AP Biology1. We’ll go over tests from before break2. Go through study guide (get some hints)3. Begin chapter 18

Cells are efficient because they conserve energy for processes that MUST be done.

Cells have the ability to turn on or off genes depending on the proteins that are present or absent within the cell.

We will learn how cells turn on or off genes to maintain cellular efficiency.

Purpose of this chapter…

Bacteria respond to environmental change by regulating transcription.

Most of what we know about gene regulation is from bacteria. We will be looking at E. coli bacteria E. coli lives in the human intestinal

tract

Chapter 18- Gene Regulation

Vocabulary1. Tryptophan- amino acid needed for

survival (bacteria)2. Feedback- allows cell to adjust the

amount of tryptophan made based on availability of the amino acid

3. Operon- the mechanism that controls gene expression

Regulation of gene expression

Vocabulary Continued:4. Regulatory Gene- on DNA that regulates a gene further away5. Promoter- A specific nucleotide sequence in DNA that binds to RNA polymerase- positioning it so it may begin transcribing mRNA6. Operator- the on and off switch of DNA 7. Repressor- the mechanics of how the operon may be turned off (blocks attachment of RNA polymerase to promoter)

Regulation of Gene Expression

1.Negative Gene Regulation (shut off by an active repressor)

A.Repressible OperonB.Inducible Operon

2.Positive Gene Regulation (turned on by an active repressor)

Types of Gene Regulation

Trp Operon

Trp Operon

Trp Operon

Trp operon is a repressible operon Its transcription can be inhibited (repressed)

when tryptophan is available Trp binds allosterically to a regulatory protein

Trp Operon

Lac operon is an inducible operon It is usually shut offBut it can be stimulated

(induced) when lactose (lac) is present

Lac Operon

Lac Operon

Lac Operon

Example is the lac operon (lac operon can be both positive and negative) Here’s why…

E. coli prefers glucose to lactose so it will preferentially breakdown glucose rather than lactose (turning lac off) inducible

However if glucose is NOT available there must be a gene that transcribes lac enzymes

The absence of glucose increases the amount of cAMP in the cell (positive)

Positive Gene Control

Positive- Lac operon

Positive- Lac operon

Review try and lac operons Finish chapter 18, begin chapter 19 today Test is February 1st

AP Biology

All organisms must regulate genes. Unicellular and multicellular organisms must

continually turn genes on and off in response to external and internal cues.

Human cells generally express 20% of its genes at a time

Different cell types are different not in DNA but because of differential gene expression

Eukaryotic Regulation

Figure 18.6 Signal

NUCLEUSChromatin

Chromatin modification:DNA unpacking involvinghistone acetylation and

DNA demethylationDNA

Gene

Gene availablefor transcription

RNA ExonPrimary transcript

Transcription

IntronRNA processing

CapTail

mRNA in nucleus

Transport to cytoplasm

CYTOPLASMmRNA in cytoplasm

TranslationDegradationof mRNA

PolypeptideProtein processing, such

as cleavage and chemical modification

Active proteinDegradation

of proteinTransport to cellular

destination

Cellular function (suchas enzymatic activity,structural support)

Stages in gene expression that can be regulated in eukaryotic cells

Regulation of Eukaryotic cells

1. Regulation of chromatin structure2. Regulation of transcription initiation 3. Mechanisms of post-transcriptional

regulation

A. Histone Modifications- when structures around chromatin are changed a decrease in Transcription of gene occurs

B. DNA methylation- long stretches of inactivated DNA

Chromatin structure

1. Enhancers- Segment of DNA containing multiple control elements, located far from where the promoter is

These allow DNA to bend which brings the enhancers closer to transcription factors

DNA folds over top of itself

Transcription Factors

Figure 18.10-1

ActivatorsDNA

Enhancer Distal controlelement

PromoterGene

TATA box

Figure 18.10-2

ActivatorsDNA

Enhancer Distal controlelement

PromoterGene

TATA boxGeneraltranscriptionfactors

DNA-bendingprotein

Group of mediator proteins

Figure 18.10-3

ActivatorsDNA

Enhancer Distal controlelement

PromoterGene

TATA boxGeneraltranscriptionfactors

DNA-bendingprotein

Group of mediator proteins

RNApolymerase II

RNApolymerase II

RNA synthesisTranscriptioninitiation complex

1. Alternative RNA splicing- some segments of the mRNA strand are treated as introns . (Regulatory strands control which genes are read as introns or exons) As a result alternative mRNA is actually synthesized.

2. mRNA degradation- doesn’t last long weeks at most

3. Initiation of translation- Some are prevented from attaching to a ribosome for translation

Post Transcriptional Regulation

Figure 18.6 Signal

NUCLEUSChromatin

Chromatin modification:DNA unpacking involvinghistone acetylation and

DNA demethylationDNA

Gene

Gene availablefor transcription

RNA ExonPrimary transcript

Transcription

IntronRNA processing

CapTail

mRNA in nucleus

Transport to cytoplasm

CYTOPLASMmRNA in cytoplasm

TranslationDegradationof mRNA

PolypeptideProtein processing, such

as cleavage and chemical modification

Active proteinDegradation

of proteinTransport to cellular

destination

Cellular function (suchas enzymatic activity,structural support)

Stages in gene expression that can be regulated in eukaryotic cells

YAY the projector is working!

Finish chapter 19 today

AP Biology

Virus- very simple, very small. Lack metabolic machinery An infectious particle consisting of a few genes

packaged in a protein coat

Are viruses living or non-living? Discussion-

Chapter 19- Viruses

Tobacco disease stunts growth of tobacco plants and gives leaves a mosaic coloration

Discovery of Viruses

Viral Structure

Rod shaped

Infect respiratory tract

Membrane envelope

Many viruses differ in the type of genetic material they carry Double-stranded DNA Single-stranded DNA Double-stranded RNA Single-stranded RNA

Viral Genomes

Capsid- protein shell enclosing the viral genome Depending on virus can be rod, polyhedral, or

more complex Viral envelope- membranes of host cell

studded with glycoprotein spikes Influenza have this membrane envelope which

encloses the capsid

Capsids and Envelopes

Lytic cycle- 1. Attachment of virus to host cell2. Virus drops off genetic material3. Genetic material goes into nucleus4. Genetic material is replicated5. Transcription occurs6. Translation makes proteins7. Lyse= break= as protein leave it lyses the cell

(programmed cell death)

Viral Replication

Virulent phage- a virus that only replicates by a lytic cycle

Why is there still bacteria? Natural selection favors bacterial mutants with

receptor sites that are no longer recognized by the phage type

Bacteria produce restriction enzymes that recognize and cut up foreign DNA including phage DNA. This prevents phage to infect the cell

Lysogenic cycle- allows replication of the phage genome without destroying the host

Temperate phage- use both lytic and lysogenic cycles

Prophage- when DNA from phage is integrated into the host. Host lives silently within the bacterium

Lysogenic cycle

Lysogenic cycle- the phage replicates without destroying the host cell

Temperate phage- use both lytic and lysogenic cycles

Lysogenic Cycle

The λ phage is temperate

1. λ binds to the surface of the cell and injects it with DNA

2. Next step depends on lytic or lysogenic cycle3. Lysogenic= the λ DNA is incorporated into a specific

site on the bacteria (E. coli) virus replicates without killing the host

4. Lytic = viral genes turn the host cell into a λ producing factory lysing the host cell and infecting more cells.

Lysogenic Cycle

Important variations - The type of nucleic acid that serves as virus’

genetic material Viruses equipped with an outer envelope use it

to enter host cell Viral envelope is derived from the host’s

plasma membrane, although viral genes specify some of the molecules in the membrane

Animal virus diversity

Retrovirus- have the most complicated cycles Reverse transcriptase – enzyme that transcribes DNA

from an RNA template provides RNA---- DNA flow Human immunodeficiency virus- HIV – the virus that

causes AIDS (acquired immunodeficiency syndrome) Contain 2 single RNA strands, 2 reverse transcriptase After HIV enters the host cell transcriptase is released

in cytoplasm and it catalyzes the synthesis of DNA The new DNA inserts itself into the DNA as a provirus

(permanent)

Retroviruses

Evolution of Virus

Viruses have been found to infect every life form (bacteria, animals, plants, fungi, algae and protists)

Because virus depends on cells for their own propagation it is likely that they evolved after the first cell appeared.

Candidates- Plasmids – circular DNA that are separate from

chromosomes, independent from rest of the cell (can be transferred from 1 cell to another)

Transposons- DNA segments that can move from 1 location to another in a cells genome

Vaccine- harmless variants or derivatives of pathogenic microbes, that stimulate the immune system to mount defenses against the actual pathogen.

REVIEW of chapter 18, 19 today- group work.

Begin chapter 20

Monday we’ll review essay writing a bit, look at great essays vs not great essays.

Essay next Wednesday

AP Biology

New seats???

Change to schedule!!!

Chapter 18-20 test January 24!!! This Thursday!!!

All labs will take place Jan 28-Feb 1

AP Biology

Recombinant DNA- DNA segments from 2 different sources

Biotechnology- the direct manipulation of organisms and their components to make useful products

Genetic engineering- the direct manipulation of organisms and their genes for practical purposes

Biotechnology

Plasmid- small circular DNA molecules with a small number of genes that replicated independently of a chromosome

Basic cloning technique begins with insertion of a foreign gene into a bacterial plasmid to produce a recombinant DNA molecule

Resulting cell is a recombinant bacterium Gene cloning- the production of multiple

copies of a single gene

Plasmids

Restriction enzymes- enzymes that cut DNA molecules at specific locations In nature bacteria use restriction enzymes to cut

DNA molecules for protection Restriction site- a specific site where DNA will be cut Restriction fragments- small cuts of DNA Sticky ends- the end of the cut plasmid DNA ligase- glues and fuses DNA back together

Restriction enzymes

Cloning vector – DNA molecule that can carry foreign DNA into a cell to replicate there.

1. Clone all hummingbird genes2. Get the plasmid DNA ready

• Carries ampR resistance to antibiotic ampicillin• lacZ as well

3. Plasmid has a recognition sequence4. Both plasmid and hummingbird DNA are

digested with the same restriction enzyme5. Fragments are mixed together (pair with

sticky ends)6. DNA ligase added to glue fragments together

Technique

NOTE: Some cells acquire recombinant plasmid Some take up a nonrecombinant plasmid Some don’t take up anything

Cells placed on agar containing ampicillin and X-gal*Only bacteria that have ampR will grow*stains will be different if lacZ was present or not lacZ presence will be white not blue

Technique Contd.

PCR (polymerase chain reaction) – makes copies of DNA without using cells and does this rapidly

Nucleic acid hybridization- depends on base pairing between a gene and a complementary sequence

Other techniques

Gel electrophoresis- separates macromolecules (nucleic acids or proteins) on the basis of their rate of movement through a polymer gel in an electrical field. Rate of movement depends on:

Molecular size Electrical charge

Electrophoresis

Gel electrophoresis contd. When the mixture undergoes electrophoresis,

it yields a banded pattern characteristic of the starting molecule and the restriction enzyme used.

The relatively small DNA molecules of viruses and plasmids can be identified by their patterns.

1. Restriction enzyme treatment2. Gel electrophoresis3. DNA transfer by blotting onto membrane4. Hybridization with radioactive probe5. Autoradiography

Gel-electrophoresis steps