6: protein function

Question 1

ubiquitination

Answer 1

adds 75 ama -> degrades unwatned protein

Question 2

add acetyl group

Answer 2

acetylation

Question 3

sumoylation

Answer 3

add SUMO, an ubiquin-like modifier
=> repress gene expression

Question 4

demonstrate the role of kinase and phosphatase

Answer 4

amino acids’ HYDROXYL is phosphorylated w/ help of kinase = an enzyme tht catalyze the transfer or PO4 to that molec
reversts back using phosphatase = catalyzes hydrolysis

Question 5

___ bind metal ions necessary for activity in enzyme

Answer 5

metalloprotein

Question 6

adds fatty acids, alter location

Answer 6

myristoylation and farnesylation

Question 7

glycosylation

Answer 7

affects protein folding solubility and binding to other molec

Question 8

how does P53 work?

Answer 8

as tumour supressor protein, when stress/UV/radiation, PMT signal to kinase, activate via phosphoryaltion, cell apoptosis & DNA repair

Question 9

protein and ligand: the general

Answer 9

priteins contains a binding site to which the ligand binds
binding: ionic, hydrophobic

Question 10

what is myoglobin? heme? histidien?

Answer 10

myoglobin consists of 8 a-helices and 1 heme prosthetic group
is O-binding protein; O is the ligand

Heme: 4 N coordination stabilizes the Fe in the centre
This binds to Histidine: O interacts with Fe; His E7 comes clower to O to stabilize

Question 11

ligand binding as described by…

Answer 11

Kd

PL <-> P + L Kd = PXL/PL

lower Kd, high affinity tight bonding

Question 12

Mb + O2 <-> MbO2 as described by

Answer 12

Y02 (fractional sat of myoglobin)= pO2 (partial P) / K + partial P

Question 13

when Kd = P02
when K = P50

Answer 13

half of the bonding iste is occupied
myoglobin’s partial P is half sat
p05 is 2.9 torr
after that, increase rapidly

Question 14

Bohr effect:

carbonic acid dissociates into ___ acid and ___
__ binds to ___

in acidic enviro, promotes a bond btw __ & ___ (salt bride) and stable T state
since __ < ___, becomes ___: Hemo release o2 into circulatory system -> lungs

Answer 14

carbon dioxide diffuses in
-> meets H20 and carbonic anhydrase
-> creates carbonic acid

=> in CO2, ___ pH ___ affinity
histidine & B-subunit
pK 6 > pH / deprotonated

Question 15

O2 binding to Hemo is ____
create

Answer 15

cooperati9ve
S shaped curve

Question 16

from T to R state

Answer 16

low ot high affinty
deoxy to oxy

a conform change occur: bind at a- & B- glohin and is oxygenated
in T state, HisF8 is proportional to Heme; in R state, becomes clower and stabilize

Question 17

role of bisphosphoglycerate BPG

Answer 17

stabilize T state; w/o it, Hemo bidns to O2 too tightly can’t realease it in tissue
in high altitudes, RBC creates more BPG
create a less steeep graph

Question 18

how harmful can Hb variants be?

Answer 18

Hb variatns causing disease

Boston, Milwauke, and Iwate: promotes methomoglobin formation
Yakima: disrupt H bond that stabilize T state

Question 19

doesnt bind to O2 well
mutation ___ in __ chains -> 2 fewer negative charges
REPLACE w/ ___ creates ___ interactions
Hb aggreates __< becomes ___

Answer 19

Sickle cell
Ê6V / B
valine hydrophobic
form / sickle-shaped

Question 20

use of OHPro

Answer 20

stabilize 3x helix via H bonds and promtoes conform of 3 a-chains
allow thermal stability at 37c

Question 21

describe collagefn 3x

Answer 21

made of 3 intertwined poly-Pro type II chains
every 3rd if Gly or kink
Gly’s side chain is amll enough tb the centre

Question 22

poly-proline type II helix vs a-helix

more extended
no intra-chain __ bonds of ___ & __ IS WIDE ENOUGH
STABILIZED BY s___ ____ of Pro;s side chains
___ residues per rurn

Answer 22

H /amide / O
steric repulsion
3

Question 23

describe collagen formation:

is synthesized as ——-
polypop catalyzed that 3 strands into __-____ ______
is dumped into extracellular by _______
collagen fibrils aggregate to form collage ___

Answer 23

pro-collagen polypep
pro-collagen molec
pro-peptidase
fibers

Question 24

___’s chain will itneract with Lys’s NH3_
-> INVOLVED IN CROSS LINKING, CREATE COV BOND
-> stabilize collagen fibrils

Answer 24

allysine

Question 25

lysine? OhLys? forming

Answer 25

lys is involved in cross linking and creates cov bond
Lys -> allysine
OHLys -> OHallysine
catalyzed by lysineoxidase

OHlys: served as a site for sugar addition; catalyzed by Lys Hydroxylase

Question 26

collagen mutation with ascorbic acid

Answer 26

Hydroxylation requires ascorbic avid
no vit C, no collagen fibril formation
=> scurvy: bleeding gum, loose teeth and unhealing woubds

Question 27

collagen mutation with Cu

Answer 27

Lysxyloxidase requires Cu
no Cu, no ross link formation
Ehlers Danlos syndrome; grp of connected tissue disorder
LOOSE skin, hypermobile joints

Question 28

collagen mutation with defect of type I collagen genes

hint: OI / mineral and bone

Answer 28

creates Osteogenesis Imperfecta
no Glyc in 3x helix: collagen fibril doesnt pack normally poor collagen mineralization
boNE FRAgility: reduced lifespan, short stature

Question 29

histone

Answer 29

protein tht package DNA
contains mostly Arg lys

Question 30

WHAT IS A HISTONE OCTOMER

Answer 30

consist of 2each of HIS 2A 2B 3 4
has a tail that extend beyond the histone_ hange DNA to RNA polym

Question 31

what is nucleosome core particle

Answer 31

146 bp that wraps aroiund the histone octomer as 1st step of DNA packaging

Question 32

EPIGENETICS

Answer 32

study of how your behaviour and enviro affect DNA
is reverssible and doesnt change the DNA sequence– change how your body reads DNA sequence