Bio Midterm 3 (gene regulation + virus)

operon

a cluster of genes organized into a single transcription unit and its associated regulatory sequences

Regulatory sequences

DNA sequences to which specific proteins bind to control the transcription of the gene or genes.

regulatory protein

a DNA-binding protein that binds to a regulatory sequence and affects the expression of an associated gene or genes

Allosteric inhibitors

• Molecules that bind to a protein at a site other than the active site (allosteric site)

• Cause a shape change that reduces or shuts down activity

Allosteric activators

• Bind at an allosteric site

• Cause a shape change that increases activity

Polyribosomes

• Multiple ribosomes translating a single mRNA at the same time

• Allows bacteria to make proteins very quickly

• transcription and translation can occur basically simultaneously

what makes the nucleosomes bind DNA less tightly

Acetylation

Epigenetics

the study of how gene expression is changed by chemical modifications to chromatin that DO NOT IMPACT gene sequence

DNA methylation

Methyl groups can be reversibly added to cytosine bases. These turn gene expression off They can be removed to turn expression back on

Genomic imprinting

an epigenetic phenomenon is which the expression of a particular allele for a gene depends on the parent its inherited from. if an allele you got from mom was methylated and thus silenced in mom, that same allele is likely methylated and still silenced in you to this day.

for Tryptophan (trp) operon, Each segment (gene) of mRNA encodes for

an enzyme that catalyzes the reaction to make Tryptophan

Repressible operon

something that is usually ‘on’ and can get turned ‘off’ (aka trp operon)

Inducible operon

something that is usually ‘off’ and get activated ‘on’ (aka lac operon)

Negative regulation

keeping or turning a gene “off”

Positive regulation

turning a gene “on”

repressor

turns off operons, to stop enzyme production

inducer

turns "on" specific operons, allowing cells to produce enzymes needed for metabolic pathway

Regulation at the DNA structural level

1. How tightly bound DNA is around nucleosomes

2. DNA methylation (in promoter area)

Transcription factors (specifically its role in gene regulation)

These proteins participate in weak interactions (non-covalent interactions) with DNA; This is what “tells” a transcription factor what DNA sequence to bind to; some activate (meaning tells RNA poly to come) while some silence gene expressionn (blocks RNA poly)

combinatorial TF-based regulation

different combinations of TFs bind to and regulate the promoters of different genes

Hormone cascades

The idea is that one hormone signal can coordinate many genes at once by activating shared TFs;

A single hormone signal can activate one or more transcription factors, and those TFs can simultaneously switch on a whole set of related genes—thanks to shared DNA binding sites and combinatorial control.

Long noncoding RNA (lncRNA)

RNA greater than 200 bases in length, They can act like transcription factors They can bind to mRNA’s themselves and prevent or promote translation; does X chromosome inactivation (Barr bodies)

Xist

the name of the lncRNA that silences an X chromosome in female placental mammals. It functions by completely coating the chromosome and epigenetically silencing them

UTR

untranslated region This sequence does not get translated by the ribosome

Regulation at the translation level

1. 3’ UTR and polyA tail largely influence mRNA half-life

2. Sequences in the 5’ UTR and 3’ UTR, and length of polyA tail influence how well the small ribosomal subunit, and therefore how quickly translation initiates

3. RNA interference (RNAi)

4. Rate of protein degradation

RNA interference (RNAi)

ncRNAs called miRNA or siRNA. (These are shorter than lncRNA)

miRNA

molecules are transcribed from an organism’s genome; usually does not perfectly base pair with target mRNA transcripts —> represses translation

blocks translation

siRNA

molecules are made in a lab or came from viruses; usually perfectly base pairs with target mRNA transcripts• Generally this results in them being cleaved then degraded

it destroys the mrna message completely.

Rate of protein degradation

When a cell wants to get rid of a protein, it covalently attaches a ubiquitin tag. Ubiquitin Ubiquitin tags recruit proteasomes, which break down the tagged protein

Regulation at the transcription level

1. transcription factors on promoter activate/silence gene expression

2. combinations of general transcription factor (TF)

3. Hormone cascades

4. Long noncoding RNA

Rhinovirus

Cold

Influenza

flu

Herpes

mono

virus

a small biological particle that can infect the cells of a living organism; NOT alive at the cellular level, but they share certain characteristics with living organisms.

virion

viral particle

Capsid

The protective layer of protein that surrounds the nucleic acid core of a virus in free form; also known as a coat.

Polyhedron

Coat proteins that form triangular units that fit together like the parts of a geodesic sphere.

Helix

Protein subunits of the coat that assemble in a rodlike spiral around the genome

Envelopes

A surface membrane derived from its host cell

Tail

The structure attached to one side of the polyhedral head

Virulent bacteriophages

kill their host cells during each cycle of infection (lytic cycle)

T-even bacteriophages T2, T4, and T6

virulent, complex viruses that infect E. coli

retrovirus

an enveloped virus with an RNA genome that replicates via a DNA intermediate

latent phase

he virus remains in the cell in an inactive form – the viral nucleic acid is present in the cytoplasm or nuclear DNA, but no complete viral particles or viral release can be detected.

At times, particularly during periods of metabolic stress, the virus may become active – viral DNA is replicated in quantity, capsid proteins are made, and completed viral particles are released from the cell.

Properties of HIV

HIV infects particular cells of the immune system.

Mild initial symptoms disappear as antibodies appear in the body and the number of viral particles drops.

Although an infected person may appear healthy for years, HIV spreads steadily to other immune system cells.

Ultimately, the body’s immune response is destroyed, making the HIV-infected person susceptible to other infections.