Bio Chemistry Exam #2 Practice quizzes

loads DNA Pol delta at sites of single-strand breaks in DNA

PCNA

initiates correction of any chemical base damage within DNA (step \#1)

repair endonuclease

reacts with G to form N-2 ethylguanosine

acetaldehyde

specifically creates an abasic site at ROS-damaged deoxcytosine within DNA

uracil-DNA glycosylase

converts cytosine to uracil

Superoxide

activates the formation of 5,5,6,6-cyclobutane thymine dimers

260 nm light irradiation

metabolic product of smoke that modifies the 2-amino group of guanosine

Benzo(a)pyrene

strips out the damaged strand which in the case of uv damage activates melanogenesis ("tanning")

Helicase

required to convert uracil to thymine on dUMP

N5,N10-Methylene tetrahydrofolate

Double-stranded DNA is the product of

Replication

Once the polymerase is finished producing DNA, it will only return to the task of template guided synthesis when there is a requirement

Prep for cell division and repair

Fidelity is only ensured by amino acids polymerase active site only during what

Durning Synthesis

Fideltiy is ensured AFTER replication by

detection by repair related proteins

When deletion happens it can happen two ways

Removal of U's by Uracil/DNA glycosylase to create an abasic site

cleavage of a damaged strand by repair endonucleases

Fidelity requires what

Template strand DNA

What does DNA polymerase do after being recruited to site

Repair to replace the damaged strand

with high levels of base damage, repair endonucleases can produce double-strand breaks which hyperactivate

ATM kinase

When ATM kinase is hyperactive what happens

Apoptosis

The substrate it uses is a nucleotide triphosphate (NTP) which it positions to attach to the end of the growing RNA strand using one phosphate to form a

Phospodiester

What is the by product of growing RNA strand

Pyrophosphate

translated by ribosomes into an amino acid sequence- (PROTEIN

mRNA sequencing

A-OH

Amino-acylation

anticodon segment

I G C

patterns of "stem" stacking and loop folding

TRNA

stylized tertiary structure of tRNAs- backbone

Tube worm

decoding the mRNA relies on base-pairing

tRNA anticodons

hypoxanthine can base-pair to the other

Bases

3rd position in the code is called the

Wobble position

amino- acylation is preformed by

aminoacyl-tRNA synthetase

Step 1

aa + ATP \=\> aminoacyl-AMP + PPi

Step 2

aminoacyl-AMP + tRNA \=\>aminoacyl-tRNA + AMP

this higher energy structure is called an

Acyl phosphate

Iniation

tRNA with mythiene start at AUG

iniation codon

AUG

Which letter corresponds with pi

E

What letter corresponds aminoacyl tRNA

J

Which letter corresponds to the tRNA

F

Which letter corresponds with the aminoacly #1 carbon is an amide bond

*I*

Which letter corresponds with the aminoacyl #1 carbon of the ester bond

J

Which letter corresponds to the free amino acid

A

Which letter identifies where the amino acyl #1 carbon is in a carboxylate

A

Which letter corresponds to H2O

G green

Which letter identifies where the amino acyl #1 carbon is an acyl-phosphate

H

Which letter corresponds to protein

I

Which letter corresponds to trigonal bipyramidal geometry

C

Which letter corresponds with amino acyl AMP

H

Which letter corresponds with AMP

G red

Which letter corresponds with ATP

B

Which letter corresponds to pyrophosphate

~~D~~

tumor-suppressor protein which is the most studied protein in scientific research

P 53

activates Chk2 kinase

ATM kinase

tag for proteins destined for proteolysis

Ubiquitin

phosphorylates S20 of p53 to block binding by Mdm2

Chk2 kinase

becomes attached in an amide bond between its own C-terminal carboxylate to a lysine on a target protein

Ubiquitin

wobble base of the anticodon of phenylalanine tRNA that base-pairs to ONLY UUU and UUC

Guanine

responds directly to single-strand and strongly to double-strand breaks in DNA

ATM kinase

wobble base of the anticodon of alanine tRNAs that base-pairs to GCX where X is any base

Hypoxanthine

produces "cuts" upstream (5') and downstream (3') on a chemically-damaged DNA strand

Repair endonuclease

directs covalent attachment of ubiquitin to p53

Mdm2

cut by caspase 3 to promote the cutting up of genomic DNA into nucleosome sized fragments, effectively killing the cell

ICDA

trimeric protein that is assembled by p21 to load DNA polymerase delta at sites of repair

PCNA

domain of CBP that bonds to acetyl-lysines to continue the spread of acetylation towards the start of transcription

Bromo

pro-apoptotic protein that is expressed in response to high levels of p53 binding to weaker response element binding sites

Bax

cut by active caspase 9 to promote apoptosis

Pro caspase 3

anti-apoptotic protein which forms inactive heterodimers with Bax to prevent apoptosis

Bcl2

uses phenylalanines to pry open A-T rich, double stranded DNA to expose single-stranded template to RNA Polymerase II

TBP

dimerized by the apoptosome so as to perform cross-proteolytic cleavage

Pro caspase 9

leaked out of the intermembrane space of the mitochondrion to the cytoplasm with cytochrome c to form the apoptosome

Apaf1

inhibited directly by p21 so as to prevent progression through the cell cycle

Start kinase

Contribution of SRP receptor alpha to SRP54 that induces the formation of trigonal bi pyramid intermediate

Arginine finger

As SRP 54 is released the nascent peptide is looped into the opened

Transcolon

The SRP complex stalls translation by preventing the ribosomes interaction with

eEF2

Cuts the polypeptide chain between the pre and the peptide B sections of preproinsulin

Signal peptidase

Bonds with high affinity of the pre portion of preproinsulin to stall translation

SRP54

Acts as a GAP on SRP54 to release it from the nascent peptide

SRP receptor alpha subunit

Small molecule that is bound to SRP54 when it's bound to the nascent peptide

GTP

Cofactor used in redox reactions that produce hydrogen peroxide

FAD

Portion of the nascent peptide that is most important for binding to SRP54

Hydrophobic leucine-rich sequence

ROS produced durning formation of the functional form of pro insulin

Hydrogen peroxide

Enzyme which oxidizes reduced PDI in the rER lumen

Ero1

The most abundant mRNA in the islet beta cell encodes

Preproinsulin

Enzyme that oxidizes the cystines of preproinsulin

Protein disulfide isomerase

organizes the assembly, movement and delivery of transport vesicles moving from the rER to the Golgi

Rab 1

organizes the assembly, movement and delivery of Islet beta cell secretory granules/vesicles from the Golgi to the plasma membrane

Rab 37

motor protein that moves secretory vesicles through the actin cortex to the plasma membrane

myosin5a

cargo receptor carrying BiP, PDI, and Ero1 recognizes what on those proteins to load them into vesicles going from the cis Golgi to the rER

KDEL-COO-

at the delivery point, acts as a GAP on Rabs

HOPS complex

organizes the assembly, movement and delivery of transport vesicles moving from the Golgi to the rER

Rab 2

Cargo receptor that recognizes proinsulin's peptide B/C boundary to load it into secretory granules at the trans Golgi

Prohormone convertase 1

cargo receptor that recognizes proinsulin to load it into vesicles in the rER

Surf4

concentrates protons into the secretory granule in order to mature proinsulin into insulin

V-ATPase

when the secretory vesicle lumen pH is low this cuts the proinsulin molecule between the C and A peptides

Prohormone convertase 2

holds together the B and A peptides in mature insulin

Disulfide bridges

motor that moves vesicles from the rER to the Golgi

kinesin

most directly "snaps" together vesicle and target membranes to effect fusion

snares

motor that moves vesicles from the Golgi to the rER

dynein

Uracil (pyrimidine)

Hypoxanthine (purine)

Cytosine (pyrimidine)

Thymine (pyrimidine)