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370 Cards in this Set

  • Front
  • Back
Gene transfer from parent to child is known as...
vertical transfer
The transfer of small pieces of genetic information from one cell to another is known as...
horizontal transfer
Genes are units of information composes of a sequence of DNA nucletides of four different types...
Adenine (A), Guanine, Thymine (T), and Cytosine (C).
What is a structural gene?
A string of nucleotides that can be decoded by an enzyme to produce a functional RNA molecule.
A string of nucleotides that can be decoded by an enzyme to produce a functional RNA molecule is known as a __________.
structural gene
Gene transfer from parent to child is known as...
vertical transfer
The transfer of small pieces of genetic information from one cell to another is known as...
horizontal transfer
Genes are units of information composes of a sequence of DNA nucletides of four different types...
Adenine (A), Guanine, Thymine (T), and Cytosine (C).
What is a structural gene?
A string of nucleotides that can be decoded by an enzyme to produce a functional RNA molecule.
A string of nucleotides that can be decoded by an enzyme to produce a functional RNA molecule is known as a __________.
structural gene
The Smallest genome known for a free-living microbe encodes a possible ______ proteins.
480
Type ____ topoisomerases cleave one strand of a DNA molecule and relieve supercoiling.
Type 1 topoisomerases;
Type ____ topoisomerases cleave both strands of DNA and use ATP to _______ supercoils.
Type 2 topoismerases; introduce
Type 2 topoisomerases...
Cleave both strands of DNA and use ATP to introduce supercoils.

-includes DNA gyrase
The active DNA gyrase complex is a tetramer composed of _____ and _________.
2 GyrA and 2 GyrB proteins.
Quinolone antibiotics specifically target...
type 2 topoisomerases
Most bacteria, archaea, and eukaryotes have _______ supercoils. Why?
negative; Because DNA is under-wound, the two strands are easier to separate than positively supercoiled DNA. This allows for easier transcription by enzymes such as RNA polymerase that must separate strands of DNA to make RNA.
What is the suspected reason why certain archaeal DNA has positive supercoils?
Archaea that live in extreme environments benefit from positive supercoils due to it being a more stable configuration. It is more tightly wound and thus, more energy is required to denature it.
________ supercoils are formed if one end of a DNA molecule is turned in the same direction as the helix.
negative supercoils; underwinding.
The boundaries of each domain are defined by ______.
anchoring proteins; a.k.a. "histone-like' proteins
The chromosome of E. coli has over ___ million bases.
4.6 million
Why is DNA with higher GC content considered more resistent to environmental stress?
Instead of having two hydrogen bonds, like AT, GC rocks out with three hydrogen bonds. Thus, higher GC content means more H-bonds and greater stability; greater stability means that more energy is required to denature or destroy DNA with high GC content.
Bacterial chromosomes range from ___ kbp to ___ kbp.
580 to 9,400 kbp
Archaeal cromosomes range from ___ kbp to ___ kbp.
935- 6,500 kbp
What is a promotor?
The DNA sequence immediately in front of a gene that is needed to activate the gene's expression.
Monocistronic RNA codes for how many proteins?
one protein; one gene
Polycistronic DNA codes for how many proteins?
several; many genes are lined up head to tail... an operon
An _______ is a series of genes lined up in tandem from head to tail.
operon
List the steps involved in the coiling of dna by type 2 topoisomerases.
1. GyrB grabs one section of double-stranded DNA.

2. GyrA introduces double-strand break in this section and holds the two ends apart while remaining covalently attached to the DNA

3. GyrA ATPase passes the intact double-stranded section through the double-stranded break

4.GyrB rejoins the cleaved DNA and opens at the other end to allow the strand that has passed through the exit.
The process of replication is divided into 3 phases. They are...
1. Initiation

2. Elongation

3. Termination
Enzymes that synthesize DNA can only connect nucleotides in a _______ direction.
5' to 3'
DNA is composed of...
Four different nucleotides linked by a phophodiester backbone.
The primary chemical difference between deoxyribose and ribose is:
The 2' carbon of ribose has a hydroxide branch.

The 2' carbon of deoxyribose has a hydrogen branch.
The base pairs in DNA are linked by _______.
Hydrogen Bonds.
What type of interaction links the 3' end of one deoxyribose/ ribose to the 5' end of the adjacent deoxyribose?
a phosphodiester bond.
What is the purpose of the protein DnaA and what gene codes for it?
DnaA initiates DNA replication, binds oriC, and DnaB loading. Coded by dnaA.
What is the purpose of the protein DnaB and what gene codes for it?
Helicase, prepriming priming, DNA-dependent rNNTPase. dnaB.
The orientation of the two strands in a nucleic acid double helix with one strand in the 5’ to 3’ orientation and the other strand in the 3’ to 5’ orientation.
Antiparallel Arrangement
What doees semiconservative DNA replication mean?
Each daughter cell receives one parental DNA strand and one newly synthesized DNA strand.
Enzymes that synthesize DNA or RNA can only connect nucleotides together in a _________ direction.
5' to 3'
List the 5 basic steps in DNA replication
1. Replication begins at origin (initiation)

2. Replication bubble forms. Replication forks progress in opposite directions.

3. One strand is synthesized continuously 5' to 3'.

4. Second strand at each fork is synthesized discontinuously in Okazaki fragments 5' to 3'.

5. Replication ends at terminus.
What occurs during the initiation phase of DNA replication?
The melting (unwinding) of the helix and the loading of the DNA polyemerase enzyme complex.
What occurs during the elongation phase of DNA replication?
The sequential addition of deoxyribonucleotides from deoxynucleotide triphosphates, followed by proofreading.
These enzymes regulate the supercoiling of DNA:
Topoisomerases
Explain how nucleic acid chemistry dictates DNA structure...
Each dioxyribose has a nitrogenous base attached to its 1' carbon. The 5' carbon and the 3' carbon of the deoxyribose are attached via a phosphodiester bond. This creates the phosphdiester backbone. The two backbones of the double-helix are arranged in an antiparallel manner so that hydrogen bonds can form between the bicyclic purines and the monocyclic pymidines (A-T and G-C). These bonds could not form otherwise.
These enzymes regulate the supercoiling of DNA:
Topoisomerases
Explain how nucleic acid chemistry dictates DNA structure...
Each dioxyribose has a nitrogenous base attached to its 1' carbon. The 5' carbon and the 3' carbon of the deoxyribose are attached via a phosphodiester bond. This creates the phosphdiester backbone. The two backbones of the double-helix are arranged in an antiparallel manner so that hydrogen bonds can form between the bicyclic purines and the monocyclic pymidines (A-T and G-C). These bonds could not form otherwise.
Linked rings of DNA found immediately after replication of circular chromosomes.
catenane
Horizontal gene transmission involving cell-cell contact. In bacteria, pili draw together the donor and recipient cell envelopes, and a protein complex transmits DNA across. In ciliated eukaryotes, a bridge forms between two cells connecting their cytoplasm, through which micronuclei are exchanged.
conjugation
The insertion of DNA into a plasmid where it can be replicated.
Cloning
Overlapping fragments of cloned DNA that are contiguous along a chromosome.
Contig
The loss of secondary and tertiary structure in a protein or nucleic acid due to high temperature or chemical treatment.
Denture
A region of DNA, such as the promoter region, that controls the expression of structural genes but does not itself code for RNA.
DNA control sequence
An enzyme cells use to create a covalent bond at a nick in the phosphodiester backbone. Also used in molecular biology laboratories to join pieces of DNA.
DNA Ligase
A non-coding DNA region in eukaryotes that can lead to activation of transcription when bound by the appropriate transcription factor. Its location on the chromosome can be far removed the regulated gene
enhancer
An enzyme that cleaves DNA from the end.
Exonuclease
QA protein that helps compact eukaryotic chromosomes in nucleosomes.
Histone
The transfer of a pathogen from one organism into another, non-progeny organism.
horizontal transmission
The annealing of a nucleic acid strand with another nucleic acid strand containing a complementary sequence of bases. The binding of one nucleic acid strand with a complementary strand.
hybridization
In eukaryotic genes, an intervening sequence that does not code for protein and is spliced out of the mRNA prior to translation.
Intron
A group of genes, operons and regulons that is co-ordinately activated in response to a particular stimulus.
modulon
Short fragments of DNA that are synthesized on the lagging strand during DNA synthesis.
Okazaki fragments
A collection of genes that are in tandem on a chromosome and are transcribed into a single RNA.
operon
The region of a bacterial chromosome where DNA replication initiates.
origin (oriC)
A DNA sequence in which the top and bottom strands have the same sequence in the 5’ to 3’ direction.
palindrome
The bond that covalently attaches to adjacent nucleotides in a nucleic acid.
phosphodiester bond
An extrachromosmal genetic element that may be present in some cells.
plasmid
A method to amplify DNA in vitro using many cycles of DNA denaturation, primer annealing, and DNA polymerization with a heat stable polymerase.
polymerase chain reaction (PCR)
An RNA polymerase that synthesizes short RNA primers complementary to a DNA template to launch DNA replication.
primase
A non-coding DNA regulatory region immediately upstream of a structural gene that is needed for transcription initiation.
promoter
An enzymatic activity of some nucleic acid polymerases that attempts to correct mispaired bases.
proofreading
A gene that is no longer functional.
pseudogene
A double-ring nitrogenous base found in nucleosides such as adenine and guanine.
purine
A single-ring nitrogenous base found in nucleosides such as cytosine, thymine or uracil.
pyrimidine
A group of antibiotic drugs that inhibit DNA synthesis by targeting bacterial topoisomerases such as DNA gyrase.
quinolones
The replacement of host DNA with donor DNA.
recombination
A group of genes and operons that is co-ordinately regulated and shares a common biochemical function.
regulon
During DNA synthesis the region of the chromosome that is being unwound.
replication fork
A bacterial enzyme that cleaves double-stranded DNA within a specific short sequence, usually a palindrome. Also called a restriction endonuclease.
restriction enzyme
A DNA sequence recognized and cleaved by a restriction enzyme.
restriction site
The mode of DNA replication whereby each new double helix contains one old, parental strand and one newly synthesized daughter strand.
semiconservative
A plasmid with origins of replication recognized by both E. coli and eukaryotes.
shuttle vector
A protein that keeps DNA polymerase affixed to DNA during replication.
sliding clamp
A string of nucleotides that encodes a functional RNA molecule.
structural gene
A sequence of DNA that halts replication of DNA by DNA polymerase.
termination (Ter) site
An enzyme that can change the supercoiling of DNA.
topoisomerase
The passage of genes from parent to offspring.
vertical transmission
The region of the ribosome that binds an incoming charged tRNA.
acceptor site (A site)
An enzyme that attaches a specific amino acid to the correct tRNA thereby charging the tRNA.
aminoacyl-tRNA transferase
Deciphering genome sequences, including identify cation of genes and prediction of gene function.
annotation
Three nucleotides in the middle loop of a tRNA that base pair with a codon in mRNA.
anticodon
A discipline at the intersection of biology and computing that analyzes gene and protein sequence data.
bioinformatics
An RNA capable of enzymatic reactions. Also known as a ribozyme.
catalytic RNA
A protein that helps other proteins fold into their correct tertiary structure.
chaperone
A functional unit of RNA, containing the information from a single gene.
cistron
A set of three nucleotides that encodes a particular amino acid.
codon
A sequence of nucleotides or amino acids with a common function at many nucleic acid or protein positions. Consists of the base pair or amino acid most frequently found at each position in the sequence.
consensus sequence
A degradation signal contained within a protein.
degron
The region of the ribosome that holds the uncharged, exiting tRNA.
exit site (E site)
An expressed or protein-coding portion of a eukaryotic gene.
Exon
A chaperone protein that is induced by high temperature stress.
Heat-shock protein
Genes that derived from a common ancestral gene.
homologous
In eukaryotic genes, an intervening sequence that does not code for protein and is spliced out of the mRNA prior to translation.
Intron
An RNA molecule that encodes a protein.
messenger RNA (mRNA)
A structural similarity between two different molecules.
molecular mimicry
The tendency of the N-terminal amino acid of a protein to influence protein stability.
N-terminal rule
A DNA sequence predicted to encode a protein.
open reading frame (ORF)
Genes present in more than one species that derived from a common ancestral gene and encode the same function.
orthologous
Genes that arise by gene duplication within a species and evolve to carry out different functions.
Paralogous
The rRNA enzymatic ability to form peptide bonds.
peptidyltransferase
The ribosomal site that contains the growing protein attached to a tRNA.
peptidyl-tRNA site (p site)
An RNA produced from an operon containing several genes and hence containing several functional sequences (usually encoding different proteins).
polycistronic
A eukaryotic messenger RNA prior to intron removal.
preliminary mRNA transcript (pre-mRNA)
A non-coding DNA regulatory region immediately upstream of a structural gene that is needed for transcription initiation.
promoter
A molecule that enters a ribosome A site containing an mRNA stop codon and initiates protein cleavage from the tRNA.
release factor
A bacterial transcription termination mechanism that requires Rho protein
Rho-dependent
A bacterial transcription termination mechanism that requires a GC-rich region near the transcript terminus.
Rho-independent
RNA molecules that include the scaffolding and catalytic components of ribosomes.
ribosomal RNA (rRNA)
See Shine-Dalgarno sequence. A stretch of nucleotides upstream of the start codon in an mRNA that binds to a specific location of the ribosome.
ribosome-binding site
Riboozyme
A catalytic RNA molecule.
In bacteria, a stretch of nucleotides upstream of the start codon in an mRNA that hybridizes to the 16S rRNA of the ribosome, correctly positioning the mRNA for translation.
Shine-Dalgarno sequence
A protein needed to bind RNA polymerase for the initiation of transcription in bacteria.
Sigma Factor
A receptor that recognizes the signal sequence of peptides undergoing translation. The complex attaches to the cell membrane of prokaryotes (or the rough endoplasmic reticulum of eukaryotes), where it docks the protein-ribosome complex to the membrane for protein membrane insertion or secretion.
signal recognition particle (SRP)
signal recognition particle (SRP)
A receptor that recognizes the signal sequence of peptides undergoing translation. The complex attaches to the cell membrane of prokaryotes (or the rough endoplasmic reticulum of eukaryotes), where it docks the protein-ribosome complex to the membrane for protein membrane insertion or secretion.
A specific amino acid sequence on the aminoterminus of proteins that directs them to the endoplasmic reticulum (of a eukaryote) or the cell membrane (of a prokaryote).
signal sequence
signal sequence
A specific amino acid sequence on the aminoterminus of proteins that directs them to the endoplasmic reticulum (of a eukaryote) or the cell membrane (of a prokaryote).
Non-protein coding regulatory RNAs that modulate translation.
"small RNA" (sRNA)
A codon (usually AUG) that signals the first amino acid of a protein.
start codon
One of three codons (UAA, UAG, UGA) that do not encode an amino acid and trigger the end of translation.
stop codon
A DNA strand (or an RNA strand in some viruses) that is used as a template for the synthesis of mRNA.
Template Strand
A molecule resembling both tRNA and mRNA that rescues ribosomes stalled on damaged mRNAs lacking a stop codon.
tmRNA
An RNA copy of a DNA template.
Transcript
The synthesis of RNA complementary to a DNA template.
Transcription
An RNA that carries an amino acid to the ribosome. The anticodon on the tRNA matches the codon on the mRNA.
Transfer RNA (tRNA)
The ribosomal synthesis of proteins based on triplet codons present in mRNA.
translation
The energy-dependent movement of the ribosome to the next triplet codon along an mRNA.
Translocation
An enzyme that cleaves the DNA backbone at regions missing a nitrogenous base.
AP endonuclease
A position in DNA where there is no base attached to the sugar of the backbone.
AP Site
A DNA site missing a purine base due to hydrolysis of the bond linking the base to the sugar.
apurinic site
A DNA repair mechanism that cleaves damaged bases off the sugar-phosphate backbone. After endonuclease activity at the AP site, a new correct DNA strand is synthesized complementary to the undamaged strand.
base excision repair (BER)
A DNA molecule formed by a single site recombination event joining two participating circular DNA molecules.
cointegrate
A species-specific secreted bacterial protein that induces competence for transformation.
competence factor
A cell that is able to take up DNA from the environment.
competent
A transposon containing a gene for the transposase enzyme which is needed for replicative transposition
complex transposon
A transposon containing genes in addition to those of transposition, such as antibiotic resistance or catabolic functions.
composite transposon
A transposon that can be transferred from one cell to another via conjugation.
conjugative transposon
Genes that are transferred together to a recipient cell during transduction.
cotransduced
The loss of nucleotides from a DNA sequence.
Deletion
A triplex DNA molecule that forms as an intermediary structure during generalized recombination.
D-loop formation
A laboratory technique that temporarily makes the cell membrane more leaky to allow the uptake of DNA.
electroporation
A DNA element that can exist as part of the chromosome or independently, as a plasmid.
episome
Low accuracy DNA repair mechanisms that allow mutations.
error-prone repair
DNA repair mechanisms that minimize the formation of mutations.
error-proof repair
The DNA recipient cell in conjugation.
F- cell
The DNA donor cell that transmits the fertility factor F+ to an F- cell during conjugation.
F+ cell
A specific plasmid (transferred by an F+ donor cell) that contains the genes needed for pilus formation and DNA export.
fertility factor (F factor)
fertility factor (F factor)
A specific plasmid (transferred by an F+ donor cell) that contains the genes needed for pilus formation and DNA export.
A fertility factor plasmid that contains some chromosomal DNA.
F-prime (F') factor or F-prime (F') plasmid
A gene mutation involving the insertion or deletion of nucleotides that cause a shift in the codon reading frame.
frameshift mutation
A mutation that enhances the activity or allows new activity of a gene product.
gain-of-function mutation
Recombination between two DNA molecules that share long regions of DNA homology.
generalized recombination
A phage-mediated gene transfer process in which any donor gene can be transferred to a recipient cell.
generalized transduction
A region of DNA sequence whose properties indicate that it has been transferred from another genome. Usually comprises a set of genes with shared function, such as pathogenicity or symbiosis support.
genomic island
A high frequency recombination bacterial strain, caused by the presence of a chromosomally integrated F factor.
Hfr
The passage of genes from one cell into another mature cell.
horizontal gene transfer
A simple transposable element that consists of a transposase gene flanked by short, inverted repeat sequences that are the target of transposase.
insertion sequence (IS)
An enzyme that catalyzes the integration, via a double cross-over, of one DNA molecule into another at a specific sequence.
integrase
A large transposon that can contain many different antibiotic resistance genes.
Integron
A flipping of a DNA fragment within a chromosome. Inversion may allow or repress the transcription of a particular gene.
Inversion
A mutation that completely eliminates the activity of the gene product.
knockout mutation
A mutation that eliminates or decreases the function of the gene product.
loss-of-function mutation
A partial diploid strain with chromosomal and F-prime factor copies of particular genes.
merodiploid
A DNA repair system that fixes misincorporation of a nucleotide after DNA synthesis. The unmethylated daughter strand is corrected to complement the methylated parent strand.
methyl mismatch repair
A point mutation that alters the sequence of a single codon, leading to a single amino acid substitution in a protein.
missense mutation
A chemical that damages DNA and leads to mutations.
mutagen
A heritable change in the DNA sequence.
mutation
The fraction of mutant cells (defective in a given gene) within the total cell population.
mutation frequency
The number of mutations introduced into DNA per generation (cell doubling).
mutation rate
A strain of cells with a high mutation rate, usually due to a mutation in a DNA repair enzyme.
mutator strain
A mutation that changes an amino acid codon into a premature stop codon.
nonsense mutation
A DNA repair mechanism that cuts out damaged DNA. New correct DNA is synthesized by DNA polymerase I.
nucleotide excision repair (NER)
A type of genomic island, a stretch of DNA that contains virulence factors and may have been transferred from another genome.
Pathogenicity island
A gene regulatory mechanism that changes the amino acid sequence of a protein from one antigenic type to another. One mechanism involves site specific recombination that flips a DNA sequence in a chromosome
phase variation
A light-induced, photolyase- catalyzed repair of pyrimidine dimers.
photoreactivation
A change in a single nucleotide within a nucleic acid sequence.
point mutation
A DNA repair mechanism that relies on recombination between an undamaged chromosome and a gap that occurred during replication of damaged DNA.
recombinational repair
A bacterial enzyme that cleaves double-stranded DNA within a specific short sequence, usually a palindrome.
restriction endonuclease
A mutation that does not change the amino acid sequence encoded by an open reading frame. The changed codon encodes the same amino acid as the original codon.
silent mutation
Recombination between DNA molecules that do not share long regions of homology but do contain short regions of homology specifically recognized by the recombination enzyme.
site-specific recombination
A coordinated cellular response to extensive DNA damage. It includes error-prone repair.
SOS response
Phage that can transfer only a specific, limited number of donor genes to the recipient cell.
specialized transduction
The transfer of host genes between bacterial cells via a phage head coat.
Transduction
The internalization of free DNA from the environment into bacterial cells.
Transformation
A type of point mutation in which a purine is replaced by a different purine or a pyrimidine is replaced by a different pyrimidine.
transition mutation
A bacterial cell membrane protein complex that imports external DNA during transformation.
translocasome
A segment of DNA that can move from one DNA region to another.
transposable element
A transposable element-encoded enzyme that catalyzes the transfer of the transposable element from one DNA region to another.
transposase
The process of moving a transposable element from one DNA region to another.
transposition
A transposable DNA element that contains genes in addition to those required for transposition.
transposon
A parasitic discicristate protist that has a cortical skeleton of microtubules culminating in a long flagellum.
transpososome
A protein that increases gene transcription.
activator
A protein that inhibits an anti-sigma factor, allowing the target sigma factor to participate in initiating transcription
anti-anti-sigma factor
An mRNA secondary structure whose formation prevents assembly of a downstream transcriptional termination stem loop. The anti-attenuator stem permits transcription of the downstream structural genes.
anti-attenuator stem loop
A non-coding RNA that binds to a complementary sequence of protein-coding RNA and (usually) prevents its translation.
antisense RNA
A protein that inhibits a specific sigma factor, preventing transcription initiation.
anti-sigma factor
An intramolecular mRNA structure consisting of a base-paired stem connected by a single-strand loop. The stem loop structure causes transcription to terminate. Its formation requires efficient translation of a leader peptide sequence
attenuator stem loop
A secreted molecule that induces quorum sensing behavior in bacteria.
autoinducer
The inhibition of transcription of an operon encoding catabolic proteins in the presence of a more favorable catabolite, such as glucose.
catabolite repression
A DNA synthesized complementary to an RNA template via reverse transcriptase.
complementary DNA (cDNA)
A small molecule that must bind to a repressor to allow the repressor to bind operator DNA.
corepressor
An increase in gene expression caused by the decrease in concentration of a corepressor.
derepression
A biphasic cell growth curve caused by the depletion of the favored carbon source and a metabolic switch to the second carbon source.
diauxic growth
Two identical sequences in a DNA molecule, aligned in the same direction.
direct repeat
A microchip containing short DNA sequences corresponding to all the open reading frames in an organism affixed to specific locations. It can be used to measure the amount of specific mRNA molecules transcribed in cells.
DNA microchip
A technique to observe DNA-protein interactions based on the ability of a bound protein to slow the voltage-driven migration of DNA through a gel.
electrophoretic mobility shift assay (EMSA)
A non-coding DNA region in eukaryotes that can lead to activation of transcription when bound by the appropriate transcription factor. Its location on the chromosome can be far removed from the regulated gene.
Enhancer
The changing of cell surface proteins by pathogens to prevent antibody detection and prolong infection.
immune avoidance
A molecule that binds to a repressor and prevents repressor binding to the operator sequence.
inducer
The ability of glucose to cause metabolic changes that prevent the cellular uptake of less favorable carbon sources that could cause unnecessary induction.
inducer exclusion
Increased transcription of target genes due to an inducer binding to a repressor and preventing repressor-operator binding.
induction
A DNA sequence that is found in an identical but inverted form at two sites on the same double helix (e.g., 5' ATCGATCGnnnnnnCGATCGAT 3').
inverted repeat
A technique that separates proteins based on their charge.
Isoelectric Focusing
The pH at which there is no net charge on an amino acid or a protein.
isoelectric point
A short DNA sequence preceding a structural gene. In amino acid operons it contains multiple codons for the amino acid synthesized by the downstream structural genes; translates ribosomes to help determine whether the structural genes are transcribed.
leader sequence
A bacterial cell that harbors a complete, yet quiescent, phage genome. Depending on the phage, the phage genome may be integrated into the bacterial chromosome or exist as an autonomous plasmid in the cell.
lysogen
A viral life cycle in which the viral genome integrates into and replicates with the host genome, but retains the ability to initiate host cell lysis.
lysogeny
A viral life cycle in which the virus produces new virions and lyses the cell, releasing virions.
lytic
A DNA sequence that binds a repressor protein, preventing transcription of a gene downstream. (Less common, refers to a sequence binding an activator protein.).
Operator
A collection of genes that are in tandem on a chromosome and are transcribed into a single RNA.
Operon
A gene regulatory mechanism that changes the amino acid sequence of a protein from one antigenic type to another. One mechanism involves site specific recombination that flips a DNA sequence in a chromosome.
phase variation
A phage genome integrated into a host genome.
prophage
All the proteins expressed in a cell at a given time. The "complete" includes all the proteins the cell can express under any condition. The "expressed" represents the set of proteins made under a given condition.
Proteome
The ability of bacteria to sense the presence of other bacteria via secreted chemical signals called autoinducers.
quorum sensing
A protein that can bind DNA and modulate transcription in response to a metabolite.
regulatory protein (regulator)
A group of genes and operons that is co-ordinately regulated and shares a common biochemical function.
regulon
The down-regulation of gene transcription.
repression
A regulatory protein that can bind to a specific DNA sequence and inhibit transcription of genes.
repressor
A cytoplasmic protein that is phosphorylated by a sensor kinase and modulates gene transcription depending on its phosphorylation state.
response regulator
A transmembrane protein that phosphorylates itself in response to an extracellular signal, and transfers the phosphoryl group to a receiver protein.
sensor kinase
A eukaryotic DNA element that can lead to decreased transcription when bound by an appropriate transcription factor.
Silencer
A cellular response to idle ribosomes (often indicating low carbon and energy stores) that includes a decrease in rRNA and tRNA production.
stringent response
A stretch of directly repeating DNA sequence (direct repeats) without any intervening DNA.
tandem repeat
A transcriptional regulatory mechanism in which translation of a leader peptide affects transcription of downstream structural genes.
transcriptional attenuation
The set of transcribed genes in a cell at given time. The "complete" includes all the possible RNA transcription products from a given genome. The "expressed" represent the set of RNAs present during a given condition.
transcriptome
A regulatory mechanism that modulates protein production by influencing the translation of mRNA
translational control
A message relay system composed of a sensor kinase protein and a response regulator protein that regulates gene expression in response to a signal (usually an extracellular signal).
two-component signal transduction system
Often reseachers will have bacteria produce a segement of DNA the researcher is interested in. To obtain the largest amount of the DNA sequence of interest, it is best to put the DNA into:
A high copy number plasmid
A shuttle vector is so named because:
It contains a replication origin compatable with E. coli and a second origin that will allow the plasmid to replicate in a eukaryote or archaea.
Eukaryotes have mostly _______ transmission of genetic material and bacteria have __________ transmission of genetic material.
mostly vertical; vertical and horizontal
The polymerase chain reaction has many cycles of three temperature steps; 95 C, 55 C, 72 C. What happens at each step?
95 C: The DNA strands denature

55 C: Primers anneal to the denatured DNA strands

72 C: Polymerization occurs
T/F Plasmids may contain antibiotic resistance genes.
T
T/F Plasmids may exist in multiple copies in a single cell.
T
T/F Plasmids may be transmitted horizontally from one bacterium to another.
T
Which protein is necessary for replicating the linear ends of eukaryotic chromosomes?
Telemerase
A gene is:
A string of nucleotides that can be decoded by an enzyme to produce a functional RNA molecule.
Restriction enzymes do not cut the bacterial DNA that produced them because:
The DNA is potected by site specific methylating enzymes; restriction enzymes only cut unmethylated DNA
The semi-conservative nature of DNA replication indicates that:
each daughter cell receives one partial strand and one newly synthesized strand.
A plasmid singly cut with a restriction enzyme that leaves cohesive ends can ligate to:
any DNA cut with the same restriction enzyme
If the deoxyadenosine methylase (Dam) enzyme is inhibited in E. coli, then the next generation time:
will increase due to the more persistent SeqA binding.
The enzyme DnaG primase is:
an RNA polymerase
E. coli DNA polymerase III has which of the following activities:

a) 5' to 3' RNA synthesis
b) 3' to 5' exonuclease
c) 3' to 5' DNA synthsis
d) DNA ligase
b)
During DNA replication each new nucleotide adds onto:
the hydroxyl group on the 3-C of the sugar
Denaturization of DNA means:
The helix separates into single strands.
List the steps involved in trranslation initiation
1) 30S subunit binds mRNA (IF3 brings them together)--this allows the ribosome-binding site to find its complementary binding site on the 16S rRNA.

2) IF1 binds and blocks the A site

3) IF2 bound to GTP interacts with the initiator tRNA (f-met-tRNA) and escorts it to the start codon at what will be the P site.

3) Once initiator is in place, IF3 is released. The 50S subunit then docks to the 30S subunit and GTP hydrolyzes. IF1 and IF3 are released.

Ribosome now locked and loaded"
The three basic steps of peptide elongation are:
1) an aminoacyl-tRNA binds to A site

2) peptide bond formation occurs between the new amino acid and the growing peptide positioned at the P site

3) the message moves on by one codon
During the first stages of elongation...this bonds to a free, charged aminoacyl-tRNA:
EF-Tu-GTP or Elongation factor bonded to GTP
What is RpoD?
Sig Factor 70--recognizes the promoter for most genes
What is RpoH?
SF 32--recoginizes the promoter for heat-shock-induced genes
What is RpoF?
SF 28--Recognizes the promoter for genes for motility and chemotaxis
What is RpoS?
SF 38--recognizes the promoter for stationary phase and stress response genes
What is the significants of the -35 and -10 regions?
Sigma factors use promoter consensus sequences to determine where to bind for transcription. The -35 and -10 regions are where these sequences most often occur.
List the four primary start codons in order of their importance/ % occurance.
1) AUG (90%)

2) GUG (8.9%)

3) UUG (1%)

4) CUG (0.1%)
List the three stop codons:
UAA, UAG, UGA
Only ___ out of the possible 64 codons specify amino acids. What are the remaining the codons?
61... the remaining 3 codons are designated as stop condons.
The very bottom or middle loop of all tRNAs harbors an _______.
anticodon--it base pairs with codons in mRNA.
Most tRNA molecules begin with a ____ and all end with a _____, to which amino acids attach.
5' G; 3' CCA
The 3' end of the tRNA molecule is called the ________.
acceptor end
What unsual characteristic is responsible for the remarkable stability of tRNA molecules?
The unusual bases... because they are poor substrates for RNases.
Where does redundancy primarily occur?
In the third postion of the codon
The charging of tRNAs is carried out by a set of enzymes called _________.
aminoacyl-tRNA transferases... There are 20 of these "match and match" proteins in the cell, one for each amino acid.
The 30S subunit contains how many ribosomal proteins?
21 assembled around one 16S rRNA molecule [labled S1-S21 (S=small)]
The 50S subunit contains how many ribosomal proteins?
31 formed around two rRNA molecules (5S and 23S)
Peptidyltransferase does what?
Located within the 50S subunit of ribosomes, it "stitches" together amino acids via the formation of peptide bonds.
What is an ORF?
An open reading frame... a sequence of DNA predicted by various sequence cues to encode an actual protein.
What is the purpose of DNA ligase?
Joins phosphodiester ends during replication
What is the purpose of DNA Pol 1?
DNA polymerase I fills the gap left by RNase H during the process of replacing the RNA primer on the lagging strand. (DNA replication).
Who is credited with the discovery of the replisome?
Arthur Kornberg
Describe the process of DNA replication initiation (12):
1. After division, SeqA is bound to hemi-methylated oriC.

2. DnaA accumulation is proportional to growth rate

3. Dam methylation of hemi-methylated DNA

4. SeqA inhibitor is displaced

6. DnaA-ATP proteins bind to the repeated 9-mer sequences within oriC

7. Binding of DnaA leads to strand separation at the 13-mer repeats

8. DNA helicase (DnaB) and DNA helicase loader (DnaC) associate with the DnaA bound origin

9. DnaC opens the DnaB ring and loads the DnaB onto the single-stranded DNA at the origin. This leads to the release of DnaC.

10. DnaB's each recruit a DNA primase, which synthesizes an RNA primer on each template.

11. The clamp loader with DNA polymerase III loads a sliding clamp onto each leading-strand DNA at RNA primer

12. DNA polymerase binds to the clamp. Leading-strand synthesis begins and continues to the end of the template. At each lagging strand, sliding clamp is then loaded.

DNA melts at oriC
DNA Replication: What recruits DNA primase? When and Why?
Helicase (DnaB) recruits DNA primase during the initiation stages after it has been loaded. DNA primase is a specific form of RNA polymerase that synthesizes the RNA primer, which launches DNA replication.
DNA Polymerase III synthesizes how many bp per second?
1000 bp/sec
DNA Replication: Describe the process of the elongation of DNA synthesis (6):
1. The leading strand DNA Pol III enzyme replicates the leading strand . SSBs cover and protect the unreplicated single strand. The DnaB remains on the lagging strand, unwinding the dsDNA moving into the replisome complex.

2. Lagging-strand DNA polymerase synthesizes the lagging strand. The lagging strand loops out after passing through the polymerase.

3. After DnaB has moved approx. 1000 bases, a second RNA primer is synthesized on each lagging strand.

4. When the lagging strand-polymerase bumps into the 5' end of a previously synthesized fragment, the DNA polymerase is released and the clamp is disengaged

5. A new clamp is assembled on the newly primed lagging strand.

6. The DNA polymerase binds to that clamp and begins synthesizing another Okazaki fragment.
What are SSBs?
single-strand binding proteins... used during the elongation stage of DNA replication to protect the single-stranded DNA.
DNA Replication: Describe the process of lagging-strand repair:
1. RNase cleaves RNA at any point along the hybrid RNA-DNA section.

2. DNA Pol 1 fills the gap using 3' OH end of DNA fragment

3. Once DNA Pol 1 is finished synthesizing, it cannot join the 3' OH of the last added nucleotide with the 5' phosphate of the abutting fragment. The resulting "nick" is repaired via DNA ligase
What prevents the build up of torsional stress during the unwinding process in DNA replication?
DNA gyrase, that is ahead of the replication of fork, removes the positive supercoils as they form.
What is the purpose of the protein called Tus?
Used during termination of DNA replication.

(Terminus Utilization Substance)...

It binds to the termination sequence and acts as a counter-helicase when it comes into contact with DnaB. This effectively halts polymerase movement.
What two enzymes are used to solve the "linked ring" problem that results from DNA replication?
XerC and XerD
What do XerC and XerD do exactly?
They are enzymes that recognize a specific site (called dif) on both DNA molecules (after replication) and catalyze a series of cutting and rejoining steps that essentially pass one molecule through the other. Fixes the "linked ring" problem.
What are two ways that plasmids can replicate?
Bidirectional and rolling circle replication
Plasmids: In rolling circle replication, what is used to "nick" the + strand at the oriC?
RepA (replication initiator)
What are plasmids?
They are autonomously replicating circular or linear DNA molecules that are part of a cell's genome and can be transferred to other cells. Extrachromosomal pieces of DNA.
DNA Pol III has ___ to ____ exonuclease activity.
3' to 5'
Two types of plasmids:
High-copy-number:
-Up to 200 copies per cell
-Divide continuously
-Segregate randomly

Low-Copy-Number plasmids:
-One or two copies per cell
-Segregate similar to chromosome
What is the function of the Epsilon subunit?
(dnaQ or mutD)

Proofreading, 3'-5' exonuclease
What does PCR stand for?
Polymerase Chain Reaction
What is PCR good for?
Can produce over a 1 million fold amplification of target DNA sequence.
An enzyme complex called _________ carries out the process of transcription.
DNA-dependent RNA polymerase
Redundancy =

Degeneracy =
The same amino acid, but different codon (slightly changed usually)

2. A position of a codon is said to be a fourfold degenerate site if any nucleotide at this position specifies the same amino acid. For example, the third position of the glycine codons (GGA, GGG, GGC, GGU) is a fourfold degenerate site, because all nucleotide substitutions at this site are synonymous
Approximately, how many ribosomes are there per cell?
10-70 K
Translation: Describe the process of Termination of translation (6):
After translocation...

1. Stop codon in A site (no tRNAs correspond to stop codons)

2. RF1 or RF2 binds to A site... (mimics tRNA)... activates step 3

3. Peptidyltransferase cuts peptide loose from tRNA in the P site

4. RF3 displaces RF1 or RF2

5. RRF, EF-G-GTP binds at A site... GTP hydrolysis undocks sudunits

6. IF3 displaces tRNA and mRNA... binds to the 30S subunit and prevent the 50S and 30S from coming together
Translation: Describe the process of initiation:
1. 30S subunit binds to mRNA... assisted by IF3 (binds to 30S to prevent 30 and 50S from associating)
--Binding occurs 4-8 bases upstrean of AUG. Where a consensus sequence called the Shine-Delgarno sequence, in the mRNA anneals near the end of the 16S rRNA.

2. IF1 blocks the A site

3. IF2-GTP, f-met tRNA, bind P site

4. IF3 released

5. 50S subunit recruited

6. GDP hydrolyzed

7. IF1, IF2 released
Translation: Describe the process of elongation:
1. EF-Tu-GTP bind to free-charged tRNAs.

2. Incoming AA-tRNA bind to A site

3. Peptidyltranferase activity catalyzes a bond between AA in P site and AA in A site

4. Peptide now attached to tRNA in A site

5. Translocation occurs until stop codon is reached
Translation: Describe the process of translocation during elongation:
1. An Elonagation factor called EF-G (assoc with GTP) binds to the ribosome.

2. The GTP is hydrolyzed, providing energy to ratchet the 50S and 30S subunits ahead one codon.

3. This opens the A site and slides the uncharged tRNA into the last site (E site). The next aminoacyl tRNA that enter the A site creates a conformational change and ejects the tRNA from the E site.
Transcription: Describe the two types of transcription termination
1. Rho-independent termination:
-Requires a GC-rich region of RNA roughly 20bp upstream from the 3' terminus.
-the GC-rich sequence contains complimentary bases and forms an RNA stem or loop
-this structure "grabs" the RNA polymerase causing it to pause
-While the RNA Pol is paused, the DNA-RNA duplex is weakened because the poly-U, poly-A base pairs at the 3' terminus contain obly 2 H-bonds per pair
-The hybrid molecule is melted and transcription is stopped

2. Rho-dependent termination
-relies on a protein called Rho and an ill-defined sequence at the 3' end of the gene that appears to be a strong pause site
-the pause site is located after the ORF, beyond the translation stop codon (for obvious reasons).
-Rho factor binds to an exposed region of RNA after the ORF at GC-rich sequences.
-This is the pause site
-Rho monomers assemble as a hexamer around the RNA and pulls itself to the paused RNA polymerase by wrapping the RNA around itself.
-once it touches the RNA polymerase termination occurs.
How to unstick stuck ribosomes:
Ribosomes stuck with peptidyl-tRNA at P site and empty A site.

1. tmRNA binds, adds Ala, and AANDENYALAA codons are translated (SsrA)

2. Stop codon on tmRNA disengages ribosome

3. SspB helper protein recognizes SsrA-tagged protein

4. SspB complex escorts protein to ClpXP for degradation
Is peptidyltransferase activity carried out by the rRNA or protein?
rRNA
List the four major chaperones seen in most species.
GroEL (60 kDa), GroES (10kDa), DnaK (70 kDa), and trigger factor (48 kDa)
What does GroEL do?
It acts as a chamber to reshape proteins... It is capped by GroES, which determines access to the chamber.
Does DnaK have a chambered structure?
No. it is an open chaperone and clamps down on peptides to assist folding.
Export of Protein into the Cell Memrane: Describe the process of SRP and cotranslational transport
1. Ribosome is "paralyzed" by SRP and move to the membrane to interact with FtsY

2. Some integral membrane proteins are inserted directly.

3. Periplasmic proteins are secreted via the Sec system (SecYEG)
Export of Protein to Periplasm: SecA- dependent patchway...
1. Trigger factor allows complete translation

2. SecB wraps pilot protein

3. SecB complex delivered to SecA-SecYEG

4. SecA plunger repeatedly plunges 20 aa's into SecYEG channel

5. LepB cleaves signal sequence. Periplasmic chaperones fold the protein.
The procress of importing free DNA into bacterial cells is known as:
Transformation
This transformation technique is used to "shoot" DNA accross the membrane:
electroporation
TEST: Mutation of which of the following genes would result in an inability to grow on lactose?

a. lac Z
b. lac Y
c. lac l
d. crp
e. all but c are correct
e. all, but C are correct

lacl is a repressor, mutation of it would increase production
The alternative sigma factor, RpoS, directs RNA polymerase holoenzyme to transcribe:
Stationary phase promoters
A polycistronic mRNA encodes information for:
an operon
Recombinant DNA (e.g. Cloning) does NOT require which of the following?

a. restriction enzymes
b. Vector
c. Ligase
d. DNA Polymerase
D. DNA polymerase
Incorporation of di-deoxy nucleotides during in vitro DNA replication
Causes DNA synthesis to stop and is a mechanism used to sequence DNA
What is the role of DNA Pol I in DNA Replication?
Synthesis of DNA & Fill in hole left by primer removal
The enzyme responsible for transcription is most correctly described as:
DNA-dependent RNA polymerase
Immediately following translocation and before the next elongation step, the A-site of the ribosome is
empty
What two things discussed in lecture control the number of a specific protein in the cell?
1. The frequency of transcription initiation of the gene that encodes the protein

2. Quality of the RBS of the mRNA that encodes the protein
The meth codon AUG indicates what?
start codon
Describe the basic mechanism of the conjugation process:
The presence of F-Factor in one cell allows for the creation of a sex pilus connect to cells together. The pilus contract bring the cells close together forming a conjugation bridge. The F-Factor nicks the oriT and the 5' end begins to move through the bridge. Each strand is replicated and the recipient is now a donor.
What type secretion system is conjugation?
Type IV
When the chromosome has integrated an F-factor, the cell is designated _____.
an Hfr... refering to the fact that there are more cells capable of transferring chromosomal DNA in an Hfr population than a F+ population where few Hfr's are present.
What is a merodiploid?
A situation where a conjugal recipient of the F' factor contains two copies of those few genes
How does Hfr relate to gene mapping?
Timing of Hfr gene transfer was used to construct the original gene maps of E. coli.
The process in which bacteriophages carry payloads of host DNA from one cell to another is known as __________.
Transduction
What are the two types of transduction?
generalized and specialized
Bacteriophages that perform generalized transduction can:
take any gene from a donor cell and transfer it to a recipient cell.
Bacteriopages that perform specialized transduction can:
only transfer a few closely linked genes.
Steps of generalized transduction:
1. P22 phage DNA infects a host cell and makes subunit components more phage

2. DNA is packaged into capsid heads. Some capsids package host DNA.

3. New phage assembly is completed

4. Cell lyses, page is released.

5. Transducing phage particle inject host DNA into new cell, where it may recombine into the chromosome.
What protects bacteria from invasion of foreign DNA?
Restriction endonucleases protect bacteria from invasion by foreign DNA. Restriction-modification enzymes methylate restriction target sites in the host DNA to prevent self digestion.
List the steps to generalized recombination:
1. RecBCD binds to the end of the donor DNA

2. RecBCD unwinds strand until it reaches the Chi site, where it nicks the DNA and continues unwinding. Then RecA filament forms.

3. RecA find homology and mediates strand invasion, D-loop.

4. RuvAB binds at the crossover and carries out branch migration, which extends base pairing between donor and recipient strands.

5. Endonuclease cleaves one end of the D loop

6. Displaced ends are ligated to opposite strands

8. RuvC can cleave across the junction in two ways.
___________ mediates generalized recombination.
RecA synaptase
What is a mutation?
A heritable change in DNA sequence. Can effect either the genotype or phenotype
List the four types of point mutations:
1. Silent mutation

2. Missence mutation

3. Nonsense mutation

4. Single base pair mutation
--transition
--transversion
Mutations that do not change the amino acids sequence of a translated ORF are called:
silent mutations
What is a point mutation?
a change in a single nucleotide.
What is a transition mutation?
A point mutation, in which, a purine is changed to a different purine or pyramidine is changed to a different pyramidine.
What is a transversion mutation?
A point mutation, in which, a purine is swapped out with a pyramidine and vice versa.
What are the three "larger" mutation types?
Insertions, Deletions, Inversions
What is a missense mutation?
A mutation where the amino acid sequence of the protein has changed as a result.
What is a loss-of-function mutation?
A missense mutation, in which, the protein's activity has been decreased or eliminated.
What is a gain-of-function mutation?
A missense mutation, in which, the protein's activity has been increased or even gained a new activity
What is a nonsense mutation?
A point mutation that changes an amino acid codon into a translation termination codon... results in a truncated protein lacking in function.
A mutation that eliminates function is known as a:
knock-out mutation... can be insertions, deletions, or nonsense mutations.
What are mutagens?
Chemical agents that damage DNA
How is a frameshift mutation created?
Through either a deletion or insertion mutation, in which, the frame is changed and causes the protein message being translated to be garbled.
List 3 types of mutagens:
Spontaneous tautomers during replication

Electromagnetic radiation

Chemicals
What is the Ames Test?
A test to determine the mutagenicity of certain compounds.
-Uses a hisG mutant that cannot grow on a defined media
-if the compound is able to mutate the hisG gene to its original state then it is capable do this to any gene.
-Uses bacterial cultures to test for mutagenicity
- more colonies = stronger mutation
la lámpara
lamp
What is mismatch repair?
Mispaired bases occasional occur during replication. These are cut out of the strand. The mutated fragment is un-methylated and is newer. It is assumed to be in error and is cleaved out and replaced by exonucleases and DNA Pol 1.
What is Nucleotide excision repair?
Removal of Thymidine dimers
-induced by UV (photoactivation)
-cut out by UvrAB
What is Base excision repair?
Removes damaged bases
-excised by specific enzymes
-replaced by DNA Polymerase 1
What is Recombinational Repair?
Occurs just after replication
-undamaged strand is copied
-damaged strand is replaced
-catalyzed by RecA recombinase
What is SOS repair?
Used for extensive DNA damage.

-damage inactivates LexA (SOS repressor)
-leads to activation of many repair genes (UmuDC = Pol V)
-Error prone, but better than nothing
-Activiation
This DNA repair method uses methylation of the parental DNA strand to discriminate it from the newly relicated DNA .
Methyl mismatch repair
This method of DNA repair excises structurally altered bases without cleaving the phosphodiester backbone.
Base excision repair
This method of DNA repair occurs at the replication fork. A good strand of DNA is used to replace a damaged strand.
Recombinational Repair