AP Biology Discussion Notes

2/25/2015

Goals for Today

• Be able to describe regions of DNA and how they are important to gene expression in Bacteria (Prokaryotes) & Eukaryotes

Question of the Day 2/25What two things would be found on a DNA sequence before (______ stream of) a coding region or genes?

Conducting the Genetic Orchestra CH18

• Prokaryotes and eukaryotes alter gene expression in response to their changing environment

18.1: Bacteria often respond to environmental change by regulating transcription

• Natural selection has favored bacteria that produce only the products needed by that cell

• A cell can regulate the production of enzymes by feedback inhibition or by gene regulation

• Gene expression in bacteria is controlled by the operon model

Repressible and Inducible Operons: Two Types of Negative Gene Regulation

An inducible operon is one that is usually ____; a molecule called an inducer inactivates the repressor and turns on transcription

What is the “inducer” in the Lac Operon?

Figure 18.4a

(a) Lactose absent, repressor active, operon off

Regulatorygene

Promoter

Operator

DNA lacZlacIDNA

mRNA5

3

NoRNAmade

RNApolymerase

ActiverepressorProtein

Figure 18.4b

(b) Lactose present, repressor inactive, operon on

lacI

lac operon

lacZ lacY lacADNA

mRNA5

3

Protein

mRNA 5

Inactiverepressor

RNA polymerase

Allolactose(inducer)

-Galactosidase Permease Transacetylase

Positive Gene Regulation

• Some operons are also subject to positive control through a stimulatory protein, such as catabolite activator protein (CAP), an activator of transcription

• When glucose (a preferred food source of E. coli) is scarce, CAP is activated by binding with cyclic AMP (cAMP)

• Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription

• When glucose levels increase, CAP detaches from the lac operon, and transcription returns to a normal rate

• CAP helps regulate other operons that encode enzymes used in catabolic pathways

Positive Gene Regulation

Figure 18.5a

Promoter

DNA

CAP-binding site

lacZlacI

RNApolymerasebinds andtranscribes

Operator

cAMPActiveCAP

InactiveCAP

Allolactose

Inactive lacrepressor

(a) Lactose present, glucose scarce (cAMP level high):abundant lac mRNA synthesized

Figure 18.5b

Promoter

DNA

CAP-binding site

lacZlacI

OperatorRNApolymerase lesslikely to bind

Inactive lacrepressor

InactiveCAP

(b) Lactose present, glucose present (cAMP level low):little lac mRNA synthesized

Fill in the blanks

Repressible and Inducible Operons: Two Types of Negative Gene Regulation

• A repressible operon is one that is usually ____; binding of a repressor to the operator shuts off transcription

• The trp operon is a repressible operon

• E. coli can synthesize the amino acid tryptophan

• Think of these questions and think about energy and natural selection:–When would “want” to do this?

–When would “not want” to do this?

trp OPERON

• By default the trp operon is on; and the genes for tryptophan synthesis are transcribed

• When tryptophan is present, it binds to the trp repressor protein, which turns the operon off

trp OPERON

• The repressor can be in an active or inactive form, depending on the presence of other molecules

• The repressor is active only in the presence of its corepressor tryptophan; – A corepressor is a molecule that cooperates

with a repressor protein to switch an operon off

• thus the trp operon is turned off (repressed) if tryptophan levels are high

trp OPERON

Figure 18.3a

Promoter

DNA

Regulatory gene

mRNA

trpR

5

3

Protein Inactive repressor

RNApolymerase

Promoter

trp operon

Genes of operon

Operator

mRNA 5

Start codon Stop codon

trpE trpD trpC trpB trpA

E D C B A

Polypeptide subunits that make upenzymes for tryptophan synthesis

(a) Tryptophan absent, repressor inactive, operon on

Figure 18.3b-1

(b) Tryptophan present, repressor active, operon off

DNA

mRNA

Protein

Tryptophan (corepressor)

Activerepressor

Figure 18.3b-2

(b) Tryptophan present, repressor active, operon off

DNA

mRNA

Protein

Tryptophan (corepressor)

Activerepressor

No RNAmade

Precursor

Feedbackinhibition

Enzyme 1

Enzyme 2

Enzyme 3

Tryptophan

(a) (b)Regulation of enzymeactivity

Regulation of enzymeproduction

Regulationof geneexpression

trpE gene

trpD gene

trpC gene

trpB gene

trpA gene

Figure 18.2

Promoter

DNA

Regulatory gene

mRNA

trpR

5

3

Protein Inactive repressor

RNApolymerase

Promoter

trp operon

Genes of operon

Operator

mRNA 5

Start codon Stop codon

trpE trpD trpC trpB trpA

E D C B A

Polypeptide subunits that make upenzymes for tryptophan synthesis

(a) Tryptophan absent, repressor inactive, operon on

(b) Tryptophan present, repressor active, operon off

DNA

mRNA

Protein

Tryptophan (corepressor)

Activerepressor

No RNAmade

Figure 18.3

Repressible and Inducible Operons: Two Types of Negative Gene Regulation

• A repressible operon is one that is usually ____

• An inducible operon is one that is usually ____

• The trp operon is a(n) ____________ operon• The Lac operon is a(n) ____________ operon

Conducting the Genetic Orchestra CH18

• Prokaryotes and eukaryotes alter gene expression in response to their changing environment

• In multicellular eukaryotes, gene expression regulates development and is responsible for differences in cell types

Figure 18.1

Eukaryotic gene expression:regulated at many stages

• All organisms must regulate which genes are expressed at any given time

• In multicellular organisms regulation of gene expression is essential for cell specialization

Figure 11.22

Interdigital tissueCells undergoing

apoptosisSpace between

digits1 mm

Differential Gene Expression

• Almost all the cells in an organism are genetically identical

• Differences between cell types result from differential gene expression,– the expression of different genes by cells with

the same genome• Abnormalities in gene expression can lead to

diseases including cancer• Gene expression is regulated at many stages

Figure 18.6 Signal

NUCLEUSChromatin

Chromatin modification:DNA unpacking involvinghistone acetylation and

DNA demethylationDNA

Gene

Gene availablefor transcription

RNA ExonPrimary transcript

Transcription

Intron

RNA processing

Cap

Tail

mRNA in nucleus

Transport to cytoplasm

CYTOPLASM

mRNA in cytoplasm

TranslationDegradationof mRNA

Polypeptide

Protein processing, suchas cleavage and

chemical modification

Active proteinDegradation

of proteinTransport to cellular

destination

Cellular function (suchas enzymatic activity,structural support)

Figure 18.6a Signal

NUCLEUSChromatin

Chromatin modification:DNA unpacking involvinghistone acetylation and

DNA demethylationDNA

Gene

Gene availablefor transcription

RNA ExonPrimary transcript

Transcription

Intron

RNA processing

Cap

TailmRNA in nucleus

Transport to cytoplasm

CYTOPLASM

Figure 18.6b

CYTOPLASM

mRNA in cytoplasm

TranslationDegradationof mRNA

Polypeptide

Protein processing, suchas cleavage and

chemical modification

Active proteinDegradation

of proteinTransport to cellular

destination

Cellular function (suchas enzymatic activity,structural support)

DNA Methylation

• DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species

• DNA methylation can cause long-term inactivation of genes in cellular differentiation

DNA Methylation

• In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development

Histone Modifications

• In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails

• This loosens chromatin structure, thereby promoting the initiation of transcription

• The addition of methyl groups (methylation) can condense chromatin; the addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen chromatin

Figure 18.7

Amino acidsavailablefor chemicalmodification

Histone tails

DNA double helix

Nucleosome(end view)

(a) Histone tails protrude outward from a nucleosome

Unacetylated histones Acetylated histones

(b) Acetylation of histone tails promotes loose chromatinstructure that permits transcription

Operon Practice

• If you can draw it you understand it

Registration Materials• See Ms. Benz in A156

Thoughts on taking the AP TEST

• You have worked hard all semester, and you should get your reward for all that hard work!

Thoughts on taking the AP TEST• IF biology major:

– You should take the test which will count as an elective credit and be much cheaper than other credits

– You will still want to take MAJORS biology at your college/university to:• Understand their specific expectations & emphasis• Meet professors and make good impressions for

potential lab/field jobs• Meet your cohort – other students who will be

going through the program with you – and form friendships & study groups

Thoughts on taking the AP TEST

• IF non-science or non-biology major:–You should take the test for easy credit

while it is all fresh in your mind.• It will be much more difficult and more

expensive to get this same credit as a college class