cell bio exam 3

gene

a segment of DNA that directs the production of a particular protein or functional RNA molecule

transcription

the mechanism by which cells copy DNA into RNA

translation

the mechanism by which cells use the information encoded in RNA to direct the synthesis of a protein

gene expression

the process by which a gene makes a product that is useful to a cell or organism by directing the synthesis of a protein or an RNA molecule with a characteristic activity

rna polymerase

the enzyme responsible for adding ribonucleotides to the growing chain

rna transcript

the RNA molecule produced by transcription is referred to as

noncoding rna

an RNA molecule that is the final product of a gene and does NOT code for a protein

messenger rnas

code for proteins

ribosomal rnas

form the core of the ribosome’s structure and catalyze protein synthesis

micro rnas

regulate gene expression

transfer rnas

serve as adaptors between mrna and amino acids during protein synthesis

small interfering rnas

provide protection from viruses and proliferating transposable elements

long noncoding rnas

act as scaffolds and serve other diverse functions, many of which are still being discovered

other noncoding rnas

used in rna splicing, gene regulation, telomere maintenance

initiation

recognizing the beginning and assembling everything needed to make transcription happen

elongation

adding nucleotides one at a time using a template strand as a guide

termination

recognizing where to stop transcribing and dissociating from DNA

promoter

dna sequence that indicates where RNA polymerase should bind to initiate prokaryotic transcription

sigma factor

subunit of RNA polymerase in bacteria that recognizes the promoter

terminator

dna sequence that indicates where RNA polymerase should stop transcribing

rna polymerase 1

makes most rRNA

rna polymerase 2

makes mRNA and some snRNA and miRNA

rna polymerase 3

makes tRNA, some rRNA, other small RNAs

transcription factors

eukaryotes require the assistance of a large set of proteins for transcription

general transcription factors

proteins that assemble on the promoters of eukaryotic genes near the start site of transcription and load the RNA polymerase in the correct position

tata box

sequence found in the promoter of many eukaryotic genes that contains repeats of AT base pairs

transcription initiation complex

other transcription factors assemble at the promoter along with RNA polymerase II

elongation factors

help RNA pol II to move along the DNA and get access to the sequences that are wound around histones

rna pol 1

stops when specific termination sequences are recognized by a termination factor

rna pol 2

doesn’t have a stop signal, keeps transcribing past the gene, unclear how/when it stops. The mRNA it is transcribing gets clipped off by a separate protein that recognizes where the transcript should stop

rna pol 3

stops when it reaches a stretch of U residues (UUUUUUU)

rna capping

modifies the 5’ end of a transcript by addition of a methylguanosine

polyadenylation

mRNA molecules in eukaryotes get polyadenylated- addition of numerous A nucleotides to the 3’ of the transcript

introns

noncoding sequence within a eukaryotic gene that is transcribed into RNA molecule but then removed to produce a mature mRNA molecule

exons

segment of a eukaryotic gene that is transcribed into RNA and dictates the amino acid sequence of part of a protein

rna splicing

process in which intron sequences are excised from RNA molecules in the nucleus during the formation of a mature mRNA, takes place in the nucleus

spliceosome

molecular complex that cuts out the intron by forming a lariat structure

ribozymes

rnas that catalyze reactions

alternative splicing

transcripts from many eukaryotic genes can be spliced in different ways in a process

translation

process by which the sequence of nucleotides in a messenger RNA molecule directs the incorporation of amino acids into protein

codon

a group of 3 consecutive nucleotides that specifies one amino acid

genetic code

the set of rules by which the nucleotide sequence of a gene through an intermediary mRNA molecule is translated into the amino acid sequence of a protein

reading frame

one of the three possible ways in which a set of successive nucleotide triplets can be translated into a protein

start codon

a special nucleotide sequence that signals where translation should start and sets the reading frame

degenerate

most amino acids have more than one codon

wobble

many tRNAs only require accurate base pairing for the first two nucleotides in a codon

aminoacyl trna synthetases

the enzymes responsible for “charging” tRNA molecules with amino acids

e site (exit site)

holds the empty tRNA that has already donated its amino acid

p site (peptidyl site)

holds the tRNA that’s `carrying the polypeptide

a site (aminoacyl site)

where charged tRNAs enter

mrna binding site

holds the mRNA being translated

initiator trna

the tRNA that carries methionine which is always the first amino acid in a polypeptide (it’s usually removed later)

polycistronic mrna

mRNA molecules that encode several proteins

ribosome binding sequence

sequences in polycistronic mRNA that tell ribosomes where to bind

formyl-methionine

modified methionine that’s always the first amino acid in bacterial proteins

stop codons

tell the ribosome where to stop translation. Do NOT code for amino acids

release factors

proteins that bind at stop codons altering the activity of a ribosome

tetracycline

blocks binding of aminoacyl-trna to a site of ribosome

streptomycin

prevents the transition from initiation complex to chain elongation; also causes miscoding

chloramphenicol

blocks the peptidyl transferase reaction on ribosomes

erythromycin

binds in the exit channel of the ribosome and inhibits elongation of the peptide chain

rifamycin

blocks initiation of transcription by binding to and inhibiting rna polymerase

proteolysis

breakdown of proteins

proteases

enzymes that cut peptide bonds

proteosomes

protein complexes where breakdown of proteins happens

ubiquitin

covalently attached unit that marks proteins for destruction

nuclear transplantation experiments

an experiment where the nucleus of a differentiated cell is placed into an egg cell with its nucleus removed to see if it can direct development of a whole organism

proteome

all the proteins made by a cell at a
given time

housekeeping proteins

proteins that are common to all the cells of a multicellular organism

transcriptome

all the RNAs made by a cell at a given time

regulatory dna sequences

indicate where regulator proteins should bind

enhancers

DNA sequences that activators bind to

silencers

DNA sequences that repressors bind to

regulator proteins

bind to DNA to control gene expression

activators

proteins that turn genes on

repressors

proteins that turn genes off

pluripotent stem cells

undifferentiated cells that can give rise to other cell types

induced pluripotent stem cells

cells can also be forced to de-differentiate making them __

epigenetic inheritence

the transmission of a heritable pattern of gene expression from one cell to its progeny that does not involve altering the nucleotide sequence of DNA

micrornas

tiny RNA molecules (~22 nucleotides) that control gene expression by base pairing with specific mRNAs, reducing their stability and translation

rna induced silencing complex

micrornas function by joining a protein complex called __

small interfering rna

small RNA molecule that like miRNAs binds to a target RNA molecule to mark it for destruction

rna interference

the process of controlling gene expression with siRNAs

dicer

foreign RNA is cut up into pieces by a protein

rna induced transcriptional silencing

while RISC+siRNA are going about destroying foreign RNA in the cytosol some of the siRNAs produced by DICER join a complex

crispr

many species of bacteria maintain a record of past infections in the form of small noncoding RNAs that they use to protect them from future infections

crispr locus

once a bacteria has encountered a virus it actually adds part of the viruses genome to its own chromosome in a location

crispr rnas

when the bacteria is exposed to the virus again it uses the stored DNA information to produce a series of small RNAs

cas

crRNA join with a proteinlo

long noncoding rna

class of large RNA molecules that does not encode proteins. Some have been identified as regulating gene expression

dna cloning

production of many identical copies of a DNA sequence

restriction enzymes

enzymes that cut DNA at specific sequences

recombinant dna

inserting DNA fragments into a vector that
can be copied involves combining DNA from
different sources

plasmids

the vectors we use to carry DNA that we want to clone

genomic libraries

the resulting cultures of bacterial cells containing the fragments from the genome

hybridization

H bonds in DNA can be disrupted by heating. When the solution is cooled the the two strands will come back together

polymerase chain reactions

a method for amplifying DNA

dideoxy sequencing

a method for sequencing DNA using PCR and chain terminating nucleotides called dideoxynucleotides (ddNTPs)

clustering

computationally sorting data such as RNA-seq data based on similarity

in situ hybridization

allows a particular nucleic acid to be visualized in its normal place