

one less oxygen

Question 28

the DNA double helix always has a uniform diameter because ___, which have one ring always pair with ___, which have two rings

Answer 28

pyrimidines
purines

Question 29

Which molecules form the backbone of DNA?

Answer 29

deoxyribose (sugar) and phosphate

Question 30

primary structure of proteins is maintained by ___ bonds

Answer 30

peptide