Genetics Exam 3-Gene Control

Structural Genes

encoding proteins

Regulatory Genes

encoding products that interact with other sequences and affect the transcription and translation of these sequences

Regulatory elements

DNA sequences that are not transcribed but play a role in regulating other nucleotide sequences

How do bacteria respond to environmental changes in regards to genes

turn them on and off

In eukaryotic cells, gene regulation brings about

cell differentiation

Constitutive expression

continuously expressed under normal cellular conditions

Positive control

stimulate gene expression

Negative control

inhibit gene expression

Domains

~60–90 amino acids, responsible for binding to DNA, forming hydrogen bonds with DNA

Motif

within the binding domain, a simple structure that fits into the major groove of the DNA

Distinctive types of DNA-binding proteins based on the

motif

Major types of motifs

• Helix-turn-helix

• Zinc finger

• Steroid receptor

• Leucine zipper

• Helix-loop-helix

• Homeodomain

Helix-turn-helix Location

Bacterial regulatory proteins; related motifs in eukaryotic proteins

Helix-turn-helix Characteristic

Two alpha helices

Helix-turn-helix Binding Site in DNA

Major groove

Zinc finger Location

Eukaryotic regulatory and other proteins

Zinc finger Characteristics

Loop of amino acids with zinc at base

Zinc Finger Binding Site in DNA

Major groove

Leucine zipper location

Eukaryotic transcription factors

Leucine zipper Characteristics

Helix of leucine and a basic arm; two leucines interdigitate

Leucine zipper Binding Site in DNA

Two adjacent major grooves

Operon

promoter + operator + structural genes

Regulatory gene

DNA sequence–encoding products that affect the operon function but are not part of the operon

Inducible Operons

Transcription is usually off and needs to be turned on

Repressible operons

Transcription is normally on and needs to be turned off

Negative inducible operons

The control at the operator site is negative. Molecule binding is to the operator, inhibiting transcription. Such operons are usually off and need to be turned on

Inducer

small molecule that turns on the transcription

Negative repressible operons

The control at the operator site is negative. But such transcription is usually on and needs to be turned off

Corepressor

small molecule that binds to the repressor and makes it capable of binding to the operator to turn off transcription

In positive transcriptional control, the regulatory protein involved is an

activator

How does positive control work

binds to DNA and stimulates transcription

The lac operon is a ___ operon

negative inducible

What is the inducer of the lac operon

allolactose

lacl

repressor encoding gene

lacP

operon promoter

lacO

operon operator

Structural genes lac operon

• lacZ

• LacY

• lacA

LacZ

encoding ß-galactosidases

LacY

encoding permease

LacA

encoding transacetylase

Does repression of the lac operon completely stop transcription?

no

Catabolite Repression

using glucose when available and repressing the metabolite of other sugars

Is catabolite repression a positive or negative control

positive

cAMP

adenosine-3′, 5′-cyclic monophosphate

The concentration of cAMP is inversely proportional to

the level of available glucose

Low glucose means cAMP levels are high, cAMP binds to CAP, the CAP-cAMP complex binds to DNA, increasing the efficiency of polymerase binding, and results are

high rates of transcription and translation of the structural genes

High glucose means low levels of cAMP, cAMP is less likely to bind to CAP, RNA polymerase cannot bind to DNA as efficiently so

transcription rate is low

The trp operon is a ____ operon

negative repressible operon

What are the five structural genes of the trp operon

• trpE

• trpD

• trpC

• trpB

• trpA

What do the structural genes function to do

these five enzymes convert chorismate to tryptophan

When tryptophan is low: the trp repressor is normally inactive, so it does not bind to the operator so

transcription does not take place

When tryptophan is high: tryptophan binds to the repressor, making it active

the trp repressor binds to the operator and shuts transcription off

Attenuation

• affects the continuation of transcription, not its initiation

• This action terminates the transcription before it reaches the structural genes

Attenuator

a specific DNA sequence within a bacterial operon that causes premature termination of transcription

Antiterminator

genetic process that allows RNA polymerase to bypass termination signals and continue transcribing RNA

What causes the change between humans and apes despite our very similar genomes

a small number of regulatory sequences

For eukaryotic cells, each gene has its own ___ and must be transcribed separately

promoter

For eu, DNA must unwind from the histone before

transcription

How are transcription and translation separated in eukaryotes

through time and space

Changes in chromatin structure affect the

expression of genes

DNase I hypersensitive sites

more open chromatin configuration site, upstream of the transcription start site

Histone modification

• Addition of methyl groups to the histone protein tails

• Addition of acetyl groups to histone proteins

Chromatin remodeling complexes reposition the ___ allowing transcription factors and RNA polymerase to bind to promoters and initiate transcription

nucleosomes

The ___ of histone proteins alters ____
and permits some transcription factors to bind to DNA

acetylation; chromatin structure

Flowering locus C (FLC) gene

encodes a regulatory protein that represses the activity of other genes that affect flowering

Flowering locus D (FLD) gene

encodes a deacetylase enzyme, which removes acetyl groups from histone proteins in the chromatin surrounding FLC

Which species if the FLD and FLC gene found in

Arabidopsis

Chromatin remodeling complexes

bind directly to DNA sites and reposition nucleosomes

Chromatin immunoprecipitat ion (ChIP) can be used to identify

DNA-binding sites of a specific protein and locations of modified histone protein

Transcription in eukaryotes is regulated by

transcription factors

Transcription factors can stimulate and stabilize

basal transcription apparatus at core promoter

Mediator

interact with transcription factors and RNA Polymerase

Transcription factors allow for the regulation of galactose metabolism through

GAL4

Where does the GAL4 bind to

UAS_G site

What does the GAL4 do

controls transcription of genes in galactose metabolism

Enhancer

DNA sequence stimulating transcription a distance away from promoter

Silencer

DNA sequence with an inhibitory effect on the transcription of distant genes

silencers are position and orientation independent, and they contain binding sites for transcription factors that decrease transcription.

true

Insulator

DNA sequence that blocks or insulates the effect of enhancers

Insulator function

cause loops of chromatin that form interacting regions of genes and regulatory elements

Insulators and their binding proteins

may help create “neighborhoods” of regulatory elements and genes that physically interact but insulated from regulatory elements in other neighborhoods

An insulator blocks the action of an ____ on a promoter when the insulator lies between the enhancer and the promoter

enhancer

Alternative splicing in drosophila XX genotype

1. XX embryos and active Sxl gene produce a protein that causes pre-mRNA to be spliced at the downstream 3’ site

2. This produces tra protein

3. Tra and Tra-2 proteins direct female specific splicing of dsx pre-mRNA, producing a protein that makes a female

Alternative splicing in drosophila XY genotype

1. Sxl gene is not activated

2. tra pre-mRNA is spliced at upstream site, producing a nonfunctional protein

3. without tra, male specific splicing of dsx protein produces a male phenotype

Degradation of RNA

• 5’ cap removal

• shortening of Poly-A tail

• degradation of 5’ UTR, coding sequence, and 3’ UTR

Dicer and RISC

RNA-induced silencing complex

Dicer function

• cleaves and processes double-stranded RNA

• produce single-stranded siRNAs or miRNAs 21 to 25 nucleotides long

• combine with proteins to form a RISC

The RNA component of RISC pairs with

complementary base sequences in specific mRNA molecules (often sequences in the 3’ UTR of the mRNA)

Small interfering RNAs base-pair perfectly with

mRNAs

microRNAs often form

less-than-perfect pairings

Mechanisms of gene regulation by RNA interference

• RNA cleavage

• Inhibition of translation

• Transcriptional silencing

• Silencer-independent degradation of mRNA

RNA cleavage

RISC containing an siRNA, pair with mRNA molecules and cleavage to the mRNA

Transcriptional silencing

altering chromatin structure

RNA silencing leads to the degradation of ___ or to the ___ of translation and transcription

mRNA; inhibition

The control of development by RNA interference

miRNA molecules are key factors in controlling development in animals, including humans and
plants

RNA crosstalk

Different RNA molecules that share binding sites for miRNAs may compete among themselves for
available miRNAs

The availability of ribosomes, charged tRNAs, and initiation and elongation factors may affect the rate of translation

true

Translation of some mRNAs is regulated by proteins that bind to the 5’ and 3’ untranslated regions of the mRNA

true

Bacterial and Eukaryotic gene control comparison

see chart