Chapters 14-17 Vocab

Electrophoresis

technique used to separate DNA fragments according to size

Helicase

during replication, this enzyme helps to open up the DNA helix by breaking the hydrogen bonds

induced mutation

mutation that results from exposure to chemicals or environmental agents

lagging strand

during replication, the strand that is replicated in short fragments and away from the replication fork

leading strand

strand that is synthesized continuously in the 5'-3' direction, which is synthesized in the direction of the replication fork

Ligase

enzyme that catalyzes the formation of a phosphodiester linkage between the 3' OH and 5' phosphate ends of the DNA

mismatch repair

type of repair mechanism in which mismatched bases are removed after replication

Mutation

variation in the nucleotide sequence of a genome

nucleotide excision repair

type of DNA repair mechanism in which the wrong base, along with a few nucleotides upstream or downstream, are removed

Okazaki fragment

DNA fragment that is synthesized in short stretches on the lagging strand

point mutation

mutation that affects a single base

Primase

enzyme that synthesizes the RNA primer; the primer is needed for DNA pol to start synthesis of a new DNA strand

Primer

short stretch of nucleotides that is required to initiate replication; in the case of replication, the primer has RNA nucleotides

Proofreading

function of DNA pol in which it reads the newly added base before adding the next one

replication fork

Y-shaped structure formed during initiation of replication

silent mutation

mutation that is not expressed

single-strand binding protein

during replication, protein that binds to the single-stranded DNA; this helps in keeping the two strands of DNA apart so that they may serve as templates

sliding clamp

ring-shaped protein that holds the DNA pol on the DNA strand

spontaneous mutation

mutation that takes place in the cells as a result of chemical reactions taking place naturally without exposure to any external agent

Telomerase

enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends

Telomere

DNA at the end of linear chromosomes

Topoisomerase

enzyme that prevents overwinding of DNA when DNA replication is taking place

Transformation

process in which external DNA is taken up by a cell

transition substitution

when a purine is replaced with a purine or a pyrimidine is replaced with another pyrimidine

transversion substitution

when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine

7-methylguanosine cap

modification added to the 5' end of pre-mRNAs to protect mRNA from degradation and assist translation

aminoacyl tRNA synthetase

enzyme that “charges” tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid

Anticodon

three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon

CAAT box

(GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors

central dogma

states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins

Codon

three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation

Colinear

in terms of RNA and protein, three “units” of RNA (nucleotides) specify one “unit” of protein (amino acid) in a consecutive fashion

Consensus

DNA sequence that is used by many species to perform the same or similar functions

core enzyme

prokaryotic RNA polymerase consisting of α, α, β, and β' but missing σ; this complex performs elongation

Degeneracy

(of the genetic code) describes that a given amino acid can be encoded by more than one nucleotide triplet; the code is degenerate, but not ambiguous

Downstream

nucleotides following the initiation site in the direction of mRNA transcription; in general, sequences that are toward the 3' end relative to a site on the mRNA

Exon

sequence present in protein-coding mRNA after completion of pre-mRNA splicing

FACT

complex that “facilitates chromatin transcription” by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by

GC-rich box

(GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter

Hairpin

structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides

Holoenzyme

prokaryotic RNA polymerase consisting of α, α, β, β', and σ; this complex is responsible for transcription initiation

initiation site

nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a “+1”

initiator tRNA

in prokaryotes, called tRNA f Met; in eukaryotes, called tRNA i; a tRNA that interacts with a start codon, binds directly to the ribosome P site, and links to a special methionine to begin a polypeptide chain

Intron

non–protein-coding intervening sequences that are spliced from mRNA during processing

Kozak’s rules

determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must appear around the AUG: 5’-GCC(purine)CCAUGG-3’; the bolded bases are most important

nonsense codon

one of the three mRNA codons that specifies termination of translation

nontemplate strand

strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA

Octamer box

(ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter

peptidyl transferase

RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation of peptide bonds

Plasmid

extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common in prokaryotes

poly-A tail

modification added to the 3' end of pre-mRNAs to protect mRNA from degradation and assist mRNA export from the nucleus

Polysome

mRNA molecule simultaneously being translated by many ribosomes all going in the same direction

preinitiation complex

cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template

Promoter

DNA sequence to which RNA polymerase and associated factors bind and initiate transcription

reading frame

sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that protein

rho-dependent termination

in prokaryotes, termination of transcription by an interaction between RNA polymerase and the rho protein at a run of G nucleotides on the DNA template

Rho-independent

termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin formation in the mRNA that stalls the polymerase

RNA editing

direct alteration of one or more nucleotides in an mRNA that has already been synthesized

Shine-Dalgarno sequence

(AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules comprising the 30S ribosome

signal sequence

short tail of amino acids that directs a protein to a specific cellular compartment

small nuclear RNA

molecules synthesized by RNA polymerase III that have a variety of functions, including splicing pre-mRNAs and regulating transcription factors

Splicing

process of removing introns and reconnecting exons in a pre-mRNA

start codon

AUG (or rarely, GUG) on an mRNA from which translation begins; always specifies methionine

TATA box

conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for transcription

template strand

strand of DNA that specifies the complementary mRNA molecule

transcription bubble

region of locally unwound DNA that allows for transcription of mRNA

Upstream

nucleotides preceding the initiation site; in general, sequences toward the 5' end relative to a site on the mRNA

3' UTR

3' untranslated region; region just downstream of the protein-coding region in an RNA molecule that is not translated

5' cap

a methylated guanosine triphosphate (GTP) molecule that is attached to the 5' end of a messenger RNA to protect the end from degradation

5' UTR

5' untranslated region; region just upstream of the protein-coding region in an RNA molecule that is not translated

Activator

protein that binds to prokaryotic operators to increase transcription

catabolite activator protein (CAP)

protein that complexes with cAMP to bind to the promoter sequences of operons which control sugar processing when glucose is not available

cis-acting element

transcription factor binding sites within the promoter that regulate the transcription of a gene adjacent to it

Dicer

enzyme that chops the pre-miRNA into the mature form of the miRNA

DNA methylation

epigenetic modification that leads to gene silencing; a process involving adding a methyl group to the DNA molecule

Enhancer

segment of DNA that is upstream, downstream, perhaps thousands of nucleotides away, or on another chromosome that influence the transcription of a specific gene

Epigenetic

heritable changes that do not involve changes in the DNA sequence

eukaryotic initiation factor-2 (eIF-2)

protein that binds first to an mRNA to initiate translation

gene expression

processes that control the turning on or turning off of a gene

guanine diphosphate (GDP)

molecule that is left after the energy is used to start translation

guanine triphosphate (GTP)

energy-providing molecule that binds to eIF-2 and is needed for translation

histone acetylation

epigenetic modification that leads to gene expression; a process involving adding or removing an acetyl functional group

inducible operon

operon that can be activated or repressed depending on cellular needs and the surrounding environment

initiation complex

protein complex containing eIF-2 that starts translation

lac operon

operon in prokaryotic cells that encodes genes required for processing and intake of lactose

large 60S ribosomal subunit

second, larger ribosomal subunit that binds to the RNA to translate it into protein

microRNA (miRNA)

small RNA molecules (approximately 21 nucleotides in length) that bind to RNA molecules to degrade them

Myc

oncogene that causes cancer in many cancer cells

negative regulator

protein that prevents transcription

Operator

region of DNA outside of the promoter region that binds activators or repressors that control gene expression in prokaryotic cells

Operon

collection of genes involved in a pathway that are transcribed together as a single mRNA in prokaryotic cells

poly-A tail

a series of adenine nucleotides that are attached to the 3' end of an mRNA to protect the end from degradation

positive regulator

protein that increases transcription

Post-transcriptional

control of gene expression after the RNA molecule has been created but before it is translated into protein

Post-translational

control of gene expression after a protein has been created

Proteasome

organelle that degrades proteins

Repressor

protein that binds to the operator of prokaryotic genes to prevent transcription

RISC

protein complex that binds along with the miRNA to the RNA to degrade it

RNA stability

how long an RNA molecule will remain intact in the cytoplasm

RNA-binding protein (RBP)

protein that binds to the 3' or 5' UTR to increase or decrease the RNA stability