Exam 1 Enzymes and Elements

Question 1

CDK

Answer 1

Cyclin-dependent-kinase: Used for phosphorylation of ORC to entire each origin is only activated once per cell cycle

Question 2

CDC6

Answer 2

ORC element binds to form Pre-RC complex

Question 3

Cdt1

Answer 3

ORC element to for Pre-RC complex

Question 4

Glycosylase

Answer 4

BER Repair - removes nucleotide base only

Question 5

AP Endonuclease/Phosphodiesterase

Answer 5

Cleaves chain and excises nucleotide (Sugar/phosphate bond)

Question 6

Nuclease/helicase

Answer 6

Cleaves a carpet of nucleotides and unwinds during NER

Question 7

In TCR, describe the enzymes involved and their function

Answer 7

TFIIH (XPB, XPD) - function as helicases

XPG (3’), XPF, ERCC1 (5’) - function as endonucleases

Question 8

Mut L/Mut S

Answer 8

MMR (mismatch repair) binds to error nucleotide and scans rest of strand - binds to nick and excises

Question 9

ATM/ATR/p53

Answer 9

Cell cycle checkpoints that activate the protein p53 and regulate the cell cycle progression as well as the apoptotic pathway

Question 10

Ku

Answer 10

Protein that catalyzes NHEJ (Heterodimers)

Question 11

RecA/Rad51

Answer 11

Complex involved in HEJ and meiosis - functions to bring in and bind 3 strands of DNA during the repair process - leads to the invasion strand forming

Question 12

Ruv A & Ruv B

Answer 12

Two proteins that act to direct the synthesis of nucleotides during repair - direct the direction of the branch point in HEJ and make it directional instead of spontaneous

Question 13

Spo11

Answer 13

Create breaks in the dsDNA during meiotic recombination. Works in tandem with Mre11 to bind to

Question 14

MRE11

Answer 14

Another factor in the mechanism of general recombination in meiosis. These are nucleases which expose and break the DNA and expose ssDNA 3’ End

Question 15

snRNA

Answer 15

direct splicing of pre-mRNA

Question 16

snoRNA

Answer 16

guide modification enzymes in rRNA synthesis

Question 17

scaRNA

Answer 17

used to modify snRNA and snoRNA

Question 18

siRNA, miRNA, lncRNA

Answer 18

regulate gene expression

Question 19

Describe: CAAT, BRE, TATA, INR, & DPE. State their location in the gene and describe the regulatory proteins that each one binds

Answer 19

CAAT - binds TBP in TFIID, BRE - binds TFIIB, TATA -TBP, INR - TFIID, DPE - TFIID

Question 20

TFIID
TFIIB
TFIIH
TFIIE
TFIIF

Answer 20

D=TBP and TAFS (tata box and recognition of non-TATA promoter elements; regulation of TBP binding to DNA, chromatin remodeling
B=recruitment of Pol II, BRE recognition and transcriptional start site
H=helicase and phosphorylation of C-term domain of Pol II
E=enhance activity of TFIIH
F=destabilizes non-sepcific binding of pol II, attracts TFIIE and H

Question 21

CPSF/CSTF

Answer 21

Cleavage and polyadenylation factor - cleaves after CA sequence in mRNA between 10-30 nucleotides after termination sequence. Allows formation of Poly A tail. CSTF - cleavage stimulation factor reside in U rich or GU rich area less than 30 nucleotides away

Question 22

SR proteins:
U1
U2(AF) & BBP -  followed by U2 snRNP
BB
U4
U5
U6

Answer 22

Remember: 5’= GU…Branch point = A…and 3’=AG
U1 binds to 5’ splice site
U2AF and BBP - bind to branch site and forms catalytic center
U4 masks the catalytic activity of U6
U5 binds the 5’ splice site; then the 3’ splice site
U6 is the catalytic subunit - splicing

Question 23

hnRNP, elF4G, elF4E, CBC

Answer 23

heterogenous ribosomal nuclear protein: elongation factors for protein synthesis; cap binding protein

Question 24

UBF, TFIIC

Answer 24

Upstream control element binding (upstream binding factor) in recruitment of Pol I for rRNA syn.
TFIIC is the complex in Pol III from which either tRNA comes from (using B-box) or TFIIA is recruited to make the 5S ribosomal subunit using C-box