Studied by 3 people
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
the strand that is synthesized continuously in the 5' to 3' direction that 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
the Y-shaped structure formed during the initiation of replication
silent mutation
mutation that is not expressed
single-stranded 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
a 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 tRNAMetf; in eukaryotes, called tRNAi; 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
the word purine and the G after "AUG" (G-3') are bolded
nonsense codon
one of the three mRNA codons that specifies termination of translation
nontemplate strand
the 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
the process of removing introns and reconnecting exons in a pre-mRNA
start codon
the 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
the strand of DNA that specifies the complementary mRNA molecule
transcription bubble
the 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 that 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; commonly found in cancer cells
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; commonly found in cancer cells
inducible operon
operon that can be activated or repressed depending on cellular needs and the surrounding environment
initiation complex
protein complex containing eIF2-2 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
Note
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