AP Bio Unit #6 Part 2: Gene Expression and Regulation

my acc for all the other units! good luck

operator

segment of dna that controls on/off switch for genes, within the promoter

operon

entire stretch of dna including: operator, promoter, and genes

repressor

switches off operon, blocks operator from rna polymerase

regulatory gene

creates the repressor

corepressor

bonds to existing repressor to activate it

trytophan (corepressor) + trp repressor

together turns off operon

repressible operon

usually on, is wanted to turn off, repressor + operator turns off transcription, anabolic (building) pathways, repressed by high levels of final product

example of repressible operon

trp operon

inducible operon

usually off, inducer inactivates the repressor and turns on transcription, catabolic (breaking down) pathways

example of inducible operon

lac operon

lac operon

genes code for enzymes for metabolism of lactose (catabolic)

inducer

inactivates repressor to turn lac operon on

negative control of genes

operons are switched off by the active form of the repressor

cylic amp receptor protein (CRP)

activator of transcription

CRP activation

CRP + cyclic amp (cAMP)

activated CRP

attaches to promoter of lac operon and accelerates transcription

lactose

glucose alternative, must be broken down for energy, when glucose is absent → more lac operon must function

negative control in lac operon

the default mechanism that prevents transcription of the lac operon when lactose is absent and glucose present,

positive control in lac operon

enhances transcription when lactose is present, but only if glucose is scarce

differential gene expression

why the same dna in cells can express different genes

chromatin

dna wrapped around histones

histone acetylation

euchromatin, opens up chromatin and promotes transcription

dna methylation

heterochromatin, tightens chromatin, slows transcription or blocks it, can cause long term inactivated of genes in cellular differentiation

genomic imprinting

methylation regulates expression of either maternal or paternal alleles or certain genes at start

cellular differentiation

young, unspecialized cell takes on individual characteristics → reach mature form

epigenetic inheritance

ways to turn genes on or off without changing nucleotide sequence

control elements

segments of noncoding dna where transcription factors bind to regulate transcription

distal control elements

groups are called enhancers, far away from a gene, generally associated with only one gene

activator

protein that binds to an enhancer and stimulates transcription of a gene

protein mediated binding of dn

brings the bound activators into contact with mediator proteins

proximal control element

close to promoter

alternative rna splicing

same mrna can make different proteins by cutting out different exons

regulatory proteins

bind to mrna and block ribosomes from starting translation

mrna degration

getting eaten by enzymes

utr sequence

untranslated, influences life span of mrna

longer mrna lasts in cytoplasm

the more proteins made

ubiquitin

mark of degradation on proteins

proteasomes

break marked proteins into monomers

MicroRNA (miRNA)

non-coding mrna, degrades mrna or blocks translation

miRNA binds fully to target mRNA

degrades mrna

miRNA does not attach to all bases

blocks translation of the mrna

small interfering RNAs (siRNAs)

only in yeast, non-coding rna, turns chromosome centromere into heterochromatin

rna interference (RNAi)

process of siRNAs blocking gene expression by condensing the centromere

cell differentation

cells become specialized in structure and function

morphogenesis

physical processes that give organism its shape

stem cell

immature cell before determination

cytoplasmic determinants

maternal chemicals in the egg that determine the cell

induction

pathway that tells cells to tell each other what to become

determination

commits cell to become a particular cell type, precedes differentiation

differentiation

turns on genes for proteins to start the cell

myoblasts

cells determined to be muscle cells

master regulatory gene

sets up pathway of transcription facts by turning on the first factor in the chain

pattern formation

how we establish a front facing and back of an organism

positional information

tells cell its location relative to other cells and body axes

drosophilia

cytoplasmic determinants in unfertilized cell determine axes before fertilization

majority of bicoid gene

front/head

homeotic genes

edward b. lewis, hox gene, control pattern formation in late embryo, larva, and adult in drosphilia

embryonic lethals

mutations cause death

maternal effect/ egg polarity genes

bicoid gene, encode cytoplasmic determinants that make axes

no functional bicoid gene

lacks front half of its body

morphogens

establish embryos axes and other features

bicoid gene

affects front half of body, distributed front to back gradient

bicoid importance

identified specific protein required for some early steps, understanding mother’s rule in embryo development, gradient of moles can affect polarity and position

low concentration of bicoid gene

abdomen

virus

nucleic acid covered by protein

wendell stanley

discovered the existence of a virus

viral genomes can be

double or single stranded dna or rna, single linear or circular

capsid

protein coat around the viral genome

capsomeres

protein subunits that make a capsid

influenza viruses

have rna protein, rna production uses rna polymerse which doesnt have checking system so more mutations

viral envelope

protein shell of virus made from host’s membrane and viral genome, glycoprotein spike to infect hosts,

bacteriophage/phage

viruses that infect bacteria, tail attaches the virus to its host

host range

what type of cell a virus can infect, viruses can only replicate in a host cell

virus infection

replication: virus does dna replication with dna polymerase

transcription/translation: virus uses rna polymerase to make proteins

assembly: replicated viral dna and protein coat assemble and exit

lytic cycle

causes the cell to lyse (explode) open exit

virulent phage

phage (bacteria) that reproduces only by lytic cycle

lysogenic cycle

replicates phage genome by integrating into host cell’s genome, can switch to lytic cycle

temperate phage

uses lytic and lysogenic cycle

prophage

intergrated viral dna in lysogenic cycle, each time host divides it copies the phage dna and passes it down, only in bacteria

restriction enzyme

cellular enzymes identify foreign dna and cut it up

CRISPR-Cas system

CRISPR: holds dna from previous infections and transcribes it to rna that bonds with the Cas protein

Cas: protein that bonds with the RNA from CRISPR and cuts the phage dna degrading it

spacer in the CRISPR-Cas system

corresponds to dna from a phage that has infected the cell previously

membranous envelope

glycoproteins on the envelope bond to specific receptor molecules on host cell’s surface

retroviruses

infect animals, use reverse transcriptase to turn RNA genome into DNA

HIV

retrovirus that causes AIDS, the illness,

provirus

dna made by reverse transcriptase that integrated into host genome, stays permanently in the host cell, only in eukaryotic cells

vaccine for viral diseases

harmless versions of the virus which makes immune system have a defense against the actual virus

allows users to search for specific dna sequence, predicted protein sequence, common stretches of amino acids

ncbi blast

gene annotation

protein coding genes within dna sequences

transposable elements

dna that dna move from one location to another, makes repetitive dna

transposons

dna is copied and moves with a transposase enzyme

retrotransposons

copied into single stranded rna then reverse transcribed back into dna and integrated into the genome

alu elements

transcribed into rna molecules, can help regulate gene expressed

simple sequence dna

many copies of short sequences, not related to transposons, common in centromeres and telomeres

short tandem repeat

series of repeating units of 2-5 nucleotides, varies from person to person,

multigene families

two or more identical or very similar genes

alpha and beta globin

polypeptides of hemoglobin on different human chromosomes, expressed at different times in development, likely transposed from common ancestor then had mutations

psuedogenes

versions of the function genes that no longer make functional proteins

mutation

underlies much of genome evolution, earliest life forms likely only had genes necessary for survival and reproduction

rate of duplications and inversions

accelerated 100 million years ago when large dinosaurs went extinct and mammals diversified