Exam 2

Chargaffs rules

amount of A=T and G=C in DNA

photo 51

Rosalind Franklin’s image showing DNA as a long thin helix

Watson-Crick model

Double helix: backbone outside, bases inside, antiparallel strands, 10 base pairs per turn

phosphodiester bond

Covalent bond linking the 5′ phosphate of one nucleotide to the 3′ OH of the next

major/minor groove

Uneven grooves formed as the strands twist around each other

karyotype

Display of an organism’s full set of chromosomes; used to detect abnormalities

Translocation

Abnormal swap of pieces between chromosomes; linked to cancer

homologous chromosomes

matching pairs of chromosomes, one from each parent

30 nm fiber

Second level: nucleosomes pulled together by H1

Chromatin loops

loops of chromatin formed by SMC protein rings, uses ATP

SMC proteins

structural maintenance of chromatin proteins that form loops

Cohesin

SMC ring complex that enlarges chromatin loops in interphase

chromatin remodeling complex

ATP-dependent enzyme that repositions DNA on nucleosomes to change accessibility

Histone modifying enzymes

Enzymes that add or remove methyl, acetyl, phosphate, etc. on histone tails (reversible)

HATs (histone acetyltransferase)

Enzyme that adds acetyl groups

HDAC (histone deacetylase)

enzyme that removes acetyl groups

Histone methyltransferase

enzyme that adds methyl groups to histones

heterochromatin

highly compacted chromatin, genes are mostly off

euchromatin

Loosely packed chromatin (genes accessible)

H3K9 methylation

methylation of lysine 9 on histone H3: marks heterochromatin

barrier DNA sequence

sequence that stops heterochromatin spreading

β-globin barrier mutation

Barrier lost, so the β-globin gene gets packed into heterochromatin and isn’t expressed, causing anemia

Sister chromatid cohesion

Holding duplicated chromatids together until separation (a centromere function)

TTAGGG

The repeated telomere sequence

origin

A-T rich (easier to separate); ~10,000 in the human genome; 1 in bacteria

replication forks

Y-shaped site where the parent strands separate and are copied

ORC (origin recognition complex)

Sits on the origin throughout the cell cycle

dNTP

Deoxyribonucleoside triphosphate (dATP, dTTP, dGTP, dCTP); DNA building block

pyrophosphate

Released from the incoming dNTP; this release powers bond formation

Primer

Short starting strand DNA polymerase needs (RNA in cells

Primase

RNA polymerase that makes RNA primers using ribonucleotides

DNA pol I

replaces RNA primers with DNA

Catalytic site (P)

polymerase site that adds nucleotides when the pair is correct

Editing site (E)

Polymerase site where a mismatched nucleotide is cut out

end replication problem

The last lagging-strand primer can’t be replaced, so linear DNA ends shrink each round

mismatch repair

Fixes replication errors that escape proofreading

Base excision repair

Fixes single damaged bases (e.g., U from deaminated C)

Uracil DNA glycosylase

Detects U in DNA and cuts the base off its sugar

Rad52 and BRCA2

help the broken strand invade the homologue

conserved sequences

sequences kept the same through evolution because replication and repair are accurate

sigma factor

bacterial protein that helps RNA pol find the promoter, released after transcription starts

-10 and -35

Sequences found in all bacterial promoters

Elongation

RNA pol moves along the template adding NTPs

terminator

Sequence that signals RNA pol to release the RNA (bacteria)

promoter polarity

Promoter direction decides which strand is the template

RNA polymerase I

in the nucleolus; makes most rRNA

RNA polymerase II

In the nucleoplasm; makes mRNA

RNA polymerase III

In the nucleoplasm; makes tRNA, 5S rRNA, microRNA

General transcription factor

Protein always required for eukaryotic RNA pol to bind promoters

TFIID

First GTF to bind; recognizes the TATA box

TBP

Subunit of TFIID that binds the TATA box

TATA box

DNA sequence in most eukaryotic promoters

TFIIB

Binds next to TFIID

TFIIH

Unwinds DNA and phosphorylates Pol II’s C-terminal tail

Pol II C-terminal tail

Phosphorylation releases Pol II to start, then recruits RNA-processing proteins

Transcription initiation complex

Full assembly of GTFs + Pol II at the promoter

Elongation factors transcription

Help Pol II move through nucleosomes by prying DNA off histones

Primary transcript

Newly made RNA before processing

RNA processing

Modifications needed before RNA can function

tRNA processing

Removal, replacement, chemical modification, excision

5` cap

7-methylguanosine joined by a 5′→5′ linkage; protects mRNA and helps ribosome positioning

Poly(A) tail

50 to 250 A’s on the 3′ end; stability, export, ribosome recognition

Poly(A) polymerase

Enzyme that adds the poly(A) tail

Polyadenylation signal

Sequence just upstream of the cut site that signals the end of transcription

Pre-mRNA

mRNA before introns are removed

R = A or G, Y = C or U, N = any nucleotide

R/Y/N (in splice signals)

snRNP

Small nuclear ribonucleoprotein; RNA-protein complex that recognizes splice sites

snRNA

RNA part of an snRNP; base pairs with the intron

spliceosome

Large RNA-protein assembly that does the splicing

Branch point A

Adenine in the intron that attacks the 5′ splice site

Lariat

Loop-shaped intron released after splicing

U2 U6

snRNAs that pair to form the spliceosome’s active site

Mg2+

Held by the RNAs; catalyzes the splicing chemistry

exon junction complex

Protein marker left at each splice junction

intracellular condensate

“Factories” in the nucleus where RNA synthesis and processing happen

redundant code

Most amino acids have more than one codon

codon

Three-nucleotide unit of mRNA

Cell-free translation system

Experimental system used to crack the code (with radioactive amino acids)

Aminoacyl-tRNA

tRNA with its amino acid attached by a high-energy ester bond at the 3′ end

Aminoacyl-tRNA synthetase

Enzyme (one per amino acid) that attaches the correct amino acid to its tRNA

ribosome

rRNA + protein particle with large and small subunits; decodes mRNA

Ribosome locations

Free in the cytoplasm, ER-bound, mitochondrial matrix, chloroplast stroma

N-terminus

End of the protein made first (mRNA read 5′→3′)

23S rRNA

rRNA that forms the peptide-bond catalytic site

pre initiation complex

initiator tRNA + small subunit + initiation factors before start

Initiator tRNA

Special Met-tRNA that binds directly to the P site and works with initiation factors

Ribosome-binding site

Where bacterial ribosomes start translation

peptidyl transferase

rRNA catalytic activity in the large subunit that forms peptide bonds

ribosome binding site

Where bacterial ribosomes start translation

release factor

Binds a stop codon; causes the chain to be released using water

Kozak sequence

gccRccAUGG around the correct start AUG in vertebrates

polyribosome

Several ribosomes translating one mRNA at once

Coupled transcription-translation

In bacteria, translation starts while the mRNA is still being made

post translational modification

Covalent changes after translation (phosphorylation, glycosylation, methylation, acetylation; >100 types)

housekeeping proteins

made in all cells (polymerases, repair enzymes, ribosomal proteins, cytoskeleton)

Glucocorticoid receptor (GR)

Cortisol receptor; a ligand-activated transcription factor (activator or repressor)

Tyrosine aminotransferase

Liver enzyme that helps convert Tyr to glucose; up in liver, down in fat with cortisol

Promoter region

DNA that starts transcription; recognized by RNA pol and its helper proteins

Transcription initiation site

Where RNA synthesis begins

Regulatory DNA sequence

DNA where regulators bind to control when, where, and how much a gene is transcribed (10 to 100,000 bp)