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147 Cards in this Set

  • Front
  • Back
What are the three components of DNA metabolism?
Replication, Repair, and Recombination
What shapes and governs DNA metabolism?
Enzymes
Which strand of DNA is copied continuously?
The Leading strand, with a polarity of 5'-3'
What are some characteristics of DNA replication?
Semi-Conservative
Bidirectional @ Replication Forks
Semi-Discontinuous
What are the three processes of DNA replication?
Initiation
Elongation
Termination
Why is DNA replication considered semiconservative?
Because the replicated strands contain one parent strand, and one daughter strand.
How was the semi-conservative nature of DNA replication demonstrated?
Through the use of Nitrogen isotopes to mark the parental strand of DNA.
How is DNA replication bidirectional?
The replication forks work in both directions from where the replication initiated.
How is DNA replication semidiscontinuous?
The leading strand synthesis is continuous, and the lagging strand synthesis is discontinuous, therefore leading to a semidiscontinuous replication mechanism.
What are Okazaki fragments?
They are fragments generated by the discontinuous replication of the lagging strand.
What links the Okazaki fragments?
DNA ligase
What is required to begin the synthesis of DNA?
Primase
Is primase made up of DNA or RNA?
RNA
How many primers are required for the synthesis of the leading strand?
One
What was the first enzyme discovered that could synthesize DNA?
DNA Polymerase I
Who found DNA Polymerase I?
Arthur Kornberg
What molecule is required to remove two phosphate groups from dNTP?
Magnesium (2+)
What is the rate of error in DNA replication?
Once in every 10^9 to 10^10 BP
What are the two enzymes that degrade DNA?
Exonuclease and Endonuclease
Name the enzyme that can only degrade DNA from one end of the molecule.
Exonuclease
Name the enzyme that can begin to degrade DNA at specific internal sites.
Endonuclease
Which DNA replicating enzyme has both 3'->5' and 5'->3' exonuclease activity?
DNA Polymerase I
What is the most abundant Polymerase?
Polymerase I
What is the role of DNA Polymerase II?
DNA Repair
How many beta clamps does DNA Polymerase III have?
Three
What keeps DNA Polymerase III from dissociating from DNA?
Beta Clamps
What does initiation require?
DnaA, DnaB, SSB and Primase
What is another term for DnaB?
Helicase
What is the component of initiation that binds to oriC to separate it into single strands?
DnaA
Which segment of DNA is AT-rich?
oriC
What is the purpose of DnaC?
It forms a complex with DnaB and is required for the loading of DnaB onto DNA
In what form does DnaB bind to DNA?
In the form of a DnaB-DnaC complex.
What enzyme makes the RNA primers?
DnaG or Primase
What is the role of SSB?
To stablize the denatured DNA strands.
What is elongation?
The synthesis of both the leading and lagging strand.
What is DNA gyrase?
It is a stablizing element of topoisomerase to stablize the unwound DNA.
What are seven proteins required for elongation?
SSB,
DnaB,
Primase,
DNA gyrase,
DNA Polymerase III,
DNA Polymerase I,
DNA Ligase
What is a replisome?
The combination of the proteins at the replication fork.
How many sites of termination exist in E. coli DNA?
Seven
What proteins bind to the Ter site?
Tus, to form a Tus-Ter complex.
What does a Tus-Ter complex accomplish?
It stops DnaB
What are the Ter proteins for the Clockwise trap?
TerG
TerF
TerB
TerC
What are the Ter proteins for the counter-clockwise trap?
TerE
TerD
TerA
Why does replication have a high fidelity?
Cells maintain balanced levels of dNTP's
Polymerase occurs in two stages, which serves as a double check
PolI and PolII have proofreading
Other enzymes repair residual errors.
What is the end of a eukaryotic chromosome called?
Telomere
What is the defining feature of Telomeric DNA?
the G-rich sequence. TTAGGG in humans.
What synthesizes Telomeric DNA?
Telomerases
What are the two negative consequences of DNA damage?
Cell Death, and Mutations.
What are four mechanisms of DNA repair?
Direct Repair
Base Excision Repair
Nucleotide Excision Repair
Mismatch Repair
What is the function of methylation?
To distinguish parent strands from newly synthesized strands.
Where does methylation occur in E. coli?
At the N6 of adenines in (5')GATC
Which enzyme binds to mismatched base pairs?
MutS-MutL complex.
What binds to a hemimethylized GATC sequence?
MutH, which cleaves the unmethylated strand to mark it for repair.
What molecules are important to the base-excision repair pathway?
DNA Glycosylase
AP endonuclease
DNA Polymerase I
DNA Ligase
What are the molecules important in the Nuleotide-Excision Repair mechanism?
UvrA
UvrB
UvrC
DNA Polymerase I
DNA Ligase
What are the two ways to generate diversity within organisms?
DNA Recombination
DNA Mutation
Where does crossover occur in meiosis?
Prophase I
Where is the recombination hotspot?
Chi sequence
What are the proteins required for recombination?
RecBCD,
RecA,
RuvAB,
RuvC
What is the function of RecBCD?
To unwind DNA (when a Chi sequence is encountered)
Which protein resolves the Holiday junction?
RuvC
What is the function of RecA?
To mediate strand exchange
What does RuvAB accomplish?
It drives branch migration.
Which strand is used to synthesize RNA?
DNA Template Strand (3'->5')
How is the DNA supercoil changed during transcription?
RNA polymerase creates a negative supercoil before it, and a positive supercoil after it.
What are the four stages of transcription?
Binding of RNA polymerase to promoter sites

Initiation of polymerization

Chain elongation

Chain termination
What is the rate of RNA synthesis?
50nt/sec
What is the elongation enzyme?
Core polymerase
What is the rate of error in the Core Polymerase?
1 in 10,000 bps.
What are the two mechanisms in transcription?
Rho
Specific Sequences
What is rho?
It is an ATP-dependent helicase, which unwinds the DNA:RNA hybrid and releases the RNA chain.
In eukaryotes, what is the function of RNA polymerase I?
It transcribes rRNA
Which polymerase transcribes mRNA in eukaryotes?
RNA polymerase II
What does RNA polymerase III transcribe?
5S rRNA, tRNA, and small RNA genes.
Which enzyme utilizes the TATA and CAAT boxes as promoters?
RNA polymerase II
How many promoters does RNA Polymerase I recognize?
One
Why do eukaryotes lack precise transcription termination sites?
Because they undergo post-transcriptional processing that will fix any cleavage errors.
What are the three major classes of RNA?
mRNA (messenger)
rRNA (ribosomal)
tRNA (tranlational)
A 5' capping (G)
Splicing
The addition of a 3' PolyA tail and specific site editing are all characteristics of what?
Posttranscriptional Processing.
What makes mRNA resistant to 5' exonucleolytic degredation?
The 5' G Cap
How can the Poly(A) tail protect mRNA?
It can protect it from degredation through PABP.
What are exons?
They are the protein-coding regions that must be joined by removing introns.
What is the process of intron removal and exon joining called?
RNA splicing.
What are the four classes of introns?
Group I introns

Group II introns
Spliceosome introns

ATP and endonuclease dependent introns
This intron is self-splicing, with no protein enzymes involved. Requires a guanine nucleoside or nucleotide cofactor. What class of intron am I?
Group I
This intron is self-splicing without the need for protein enzymes. It formes a branched lariat as an intermediate. What class of intron am I?
Group II introns.
I am the largest class of intron. I am found in nuclear mRNA. I require a large protein complex called spliceosome. What class of intron am I?
Spliceosome intron.
I am found in certain tRNA's. I require ATP and endonuclease in action. What class of intron am I?
ATP and endonuclease dependent intron.
What are degenerate codons?
Codons that are decoded into the same amino acid.
How is the nucleotide sequence read?
Sequentially, triplet by triplet
What are the trinucleotide sequences of tRNA?
Anticodons
What is the codon for initiation?
AUG (Met)
What are the three stop codons?
UAA
UAG
UGA
What are the two amino acids that are represented by only one sequence of codons?
Met and Trp
How do anticodons bind to mRNA?
Through Hydrogen bonding
What allows three tRNA molecules to simultaneously bind in close proximity to adjacent codons on mRNA?
The narrow width (2-2.5nm)
What must occur for accurate translation? (Two Steps)
Correct amino acid must be attacted to a tRNA

The correct aminoacyl-tRNA must pair with a correct mRNA codon.
What allows the correct attachment of an amino acid to a tRNA?
Aminoacyl-tRNA synthetase (aaRS)
The idea that the first two codon - anticodon pairings follow Watson-Crick geometry and the third wobbles, or does not necessarily follow the pattern is called?
The Wobble Hypothesis
What are two characteristics of ribosomes?
Enormous, and complex
What are the vital functions of ribosomes?
Binds mRNA
Has Specific binding sites for tRNA
Oversees nonribosomal protein factors, and polypeptide chain initation, elongation, and termination.
Catalyzes peptide bond formation
Undergoes movement to translate sequential codons.
What is the size of the large ribosomal subunit(prokaryote)? And What does it contain?
50S, 5S and 23S rRNA with 31 different proteins.
What is the size of the small ribosomal subunit(prokaryote)? and what does it contain?
30S, 16S rRNA and 21 different proteins.
What are the sizes of the subunits of the eukaryotic ribosome?
40S and 60S
Which site in the ribosome houses an aa-tRNA?
A site
Which site in the ribosome houses a peptidyl-tRNA?
P site
Which site in the ribosome houses a deacylated tRNA?
E site
What are polysomes?
Multiple ribosomes acting on the same mRNA molecule sequentially.
Which protein factors are associated with initation?
IF (Initiation Factors)
Which protein factors are associated with elongation?
EF (Elongation Factors)
Which protwin factors are associated with termination?
RF (Release Factors)
What are the three translation stages?
Initiation
Elongation
Termination
What is the tRNA that initiates translation?
Met-tRNAf (N-Formylmethionine-tRNA)
What is the tRNA that carries internal Met residues?
Met-tRNAm
What is the Shine-Dalgarno sequence?
A purine rich (G and A) tract of 3-10nt which is found before the initation codon.
What does the mRNA's Shine-Dalgarno sequence base-pair with?
16S rRNA
In which step of initation does IF-3 bind to the 30S subunit?
Step 1
The binding of IF-2, IF-1, 2GTP, and fMet-tRNA is which step of initation?
Step 2
In step 2 of initation, what purpose does IF-1 in the A site serve?
Prevents the inappropriate binding of a tRNA.
The release of IF-1, IF-2, and IF-3 occurs in which step of initiation?
The third step
What are the three stages of chain elongation?
Decoding
Transpeptidation
Translocation
What delivers the right aa-tRNA into the empty A site in the ribosome?
EF-Tu
What mediates the GDP exchange by GTP?
EF-Ts
What is a G protein?
Any protein that associates and hydrolyzes GTP
What is the most abundant protein in E.coli?
EF-Tu
What is the proofreading for accurate tRNA selection?
GTP hydrolysis from EF-Tu
What is transpeptidation?
It is the transfer of the peptidyl group on the P-site of tRNA to the A site.
What plays a catalytical role in peptidyl transfer?
rRNA, found in the large subunit. Called peptidyl transferase center
What enables the ribosome to move to the next codon?
EF-G & GTP hydrolysis
Which codons does the protein release factor, RF-1 recognize? (in E.coli)
UAA, and UAG
Which codons do the protein release factor RF-2 recognize? (In E.coli)
UAA, and UGA
Where in the ribosome is the stop codon recognized?
The A Site
What causes the release of the polypeptide?
The binding of RF-1 or RF-2 to the A site
What causes the release of the deacylated tRNA, release factor, and mRNA from the ribosome?
RRF, IF-3, and energy from GTP hydrolysis.
What gene products are present in large amounts?
Elongation factors required for protein synthesis in bacteria.
What gene products are present in small amounts?
Enzymes that repair DNA lesions
What are the seven processes that affect cellular concentration of a protein?
1) Synthesis of primary RNA transcript
2) Post transcriptional modification of mRNA
3) Messenger RNA degredation
4) Protein Synthesis
5) Posttranslational mod of proteins
6) Protein targeting and transport
7) Protein degredation
What are housekeeping genes?
Genes for products that are required at all times.
What is the term for varying expression of genes in response to molecular signals?
Regulated gene expression
What affects binding affinity of RNA polymerases?
Different nucleotide sequences
What are three proteins that regulate transcription initiation?
Specificity Factors
Repressors
Activators
What is the σ subunit of E. coli?
It is a specificity factor that changes when it is subjected to heat stress
What are operators?
Binding sites in prokaryotic cells (near a promoter)
What is an enhancer?
Binding site in eukarotic cells (distant from a promoter)
Where does gene expression controlled in prokaryotes?
At the level of transcription
What is an example of a negative regulatory element in E.coli?
lac repressor
What is an example of a positive regulatory element in E.coli?
CRP-cAMP