Exam 4 Danhart

Gene expression

set of processes that convert information in DNA into a product and something you can see

Central dogma of molecular biology

DNA → mRNA → Protein

Transcription

uses DNA template to make an RNA molecule with a complementary sequence

Translation

uses information in mRNA to synthesize protein

Ribozymes

RNA molecules that do not code for protein

Reverse transcriptase

enzyme that makes DNA from RNA, used by many viruses and an important tool for researchers

Codon

a group of three DNA bases the specifies a particular amino acid

Start Codon

AUG

Stop codons

UAA, UAG, UGA

Template strand

template for mRNA synthesis

Redundant

most amino acids are coded for by multiple codons

Unambiguous

each codon codes for only one amino acid

Non-overlapping

codons are read one after another

Universal

codons code for the same amino acids in most organisms

Convervative

when multiple codons code for the same amino acid, usually only the third base differs

Point mutation

alters the sequence of one or a small number of base pairs. Can be beneficial, deleterious, or neutral

Silent

change in nucleotide sequence that does not change the amino acid specified by a codon, no change in phenotype

Missense

change in nucleotide sequence that changes the amino acid specified by codon, change in primary structure of protein

Nonsense

change in nucleotide sequence that results in an early stop codon, leads to mRNA breakdown

Frameshift

addition or deletion of a nucleotide, reading frame is shifted, altering the meaning of all subsequent codons

Chromosome mutation

changes in the structure or number of chromosomes

Inversion

segments of a chromosome are detached, flipped, and rejoined

Translocation

segments of a chromosome are detached and joined to a different chromosome

Deletion

loss of a segment of a chromosome

Duplication

segment of a chromosome is duplicated

Promoter

short sequence of DNA where proteins bind to initiate transcription (what RNA polymerase is looking for)

Transcription factors

proteins that bind to DNA and are involved in the process of transcription

Sigma

main transcription factor in bacteria, binds to -10 and -35 boxes, guides RNAP to where transcription will begin

RNAP holoenzyme

sigma + core enzyme that forms the complete RNA polymerase complex, essential for initiating transcription in bacteria.

Initiation (bacteria)

sigma binds to promoter and RNAP binds to sigma, RNAP opens up DNA helix and begins transcription, sigma is released

Elongation (bacteria)

RNAP moves along DNA continuously

Termination (bacteria)

A signal is transcribed that folds RNA into a hairpin structure and causes the release of RNA from RNAP

Eukaryotic transcription

3 RNAP’s, diverse promoters, GTFs, multiple methods of termination, transcription and translation are separated

Exons

genes that remain part of mRNA

Introns

sections removed from mRNA

snRNPs (small nuclear ribonucleoproteins)

bind to pre-mRNA and assemble to form spliceosome

Splicing

intron is cut out and removed as a ‘lariat’ structure

5’ cap

modified general transcription factor added to the 5’ end that serves as protective shield

Poly(A) tail

long chain of As added to 3’ end, enables ribosome to bind to mRNA and terminates RNA transcription

tRNA secondary structure

between mRNA and amino acids, 3’ end attaches to amino acid, tRNA is antiparallel to mRNA

Aminoacyl

tRNA + amino acid, “charged RNA” due to negative charge of phosphate groups

Aminoacyl-tRNA synthetases (ARS)

catalyze addition of amino acids to tRNA “charge” tRNAs

Wobble hypothesis

bases at the 3’ end of a codon can bind anticodons in ways that don’t match Watson-Crick base pairing (flexibility in base pairing). Allows one tRNA to read more than one codon

A site

aminoacyl tRNA

P site

tRNA with growing polypeptide attached

E site

tRNA that will EXIT ribosome

Small subunit

holds mRNA in ribosomes

Large subunit

contains tRNA binding sites; where peptide bond formation occurs in ribosomes

Initiation (eukaryotes)

mRNA binds to small subunit of ribosome at ribosome binding site, first aminoacyl tRNA binds to start codon, large subunit of ribosome binds in P site

Elongation

new aminoacyl tRNA enters A site, peptide bond is formed between amino acids by ribosome, ribosome moves one codon (translocates)

Termination

release factor binds to stop codon, polypeptide (amino acids) and tRNAs released, ribosome subunits separate

Post-translational modifications

protein folding guided by molecular chaperones and chemical modifications in Golgi and Rough ER (phosphorylation, glycosylation)

Gene expression

the set of processes converting information in DNA into a functional product, regulated by central dogma

Galactoside permease

transports lactose into cell

B-galactosidase

breaks down lactose into glucose and galactose

Inducer

small molecule that triggers transcription (lactose)

lacZ gene

codes for B-galactosidase

lacY gene

codes for galactoside permease

lacI

shuts down lacZ and lazY genes when they aren’t needed

Operon

set of coordinately regulated bacterial genes that are transcribed together into one mRNA

Negative control

repressor protein binds to DNA and shuts down transcription (on/off switch)

Positive control

activator protein bind to DNA and triggers transcription (volume control)

Turning on operon

lactose (inducer) binds to repressor, repressor changes shape and can no longer bind to DNA

Turning off operon

repressor is bound to DNA, transcription is blocked

Repressor

bound to operator and blocks transcription

CAP (catabolite activator protein)

when bound to cAMP (second messenger), binds to DNA to increase transcription

Expression is greatest

high lactose, low glucose, high cAMP

Inducer exclusion

glucose inhibits the activity of galactoside permease, prevents lactose from entering cell

Regulons

separate genes or operons with the same regulatory sequences that are controlled together

Differential gene expression

cells with the same genome express different sets of genes

Histones

proteins that wrap around DNA

Nucleosome

DNA + histones

DNA methylation

methyl groups (CH3) added to C nucleotides (leads to condensing of chromatin)

Histone acetylation

acetyl groups added to lysine residues on histone tails and decondenses (opens) chromatins

Chromatin-remodel complexes

large enzyme complex that use ATP to reshape chromatin

Epigenetics

any mechanism of inheritance due to something other than changes in DNA sequence

Core promoter

binding site for RNA Polymerase (same for prokaryotes)

Promoter-proximal elements

close to promoter, allow coordinated regulation of genes of the same type

Enhancers

far from promoter, bound by activator proteins to begin or increase transcription

Silencers

far from promoter, bound by repressor proteins to shut down transcription

General transcription factors (GTFs)

bind to core promoter to initiate transcription in many genes, not involved much in regulation

Regulatory transcription factors (TFs)

bind to enhancers, silencers, promoter-proximal elements, specific for different types of cells and responsible for making cell types

Histone acetyltransferases (HATs)

add acetyl groups

Histone deacetylases (HDACs)

remove acetyl groups

Mediator

large protein complex that interacts with TFs and recruits RNAP for transcription

Alternative splicing

same primary transcript (pre-mRNA) can be spliced in different ways, same gene can yield more than one mature mRNA

Ubiquitin

protein that marks another protein for degradation

Proteasome

garbage disposed, breaks down ubiquitinated proteins

Biotechnology

the engineering of genes, cells, and organisms for research

Recombinant DNA

mix/match DNA sequences from any organism to produce large amounts of a gene product

PCR

quickly make unlimited copies of any DNA

DNA sequencing

discover new or modified proteins; determine evolutionary relationships; understand disease

CRISPR-Cas

editing genomes at specific locations

Gene therapy

replacing genes to cure genetic diseases

DNA cloning

producing many copies of a DNA sequence of interest

Plasmid

small, circular DNA molecule common in many bacterial cells, used for DNA cloning

Vector

a plasmid used to make copies of a foreign DNA sequence

Restriction endonucleases

bacterial enzymes that cut DNA at specific base sequences

Sticky ends

single-stranded base on a fragment cut by restriction enzymes (two ends are complementary and can specifically rejoin)

Recombinant plasmid

Sticky ends on plasmid and on foreign DNA complementary base pairs connect to each other