Cell and Molecular Bio Exam 2

Two proteins for folding DNA (chromosomes)

condensin and scaffold

Two parts of condensin

anchor and motor ring

Anchor function

binds to heterochromatin

Motor-ring function

opens and closes around heterochromatin and binds ATP, creates heterochromatin loop as it moves down structure

result of transcriptional dysregulation

diseases, ex. alzheimers

DNA elements

chromatin (hetero vs eu), promoters, enhancers, epigenetics

mediator complex function

bridges transcription factors

lac operon during low amount of lactose

inactivated, repressor bound to operator

lac operon with high lactose

rna holoezyme binds promoter, active and repressor leaves

CAP function lac operon

activator protein, binds to enhancer (CAP) to further promote transcription

transcribes all coding regions (mRNA)

RNA polymerase II

transcribes rRNA

RNA polymerase I

produces tRNA

RNA polymerase III

Scientist responsible for crystallizing RNA polymerase II

Roger Kornberg

C-terminal of RNA polymerase II

364 aa, 52 tandem heptapeptide repeats

C-terminal RNA polymerase II rich in what aa?

serine, hyperphosphorylated

Resting stage RNA pol II

unphosphorylated

enzyme responsible for phosphorylation in rna pol II

cyclin dependent kinase (CDK)

eukaryotic promoter sequence

TATA box

site-directed mutagenesis

introduce nucleotide changes into target dna

Reporter genes ex (4)

GFP and luciferase, thymine kinase, lacz

scrambling mutation analysis

5’ deletion analysis

DNase I footprinting

method used to identify where dna-binding protein (ex. transcription factor) binds to DNA sequence

HMG1

enhancers

spliceosome function

protein complex that binds to enhancers and recruits mediator complex

TBP

all processes that regulate gene expression following transcription

post-transcriptional control

what level of control for gene expression to generate most diversity

post-transcriptional control

methods of post transcriptional control (5)

Passage of mRNA through nuclear membrane, RNA editing, RNA processing, destruction of RNA, rate of protein synthesis

3 key steps of mRNA processing (in order)

5’ capping, splicing, 3’ polyadenylation

RNA splicing is done by the?

Spliceosome, molecular machine of snRNPs

snRNPs + scientist who discovered

snRNA + protein, Joan Steitz

discovered mRNA splicing

Philip Sharp

5’ cap made of and purpose?

7-methylgaunosine, 5’-to-5’ triphosphate linkage, methylated ribose, protects mRNA and allows nuclear exit

3’ poly adenylation purpose

protects from exoribonucleases and allows binding of poly-A binding proteins (PABP)

Poly adenylation steps (2)

endonuclease cuts transcript to free 3’OH, PolyA polymerase adds adenine residues by using ATP as substrate

Sequences recognized for Poly adenylation

AAUAAA and G/U

Which recognition sequence remains after poly adenylation

AAUAAA

scientists that discovered ribozymes

Thomas Cech and Sidney Altman

transesterification of pre-mRNA (2 steps)

branch point of intron attacks GU sequence of 5' exon, 3’OH of exon attacks AG sequence of 3’ exon

What do spliceosome snRNPs assist with chemically?

transesterification

Why are spliceosome snRNPs named U

contain uracil rich regions

Example of RNA editing

ApoB-100 to ApoB-48, changes CAA codon to UAA, liver vs. intestine

T or F RNA editing is a rare occurrence

F, A to I happens commonly

T or F RNA editing happens in many species

T

enzyme that converts ApoB100 to ApoB48

cytidine deaminase

largest protein complex that passes nuclear pore

large ribosomal subunit

AAs that line nucleoporin protein

FG - phenylalanine and glycine

molecular interaction that facilitates nucleoporin passage

hydrophobic interaction

Ticket needed for molecule to be transported back to nucleus

Nuclear localization signal

What AA must be present on NLS for nuclear entry?

Basic (K or R), interacts with negative porin

Examples of proteins that need NLS (4)

DNA polymerase, RNA polymerase, snRNPs, ribosomal proteins

3 methods of mRNA degradation

Deadenylase, decapping enzyme, endonuclease

Protein complex capable of degrading mRNA from 3’ end

Exosome

RNA interference molecule with best complementary

siRNA

4 steps of tRNA processing

trim 5’ sequence, remove introns, replace 3’UU with CCA, modify internal bases

What’s unique about tRNA promoter

intragenic

CTD domain of RNA polymerase II

serine heavy region

What is necessary for rna polymerase II activation (CTD)

phosphorylation of serine residues

enzyme that phosphorylates CTD domain

cyclin dependent kinase

Steps of gene knockout traditional (3)

disruption sequence, transformation, recombination

Cre codes for what enzyme

recombinase

transposase function

binds to and cuts DNA transposon so it can jump around

blunt end cuts occur in the _____

donor end DNA

staggered end cuts occur in the _____

target DNA

primer for negative sense DNA synthesis - retrotransposons

tRNA

protein that removes acetyl groups from euchromatin

HDAC - histone deacetylase

Protein that marks DNA as transcriptionally inactive

HP1

target of methylation/acetylation for histone

K - Lysine

What enzyme part of the chromosome folding process requires ATP?

Condensin

Discovered the structure of RNA polymerase II

Roger Kornberg

Common proximal element sequences

GGGAGG CCAAT

most common promoter sequence

TATATATA

Bends DNA to stabilize for nucleoprotein attachment

HMG1

Determines the location of DNA sequence regulating transcription

Site-directed mutagenesis

Determines the location of DNA binding proteins

DNase I footprinting

binds to promoter and bends DNA to mark readiness for transcription

TBP

Explain the Glucocorticoid receptor steps (4)

Receptor bound to chaperone (HSP70), finds hormone and dissociates with chaperone, travels to nucleus, hormone regulates transcription

Motif with 2 cysteine and 2 histidine residues and zinc, binds to MAJOR groove

zinc-finger

Motif with hydrophobic residues that dimerize

Leucine zipper

Enzyme necessary for cholesterol production, inhibited by statin

HmG-CoA reductase

Location of lipid production

SER

prenylated protein

Ras GTP protein

acyetylated protein

Src protein kinase

integral protein that takes of sugars

glycophorin

light-driven proton pump found in bacteria

bacteriorhodopsin

T or F bacteriorhodopsin pumps hydrogen protons IN

F

What do GPI-anchored proteins do?

cell adhesion

enzyme that breaks down fatty acids + motifs

phospholipase, c2 and ph motifs

protein necessary for fusion of vesicles to membrane + characteristic motif

SNARE, amphipathic helix

binds to lipid bilayer by insertion of hydrophobic loop

Annexin V

contain beta barrels

porins

method used to observe fluidity of lipid membrane

FRAP

Only 50% recovery after FRAP

lipid raft regions

Primary PL for inner leaflet of membrane

PE

Primary PL for outer leaflet of membrane

PC

Examples of cone shaped PLs

PE and phosphatidic acid

Example of cylinder shaped PLs

PC