big questions… chapter 16 biology/ap lecture notes pdf...cchs ap biology goldberg chapter 16...

CCHS AP Biology Goldberg

Chapter 16

Regulation of Gene

Expression

Some of the BIG Questions…

How are genes turned on & off?

How do cells in a multicellular organism,

all with the same genes, differentiate to

perform completely different, specialized

functions in eukaryotes?

But first…

Bacterial Metabolism

Bacteria need to respond quickly to

changes in their environment

ex. if have enough of a product,

need to stop production

why? waste of energy to produce more

how? stop production of anabolic enzymes

ex. if find new food/energy source,

need to utilize it quickly

why? metabolism, growth, reproduction

how? start production of catabolic enzymes

Reminder: Regulation of Metabolism

One way: Feedback inhibition

product acts

as an allosteric

inhibitor of

1st enzyme in

synthesis

pathway

= inhibition-

Another Way to Regulate Metabolism

Another way: Gene regulation

block transcription of genes for all enzymes in synthesis pathway saves energy by

not wasting it on unnecessary protein synthesis

= inhibition-

Gene Regulation in Bacteria

Control of gene expression enables

individual bacteria to adjust their

metabolism to environmental change

Cells vary amount of specific enzymes

by regulating gene transcription

turn genes on or turn genes off

ex. if you have enough of something in your

cell then you don’t need to make enzymes

used to build more of that thing

it’s a waste of energy!

turn off genes which codes for enzymes


Genes Grouped Together

Operon genes grouped together with related functions

ex. enzymes in a certain metabolic pathway

promoter = RNA polymerase binding site single promoter controls transcription of all

genes in operon

transcribed as 1 unit & a single mRNA is made

operator = DNA binding site of regulator protein

So how can genes be turned off?

First step in protein production?

transcription

stop RNA polymerase!

Repressor protein

binds to DNA near promoter region

blocking RNA polymerase

binds to operator site on DNA

blocks transcription

operatorpromoter

Repressor Protein Model

DNATATA

RNApolymerase

repressor

repressor repressor protein

Operon: The operator, promoter & genes they control

serve as a model for gene regulation

gene1 gene2 gene3 gene4RNA

polymerase

Repressor protein turns off gene by

blocking RNA polymerase binding site.operatorpromoter

Repressible Operon: Tryptophan

DNATATA

RNApolymerase

repressor

tryptophan (a corepressor)


repressortryptophan – repressor protein

complex

Synthesis Pathway Model

When excess tryptophan is present,

binds to tryp repressor protein &

triggers repressor to bind to DNA.

(blocks [represses] transcription)

gene1 gene2 gene3 gene4RNA

polymerase

conformational change in

repressor protein!

Tryptophan Operon

What happens when tryptophan is present?

Don’t need to make tryptophan-building enzymes!

Tryptophan binds allosterically to regulatory protein.

operatorpromoter

Inducible Operon: Lactose

DNATATA


repressorlactose – repressor protein

complex

lactose

repressor gene1 gene2 gene3 gene4

Digestive pathway model

When lactose is present, binds to

lac repressor protein & triggers

repressor to release DNA

(induces transcription)

RNApolymerase

conformational change in

repressor protein!

repressorRNA

polymerase


Lactose Operon

What happens when glucose is not available

and lactose is present?

Need to make lactose-digesting enzymes!

Lactose binds allosterically to regulatory protein.

Operon Summary

Repressible operon

usually functions in anabolic pathways

synthesizing end products

when end product is present in excess,

cell allocates resources to other uses

Inducible operon

usually functions in catabolic pathways

digesting nutrients to simpler molecules

produce enzymes only when nutrient is

available

cell avoids making proteins that have nothing

to do, cell allocates resources to other uses

Jacob & Monod: lac Operon

Francois Jacob & Jacques Monod

first to describe operon system

coined the phrase “operon”

1961 | 1965

Francois JacobJacques Monod

Viral Gene Expressionbacteriophageinfluenza

A package of

genes in transit

from one host

cell to another

“A piece of bad news

wrapped in protein”

– Peter Medawar

Viral Diseases

Measles

Polio

Hepatitis

Chicken

pox


Smallpox

Eradicated in late 1970’s

vaccinations ceased in 1980

at risk population?

Influenza: 1918 Epidemic 30-40 million deaths world-wide

Influenza A H1N1

H – hemagglutinin

N – neuraminidase

Emerging Viruses Viruses that “jump” host

switch species

Ebola, SARS, bird flu, hantavirus

The Coming Plague by Laurie Garrett SARS

Ebola hantavirus

A Sense of Size

Comparing size

eukaryotic cell

bacterium

virus

What is a virus? Is it alive?

DNA or RNA enclosed in a protein coat

Viruses are not cells

Extremely tiny

need an electron microscope to see

smaller than ribosomes

~20–50 nm

1st discovered in plants (1800s)

tobacco mosaic virus

couldn’t filter out

couldn’t reproduce on media

like bacteria

Variation in Virusesplant virus pink eye

Parasites? NO!

lack enzymes for metabolism

lack ribosomes for protein synthesis

need host “machinery”


Viral Genomes

Viral nucleic acids

DNA double-stranded

single-stranded

RNA double-stranded

single-stranded

Linear or circular smallest viruses

have only 4 genes, while largest have several hundred

Viral Protein Coat

Capsid

crystal-like

protein shell

1-2 types of

proteins

many copies of

same protein

Viral Envelope

Lipid bilayer membranes

cloaking viral capsid

envelopes are derived from

host cell membrane

glycoproteins on surface

HIV

Entry

virus DNA/RNA enters host cell

Assimilation

viral DNA/RNA takes over host

reprograms host cell to copy viral nucleic acid & build viral proteins

Self assembly

nucleic acid molecules & capsomeres then self-assemble into viral particles

exit cell

“Generalized” Viral Lifecycle

Symptoms of Viral Infection

Link between infection & symptoms varies

can kill cells by lysis

can cause infected cell to produce toxins

fever, aches, bleeding…

viral components themselves may be toxic

envelope proteins

Damage?

depends…

lung epithelium after the flu is repaired

nerve cell damage from polio is permanent

Viral Hosts

Host range

most types of virus can infect & parasitize

only a limited range of host cells

identify host cells via “lock & key” fit

between proteins on viral coat &

receptors on host cell surface

broad host range

rabies = can infect all mammals

narrow host range

human cold virus = only cells lining upper

respiratory tract of humans

HIV = binds only to specific protein

(CD4 receptor) on human white blood cells


Defense Against Viruses

Bacteria have defenses against phages

bacterial mutants with receptors that

are no longer recognized by a phage

natural selection favors these mutants

bacteria produce restriction enzymes

recognize & cut up foreign DNA

bacteria used CRISPR!

sort of an immune system… (more later)

It’s an escalating war!

natural selection favors phage mutants

resistant to bacterial defenses

RNA Viruses

Retroviruses

have to copy viral RNA into host DNA enzyme = reverse transcriptase

RNA DNA mRNA

host’s RNA polymerase now transcribes viral DNA into viral mRNA mRNA codes for viral components

host’s ribosomes produce new viral proteins

proteinRNADNA

transcription translation

replication

Vaccinations

Immune system exposed

to harmless version of pathogen

triggers active immunity

stimulates immune system to produce

antibodies to invader

rapid response if

future exposure

Most successful

against viral diseases

Transcription – Another Look…

The process of transcription includes

many points of control

when to start reading DNA

where to start reading DNA

where to stop reading DNA

editing the mRNA

protecting mRNA as it travels through

cell

Eukaryotic Transcription

Roger Kornberg

for his studies of the molecular basis of

eukaryotic RNA transcription

1990s | 2006

Roger KornbergRNA polymerase

molecules bound to

bacterial DNA

Transcription

Promoter sequences upstream of gene


Transcription

Initiation complex

transcription factors

bind to promoter

region upstream of

gene

proteins which bind to

DNA & turn on or off

transcription

TATA box binding site

only then does RNA

polymerase bind to

DNA

Transcription Initiation

Control regions on DNA

promoter nearby control sequence on DNA

binding of RNA polymerase & transcription factors

“base” rate of transcription

enhancers/activators distant control

sequences on DNA

binding of activator proteins

“enhanced” rate (higher level) of transcription

Model for Enhancer Action

Enhancer DNA sequences

distant control sequences

Activator proteins

bind to enhancer sequence & stimulates transcription

Silencer proteins

bind to enhancer sequence & block gene transcription

Transcription in Eukaryotes

Prokaryote vs. Eukaryote Genome Prokaryotes

small size of genome

circular molecule of naked DNA DNA is readily available to RNA polymerase

control of transcription by regulatory proteins

operon system

most of DNA codes for protein or RNA no introns, small amount of non-coding DNA

regulatory sequences: promoters, operators

Prokaryote vs. Eukaryote Genome Eukaryotes

much greater size of genome how does all that DNA fit into nucleus?

DNA packaged in chromatin fibers how to regulate access to DNA by RNA polymerase?

most of DNA does not code for protein 97% “junk DNA” in humans; purpose?

cell specialization need to turn on & off large numbers of genes


Why turn genes on & off?

Specialization each cell of a multicellular eukaryote

expresses only a small fraction of its genes

Development different genes needed at different points

in life cycle of an organism afterwards need to be turned off permanently

Responding to organism’s needs homeostasis

cells of multicellular organisms must continually turn certain genes on & off in response to signals from their external & internal environment

ex: Fertilization causes changes…

yolk found at vegetal hemisphere

embryo at animal hemisphere (pigmented)

post fertilization, animal pole rotates to where

sperm penetrates the egg—forming the gray

cresent

…which sets up signal cascades

to help set up the body plan.Hox Genes

found in animals to determine body plan!

Chapter 19!

Hox Genes Hox Genes

genes that control

differentiation on

anterior-posterior

axis

hedgehog v. sonic

hedgehog


Hox Genes

Eric Wieschaus

for his discoveries concerning the genetic

control of early embryonic development

1980s | 1995

Eric Wieschaus

Why turn genes on & off?

Specialization each cell of a multicellular eukaryote

expresses only a small fraction of its genes

Development different genes needed at different points

in life cycle of an organism afterwards need to be turned off permanently

Responding to organism’s needs homeostasis

cells of multicellular organisms must continually turn certain genes on & off in response to signals from their external & internal environment

Points of Control The control of gene expression

can occur at any step in the pathway from gene to functional protein

unpacking DNA

transcription

mRNA processing

mRNA transport out of nucleus

through cytoplasm

protection from degradation

translation

protein processing

protein degradation

DNA PackingHow do you fit all that DNA into the nucleus?

DNA coiling & folding double helix

nucleosomes

chromatin fiber

looped domains

chromosome

from DNA double

helix to condensed

chromosome

Nucleosomes

“Beads on a string”

1st level of DNA packing

histone proteins 8 protein molecules

many positively charged amino acids arginine & lysine

bind tightly to negatively charged DNA

8 histone

molecules DNA Packing

Degree of packing of DNA regulates transcription

tightly packed = no transcription

= genes turned off

darker DNA (H) = tightly packed

lighter DNA (E) = loosely packed


Histone Acetylation

Acetylation of histones unwinds DNA

loosely packed = transcription

= genes turned on

attachment of acetyl groups (–COCH3) to histones

conformational change in histone proteins

transcription factors have easier access to genes

DNA Methylation

Methylation of DNA blocks transcription factors

no transcription = genes turned off

attachment of methyl groups (–CH3) to cytosine

C = cytosine

can be a permanent inactivation of genes

ex. inactivated mammalian X chromosome

X Chromosome Inactivation

Female mammals inherit two X

chromosomes

one X becomes highly methylated

(INACTIVATED!) during embryonic

development – EPIGENETICS!

condenses into compact object = Barr body

X-Inactivation & Tortoise Shell Cat

2 different cell lines in cat

Regulation of mRNA Degradation

“Life” span of mRNA determines

pattern of protein synthesis

mRNA can last from hours to weeks

RNA Interference

Small RNAs (miRNA, siRNA, RNAi)

short segments of RNA (21-28 bases) bind to mRNA

create sections of double-stranded mRNA

“death” tag for mRNA triggers degradation of mRNA

cause gene “silencing” even though post-transcriptional control,

still turns off a gene


RNA Interference

Small RNAs

double-stranded RNA

sRNA + mRNA

mRNA

mRNA degraded

functionally turns

gene off!

1990s | 2006

Andrew Fire Craig Mello

Points of Control The control of gene expression

can occur at any step in the pathway from gene to functional protein

unpacking DNA

transcription

mRNA processing

mRNA transport out of nucleus

through cytoplasm

protection from degradation

translation

protein processing

protein degradation

Control of Translation

Block initiation stage

regulatory proteins attach to

5’ end of mRNA

prevent attachment of ribosomal subunits &

initiator tRNA

block translation of mRNA to protein

Protein Processing & Degradation

Protein processing

folding, cleaving, adding sugar groups, targeting for transport

Protein degradation

ubiquitin tagging

proteosome degradation

transcription

1

mRNA

processing2mRNA transport

out of nucleus

3

translationmRNA

transport

in

cytoplasm

4

1. transcription

-DNA packing

-transcription factors

2. mRNA processing

-splicing

3. mRNA transport

out of nucleus

-breakdown by sRNA

4. mRNA transport

in cytoplasm

-protection by 3’ cap &

poly-A tail

5. translation

-factors which block

start of translation

6. post-translation

-protein processing

-protein degradation

-ubiquitin, proteasome

post-

translation

5

6

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