biochem 7

Helicase enzymes

Separation of the double helix for DNA replication to occur

Primase

Synthesizes a short strand of RNA complementary to a part of the template DNA strand

The presence of multiple origins at which replication takes place

Causes increased rate of DNA synthesis in eukaryotic cells

pyrophosphate

Released during the addition of deoxyribonucleotides to the nascent DNA chain

DNA polymerase

Catalyzes the addition of deoxyribonucleotides to DNA

Trombone slide model

Lengthening of the loop formed by the lagging strand during replication

Topoisomerase

Strands of DNA must be relaxed or unwound for replication by ____

Template

Role of DNA to direct synthesis of the complementary strand of DNA or RNA

Okazaki fragment

Small fragments of DNA synthesized on the lagging strand

Helicase

Proteins that use ATP hydrolysis to separate the DNA during replication

Telomeres

The ends of chromosomes

G-rich strand

Critical in the formation of a telomere

UV light

Results in covalent formation of pyrimidine dimers involving adjacent pyrimidines in a DNA strant

Cell death, alteration to DNA sequences that can be inherited, stalling of DNA replication, cell transformation and cancer

Events that can result from damage to DNA that is not repaired

Huntington disease

Disease caused by trinucleotide expansion

Deamination of cytosine to uracil

Does not cause a problem in the next round of DNA replication because the repair machinery recognizes uracil in DNA as a mistake and replaces it with cytosine

RNA polymerase

Searhes for promoter sites, unwinds short stretches of DNA, detects termination signals

Sigma

The protein that binds DNA sequences and helps RNA polymerases initiate transcription

3' hydroxyl group

Attacks the 5' hydrogen of the incoming nucleotide

Pribnow box

Is found -10 base pairs from the enzyme

Bromodomain

Region of a protein that regulates transcription by interacting with the acetylated lysine of histones

Agonists

Molecules that bind to a receptor and trigger a signaling pathway

Zinc fingers

DNA-binding domain found in steroid hormone receptors

Enhancers

Binding sites in DNA for specific regulatory proteins

Coactivators

Proteins that act in a coordinated manner with hormone receptors to mediate gene expression

Histone deacetylase

Enzyme that removes the acetyl group for a lysine of a histone

Ligand

A general term for molecules that bind to receptors

TATA box

In eukaryotes, transcription is initiated by the binding of the transcription factor to the

Introns

Spliced transcribed and spliced out before translation

Modification of sequences, adding a poly(A) fail to the 3' end, splicing together the exons, Methylation of certain residues, adding a 5' methylguanylate cap

Features of post-transcriptional processing of RNA

RNA polymerase II

Eukaryotic RNA polymerase involved in synthesis of pre-MRNAs

RNA molecules associated with the spliceosomes

Catalyze the removal of introns during splicing

Small nuclear ribonucleoproteins

snoRNP

Stability against nucleases

The capping process at the 5' end of the eukaryotic mRNA contributes to

Degenerate

A single amino acid may be specified by more than one codon

5-3

mRNA is read in this direction

Amino to carboxyl

Protein is synthesized in this direction

Contains an amino acid attachment site, contains unusual bases, L-shaped

tRNA

Aminoacyl tRNA stynthetase

Enzymes responsible for attaching amino acids to tRNA

Shine-dalgarno

The sequence in prokaryotes that interacts with a complementary complementary sequence on the 3' end of the 16S rRNA to set the reading frame is

Initiation factors

Includes 1F1, 1F2, 1F3 in prokaryotes

N-formylmethionine

The first amino acid in bacterial translation

GTP

EF-G translocase proteins use the energy of ____ hydrolysis

elongation factor TU

The biomolecule ___ delivers the aminoacyl-tRNA to the "A site" in E coli

Release factors

These proteins recognize UAA, UAG, UGA

Signal sequence

A sequence of 9-12 hydrophobic amino acid residues directing ribosomes to the endoplasmic reticulum

ATP

The energy of hydrolysis of this molecule drives the scanning of eukaryotic mRNA until the first AUG is reached

Origin of replication

Location of DNA replication in E. coli

DNA polymerase I and DNA ligase

Achieves filling the gap between the fragments of the lagging strand after the removal of multiple RNA primers

Polymerase switching

Higher processivity of DNA replication

Phosphodiester linkage

The bond whose formation is catalyzed by DNA polymerase during chain elongation

Polymerase III is a dimeric holoenzyme and the looped lagging strand allows the enzyme to proceed

How can the leading and lagging strands be synthesized in a coordinated fashion

Replication of telomeres

RNA dependent DNA polymerase

Trinucleotide repeats

Found to cause alternative structures during DNA replication

Mutagen

Chemically changes the nature of a base in DNA

Ligases

Involved in joining DNA molecules together

Direct repair

Process for correcting for base-pair mismatches without excising bases

Photolyase

Enzyme that uses light energy to form an excited state to cleave the dimer into individual bases

Glycosylase

Enzyme that cleaves a glycosidic bond to release a damaged base

Ames

An assay used to determine the carcinogenic potential is the ___ test

DNA polymerase exonuclease

First line of defense against errors in replication

Operon

A group of prokaryote genes that are closely related and are produces as a single mRNA transcript

Transcription

RNA synthesis (tRNA, mRNA, rRNA) is called ____

Divalent cofactor

Required cofactor for RNA polymerase

Promoters

DNA sequences that direct RNA polymerase to the initiation site are called

Primer

Unlike DNA synthesis, RNA synthesis does not require ____

Transcription bubble

The region of RNA synthesis containing DNA, RNA, and enzymes is called ___

Consensus

Sequences deduced from the analysis of many related DNA sequences

repressor

Expression of galactosidase requires the induction of an operon dissociation of ______

Stem loop

RNA structure that signals termination of transcription

Catabolite repression

An increase in cellular metabolism that inhibits expression of the genes for that metabolism is a process known as ____

Control of transcription

Regulates differential gene expression

Enhances transcription and recruits factors for mRNA processing

When phosphorylated, the carboxyl-terminal domain of RNA polymerase II

Combinatorial control

Interaction of many different protein factors to stimulate or repress transcription

At a distance from the transcription start site

Location of enhancer sites

Binding of a tata box binding protein

First step in transcription initiation in eukaryotes

Spliceosomes

mRNA precursors may be splices by ____ complexes

Spliced

Nearly all mRNA precursors in higher eukaryotes are

PolyA tail

An elongated sequence that stabilizes the 3' end of mRNA

RNA polymerase I

Transcription _____ gives rise to three ribosomal components

Methylation

Common rRNA modification
Allows E. Coli to distinguish between parent and daughter DNA strands immediately after replication

U2 and U6

Small nuclear RNAs that form the catalytic center of the spliceosome

RNA editing

A change, other than splicing, made to the base sequence of RNA following transcription

Alternative splicing

A mechanism of splicing that allows diversity in the proteins generated from a particular gene

Ribozyme

An RNA molecule that is catalytic is called

CCA

Added to 3' end of tRNA

Translation

Term applied to the process of protein synthesis

CCA

Amino acid attached to the tRNA molecule

Charged tRNA

Amino acid ester of tRNA

Wobble

____ hypothesis explains why some tRNA molecules can bind to more than one codon

5' linkage

The 5' end of a tRNA has a ____

Aminoacyl tRNA synthetase

____ Can recognize both a specific amino acid and a specific tRNA molecule

Transcription

Closely coupled with translation in prokaryotic gene expression in time and space

Anti codon loop

Recognize by aminoacyl tRNA synthetase

AUG

Anticodon for CAU

mRNA

Contains signals that define the beginning and end of protein synthesis

Shine-dalgarno sequence with 16S rRNA

Establishes the reading frame in prokaryote translation

Circular

Eukaryotic mRNA is ___

incoming charged tRNA binds to the A site, growing peptide is transferred from the tRNA in the P site to the tRNA in the A site, the tRNAs and the mRNA are translocated through the elongation factor, release factors facilitate the hydrolysis of the ester

During protein synthesis