KH1-5

Question 1

informational biopolymers
是什么+特点

Answer 1

DNA RNA proteins

-linear
-asymmetry monomer
-unidirectional growth
-covalently linked

Question 2

Why DNA is stable

Answer 2

1. 2-H（lack of 2-OH）：more resistant to chain cleavage
   2.Thymine：比uracil多一个CH3， makes some chemical damage easier to repair

Question 3

bond in 核酸

Answer 3

N-glycoside bond
phosphate-dieaster

Question 4

nucleotide

Answer 4

with phosphate

Question 5

DNA：（）handed helix

Answer 5

right
B DNA

Question 6

amino acid （）stereoisomers

Answer 6

L-stereoisomers

Question 7

direction of growth of amino acid

Answer 7

C terminus

Question 8

() strand is identical to the newly synthesized strand

Answer 8

non-template

Question 9

start codon
stop codon

Answer 9

AUG
UAA UGA UAG

Question 10

energized monomer

Answer 10

dNTP
rNTP
aminoacyl tRNA

Question 11

secondary structure

Answer 11

local
H-bond in backbone (C=O and N-H)

Question 12

alpha helix

Answer 12

N and N+4
3.6 resides/turn
side-chain determine properties

Question 13

beta sheet

Answer 13

2 faces

Question 14

tertiary structure

Answer 14

overall conformation of protein
domain and motif

Question 15

coiled-coil motif

Answer 15

2 helix
heptad repeat (1,4 hydrophobic, distance 3.5 residues)

Question 16

EF hand

Answer 16

2 helix + loop
Ca2+ binding

Question 17

Zinc finger

Answer 17

1 helix + 2 sheets
common in transcription factors
bind to DNA/RNA

Question 18

Domain vs. Motif

Answer 18

motif: local small, not independent

Question 19

example of domain

Answer 19

Hemagglutinin HA2

Question 20

size of domain

Answer 20

> 40 aa

Question 21

bond type in 2 3 4 protein structure

Answer 21

non covalent

Question 22

superamolecular complexs

Answer 22

multi proteins
euka
dynamic
transcription intiation complex

Question 23

non covalent structural interactions in protein

Answer 23

H bond: 2/ polar side chain
ionic : charged side chain
van der waal: hydrophobic side chain

Question 24

covalent structural interaction

Answer 24

disulfide bonds
cysteine (intra/interchain)
ex.insulin

Question 25

what will misfolded protein do?

Answer 25

aggregation (hydrophobic parts)

Question 26

N terminus start folding when

Answer 26

C terminus is still synthesize

Question 27

Chaperons

Answer 27

permit partially misfolded protein return to proper folding pathways
looking for hydrophobic patches
ATP dependent
can be unregulated

Question 28

2 main classes of Chaperons

Answer 28

molecular chaperones
chaperonins

Question 29

molecular chaperones

Answer 29

Hsp 70
newly synthesized and wrong confirmation
bind to hydrophobic residues prevent aggregation

Question 30

Hsp 60
what
structure
process

Answer 30

group 1 chaperonins (bacteria and mitochondria in our cell)
Gro EL (tall or short)
Gro ES
2 different shape chamber
3 ATP
EL change shape change
what happened inside unclear: maybe the change in shape is important in folding or the water inside the chamber has different properties than outside

Question 31

group 2 chaperonins

2 difference with group 1

Answer 31

(eukaryotic cytoplasm)

1. 8 different proteins in each chamber
2. no separate lid

Question 32

irretrievably proteins

Answer 32

destroy be proteolytic cleavage

Question 33

what does E1 E2 E3 do

Answer 33

E1: first bind with Ub in cytoplasm
E2: replace E1
E3: recognize the target protein
let E2 transfer Ub to covalently link to lysine

Question 34

Ub

Answer 34

76 residue aa

Question 35

structure and function of proteasome

Answer 35

2 19S cap: Ub-receptor, ATPase, DUB
Ub-receptor: recognize and bind poly ub
DUB: remove Ub by hydrolysis
ATPase: unfold the protein using ATP

then feed into 20S core
protease on inward surface degrade the protein

Question 36

advantage of the central core of proteasome

Answer 36

avoid destroy other protein in the cytoplasm

Question 37

how amyloid cause disease

Answer 37

amyloid precursor: contain alpha helix
cleavage of the helix
unstable, transfer to beta sheet
aggregation into filaments resistant to proteolysis

Question 38

amyloid cause what disease

Answer 38

帕金森 阿尔兹海默症 疯牛病

Question 39

what is Kd

Answer 39

lower Kd, stronger interaction

Question 40

what is CDR

Answer 40

binding site of antibody and antigen

Question 41

Vmax

Answer 41

max reaction rate
depends on amount and efficiency

Question 42

Km

Answer 42

the substrate concentration that supports a rate of a catalysis equal to 1/2 of Vmax depend on affinity of enzyme

Question 43

what does Trypsin cut

Answer 43

positively charged (Asp-189 negatively charged)

Question 44

what does Chymotrypsin cut

Answer 44

non charged (Ser-189 neutral)

Question 45

what does elastase cut

Answer 45

small molecule (Val 190, Val216)

Question 46

trypsin catalytic reaction

Answer 46

step 1
form the enzyme-substrate complex (Ser 195 acyl enzyme)
release the N terminus

Step 2
break the bond of the complex
release the C terminus

both depends on the His-57’s ability to bind and release enzyme

Question 47

allosteric effects

Answer 47

Binding of a ligand at one site on a protein can lead to conformational
changes that affect the binding of another ligand molecule at a different
site.

ex. Hsp 70 ATP binding and the target protein binding

Question 48

how Ca2+ involve in allosteric switch in EF hands

Answer 48

Ca2+ open the structure, give a empty space for peptide binding

Question 49

how G protein switch on/off

Answer 49

On: GTP, GAP come facillitate hydrolysis, inactive G protein

Off: GDP, GEF come facilitate GTP binding