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Foundations in Molecular Biology and Genetics: Final
University of Guelph MBG*2040
470
Microbiology
Undergraduate 2
12/08/2015
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Term
+1 sequence
 Definition
The site where transcription begins.
Term
2-aminopurine (2-AP)
 Definition
A base analog. An adenine or guanine analog.
Term
3' - 5' exonuclease activity
 Definition
Cuts DNA strands, starting at the 3' termini. The DNA polymerase goes "backwards". Allows for proofreading.
Term
5' - 3' exonuclease activity
 Definition
Cuts DNA strands, starting at the 5' termini.
Term
5-bromouracil (5-BU)
 Definition
A base analog. A thymine analog that pairs with adenine or guanine, depending on if it is in keto or enol form. If it is in enol form before incorporation, it produces C:G → A:T transitions. If it is in enol form after incorporation, it produces A:T → C:G transitions.
Term
7-methyl guanosine cap
 Definition

5' cap

A 7-methyl guanosine residue joined to the initial nucleotide of the transcript by a 5' - 5' phosphate linkage. Added to the nascent RNA transcript during elongation when it is about 30 nucleotides long. Protects the 5' end from degradation.
Term
-10 sequence
 Definition
A promoter. Part of the Pribnow box. An upstream sequence about 10 nucleotides from the initiation site in E. coli. Its consensus sequence is TATAAT. Facilitates localized unwinding of DNA because it is A:T rich.
Term
-35 sequence
 Definition

Recognition sequence

A promoter. Part of teh Pribnow box. An upstream sequence about 35 nucleotides from the initiation site in E. coli. Its consensus sequence is TTGACA. The sigma subunit binds to this sequence.
Term
α-amanitin
 Definition
An inhibitor of RNA polymerase II. A deadly toxin. Found in death angel mushrooms.
Term
α-helix
 Definition
A secondary structure in proteins. Rigid cylinders in which each peptide bond is hydrogen bonded to the peptide bond three/four amino acids away. Proline cannot be present in α-helices.
Term
β-sheet
 Definition
A secondary structure in proteins. The polypeptide folds back onto itself, sometimes repeatedly, and the parallel segments are held by hydrogen bonds.
Term
A-DNA
 Definition
Right-handed, compact DNA. Created artificially by exposing DNA to salts.
Term
Ac/Ds elements
 Definition
Cut-and-paste transposons found in maize. Discovered by Barbara McClintock. Cause clear corn kernels to become mosaic brown/purple kernels.
Term
Acquired immune deficiency syndrome (AIDS)
 Definition
A disease caused by HIV virus. Affects tens of millions of people. Loss of ability to fight infections from pathogens, including normally benign organisms.
Term
Acquired traits
 Definition
Traits imposed on an organism by environmental factors. Jean Lamarck and Trofim Lysenko thought that they were inherited, but actually they are not.
Term
Acridine dyes
 Definition
A class of chemical mutagens. Intercalates into DNA, sandwiching between base pairs, increasing the probabilit of mistakes in replication. The DNA molecules are more rigid, and may have kinks. Causes frameshift mutations. Includes 2,8-diamino acdiride (proflavin), and acridine orange.
Term
Acridine orange
 Definition
An acridine dye.
Term
Activator
 Definition
The product of regulator genes in positive control mechanisms. They are needed to turn on expression of one or more structural genes.
Term
Adenine
 Definition
Has a common amino form, and a rare imino form, with the H at C6 rather than C1. If treated with nitrous acid, it changes to hypoxanthine, which pairs with cytosine.
Term
Alkylating agents
 Definition
A class of chemical mutagens. Mutagenic to replicating and non-replicating DNA. Donates alkyl groups (ethyl, methyl, et cetera) to other molecuels, altering base pairing, or activating error-prone DNA repair processes that introduce mutations during repair. Induce all types of mutations, including chromosome aberrations. Includes di-(2-chlorethyl) sulfide (mustard gas), ethyl methane sulfonate (EMS), and ethyl ethan sulfonate (EES).
Term
Allolactose
 Definition
The affector molecule of the lac operon. An inducer. Produced from lactose by β-galactosidase, the product of lacZ, which has a low background level of expression at all times.
Term
Allosteric transition
 Definition
Conformational change in protein structure due to binding with another molecule.
Term
Amber mutation
 Definition
Named after one of the researchers who discovered them. Nonsense mutations in E. coli that produce stop codons, and result in synthesis of truncated polypeptides. Mutant tRNAs that recognize stops codons as amino acids are suppressor mutations for amber mutations.
Term
Amino
 Definition
The common form of cytosine and adenine.
Term
Amino acid
 Definition
The constituent of polypeptides. Has an amino group, a free carboxyl group, and a side group.
Term
Aminoacyl site (A)
 Definition
The A site on a ribosome. Binds incomping aminoacyl-tRNAs.
Term
Aminoacyl-tRNA
 Definition
tRNA with an amino acid attached by a high-energy bond. Created by aminoacyl-tRNA synthetase.
Term
Aminoacyl-tRNA synthetase
 Definition
Catalyzes the binding of amino acids to the correct tRNA, converting ATP into AMP. There is at least one for each amino acid.
Term
Anabolic pathways
 Definition

Biosynthetic pathways

Often repressible. Repressed in the presence of the molecule they produce.
Term
Anticipation
 Definition
Increased copy number of a trinucleotide repeat with each generation, leading to increased severity or early onset of the disease.
Term
Antisense strand
 Definition
Strands of RNA that are complementary to sense strands. Do not code for polypeptides.
Term
apo-B
 Definition
Genes which regulate apolipoproteins: blood proteins in rabbits and humans which carry fat molecules. The mRNA has a change in structure of bases during RNA editing. This enables the mRNA to produce different products in different parts of the body, to perform different functions.
Term
ARS elements
 Definition

Autonomously Replicating Sequences

Sequences in prokaryote DNA that have their own origin of replication, and replicate independently from the rest of the chromosome. About 50 bp in length, with a conserved core A:T rich 11 bp sequences. Found in Saccharomyces cerevisiae.
Term
Arthur Kornberg and coworkers
 Definition
First demonstrated in vivo DNA replication in 1957, and won the Nobel Prize in 1959.
Term
Ataxia-telangiectasia
 Definition
An inherited disease caused by defects in DNA repair mechanism. Radiation sensitivity, chromosome instability, early onset of progressive neurodegeneration, and prone to cancer. Caused by defects in kinases involved in the control of cell cycle. Caused by mutations in ATM.
Term
ATM
 Definition
A gene on chromosome 11 for serine/threonine kinase. Mutation in this gene can lead to ataxia-telangiectasia.
Term
AUG
 Definition
The initiation sequence in eukaryotes. Codes for tRNAiMet. The ribosome moves down from the 5' end, scanning for this sequence. At all other positions in the mRNA, it codes for tRNAMet.
Term
Autoradiography
 Definition
Detecting radioactive isotopes by exposing the experiment to a photographic emulsion containing silver halides. Black spots form where radioactive isotopes are present.
Term
Back mutation
 Definition
A type of reversion. A second mutation at the same site in the genome. Restores the nucleotide sequence of the gene. If back-crossed to a wild-type individual, all progeny are wild-type.
Term
Balbiani rings
 Definition

Puffs

Sites of localized unwinding due to gene transcription in eukaryotes. Occurs in the polytene chromosomes of Drosophila salivary glands.
Term
Barbara McClintock
 Definition
Studied maize chromosome breakage at University of Missouri 1936 - 1941. Discovered Ac/Ds transposable elements in 1940. Proposed the idea of transposable elements. The concept was not accepted immediately; people thought that DNA was stable, and didn't "jump around". Won the Nobel Prize in 1983.
Term
Basal transcription factor _ (TFII_)
 Definition

Transcription Factor for RNA polymerase II [letter of denotation]

Transcription factors which initiate transcription by RNA polymerase II. Must interact with promoters in the correct sequence to initiate translation. Incldues TFII A, B, D, E, F, and H.
Term
Base analogs
 Definition
A class of chemical mutagens. Mutagenic only to replicating DNA. Have structures similar to normal bases, and are incoroprated into DNA during replication. Increase the frequency of mis-pairing. Includes 5-bromouracil (5-BU), and 2-aminopurine (2-AP).
Term
Base excision repair
 Definition
A form of excision repair. Systems remove abnormal or chemically modified bases from DNA. Initiated by DNA glycosylases that recognize abnormal bases in DNA: each recognizes a specific type of altered base. DNa glycosylase cleaves the glycosidic bond between base and deoxyribose, creating apyrimidine sites (AP sites) with missing bases. AP endonuclease acts with phosphodiesterases to excise sugar-phosphate groups.
Term
Benno Müller-Hill and coworkers
 Definition
Showed that O2 and O3 operators of the lac operators have effects on levels of transcription in the operon.
Term
Bidirectional replication
 Definition
Replication forks travel in opposite directions from the origin of replication. Mario Schnös and Ross Inman provided evidence for this.
Term
bla
 Definition
A gene on a Tn3 element. Codes for beta lactamase enzyme, which produces resistance to ampicillin.
Term
BLM
 Definition
A gene on chromosome 15 for BLM REcQ helicase. Mutation in this gene can cause Bloom syndrome.
Term
Bloom syndrome
 Definition
An inheritance disease caused by defects in DNA repair mechanism. Chromosome instability, mental retardation, and prone to cancer. Increased chromosome aberration. Alterations in specific DNA helicases. Caused by mutation in BLM.
Term
CAAT box
 Definition
An element of a promoter for RNA polymerase II. A conserved element at about -80. The consensus sequence is GGCCAATCT.
Term
Caenorhabditis elegans
 Definition
A eukaryote which has multi-genic mRNAs that contain many genes.
Term
CAF-1
 Definition
Chromatin assembly factor 1. Carries histones to chromosomal sites of nucleosome assembly during DNA replication.
Term
Catabolic pathways
 Definition

Degradative pathways

Usually catalyzed by inducible enzymes. Induced by presence of the molecule they break down.
Term
Catabolite activator protein (CAP)
 Definition

Cyclic AMP receptor protein

A dimer that binds to the CAP/cAMP binding site on the lac operon in the presence of glucose. It has positive control. It bends the DNA, making it easier for RNA polymerase to attach. It binds to loops formed when lac repressor is bound to O1 and O3.
Term
Catbolite repression
 Definition
Glucose effect. In the presenceof glucose CAP prevents induction of the lac (lactose), ara (arabinose), and gal (galactose) operons. Assures that glucose is metabolized in preference to other, less efficient carbohydrates. CAP has positive control of the operons, and cAMp is the effector molecule, present only in the absence of glucose.
Term
Central Dogma of molecular biology
 Definition

First described by Francis Crick.

DNA -(transcription)--> RNA -(translation)--> polypeptides
Term
Chain termination codon
 Definition

UAA, UAG, or UGA

Triggers termination of translation when they enter the A site of the ribosome. Recognize by release factors.
Term
Chaperones
 Definition
Proteins that help some nascent polypeptides fold into their correct formation.
Term
Charles Yanofsky and colleagues
 Definition
First demonstrated evidence for colinearity between genes and polypeptides. Compared the nucleotide sequences of trpA with the amino acid sequence of the polypeptide it codes for in wild-type and mutant E. coli.
Term
Charlotte Auberach and associates
 Definition
Discovered the mutagenic effects of mustard gas. Their research was classified during WWII due to its use as a weapon, and results were not published until after the war.
Term
Chemical mutagen
 Definition
Chemicals which are mutagens. May affect replicating or non-replicating DNA, or replicating DNA only. Includes alkylating agents, base analogs, acridines, deaminating agents, and hydroxylating agents.
Term
Chromosome remodeling
 Definition
Modification of nucleosomes, to interact with proteins and express only genes which need to be expressed. Occurs before transcription.
Term
ClB chromosome
 Definition

An X chromosome in Drosophila which is altered. Examined in the ClB method. Has three characteristics:

C: Crossover suppressor. A long inversion that suppresses recombination between ClB and normal X chromosomes. Causes recombinant progeny to abort.

l: Lethal mutation. Homozygous females and hemizygous males with the ClB chromosome are not viable.

B: Bar-eye phenotype. The eyes are narrowed and bar-shaped. It is partially dominant, so heterozygotes can be identified.
Term
ClB method
 Definition
An accurate method of identifying lethal mutations on the X chromosomes of Drosophila, developed by Hermann J. Muller. Performed with females heterozygous for the ClB chromosome. If there is a recessive lethal mutation on the X chromosome, all progeny from a cross with a normal male will be female.
Term
Co-repressors
 Definition
Effector molecules that cause repression of genes. Cause activators to detach from the RPBS. Cause repressors to attach to the RPBS.
Term
Cockayne syndrome
 Definition
An inherited disease caused by defects in DNA repair mechanisms. UV sensitivity, neurological and developmental disorders, and premature aging. Caused by mutation in CSA or CSB.
Term
Codon
 Definition
A three-nucleotide sequence that specifies an amino acid, according to the genetic code.
Term
Cointegrate
 Definition
A Tn3 element fused to a plasmid. Tn3 is replicated and the cointegrate folds, producing site-specific recombinations at res sites, splitting the cointegrate apart producing two genetic elements with Tn3 genes.
Term
Composite transposon
 Definition
A cut-and-paste transposon found in bacteria. Includes Tn3. Created when two IS elements insert into each other. The region between them can be transposed when the elements act joinly. The flanking IS element may be identical, inverted, or different IS elements.
Term
Conjucative R plasmids
 Definition
Plasmids which transfer genes for antibiotic resistance between bacteria cells. May be rapidly exchanged between bacteria, even across species. Some carry multiple resistance genes. Evolved through IS-mediated recombination events. Cause many bacterial diseases to be difficult to treat for. Includes a resistance transfer factor and R-determinant.
Term
Consensus sequence
 Definition
Sequences which are most often preserved.
Term
Conservative replication
 Definition
A possible method of DNA replication. A completely new DNA molecule is produced. In Meselson and Stahl's experiment, one DNA strand would be heavy density, and the rest would be normal density. There is no evidence to support this.
Term
Continuous replication
 Definition
Occurs on the strand of the replication fork going in the 5' - 3' direction. Synthesizes the leading strand.
Term
Constitutive genes
 Definition

Continuously expressed

Genes which code for housekeeping functions.
Term
copia
 Definition
A retroviruslike element found in Drosophila. Produces copious amounts of RNA.
Term
Circk's wobble hypothesis
 Definition
Hypothesized by Francis Crick. In a tRNA, the first two bases in the codon/anti-codon are very important. Pairing at the third base, the wobble position is less important: supports some, but not all types of base pairing.
Term
CSA
 Definition
A gene on chromosome 5 for DNA excision repair protein. Mutation in this gene can cause Cockayne syndrome.
Term
CSB
 Definition
A gene on chromosome 10 for DNA excision repair protein. Mutation in this gene can cause Cockayne syndrome.
Term
Cut-and-paste transposon
 Definition
Transposition of cut-and-paste transposons. The transposon is excised from one position in the chromosome and inserted into another position.
Term
Cut-and-paste transposon
 Definition
A type of transposon. The element is moved by cut-and-paste transposition. Found in eukaryotes and prokaryotes. Encode for transposase. Includes IS elements, composite transposons, Ac/Ds elements, P elements, hobo elements, piggyBac elements, and Sleeping Beauty.
Term
Cyclic AMP (cAMP)
 Definition

Adenosine-3'-5'-monophosphate

The effector molecule of CAP. An inducer. CAP can only bind to the CAP/cAMP binding site when cAMP is bound to it. It is derived from ATP. Glucose inactivates the enzyme which converts ATP into cAMP.
Term
Cytosine
 Definition
Has a common amino form, and a rare imino form, with the H at C4 rather than C3. If treated with nitrous acid it changes to uracil, which pairs with adenine.
Term
David Baltimore, Howard Temin, and Stoshi Mizutani
 Definition
In 1970, discovered reverse transcriptase. This discovery initiated research into reverse transcription.
Term
Deaminating agent
 Definition
A class of chemical mutagens. Remove amino groups. Mutagenic to replicating and non-replicating DNA. Includes nitrous acid.
Term
Death angel mushroom
 Definition

Amanita sp.

Mushrooms which contain the deadly toxin α-amanitin.
Term
Degeneracy
 Definition
A characteristic of the genetic code. All amino are specified by more than one codon except methionine and tryptophan. Includes partial degeneracy, where the last nucleotide can be either pyrimidine or either purine, and complete degeneracy, where the last nucleotide can be any base.
Term
Delicious Apples
 Definition
A somatic mutation. The original tree was a genetic mosaic, and vegetative propagation allowed the mutation to be perpetuated.
Term
Depression
 Definition
When a gene is deactivated by a repression.
Term
Discontinuous replication
 Definition
Occurs on the strand of the replication fork going in the 3' - 5' direction. Synthesizes the lagging strand in Okazaki fragments.
Term
Dispersive replication
 Definition
A possible method of DNA replication. Both new DNA strands contain segments from the original molecule. In Meselson and Stahl's experiment, all DNA strands would have hybrid density, decreasing as generations progress.
Term
DNA
 Definition

B-DNA

Found in most cells. Complementary base pairs (A with T, C with G) on antiparallel strands. A right-handed double helix is found in most living cells. There are ten base pairs per turn, 0.34 nm between stacked bases, 3.4 nm length per turn.
Term
DNA gyrase
 Definition
A DNA topoisomerase II in E. coli. A tetramer of two α subunits encoded by gyrA, and two β subunits encoded by gyrB.
Term
DNA helicase
 Definition
A component of the primosome and the replisome. Unwinds the DNA strand for replication, using ATP. Two are present: one for each direction of replication. Encoded by dnaB.
Term
DNA ligase
 Definition
Required for DNA replication, repair, and recombination in all organisms. Seals nicks between Okazaki fragments on the lagging strand, using energy from NAP or ATP, depending on species. Cannot work if a nucleotide is missing. Involved in excission repair and mismatch repair.
Term
DNA photolyase
 Definition
The enzyme which carries out light-dependent repair. Activated by light. Uses the energy from blue light to cleave cross-links and repair thymine, cytosine, or cytosine-thymine dimers.
Term
DNA polymerase
 Definition
Can add nucleotides to the 3' end of a primer strand, matching the opposite strand. Can only add in the 5' - 3' direction. A nucleophilic attack of the -OH group of the 3' end. Cannot produce DNA de novo. Makes one mistake out of every 105 - 106 nucleotides. Prokaryotes have 5 DNA polymerases. Eukaryotes have at least 15, some lacking 3' - 5' exonuclease activity.
Term
DNA polymerase eta (η)
 Definition
Replicates damaged DNA. Coded by POLH.
Term
DNA polymerase I
 Definition

Kornberg's enzyme

A replicative polymerase. Has a molecular mass of 103,000. A single polypeptide, encoded by polA. Catalyzes covalent addition of nucleotides to pre-existing DNA strands. Requires Mg2+ ions. Plays a role in chromosome replication and DNA. In E. coli it excises RNA primers and replaces then with DNA nucleotides using 5' - 3' exonuclease activity. Also has 3' - 5' exonuclease activity for proofreading. Not highly processive: has short tract synthesis.
Term
DNA polymerase II
 Definition
Involved in DNA repair.
Term
DNA polymerase III
 Definition
A replicative polymerase. A component of the replisome. A complex enzyme of at least 20 subunits. Has a molar mass of 900,000 Da in its holoenzyme form. Catalyzes the addition of DNA nucleotides to RNA primers. Terminates an Okazaki fragment when it encounters the RNA primer of the preceding fragment. The β-dimer subunit, encoded by dnaN, is a ring that clamps the enzyme to the template strands so that it does not fall off easily. Has 5' - 3' exonuclease activity, only active on single-stranded DNA, and 3' - 5' exonuclease activity for proofreading. Involved in mismatch repair.
Term
DNA polymerase IV
 Definition
Involved in error-prone repair. High error frequency.
Term
DNA polymerase V
 Definition
Involved in error-prone repair. High error frequency.
Term
DNA primase
 Definition
A component of the primosome and the replisome. Synthesizes RNA primers. Encoded by dnaG.
Term
DNA repair endonuclease
 Definition
Involved in excision repair. Recognizes, binds to, and excises damaged base(s).
Term
DNA replication
 Definition

Catalyzed by DNA polymerase

(dNMP)n + dNTP → (dNMP)n+1 + PPi
Term
DNA topoisomerase
 Definition
A component of the replisome. Provides axes of rotation for replication of circular DNA by adding nicks ahead of DNA helicase. Prevents DNA from being positively supercoiled as it rotates for DNA replication. Includes DNA topoisomerases I and II. It is necessary for DNA replication.
Term
DNA topoisomerase I
 Definition
A DNA topoisomerase. Catalyzes a single-strand nick in the DNA. The remaining phosphodiester bond acts as a swivel, allowing the supercoil to undwind itself. Removes supercoils one at a time. Energy efficeint.
Term
DNA topoisomerase II
 Definition
A DNA topoisomerase. Produces double-stranded breaks in the DNA, adds a negative supercoil, and reseals the break. Removes positive supercoils two at a time, using ATP. Includes DNA gyrase.
Term
dnaA
 Definition
An E. coli gene that codes for the prepriming protein DnaA, which binds to the 9-bp sequence in oriC, then forms a 20 - 40 protein complex, opening the DNA strand.
Term
dnaB
 Definition
Encodes for DNA helicase, which unwinds the DNA strand.
Term
dnaG
 Definition
Encodes for DNA primase, which synthesizes RNA primers.
Term
dnaN
 Definition
Encodes for the β-subunit of DNA polymerase III, which clamps the enzyme to the DNA strand.
Term
dNTP
 Definition
Deoxynucleotide triphosphate
Term
Downstream
 Definition
Towards teh 3' end of the RNA transcript.
Term
Downstream sequences (+)
 Definition
DNA sequences that follow the intiation site.
Term
dsRNA
 Definition
Double-stranded RNA. Rotavirus has dsRNA.
Term
Effector molecule
 Definition
Small molecules such as amino acids, sugars, or other metabolites. Causes allosteric transition in an activator or repressor which affects its ability to bind to RPBS. Includes inducers and co-repressors.
Term
Elizabeth Blackburn and Carol Greider
 Definition
Discovered telomerase in 1985. Won the Nobel Prize in Physiology or Medicine with Jack Szostak in 2009.
Term
Elongation factor G (EF-G)
 Definition
The tRNA at the A site is moved to the P site, the tRNA at the P site is moved to the E site, and the tRNA at the E site is released. Requires GTP. The ribosome changes conformation.
Term
Elongation factor Tu (EF-Tu-GTP)
 Definition
Contains a molecule of GTP. Provides GTP to peptidyl transferase. It is released as EF-Tu-GDP after the polypeptide bond forms, and it is converted back into EF-Tu-GTP by EF-Ts. Interacts with all aminoacyl tRNAs except methionyl-tRNA.
Term
Elongation factor Ts (EF-Ts)
 Definition
Converts EF-Tu-GDP into EF-Tu-GTP.
Term
End-product binding site
 Definition
Regulatory binding site. The site or sites where the end product binds to an enzyme. Often on a separate subunit from where the substrate binds. The enzyme undergoes allosteric transition which reduces its affinity for the subtrate.
Term
Endogenous retrovirus
 Definition
Retrovirus DNA which can be transmitted to subsequent generations of an organism. Some retroviruses lose their ability to produce viral particles, and become innocuous.
Term
Enhanceosome
 Definition
A protein complex in mammals that initiates activation of genes via chromatin remodeling. Adds acetyl groups to histone tails upstream from the promoter region.
Term
Enhancer
 Definition
Modulates the efficiency of transcription initiation in eukaryotes.
Term
Enol
 Definition
The rare form of guanine and thymine.
Term
env
 Definition
A gene in a retrovirus. Codes for protein components of the virus envelope.
Term
Equilibrium density-gradient centrifugation
 Definition
Meselson and Stahl used this method to separate isotopic DNA from regular DNA, using cesium chloride salts, which have approximately the same density as DNA.
Term
eRF
 Definition
The release factor in eukaryotes. Recognizes all three termination codons.
Term
Error-prone repair system (SOS response)
 Definition
A DNA repair mechanism. Activated after extreme damage to DNA: a survival mechanism. DNA repair, recombination, and replication proteins are synthesized. Excision repair may fix much of the DNA. DNA polymerase IV and V replicates across damaged segments. It has a high frequency of replication errors.
Term
Ethyl ethane sulfonate (EMS)
 Definition
An alkylating agent.
Term
Ethyl methane sulfonate (EMS)
 Definition
An alkylating agent.
Term
Eukaryotes
 Definition
Shorter RNA primers and Okazaki fragments. DNA replication occurs only in S phase. There are multiple origins of replications, nucleosomes, and telomeres. Eukaryotes have at least 15 DNA polymerases. DNA polymerase α, δ, and ε replicate the chromosomes. Eukaryotes have 5 RNA polymerases. Transcription and translation are not coupled, and most transcripts are modified and transported to the cytoplasm.
Term
Evolution
 Definition
Mutations occur in all organisms and viruses, and increases genetic variability. Natural selection preserves combinations of genes adapted to the environment.
Term
Excinuclease
 Definition
A nuclease that cleaves on either side of damaged base(s). Distinct from endonucleases and exonucleases. Involved in nucleotide excision repair.
Term
Excision repair
 Definition
A DNA repair mechanism. DNA repair endonuclease or endonuclease-containing enzymes recognize and bind to damaged strands of DNA as a template. DNA ligase seals the nicks left by DNA polymerase. Includes base excision repair and nucleotide excision repair.
Term
Excited state
 Definition
Electrons in higher energy levels. Caused by nonionizing radiation. Causes increased reactivity in DNA.
Term
Exit site (E)
 Definition
The E site on a ribosome. Binds to the departing uncharged tRNA.
Term
Exon
 Definition
Expressed sequences. Coding sequences. Remain present in mRNA after introns are spliced out.
Term
Exonuclease activity
 Definition
Corrections. Nucleotides are removed. Incorrect base pairs are detected due to their incorrect geometry.
Term
Eye
 Definition
A structure that forms during replication of the linear chromosome of phage T7.
Term
F, G, and I elements
 Definition
A group of retroposons found in Drosophila.
Term
FA
 Definition
Eight genes, A - H, on 5 different chromosomes. Mutations in these genes can cause Fanconi anemia.
Term
FACT
 Definition

Facilitates Chromatin Transcription

A protein which removes H2a and H2b histones as RNA polymerase II passes over nucleosomes, then re-attaches them afterwards.
Term
Fanconi anemia
 Definition
An inherited disease caused by defects in DNA repair mechanisms. Sensitivity to DNA cross-linking agents, chromosome instability, and prone to cancer. Impaired removal of DNA inter-strand cross-links, such as those formed by mitomycin C antibiotic. Caused by mutation in FA.
Term
Feedback inhibition
 Definition
End-product inhibition. The product of a synthetic pathway inhibits the first enzyme in the pathway. Results in an almost instantaneous arrest of synthesis. Not to be confused with repression.
Term
Forward mutation
 Definition
A mutation of a wild-type allele that results in a mutant allele.
Term
Frameshift mutation
 Definition
An insertion or deletion of a number of base pairs that is not a multiple of three within the coding regions of a gene. Alters the reading frame of codons in mRNA translation. Amino acid sequence is dramatically altered, almost always leading to a non-functional protein.
Term
Francis Crick
 Definition

First described the Central Dogma of molecular biology, and suggested that there was an adaptor molecule between RNA and polypeptides (tRNA) in 1958.

In 1961, published the first evidence for triplet codes after doing experiments with T4 bacteriophages: found that single and double-base mutations caused mutant phenotype, but triple-base mutations preserved the wild phenotype. Also proposed the wobby hypothesis.
Term
François Jacob and Jacques Monod
 Definition
Developed the operon model in 1961 to explain regulation of genes for lactose metabolism in E. coli. Won the Nobel Prize in 1965.
Term
FRAXA
 Definition
A site on the X chromosome. If there is a CGG trinucleotide repeat, it causes fragile X syndrome, the most common form of inherited mental retardation in humans. Normal X chromosomes have 6 - 50 copies, and fragile X patients can have up to 1000 copies.
Term
gag
 Definition
A gene in a retrovirus. Codes for structural proteins of the virus capsule.
Term
GC box
 Definition
An element of a promoter for RNA polymerase II. Consensus sequence is GGGCGG.
Term
Genetic code
 Definition
Specification of amino acids by codons. Composed of nucleotide triplets, does not overlap, does not have punctuation, has degeneracy, order, start and stop codons, and is nearly universal.
Term
George Beadle and Edward Tatum
 Definition
Won the Nobel Prize in 1958. Irradiated Neruospora crassa spores with X or UV rays, and screened the clones for growth-factor requirements. Each mutation resulted in a requirement of just one metabolite. Demonstrated the one-gene-one polypeptide concept.
Term
Gerald Rubin and Allan Spralding
 Definition
Tried to use a transposon to carry a cloned gene into an organism. They were successful in returning rosy eye colour Drosophila mutants into wild-type by inserting the wild gene from a bacterial plasmid.
Term
Germinal mutation
 Definition
A mutation that occurs in germ-line cells, which gives rise to gametes. If it occurs in the gamete cell, one progeny is affected. If it occurs in a cell which then gives rise to gametes, many progeny may be affected.
Term
Guanine
 Definition
Has a common keto form, and a rare enol form, with the H at the C6 rather than C1. If treated with nitrous acid, it changes to xanthine, which pairs with cytosine, so there is no change.
Term
Guide RNAs
 Definition
RNAs that assist in RNA editing where uridine monophosphate is inserted or deleted from a sequence, dramatically changing the polypeptide it codes for. Has complementary sequence to the transcript being edited, and acts as a template for U insertion.
Term
gypsy
 Definition
A retroviruslike element found in Drosophila. Larger than copia.
Term
gyrA
 Definition

nalA

Encodes for the α subunit of DNA gyrase. Inhibited by Nalidixic acid.
Term
gyrB
 Definition

cou

Encodes for the β subunit of DNA gyrase. Inhibited by coumermycin antibiotic.
Term
Hermann J. Muller
 Definition
In 1927, discovered that X rays could induce mutations in Drosophila sperm. This changed the field of genetics. Received the Nobel Prize for Physiology or Medicine in 1946. Developed the ClB method.
Term
HeT-A
 Definition
Regenerates lost chromosome ends in Drosophila.
Term
Heterogeneous nuclear RNA (hnRNA)
 Definition
The populatoin of RNA transcripts in the nucleus of a eukaryote. Vary in size. Mostly pre-mRNA undergoing processing events before leaving the nucleus.
Term
hobo elements
 Definition
Cut-and-paste transposons found in Drosophila.
Term
Holoenzyme
 Definition
The complete enzyme.
Term
Housekeeping functions
 Definition
Gene products such as tRNA, rRNA, ribosomal proteins, RNA polymerase, and enzymes catalyzing basic metabolic processes. Coded by constitutive genes.
Term
Human immunodeficiency virus (HIV)
 Definition
A retrovirus in humans which causes AIDS. Transmitted by blood or semen. Intravenous drug users and sex industry workers are at high risk.
Term
Hutchinson-Gilford syndrome
 Definition
A severe form of progeria. Wrinkles, baldness, and other symptoms of age begin immediately after birth. The patient usually dies in their teens. Caused by a dominant mutation that affects the shape of nuclei in cells.
Term
Hydrogen bonds
 Definition
An element of tertiary structure of proteins. Weak interactions between electronegative atoms and hydrogen atoms bound to other electronegative atoms.
Term
Hydrophobic interactions
 Definition
An element of tertiary structure of proteins. Associations of nonpolar groups with each other in aqueous solution.
Term
Hydroxylamine (NH2OH)
 Definition
A hydroxylating agent. Produces C:G → A:T transitions. The amino group of cytosine is hydroxylated, producing hydroxylaminocytosine, which pairs with adenine. Due to its specific activity, it can be used to examine the nature of mutations.
Term
Hydroxylating agent
 Definition
A class of chemical mutagens. Add hydroxyl groups. Includes hydroxylamine.
Term
I
 Definition
The repressor gene of the lac operon. Codes for lac repressor, a tetramer with four copies of the gene product. It binds to operators two at a time to prevent RNA transcription, unless allolactose is bound to it. WHen bound to O1 and O2, a hairpin is formed in the DNA. When bound to O1 and O3, a loop is formed in the DNA. It has mutations I-, I-d, and Is.
Term
I-
 Definition
A mutation of I in the lac operon. Causes constitutive synthesis of lac gene products. I+ is dominant to it. Can act in cis or in trans. May affect genes on other DNA molecules in the bacteria.
Term
I-d
 Definition
A mutation in I of the lac operon. Dominant to I+ because its products form heteromultimers with I+ gene products, forming repressors which can bind to operators, but cannot bind to the affector molecule allolactose.
Term
Is
 Definition
A mutation of I in the lac operon. Produces uninducible repressors which require high amounts of lactose to produce induction.
Term
Imino
 Definition
The rare form of cytosine and adenine.
Term
Induced mutations
 Definition
Mutations that result from exposure to physical or chemical mutagens.
Term
Inducer
 Definition
Effector molecules that cause induction of genes. Cause activators to bind to RPBS. Cause repressors to fall off the RPBS.
Term
Inducible enzymes
 Definition
Enzymes encoded by inducible genes. Often catalyze catabolic pathways.
Term
Inducible genes
 Definition
Genes whose expression is regulated by induction. Produce inducible enzymes.
Term
Induction
 Definition
The activation of genes with the presence or absence of a subtance. Alters the rate of enzyme synthesis.
Term
Initiation codon
 Definition
Initiates translation. Usually AUG, but in prokaryots it is sometimes GUG. In prokaryotes it cods for tRNAfMet.
Term
Initiation factors
 Definition

Proteins in E. coli which are necessary for initiation of translation. Includes IF-1, IF-2, and IF-3

IF-2 interacts with fMet

IF-1 and IF-3 bring the 30S subunit to mRNA using GTP.
Term
Inosine
 Definition
A modified guanine/adenine derivative.
Term
Integrase
 Definition
An enzyme which integrates DNA produced by reverse transcriptase into a random site in the DNA. Coded for by retrotransposons.
Term
Intein
 Definition
Short amino acid sequences that excise themselves from nascent polyptpides. First discovered in Mycobacterium tuberculosis.
Term
Intron
 Definition

Intervening sequences

Non-coding sequences. Found in split genes. Introns can be up to 7,000 nucleotides long. May play a role in gene expression, or are remnants from gene evolution. There can be alternate splicings for one gene, producing multiple products. 60% - 80% of our genes have alternate products. Some introns have sequences that play a role in transcription. There are conserved sequences at the ends of introns: GU-intron-AG. Removed by splicing reactions carried out by splicing endonucleases, self-splicing, or spliceosomes.
Term
Ionic bonds
 Definition
An element of tertiary structure of proteins. Occurs between amino acid side chains with opposite charges. Strong under some conditions, but relatively weak in aqueous environments due to polar water molecules.
Term
Ionizing radiation
 Definition
A mutagen. Lower wavelength, higher energy radiation, including X-rays, gamma rays, and cosmic rays. Penetrates living tissues, causing release of electrons. Produces free radicals: positively charged ions which create more free radicals. Breaks chromosomes and causes deletions, duplications, inversions, and translocations. Dosage is measured in roentgen. Dosage rate is directly correlated with amounts of mutations.
Term
IS element
 Definition

Insertion sequences

Cut-and-paste transposons found in bacteria. Includes IS50. The simplest type of transposon: contains only genes that encode for its own transposition. Inserts at many sites in bacterial chromosomes and plasmids. Short and compactly organized: usually fewer than 2500 bp. There may be up to 10 copies of a single SI element in the genome. Allows for homologous recombination between chromosomes and plasmids, or between plasmids. Causes target site duplications when inserted.
Term
J. Herbert Taylor, Phillip Woods, and Walter Hughes
 Definition
Used autoradiography to examine radioactive chromosomes as they replicate, providing proof of semiconservative replication in the root tips of Vicia faba. Labelled chromosomes with a radioactive isotope of thymine, and transferred it into a solution containing colchicine, causing chromosomes to double in the cell.
Term
James Herrick and Ernest Irons
 Definition
A physician and medical intern in Chicago who discovered sickle cell anemia in 1904.
Term
Jean Lamarck and Trofim Lysenko
 Definition
Believed in the inheritance of acquired traits. Lysenko sold this concept to the Soviet Union from 1937 to 1964. Actually, acquired traits are not heritable, the environment simply selects fro pre-existing mutations. This was proved by Joshua and Esther Lederberg.
Term
Jessie Hiatt
 Definition
An Iowa farmer who discovered Delicious Apples in 1881.
Term
Joel Huberman and Arthur Riggs
 Definition
In 1968, used autoradiography of labelled DNA from Chinese hamster cells to show that in eukaryotes, DNA replication occurs bidirectionally from multiple origins.
Term
John Cairns
 Definition
Established the existence of the origin of replication. In 1963, showed that the chromosome of E. coli was a single molecule of DNA, using autoradiography. Replication of the circular chromosome during cell division produces a θ-shaped structure with two forks.
Term
John Lim
 Definition
Suggested that transposons play a role in the evolution of chromosome structure. Transposons on the same chromosome can have crossing-over to cause deletions. Transposons on sister chromosomes can cause transfer of selections from chromosome to chromosome.
Term
Joshua and Esther Lederberg
 Definition
In 1952, definitively proved that acquired traits were not inherited, by devloping replica plating.
Term
Keto
 Definition
The common form of guanine and thymine.
Term
Kozak's rules
 Definition

Named after Marilyn Kozak, who proposed them. A series of rules of how the efficiency of initiation is changed by changes of bases from the optimal initiation sequence in eukaryotes:

5' - GCC(A/G)CCAUGG-3'
Term
L1
 Definition
A LINE found in humans. 6 kbp long, with internal promoters that are recognized by RNA polymerase II. Two open-reading frames that encode for a nucleic-acid binding protein, and an endonuclease with reverse transcriptase activity. The human genome has 3000 - 5000 L1 elements, and over 500,000 truncated (from the 5' end) non-functional L1 elements. Flanked by short target site duplications.
Term
lac-
 Definition
Mutations in E. coli caused by inertion of an IS element into lac genes. Reversion to wild-type is caused by excision of the IS element, and occurs at a high rate.
Term
lac operon
 Definition
An inducible operon. Induced only if lactose is present, and glucose is absent. Its products break down lactose. Consists of P, I, three operators O1, O2, O3, and three structural genes lacZ, lacY, and lacA. The operaotrs may have Oc mutation. All structural genes are activated at low background levels at all times. Operators overlap with initiation start sites.
Term
lacA
 Definition
A structural gene of the lac operon. Codes for β-galactoside transacetylase.
Term
lacY
 Definition
A structural gene of the lac operon. Codes for β-galactoside permease. Transports lactose.
Term
lacZ
 Definition
A structural gene of the lac operon. Codes for β-galatosidase. Converts lactose into allolactose. Cleaves lactose into glucose into galactose.
Term
Lagging strand
 Definition
Synthesized by discontinuous replication. Consists of Okazaki fragments.
Term
Lariat formation
 Definition
The 5' phosphate of the G end of the 5' end of the intron is formed to the 2'-OH of the A at the 3' end of the intron by the spliceosome.
Term
Leading strand
 Definition
Synthesized by continuous replication.
Term
Light-dependent repair
 Definition

Photoreactivation

A DNA repair mechanism found only in bacteria. Works only in light. Carried out by DNA photolyase. Repairs thymine, cytosine, or cytosine-thymine dimers caused by nonionizing radiation. Used as a tool to detect thymine dimers.
Term
LINEs
 Definition
Long interspersed nuclear elements. Retroposons found in humans. Includes L1.
Term
Linus Pauling
 Definition
Thought that DNA may have been triple-stranded. This does sometimes occur in deformed cells.
Term
Maria Schnös and Ross Inman
 Definition
Used A:T rich markers in phage λ to prove that it is bidirectional replicatio. A:T pairs separate at high temperatures or pH, where C:G pairs do not, causing denaturation bubbles. Exposed replicating chromosomes to high pH at different stages of replication and examined the denaturation bubbles.
Term
Marilyn Kozak
 Definition
Proposed Kozak's rules.
Term
Marshall Nirenberg, Severo Ochoa, H. Ghobind Khorana, Philip Leder, and colleagues
 Definition
Worked out the meaning of all 64 codons of the entire genetic code. Nirenberg and Khorana shared the Nobel Prize in Physiology or Medicine in 1968.
Term
Mary Lou Pardue, Robert Levis, Haral Beissman, James Mason, and colleagues.
 Definition
Showed that HeT-A and TART regenerate lost chromosome ends in Drosophila.
Term
Masayasu Nomura and colleagues
 Definition
Disassembled the E. coli 30S ribosomal subunit into its individual proteins and rRNAs to study it.
Term
Matthew Meselson and Franklin Stahl
 Definition
In 1958, proved that E. coli replicates its DNA using semiconservative replication. Grew E. coli in a solution containing a heavy isotope of nitrogen, 15N. DNA which contains this isotope is denser than regular DNA. They separated it using equilibrium density-gradient centrifugation with cesium chloride salts. Results were consistent with semiconservative replication: two DNA strands had intermediate density, and the rest had normal density.
Term
Merozygotes
 Definition
Partially diploid bacteria with F' factors.
Term
Messenger RNA (mRNA)
 Definition
A type of RNA. It is translated into proteins on ribosomes. The product of pre-mRNA processing: removal of introns, modification of termini.
Term
Methionine
 Definition
One of the only amino acids which is specified by a single codon.
Term
Micro RNA (miRNA, siRNA, RNAi)
 Definition
A type of RNA. 20 - 22 nucleotide segments. Cleaved from small hair-pin shaped precursors. Block the expression of complementary or partially complementary mRNAs by either causing their degradation or repressing translation.
Term
Minimal medium
 Definition
Ionic salts, a simple sugar, and the vitamin biotin. Wild-type Neurospora crassa can survive in this medium.
Term
Mismatch repair
 Definition
A DNA repair mechanism. A backup to replicative proofreading. A universal mechanism. Scans for and corrects mismatched nucleotides in DNA post-replication. The template strand and non-template strand are differentiated by their methylation patterns after DNA replication: the newly synthesized strand is unmethylated. In E. coli, MutS, MutH, MutL, UvrD, exonuclease, DNA polymerase III, and DNA ligase are involved.
Term
Missense mutation
 Definition
A mutation that changes a codon to produce a different amino acid. Causes impaired function of the gene product.
Term
MSH1
 Definition
A gene on chromosome 3 for a homolog of E. coli mismatch repair protein MutL. Mutation of this gene can cause nonpolyposis colon cancer.
Term
MSH2
 Definition
A gene on chromosome 2 for a DNA mismatch recognition protein, similar to MutS in E. coli. Mutation in this gene can cause nonpolyposis colon cancer.
Term
MSH6
 Definition
A gene on chromosome 2 for MutS homolog 6. Mutation in this gene can cause nonpolyposis colon cancer.
Term
Mustard gas
 Definition

Di-(2-chlorethyl) sulfide

An alkylating agent. Its effects were studied by Charlotte Auberach and associates.
Term
Mutagen
 Definition
Physical or chemical factors which cause induced mutations. Increases frequency of mutation up to 1% per gene. Includes ionizing radiaton, nonionizing radiation, and chemical mutagens.
Term
Mutant
 Definition
An organism which exhibits a novel phenotype as a result of a mutation.
Term
Mutation
 Definition
A change in genetic material, and the process by which this change occurs. The ultimate source of all genetic variation: the raw material for evolution.
Term
MutH
 Definition
Involved in mismatch repair in E. coli. Joins the complex formed by MutS. Cleaves unmethylated strand at hemi-methylated GATC sequences on either side of the mismatch, comparing old and new strands based on methylation.
Term
MutL
 Definition
Involved in mismatch repair in E. coli. Joins the complex formed by MutS.
Term
MutS
 Definition
Involved in mismatch repair in E. coli. Recognizes mismatches and binds to initiate the repair process.
Term
Mycobacterium tuberculosis
 Definition
The bacteria which causes tuberculosis. Inteins were first discovered in this species.
Term
Nap-1
 Definition
Nucleosome assembly protein 1. Transports new histones from the cytoplasm to the nucleus during DNA replication.
Term
Negative control mechanism
 Definition
Repressors are needed to shut off expression of structural genes.
Term
Neurospora crassa
 Definition
A salmon-coloured bread mould. Can survive in minimal medium. George Beadle and Edward Tatum used this species in their experiments proving the one geneone polypeptide concept.
Term
Neutral mutation
 Definition
A mutation that causes a change in amino acid to an amino acid with similar properties. The function of the mutated polypeptide is not altered.
Term
Nick
 Definition
A break in the phosphoriester bond of one of the strands of DNA. All nucleotides are present. DNA ligase seals the nick.
Term
Nijmegan breakage syndrome
 Definition
An inherited disease caused by defects in DNA repair mechanisms. Chromosome instability, microcephaly, and prone to cancer. Increased chromosome aberrations. Caused by mutation in NBSI.
Term
Nitrous acid (HNO2)
 Definition
A deaminating agent. A potent mutagen. Causes oxidative deamination of amino groups in adenine, guanine, and cytosine. Converts amino groups into keto groups. Adenine changes to hypoxanthine. Cytosine changes to uracil. Guanine changes to xanthine.
Term
Nonionizing radiation
 Definition
A mutagen. Higher wavelength, lower energy radiation, including ultraviolet radiation. Does not have enough energy to cause ionizations. Penetrates only the surface layer of cells of the body, but can be highly damaging to single-celled organisms. Raises electrons into an excited state. PRoduces pyrimidine hydrates and dimers. Hydrates cause mis-pairing. Dimers disturb the structure of DNA, interfering with replication and repair.
Term
Nonpolyposis colon cancer
 Definition

Lynch syndrome

An inherited disease caused by defects in DNA repair mechanism. High rist of familial colon cancer. Occurs in 1/200 individuals. Caused by mutation in MSH2, MSH1, MSH6, PMS2, or PMS1.
Term
Nonsense mutation
 Definition
A mutation that produces chain-termination codons. Results in truncated polypeptides.
Term
Nontemplate strand
 Definition

Sense strand

The DNA strand which is not transcribed. Identical to the RNA transcript, but has T rather than U.
Term
NPSI
 Definition
A gene on chromosome 8 for DNA double strand break recognition protein. Mutation in this gene can cause Nijmegan breakage syndrome.
Term
Nuclear organizer regions
 Definition
Regions of the chromosome with redundant, tandem rRNA coding sequences. There may be multiple.
Term
Nuclease activity
 Definition

Synthesis

Nucleotides are added.
Term
Nucleolus
 Definition
A region of rRNA synthesis and ribosome assembly in the nucleus.
Term
Nucleoside
 Definition
A pentose sugar and a nitrogenous base, without a phosphate group.
Term
Nucleotide
 Definition
A pentose sugar and a nitrogenous base, with a phosphate group.
Term
Nucleotide excision repair
 Definition
A type of excision repair. Removal of larger defects such as thymine dimers. Involves excinucleases. In E. coli three proteins are involved, and in humans twelve are involved, including XPA. Mutation in nucleotide excision repair genes can cause xeroderma pigmentosum.
Term
O1
 Definition
An operator in the lac operon discovered by Jacob and Monod. Located between P and lacZ.
Term
O2
 Definition
An operator in the lac operon. Located downstream from O1 within lacZ.
Term
O3
 Definition
An operator in the lac operon. Located upstream of P.
Term
Oc
 Definition
A mutation of any of the operators in the lac operon. Causes constitutive synthesis of lac gene products. Acts only in cis; cannot affect genes on other DNA molecules.
Term
Octamer box
 Definition
An element of a promoter for RNA polymerase II. Consensus sequence is ATTTGCAT.
Term
Okazaki fragments
 Definition
Short fragments of DNA 100 - 200 bp on the lagging strand. Replicated in the 5' - 3' direction, overall in the 3' - 5' direction.
Term
One gene-one polypeptide
 Definition
A concept demonstrated by George Beadle and Edward Tatum. Each gene encodes one polypeptide. Modified from "one gene-one enzyme" concept, because some enzymes are multimeric.
Term
Operator
 Definition
A gene which is contiguous with structural genes that it regulates. Repressors bind to the operator to turn off transcription. An operon may have several operators.
Term
Operon
 Definition
A negative control system. Consists of structural genes, operators, and a promoter. In an inducible operon, free repressors turn off transcription. In a repressible operon only a repressor/effector complex can turn off transcription. All genes in the operon are transcribed onto a single mRNA molecule, so all genes are expressed simultaneously, and products are in equal proportions in the cell.
Term
Operon model
 Definition
A negative control mechanism proposed by François Jacob and Jacques Monod. A regulator gene encodes for a repressor which binds to an operator. This controls expression of the operon.
Term
Order
 Definition
A characteristic of genetic code. Amino acids with similar properties have similar codons. Evolved as a way of minimalizing mutation lethality.
Term
oriC
 Definition
The origin of replication in E. coli. 245-bp, with two conserved repeat sequences. An A:T rich 13-bp sequence is repeated four times, facilitating formation of the replication bubble. A 9-bp sequence is repeated four times, facilitating binding of prepriming proteins.
Term
Origin of replication
 Definition
The site of initiation of DNA replication. There is usually one per chromosome on bacterial and viral DNA. There are multiple per chromosome in eukaryotes, each controlling one replicon. In eukaryotes, origins of replication may be very long. In E. coli it is oriC.
Term
Oscar Miller, Barbara Hamkalo, and colleagues
 Definition
Developed imaging techniques to allow observation of transcription and translation occuring on the same RNA molecule in a prokaryote.
Term
P
 Definition
The promoter of the lac operon.
Term
P elements
 Definition
Cut-and-paste transposons found in Drosophila. Cause mutations.
Term
Paula DeLucia and John Cairns
 Definition
In 1969, discovered that DNA polymerase I was not the only DNA polymerase in E. coli.
Term
Peptide
 Definition
Two or more amino acids.
Term
Peptide bond
 Definition
Covalent linkage between amino acids and polypeptides. Formation on ribosomes is catalyzed by peptidyl transferase.
Term
Peptidyl site (P)
 Definition
The P site on a ribosome. Binds the tRNA to the growing polypeptide.
Term
Peptidyl transferase
 Definition
Enzymatic activity built into the 50S subunit of the ribosome, on an rRNA molecule. Catalyzes the formation of a covalent peptide bond between the amino acid at the P site and the aminoacyl-tRNA at the A site, uncoupling the amino acid and tRNA at the P site. Uses GTP provided by EF-Tu-GTP.
Term
piggyBac elements
 Definition
Cut-and-paste transposons found in moths. Can be a transition vector for many species.
Term
Plasticity
 Definition
Ability to turn genes on and off rapidly to acheive maximal growth and reproduction under a wide range of environmental conditions. In prokaryotes, there may be preprogrammed circuits or cascades of gene expression. Genes cannot be turned on out of sequence.
Term
PMS1
 Definition
A gene on chromosome 2 for a yeast mismatch repair protein homolog. Mutation in this gene can cause nonpolyposis colon cancer.
Term
PMS2
 Definition
A gene on chromosome 7 for endonuclease PMS2. Mutation in this gene can cause nonpolyposis colon cancer.
Term
Point mutation
 Definition
A mutation at a speciifc site in a gene. Substitution of one base pair for amother, or the insertion or deletion of a few nucleotide pairs at a specific site in the gene.
Term
pol
 Definition
A gene of a retrovirus. Codes for reverse transcriptase or integrease.
Term
POLH
 Definition

XPV

Codes for DNA polymerase eta. Loss of this gene leads to xeroderma pigmentosum.
Term
Poly(A) polymerase
 Definition
Performs polyadenylation: adds poly(A) tails to the cleaved 3' end of transcripts following a AAUAAA sequence.
Term
Poly(A) tail
 Definition
A polyadenosine tract 20 - 200 nucleotides long, joined to the cleaved 3' end of an RNA transcript. Gives the transcript stability, and plays a role in transport out of the nucleus. Added by poly(A) polymerase. Binds to proteins and protects the 3' end from degradation.
Term
Polyadenylation
 Definition
The addition of poly(A) tails to the cleaved 3' end of mRNAs in eukaryotes.
Term
Polypeptide
 Definition
The constituents of proteins. Long chains of amino acids.
Term
Positive control mechanisms
 Definition
Activators are needed to turn on expression of structural genes.
Term
Postreplication repair
 Definition
A DNA repair mechanism. Activated in mutants deficient in more than one repair system. DNA polymerase III stops when it encounters a thymine dimer, and replication is continued past the dimer, forming a gap in the nascent strand. RecA mediates exchange of singel strands between homologous DNA molecules. There is recombination, inserting the sequence for the nascent strand, and the thymine dimer remains on the other side. If the nucleotide excision repair system does not repair it, this process is repeated at each replication of the DNA.
Term
PPi
 Definition
Pyrophosphate
Term
Pre-mRNA
 Definition
The product of transcription in eukaryotes. It is processed by excision of introns, and modification of termini before translation.
Term
Prepriming proteins
 Definition
Aid in the formation of the replication bubble by forming multi-protein complexes that bend the DNA molecule. In E. coli, they bind to the 9-bp repeat sequences. Includes DnaA.
Term
Pribnow box
 Definition
The -35 sequence and the -10 sequence.
Term
Primary structure
 Definition
A level of structure in proteins. The amino acid sequence, specified by the nucleotide sequence.
Term
Primary transcript
 Definition
The product of transcription in prokaryotes.
Term
Primer DNA
 Definition
Provides DNA polymerase with a 3' terminus with a free -OH.
Term
Primosome
 Definition
A protein complex containing DNA primase and DNA helicase. DNA helicase unwinds the DNA, and DNA primase adds RNA primers to the lagging strand, initiating Okazaki strands.
Term
Proflavin
 Definition
2,8-diamino acridine. An acridine dye.
Term
Progeria
 Definition
A disorder in humans characterized by premature aging. Exact mechanism is unknown. The most severe form is Hutchinson-Gilford syndrome. A less severe form is Werner syndrome.
Term
Prokaryotes
 Definition
Have on RNA polymerase. Transcription and translation are tightly coupled, and may take place simultaneously on the same RNA transcript. No modification of the transcript occurs: mRNA is short-lived.
Term
Promoters
 Definition
Specific nucleotide sequences that bind to RNA polymerase. Near transcription start sites. More complex in eukaryotes than in prokaryotse. Includes the -10 and -35 sequences in E. coli. Promoters for RNA polymerase II includes the TATA box, CAAT box, GC box, and octamer box.
Term
Proofreading
 Definition
Uses 3' - 5' exonuclease activity by DNA polymerase I and III. Reduces the expected error rate of DNA replication from 1/104 times to 1/106 times. The nascent strand is scanned for errors, which are corrected using 3' - 5' exonuclease activity.
Term
Protein
 Definition
Made of polypeptides.
Term
Quaternary structure
 Definition
A level of structure in proteins. The association of two or more polypeptides in a multimeric protein.
Term
R-determinant
 Definition
A component of a conjugative R plasmid. Genes for antibiotic resistance.
Term
R loop
 Definition
A region where RNA binds to one of the strands of DNA, displaicng the other strand. Can be visualized using electron microscopy. First observed by Shirtley Tilghman, Philip Leder, and colleagues.
Term
Reading frame
 Definition
Where each codon beings and ends on an mRNA. If there is a frameshift mutation, the reading frame is altered, producing a mutant phenotype. If there is a mutation involving a number of nucleotides that is a multiple of three, the reading frame is not altered.
Term
RECQLA
 Definition
A gene on chromosome 8 for RecQ helicase L4. Mutation in this gene can cause Rothmund-Thomson syndrome.
Term
Regulator genes
 Definition
Encode products that regulate the expression of other genes. Bind to RPBS. Regulators produced are either activators or reprssors. Their ability to bind to RPBS is affected by effector molecules.
Term
Reiji and Tuneko Okazaki
 Definition
In the 1960s, discovered discontinuous relpication using isotope labelling in T4-infected E. coli.
Term
Release factors (RFs)
 Definition
Recognize termination codons. Attach a water molecule to the carboxyl terminus of the polypeptide, releasing the polypeptide from the tRNA at the P site. Prokaryotes have two: RF-1 and RF-2. Eukaryotes have one: eRF.
Term
Replica plating
 Definition
A technique developed by Joshua Esther Lederberg in 1952. Demonstrates the presence of antibiotic resistant mutants in bacterial cultures prior to introduction of antibiotic. Cultures that had been exposed to the antibiotic were much more likely to contain antibiotic resistant bacteria that ones which had not been exposed. If mutations for resistance occured after exposure to the drug, and were not randomly pre-existing in the population, then cultures that had not been exposed to the antibiotic would be just as likely to contain resistant bacteria as cultures that had been.
Term
Replication bubble
 Definition
The two strands of DNA come apart for replication. Facilitated by prepriming proteins. In E. coli it is facilitated by A:T rich in 13-bp repeat sequences in oriC.
Term
Replication fork
 Definition
Y-shaped structures that occur during DNA replication. They have bidirectional replication, in opposite directions. One side of the fork has continuous replication, and the other has discontinuous replication.
Term
Replicative transposition
 Definition
Transposition of replicative transposons. Catalyzed by transposases. The element is replicated and one copy is inserted at the new site, and one copy remains at the original site.
Term
Replicative transposon
 Definition
A type of transposon. The element is moved by replicative transposition. Found in prokaryotes. Contain genes for transposase. Includes Tn3 elements.
Term
Replicative polymerases
 Definition
DNA polymerases I and III. Involved in DNA replication. They both add 30,000 nucleotides per minutes: one error per 108 - 109 nucleotides.
Term
Replicon
 Definition
A segment of DNA which is replicated by one origin of replication. In prokaryotes the entire chromosome is one replicon. Eukaryotes have around 10,000 replicons. The number of replicons is not fixed throughout growth and development.
Term
Replisome
 Definition
The complete replication apparatus that moves along the replication fork: topoisomerase, DNA helicase, SSB proteins and other prepriming proteins, DNA primase, and replicative polymerases, DNA I and III.
Term
Repression
 Definition
The deactivation of a gene. Produces depression of a gene. Anabolic pathways are often repressed. Not to be confused with feedback inhibition.
Term
Repressor
 Definition
The product of regulator genes in negative control mechanisms. It is needed to shut of expression of one or more structural genes.
Term
res
 Definition

Resolution site

Sites on the Tn3 element where site-specific recombination occurs in the cointegrate.
Term
Resistance transfer factor (RTF)
 Definition
A component of a conjugative R plasmid. Genes needed for conjugative transfer between cells.
Term
Retroposon
 Definition

Non-LTR retrotransposons

A type of retrotransposon. Not related to viral genes. Large and widely distributed. Codes for reverse transcriptase and endonuclease activity. Flanked by untranslated regions (UTR), and homogenous sequences of A:T base pairs at the ends, derived from poly(A) tails of the RNAs from which they are produced. Include F, G, and I elements, telomeric retrotransposons, LINEs, and SINEs.
Term
Retrotransposition
 Definition
Transposition of retrotransposons. The RNA of the element is used as a template to generate DNA that is inserted into new chromosomal sites.
Term
Retrotransposon
 Definition

"Backwards"

A type of transposon. The element is moved by retrotransposition. Found only in eukaryotes. Includes retrovirus like elements and retroposons.
Term
Retrovirus
 Definition
Viruses whose life-cycle depends on retrotransposition. Their genomes are RNA strands, which are retrotransposed into the DNA of their host. Genes include gag, pol, and env. Includes HIV.
Term
Retrovirus-like elements
 Definition

LTR retrotransposons

A type of retrotransposon. Related to viral genes. Found in many eukaryotes, including yeasts, plants, and animals. Codes for reverse transcriptase and integrase, flanked by a long terminal repeate (LTR) and short target site duplications. There are about 400,000 in the human genome. Includes Ty1, copia, and gypsy.
Term
Reverse transcriptase
 Definition
Catalyzes the reverse transcription of RNA into DNA. Goes backwards from the central dogma. Discovered by David Baltimore, Howard Temin, and Satoshi Mizutani. Coded for by retrotransposons.
Term
Reversion
 Definition

Reverse mutation

A mutation which restores a mutant allele to the wild-type allele. Includes back mutations and suppressor mutations; distinguished by back-crossing the mutation to a wild-type individual. Genes vary in which type of reversion is more common.
Term
RF-1
 Definition
A release factor in prokaryotes. Recognizes UAA and UAG.
Term
RF-2
 Definition
A release factor in prokaryotes. Recognizes UAA and UGA.
Term
Rho (ρ)
 Definition
A protein that binds to rut near the 3' end of a transcript, and then moves 5' - 3' down the nascent strand RNA, after RNA polymerase. When RNA polymerase slows at the hairpin, it uses helicase activity to unwind the DNA/RNA base-pairing at the terminus.
Term
Rho-dependent terminator
 Definition
A type of termination signal in E. coli. Termination occurs only in the presence of rho.
Term
Rho-independent terminator
 Definition
A type of termination signal in E. coli. Termination can occur without rho. Contains a C:G rich region followed by six or more A:T base pairs, with A's in the template strand. When transcribed, it forms a hairpin in the nascent RNA. This slows RNA polymerase, and the weak A:U section causes RNA polymerase and the nascent RNA strand to simply fall off the DNA.
Term
Ribonucleoside triphosphate (RTP)
 Definition
The precursors for RNA synthesis.
Term
Ribosomal RNA (rRNA)
 Definition
A type of RNA. A structural and catalytic component of ribosomes.
Term
Ribosome
 Definition
Intricate macromolecular machines composed of 3 - 5 rRNAs, and 50 - 90  proteins. Perform translation. Found throughout the prokaryote cells, and in the cytoplasm and ER of eukaryote cells. Composed of rRNA and proteins. Consists of two subunits, one large and one small, which associate when they bind to mRNA and dissociate when they detach. Size and structure of ribosomes varies between species. Size is measured in Svedberg units. Has an A, P, and E site.
Term
Ribozyme
 Definition
An RNA enzyme. In self-splicing, the intron is a ribozyme for its own splicing reaction.
Term
RNA editing
 Definition
Alteration of the content of RNA transcripts by changing the structure of bases (rare), or by inserting or deleting uridine monophosphate residues. Example: apo-B.
Term
RNA polymerase
 Definition

Catalyzes the addition of RTPs to 3' end of an RNA strand. Moves in the 5' - 3' direction on the DNA, using it as a template. A nucleopilic attack of the 3'-OH on the nucleotide phosphorus atom of the RTP. Eliminates pyrophosphate. Binds to promoters on DNA. Eukaryotes have five RNA polymerases for different types of RNA, and prokaryotes have one. Produces a transcription bubble by winding DNA ahead of the polymerization side, and rewinding it behind. RNA polymerase holoenzyme in E. coli has a molecular weight of 480,000, consisting of 5 polypeptides, two of which are identical. Includes the tetrameric core and sigma factor. Adds 40 ribonucleotides per second. The region where RNA and DNA are base-paired is about 3 base pairs in length.

n(RTP) - (DNA template, RNA polymerase) → (RMP)n + n(PP)
Term
RNA polymerase I
 Definition
Found in almost all eukaryotes. Located in the nucleolus. Produces rRNAs, but not 5S rRNA.
Term
RNA polymerase II
 Definition
Found in almost all eukaryotes. Located in the nucleus. Produces nuclear pre-mRNAs, and other hnRNAs.
Term
RNA polymerase III
 Definition
Found in almost all eukaryotes. Located in the nucleus. Produces tRNA, 5S rRNA, and other snRNAs.
Term
RNA polymerase IV
 Definition
Found only in plants and some fungi. Plays a role in chromatin remodeling. Located in the nucleus. Produces siRNAs.
Term
RNA polymerase V
 Definition
Found only in plants and some fungi. Plays a role in chromatin remodeling. Located in the nucleus. Produces some siRNAs, plus noncoding transcripts of siRNA target genes, which interact and condense chromatin in chromatin remodelling.
Term
RNA primer
 Definition
RNA segments bound to the lagging strand which initiates an Okazaki strand. Synthesized by DNA primase. 10 - 60 nucleotides long in prokaryotes, about 10 nucloetides long in eukaryotes.
Term
Robert W. Holley and colleagues
 Definition
In 1965, published the proposed cloverleaf structure of tRNA. Holley shared the Nobel Prize in Physiology or Medicine in 1968.
Term
Roentgen (r)
 Definition
The unit in which dosage of ionizing radiation is measured. Equal to 2.083 x 109 ion pairs produced in one cm3 of air at 0º C and a pressure of 760 mmHg.
Term
Rolling-circle replication
 Definition
Used by many viruses, in bacteria during genetic exchange, and in some amphibians during amplification of extracrhomosomal DNA during oogenesis. A circular DNA segment stays intact, and "rolls" as it acts as the template for DNA synthesis. It may roll more than once, producing a linear DNA longer than the parent DNA, with its sequences repeated.
Term
Rotavirus
 Definition
A virus that contains dsRNA. Kills infants in 3rd world countries.
Term
Rothmund-Thomsun syndrome
 Definition
An inherited disease caused by defects in DNA repair mechanisms. Chromosome instability, mental retardation, and prone to cancer. Alterations in specific DNA helicases. Caused by mutation in RECQL4.
Term
RPBS
 Definition
Regulator protein-binding sites. Sites adjacent to promoter regions for genes, where activators or repressors bind.
Term
rut
 Definition

Rho utilization

A binding site for rho.
Term
Saccharomyces cerevisiae
 Definition
A test organsim in which splicing endonucleases were studied.
Term
Science
 Definition
If you cannot disprove a hypothesis, you must accept it.
Term
Secondary structure
 Definition
A level of structure in proteins. The spatial interrelationship of amino acids in segments of the polypeptide, maintained by hydrogen bonds. Includes α helices and β sheets.
Term
Self-splicing
 Definition

Autocatalytic activity

Discovered by Thomas Check and Sidney Altmari. Splicing reactions are intrinsic to the RNA, and occur without enzymes in rRNA, tRNA, and mRNA of mitochondria and chloroplasts. Uses no energy source: a series of phosphoester bond transfers occur, requiring guanosine nucleoside or nucleotides (GTP, GDP, GMP, or guanosine), with a free 3' -OH group. Splicing depends on the secondary structure of the RNA precursor to bring reactive groups together: the intron is a ribozyme. Rapid degradation of excised introns drive the reaction. Studied in Tetrahymena thermophila.
Term
Selenocystein
 Definition
An additional amino acid to the regular 20. Contains a trace element of selenium. Coded by UGA. Terminates the polypeptide.
Term
Selenoproteins
 Definition
Proteins that contains selenocystein. The selenium usually plays a role in binding at active sites. Play an important role in all organism.
Term
Semiconservative replication
 Definition
A possible method of DNA replication. Two strands are unwound, and a complementary nascent strand is formed to each, producing 2 identical DNA molecules. In Meselson and Stahl's experiment, two DNA strands have hybrid density, and the rest have normal density. There is evidence that this method is used in bacteria, and all eukaryotes.
Term
Sense strand
 Definition
Strands of RNA that code for polypeptides.
Term
Sequence-specific protein-nucleic acid interactions
 Definition
Bonds between proteins and nucleic acids, such as between RNA polymerase and promoters, CAP/cAMP and its binding site, or repressors/activators and operators. Proteins bind to specific DNA sequences, alter the structure of DNA to stimulate or repress transcription.
Term
Seth Wright
 Definition
A sheep farmer from Dover, Massachusetts who in 1791 discovered a germinal mutation in sheep that causes short legs.
Term
Shine-Dalgarno sequence
 Definition

AGGAGG

Named after the scientist who discovered it. A conserved sequence 7 nucleotides upstream from the initiation codon in prokaryotes. Forms base-pairing with an rRNA on the 30S subunit during initiation.
Term
Shirley Tilghman, Philip Leder, and colleagues
 Definition
Hybridized purified mouse β-globulin mRNA to the DNA that coded for the gene. Observed two R loops, demonstrating the existence of introns.
Term
Sickle-cell anemia
 Definition
Caused by a missense mutation in one of the proteins that make up hemoglobin in red blood cells.
Term
Side groups (R)
 Definition

Radicle

The group that differs between amino acids. Highly varied, producing the structural and functional versatility of proteins. Can be hydrophobic, hydrophilic, acidic, or basic.
Term
Sigma (σ) factor
 Definition
A component of RNA polymerase in E. coli. A subunit involved only in initiation of transcription. It is released after initiation. Recognizes and binds to promoters. If absent, the tetrameric protein will initiate transcription at random sites on the DNA in vitro.
Term
Signal sequence
 Definition
A short amino acid sequence at the amino or carboxyl terminus of a nascent polypeptide which signals for transport into a specific cellular compartment. Often it is removed when the polypeptide reaches its destination.
Term
Silencer
 Definition
Modulates the efficiency of transcription initiation in eukaryotes.
Term
Silent mutation
 Definition
A mutation that has no effect on phenotype. This is due to degeneracy in genetic code.
Term
Simple tandem repeats
 Definition
Repeated sequences of 1 - 6 nucleotide pairs. Dispersed throughout the human genome.
Term
SINEs
 Definition

Short interspersed nuclear elements

Retroposons found in humans. Less than 400 bp. Do not encode proteins: rely on retrotransposition activity of LINEs. Includes Alu.
Term
Single-strand DNA-binding proteins (SSB proteins)
 Definition
A component of the replisome. Bind to single-strand DNA strands in the replication bubble, after DNA helicase has opened it, preventing it from binding to itself, forming hairpins, and slowing or halting DNA replication. Binding of one SSB leads to the binding of another SSB. Encoded by ssb.
Term
Sleeping Beauty
 Definition
A cut-and-paste transposon found in salmon. A transition vector which works well in many vertebrates. Potentially useful for human gene therapy.
Term
Small interfering RNA (siRNA)
 Definition
A type of RNA. Important regulators of gene expression. Interact with proteins to modify chromatin structure.
Term
Small nuclear RNA (snRNA)
 Definition
A type of RNA. Structural components of spliceosomes. Found in the nucleus. Includes U1, U2, U4, U5, and U6.
Term
Small nucleolar RNA (snoRNA)
 Definition
Small nuclear RNAs. Found in the nucleolus. Function in rRNA and tRNA modification.
Term
snRNPs
 Definition

Small nuclear ribonucleoproteins

"Snurps"

Complexes of snRNA and protein that are the constituents of spliceosomes.
Term
Somatic mutation
 Definition
A mutation that occurs in somatic cells, which do not give rise to gametes. Mutant phenotype occurs only in cells that descent from that cell, and will not pass onto progeny. Incldues Delicious apples, and navel oranges: the original mutants were genetic mosaics, and the mutation is reproduced by vegetative propagation.
Term
Spliceosomes
 Definition
Macromolecular structures containing about 40 different proteins and five snRNAs. Composed of snRNPs. Carry out splicing reactions, removing introns in nuclear pre-mRNA. Recognition of the correct site involves base-pairing between the consensus sequence and complementary sequence at the 5' end of an snRNA. The lariat formation is formed using ATP. The 3' end of the intron is cut, and the 5' end on the exon is joined to the 3' end on the other side by a normal 5' - 3' phosphodiester linkage.
Term
Splicing endonucleases
 Definition
Carry out splicing reactions in tRNAs. Two cuts are made at the ends of the intron, and splicing ligase joins the two halves. Studied in Saccharomyces cerevisiae.
Term
Splicing ligase
 Definition
Joines the to halves cut by splicing endonuclease.
Term
Splicing reactions
 Definition
Carried out by spliceosomes. Removes introns.
Term
Split genes
 Definition
Gene which have introns. Almost all eukaryotic genes have introns, some as many as 50.
Term
Sponanteous mutation
 Definition
Mutations with no known cause. May result from a low level of metabolic errors, or be caused by unknown agents in the environment. Occurs infrequently, but frequency varies with gene and organism. For bacteria and phages, frequency is 10-8 - 10-10, and for eukaryotes 10-7 - 10-9 per nucleotide.
Term
ssb
 Definition
Encodes for SSB proteins, which bind to single-stranded DNA in the replication bubble.
Term
Suppressor mutation
 Definition
A type of reversion. A second mutation at a different location in the genome compensates for the effects of the first muation, producing wild-type phenotype. Restores the reading frame, or changes the anticodon on a tRNA. If back-crossed to a wild-type individual, half the progeny are wild-type, a quarter have the muation, and a quarter have the second mutation without the first mutation.
Term
Suppressor tRNA
 Definition
tRNA which have a mutated anticodon that recognizes a termination codon: UAG, UAA, or UGA with varying efficiency. A suppressor mutation that negates nonsense mutations.
Term
Svedberg unit (S)
 Definition
The unit that the size of ribosomal complexes are measured in. A sedimentation coefficient = (velocity/centrifugal force) of 10-13 seconds.
Term
Sylvie Doublié and colleagues
 Definition
In 1998, determined the structure of phage T7 polymerases, similar to DNA polymerase I of E. coli. Found its shape is somewhat like a hand grasping the primer DNA.
Term
Tanning beds
 Definition
Cause cancer. Are as dangerous as cigarettes or asbestos.
Term
Target site duplications
 Definition
2 - 13 bp repeats caused by staggered cleavage of DNA when transposons are inserted.
Term
TART
 Definition
Telomere-assited retrotransposition. Regenerates lost chromosome ends in Drosophila.
Term
TATA box
 Definition
An element of a promoter for DNA polymerase II. A conserved element at -30. The consensus sequence is TATAAAA (5' - 3' on the nontemplate strand). Plays a role in positioning the transcription start point.
Term
Tautomeric shift
 Definition
A hydrogen atom moves its position on a nucleic base, changing its propertis. Rare, but causes alteration in pairing of bases. A change from keto to enol form, or from amino to imino form. The more rare forms are less stable, and exist only for short amounts of time, and have irregular base pairing. Form A:C and G:T base pairs, due to altered numbers of hydrogen bonds from the moved hydrogen.
Term
Telomerase
 Definition
An RNA-containing enzyme which adds telomeres to a new DNA strand. Discovered in 1985 by Elizabeth Blackburn and Carol Greider. It extends the 3' end of the telomere with repetitive sequences. In humans the sequence is TTAGGG. Without telomerase, the chromosome would become shorter with every replication, since DNA polymerase cannot work without a 3' end. Somatic cells have low telomerase activity. Cancer cells have high telomerase activity. There is a correlation between telomere length and the age of cells. Shortening of the telomere with age leads to death.
Term
Telomeric retroposons
 Definition
A retroposon found in Drosophila.
Term
Template strand
 Definition

Anti-sense strand

The DNA strand which is transcribed. Complementary to the RNA transcript.
Term
Template strand
 Definition

Anti-sense strand

The 
Term
terA
 Definition
Blocks movement of the replication fork in a counter-clockwise direction.
Term
terB
 Definition
Blocks movement of the replication fork in a clockwise direction.
Term
Termination signal
 Definition
A DNA sequence which causes the RNA polymerase to dissociate with the DNA, releasing the nascent RNA molecule. In E. coli this includes Rho-dependent and Rho-independent terminators.
Term
Tertiary structure
 Definition

Conformation

A level of structure in proteins. The overall folding of the polypeptide. Ionic bonds, hydrogen bonds, hydrophobic interactions, Van der Waals interactions, and covalent disulfide bonds are elements of tertiary structure.
Term
Tetrahymena thermophila
 Definition
A test organism in which self-splicing was studied.
Term
Tetrameric core (α2ββ')
 Definition
A component of RNA polymerase in E. coli. The α subunit is involved in its assembly. The β subunit is the RTP binding site. The β' subunit is the DNA template binding site. Catalyzes transcript elongation.
Term
TFIIA, B, D, and F
 Definition
Basal transcription factors. Forms a pre-initiation complex that prepares DNA for unwinding and recruits RNA polymearse and TFIIE to form a transcription bubble and initiate transcription.
Term
TFIIE
 Definition
A basal transcription factor. It is recruited by TFIIA, B, D, and F to form a transcription bubble and initiate transcription.
Term
TFIIH
 Definition
A basal transcription factor. Associates and aids in DNA helix unwinding.
Term
Thermus thermophilus
 Definition
A bacteria. The structure of its 70S ribosome was solved to a resolution of 0.55 nm using X-ray crystallography.
Term
Thomas Cech and Sidney Altmari
 Definition
Discovered self-splicing in 1982. Won the Nobel PRize in Chemistry in 1989.
Term
Thymine
 Definition
It has a common keto form, and a rare enol form, with the H at C4 rather than C3.
Term
Tn3 element
 Definition
A replicative transposon in bacteria. Terminate in simple inverted 38 - 40 bp repeats. Contain three genes: tnpA, tnpR, and bla. Fuses with plasmids to form cointegrates. The plasmid and chromosome are split at the res site, thus replicating and passin Tn3 on to the other plasmid.
Term
tnpA
 Definition
A gene in a Tn3 element. Codes for transposase.
Term
tnpR
 Definition
A gene in a Tn3 element. Codes for resolvase or repressor. Binds to the res site to prevent transcription.
Term
Transcript
 Definition
A strand of RNA produced by transcription. Identical sequence to the nontemplate strand of DNA. In prokaryotes, the half-life of a transcript is less than 5 minutes. In eukaryotes, the transcripts have proteins bound to them which protect them from degradation, increasing their half-life to 5 hours.
Term
Transcription
 Definition
An RNA transcript is produced, using DNA as a template.
Term
Transcription bubble
 Definition
A locally unwound segment of DNA where RNA transcription takes place. Produced by RNA polymerase. In E. coli it is about 18 nucleotide pairs wide.
Term
Transcription factor
 Definition
Proteins that bind to the promoter region and form a complex before RNA polymerase II can bind in eukaryotes. Forms a locally unwound segment of DNA. Includes basal transcription factors.
Term
Transcription unit
 Definition
A segment of DNA that is transcribed to produce on RNA molecule. May be equivalent to one gene, or include several genes. Large transcripts with many genes are common in bacteria.
Term
Transfer RNA (tRNA)
 Definition
A type of RNA. Small RNA molecuels. Adaptors between amino acids and the codons in mRNA during translation. Have 1 - 4 unusual nucleotides that are modified post-transcriptionally by enzymes. Attach to amino acids by high energy bonds. Have an anticodon.
Term
Transition
 Definition
A mutation caused by a tautomeric shift where a pyrimidine is replaced by the other pyrimidine, or a purine is replaced by the other purine. There are four possible transitions.
Term
Transition vector
 Definition
The transposon used to carry genes into an organism. Gerald Rubin and Allan Spralding used a P element from bacteria. Different transition vectors work differently for different species.
Term
Translation
 Definition
The sequence of nucleotides in an mRNA is converted into amino acids of a polypeptide, based on the genetic code. Takes place on ribosomes in the cytoplasm.
Term
Translesion polymerase
 Definition
Replicate over lesions or defects which block replciation by most DNA polymerases.
Term
Transposase
 Definition
A protein that enables cut-and-paste and replicative transposition. Encoded by cut-and-paste and replicative transposons. Binds at or near the ends of the element and cuts both strands of the DNA.
Term
Transposition
 Definition
The movement of transposons.
Term
Transposon
 Definition

Transposable element

Transposable genetic element

Discovered by Barbara McClintock. DNA elements that can move from site to site in the genome. Constitute over 40% of the human genome, 85% of the maize genome. Insertion of a transposon into a gene often renders genes non-functional. Can confer selective advantage, or act as a genetic parasite. Many mutations are caused by transposon insertion. Includes cut-and-paste transposons, replicative transposons, and retrotransposons.
Term
Transposon tagging
 Definition
Identifying genes by using transposon-insertion mutations as markers.
Term
Transversion
 Definition
A mutation caused by a tautomeric shift where a pyrimidine is replaced with a purine, or vice versa. There are eight possible transversions.
Term
Trichothiodystrophy
 Definition
An inherited disease caused by defects in DNA repair mecahnisms. UV sensitivity, neurological disorders, and mental retardation. Individuals have short stature, brittle hair, and scaly skin. Caused by mutations in TTD, XBA, or XPD.
Term
Trinucleotide repeats
 Definition
Simple tandem repeats with 3 nucleotide pairs. Increase in copy number causes inherited diseases. The higher the copy number, the more severe the symptoms. There can be anticipation. Incldues FRAXA.
Term
Triplet code
 Definition
The nucleotide codons. Evidence for this was first found by Francis Crick in 1961.
Term
tRNAfMet
 Definition
The aminoacyl-tRNA that the initiation codon codes for in prokaryotes. Adds a methionine with a formyl group. The amino terminus amino acid in prokaryotes is alwas f-methionine, and is often cleaved post-translationally.
Term
tRNAiMet
 Definition
The aminoacyl-tRNA that the initiation codon, AUG, codes for in eukaryotes. Adds a methionine without a formyl group.
Term
tRNAMet
 Definition
The aminoacyl-tRNA that AUG codon codes for, excepting the initiation codon in prokaryotes. Adds methionine without a formyl group.
Term
trpA
 Definition
A gene in E. coli that encodes for the α subunit of tryptophan synthetase. It was studied by Charles Yanofsky and colleagues.
Term
trpB
 Definition
A gene in E. coli that encodes for the β subunit of tryptophan synthetase.
Term
Tryptophan
 Definition
One of the only amino acids which is specified by a single codon.
Term
Tryptophan biosynthesis
 Definition
The genes for biosynthesis of tryptophan are depressed in the presence of tryptophan.
Term
TTDA
 Definition
A gene on chromosome 6 for basal transcription factor IIH. Mutation in this gene can cause trichothiodystrophy.
Term
Ty1
 Definition
A retrovirus-like element found in yeast. 5.8 kbp, with 340 bp LTRs. Creates a 5 bp target site duplication when inserted. Most yeast strains have about 35 copies of it. Incldues TyA and TyB genes, homologous to gag and pol, respectively.
Term
Ultraviolet radiation (UV)
 Definition
A nonionizing radiation. Induces mutations through excidation of electrons. Causes cross-linking of adjacent thymines, to form thymine dimers that can block DNA replication and activate DNA repair mechanisms.
Term
Unidirectional replication
 Definition
One replication fork remains stationary while the other moves away. Occurs in the circular chromosome of coliphage P2.
Term
Universal
 Definition
A characteristic of genetic code. Virtually all organisms use the same genetic code. Exceptiosn in mitochondria and yeast. Mutations in tRNA cause deviations from the genetic code, and can arise as suppressor mutations.
Term
Upstream
 Definition
Towards the 5' end of the RNA transcript.
Term
Upstream sequence (-)
 Definition
DNA sequences that precede the initiation site.
Term
UvrD
 Definition

MutU

DNA helicase

Involved in mismatch repair in E. coli. Necessary for excision.
Term
Van der Waals interactions
 Definition
An element of tertiary structure of proteins. Weak attraction between atoms in close proximity.
Term
Vernon Ingram
 Definition
In 1957, demonstrated that in a normal person, the 6th amino acid of the β-subunit of hemoglobin is gluatmine, but in someone with sickle-cell anemia, it is valine.
Term
Vicia faba
 Definition
Broad beans. Used in the experiments of Taylor, Woods, and Hughes.
Term
Werner syndrome
 Definition
An inherited disease caused by defects in DNA repair mechanisms. Chromosome instability, progressive neurodegeneration, and prone to cancer. A less severe form of progeria. Sensesnce begins in the patient's teen years, and death occurs in the patient's 40s. Alterations in specific DNA helicases. Caused by a recessive mutation in WRN.
Term
Wobble position
 Definition
The third base in a codon. It is not as important as the other bases, according to Crick's wobble hypothesis.
Term
WRN
 Definition
A gene on chromosome 8 for WRN RecQ helicase. Mutation in this gene can cause Werner syndrome.
Term
X-ray diffraction
 Definition
Used to create models of proteins.
Term
X-ray radiation
 Definition
An ionizing radiation. Induces mutations through ionization.
Term
Xenopus laevis
 Definition

South African clawed toad

Its nuclear organizer region is on the sex chromosome.
Term
Xeroderma pigmentosum (XP)
 Definition
An inherited disease caused by defects in DNA repair mechanisms. UV sensitivity, early onset of skin cancers, and neurological disorders. DNA polymerase eta is absent. Caused by mutations in XPA, XPB, XPC, XPD, XPE, XPF, XPG, or XPV: genes for nucleotide excision repair.
Term
XPA
 Definition
A gene on chromosome 9 for DNA damage recognition protein. Mutation in this gene can lead to xeroderma pigmentosum.
Term
XPB
 Definition
A gene on chromosome 2 for 3' - 5' helicase. Mutation in this gene can lead to xeroderma pigmentosum or trichothiodystrophy.
Term
XPC
 Definition
A gene on chromosome 3 for DNA damage recognition protein. Mutation in this gene can lead to xeroderma pigmentosum.
Term
XPD
 Definition
A gene on chromosome 19 for 5' - 3' helicase. Mutation in this gene can lead to xeroderma pigmentosum or trichothiodystrophy.
Term
XPE
 Definition
A gene on chromosome 11 for DNA damage recognition protein. Mutation in this gene can lead to xeroderma pigmentosum.
Term
XPF
 Definition
A gene on chromosome 16 for nuclease 3' incision. Mutation in this gene can lead to xeroderma pigmentosum.
Term
XPG
 Definition
A gene on chromosome 13 for nuclease 5' incision. Mutation in this gene can lead to xeroderma pigmentosum.
Term
XPV
 Definition
A gene on chromosome 6 for translesion DNA polymerase η. Mutation in this gene can lead to xeroderma pigmentosum.
Term
Z-DNA
 Definition
Left-handed, open DNA. Found in some living cells.
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