Transcript AP Biology - ReicheltScience.com

AP Biology
1.
2.
3.
We’ll go over tests from before break
Go through study guide (get some hints)
Begin chapter 18
Purpose of this chapter…
 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.
Chapter 18- Gene Regulation
 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
Regulation of gene expression
Vocabulary
1. 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 away
5. Promoter- A specific nucleotide sequence in DNA
that binds to RNA polymerase- positioning it
so it may begin transcribing mRNA
6. 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)
Types of Gene Regulation
1. Negative Gene Regulation
(shut off by an active repressor)
A. Repressible Operon
B. Inducible Operon
2. Positive Gene Regulation
(turned on by an active repressor)
Trp Operon
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
Lac Operon
 Lac operon is an inducible operon
 It is usually shut off
 But it can be stimulated (induced)
when lactose (lac) is present
Lac Operon
Lac Operon
Positive Gene Control
 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- Lac operon
Positive- Lac operon
AP Biology
 Review try and lac operons
 Finish chapter 18, begin chapter 19 today
 Test is February 1st
Eukaryotic Regulation
 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
Figure 18.6
Signal
NUCLEUS
Chromatin
Stages in gene
expression that
can be
regulated in
eukaryotic cells
DNA
Chromatin modification:
DNA unpacking involving
histone acetylation and
DNA demethylation
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Cap
Tail
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypeptide
Protein processing, such
as cleavage and
chemical modification
Degradation
of protein
Active protein
Transport to cellular
destination
Cellular function (such
as enzymatic activity,
structural support)
Regulation of Eukaryotic cells
1. Regulation of chromatin structure
2. Regulation of transcription initiation
3. Mechanisms of post-transcriptional regulation
Chromatin structure
A. Histone Modifications- when structures around
chromatin are changed a decrease in Transcription
of gene occurs
B. DNA methylation- long stretches of inactivated DNA
Transcription Factors
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
Figure 18.10-1
Activators
Promoter
DNA
Enhancer
Distal control
element
TATA box
Gene
Figure 18.10-2
Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA box
General
transcription
factors
DNAbending
protein
Group of mediator proteins
Figure 18.10-3
Promoter
Activators
DNA
Enhancer
Distal control
element
Gene
TATA box
General
transcription
factors
DNAbending
protein
Group of mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
initiation complex
RNA synthesis
Post Transcriptional Regulation
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
Figure 18.6
Signal
NUCLEUS
Chromatin
Stages in gene
expression that
can be
regulated in
eukaryotic cells
DNA
Chromatin modification:
DNA unpacking involving
histone acetylation and
DNA demethylation
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intron
RNA processing
Cap
Tail
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypeptide
Protein processing, such
as cleavage and
chemical modification
Degradation
of protein
Active protein
Transport to cellular
destination
Cellular function (such
as enzymatic activity,
structural support)
AP Biology
 YAY the projector is working! 
 Finish chapter 19 today
Chapter 19- Viruses
 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-
Discovery of Viruses
 Tobacco disease
stunts growth
of tobacco
plants and gives
leaves a mosaic
coloration
Viral Structure
Rod shaped
Infect respiratory
tract
Membrane
envelope
Viral Genomes
 Many viruses differ in the type of genetic material
they carry
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

Double-stranded DNA
Single-stranded DNA
Double-stranded RNA
Single-stranded RNA
Capsids and Envelopes
 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
Viral Replication
 Lytic cycle1.
2.
3.
4.
5.
6.
7.
Attachment of virus to host cell
Virus drops off genetic material
Genetic material goes into nucleus
Genetic material is replicated
Transcription occurs
Translation makes proteins
Lyse= break= as protein leave it lyses the cell
(programmed cell death)
 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
 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 cycle
3. 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.
Animal virus diversity
 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
Retroviruses
 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)
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.
AP Biology
 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
Biotechnology
 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
Plasmids
 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
Restriction enzymes
 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
 Cloning vector – DNA molecule that can carry foreign
DNA into a cell to replicate there.
Technique
1. Clone all hummingbird genes
2. Get the plasmid DNA ready
• Carries ampR resistance to antibiotic ampicillin
• lacZ as well
3. Plasmid has a recognition sequence
4. Both plasmid and hummingbird DNA are digested
with the same restriction enzyme
5. Fragments are mixed together (pair with sticky
ends)
6. DNA ligase added to glue fragments together
Technique Contd.
 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
Other techniques
 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
Electrophoresis
 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
 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.
Gel-electrophoresis steps
1.
2.
3.
4.
5.
Restriction enzyme treatment
Gel electrophoresis
DNA transfer by blotting onto membrane
Hybridization with radioactive probe
Autoradiography