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