AP+ +Unit+6+ +Gene+Expression+and+Regulation
AP+ +Unit+6+ +Gene+Expression+and+Regulation
AP Biology
Unit 6: Gene Expression and
Regulation
• 6.1: History of DNA
• 6.2: DNA
• 6.3: Replication of DNA
• 6.4: Central Dogma
• 6.5: Transcription
• 6.6: Translation
• 6.7: Mutations
• 6.8:Gene Mutations
• 6.9: Chromosome Mutations
• 6.10: Prokaryotic Regulation
• 6.11: Eukaryotic Regulation
6.1: History of DNA
• 1869: Friedrich Miescher.
• First to discover DNA.
• Extracted white blood cells
from blood and lysed the
cells.
• Called it ‘Nuclein’.
6.1: History of DNA
• 1928, Griffith Experiment
• Griffith was working with bacteria that
caused pneumonia.
• S (Smooth) strain of bacteria would kill the
mouse.
• R (Rough) strain would not kill the mouse.
• Boiled S strain, killing the cells. Injected
boiled S strain into the mouse and the
mouse was ok!
• Mixed boiled S strain and R strain and
injected it into the mouse. Killed the mouse.
• Hypothesis: There is some kind of chemical
substance that isn’t alive that is capable of
transforming a cell.
• Came up with Transformation Principle.
6.1: History of DNA
• 1952
• 1950s
• Scientists knew
DNA was made of
nucleotides, but
didn’t understand
total structure.
• Rosalind Franklin
studied x-ray
diffraction and was
studying DNA.
• Took “Photo 51”
6.1: History of DNA
• 1953
• Wilkins “shared” photo with
James Watson and Francis
Crick.
• Watson and Crick created
first accurate model of DNA
with Franklin’s work.
6.1: History of DNA
• Franklin published her research, but it was
placed behind Watson and Cricks’ paper, which
made it look like it just supported their work.
• Franklin died in 1958 from Cancer, most likely
from working so much in the X-ray Diffraction
machines which were radioactive.
• Watson, Crick, and Wilkins received Nobel Prize
in Medicine in 1962.
• People cannot receive the award after they’ve died.
• Watson and Crick wrote a book about their
discovery, misleading statements about
Rosalind.
6.1: History of DNA
Year Scientist(s) What They Did How They Did It Conclusion
1869 Friedrich Miescher Discovered a substance in white Isolated material from the nuclei First identification of DNA, though
blood cells called nuclein. of pus cells in bandages function unknown
1928 Frederick Griffith Found a "transforming Injected mice with live & dead Something in dead S bacteria
principle" that transferred traits forms of bacteria (S and R strains) transformed live R bacteria
Proved DNA, not protein, is the Used viruses (bacteriophages) Only DNA entered bacteria,
1952 Hershey & Chase genetic material labeled with radioactive sulfur confirming it's the genetic material
(protein) & phosphorus (DNA)
1953 Watson & Crick (w/ Discovered the double helix Used Franklin’s X-ray image to DNA is a double helix with base-
build 3D model with base pairing pairing rules
Franklin & Wilkins) structure of DNA (A=T, C≡G)
1961–66 Nirenberg, Khorana & Cracked the genetic code Used synthetic RNA in test tubes Showed how DNA codes for
others to link codons to amino acids proteins using codons
6.2: DNA
• Nucleotides
(monomers) are the
building blocks of DNA
(polymers).
• DNA is blueprint of life.
6.2: DNA
• Nucleotides
• Phosphate Group
• Ring Shaped Sugar
Molecule: Deoxyribose
• Nitrogen containing base:
Single or Double Ring
6.2: DNA
• 4 different types in
nucleotides.
• Adenine (A)
• Guanine (G)
• Thymine (T)
• Cytosine (C)
• Sugar and phosphate group
are identical in each
nucleotide.
6.2: DNA
• Pyrimidines: Single ring
nucleotide.
• Cytosine
• Thymine (DNA Only)
• Uracil (RNA Only)
• Purines: Double ring nucleotide.
• Adenine
• Guanine
6.2: DNA
• Chargaff’s Rule
• Erwin Chargaff discovered:
• Percent of A approximately equals T.
• Percent of G approximately equals C.
• This is true for all species!
Chargaff Example Question 1
You find a new type of bacteria and sequence the
genome and find the percentage of thymine is
21%, what is the percentage of adenine?
21%
Chargaff Example Question 2
A geneticist sequences the genome of a lion and finds
the percentage of guanine is 34%, what is the
percentage of adenine?
G = 34% 100% 32%/2 = 16%
C = 34% -68% A = 16%
32% = A/T T = 16%
G/C=68%
6.2: DNA
• Complementary Base
Pairing: Each purine is
always bonded to a
specific pyrimidine.
• A:T
• G:C
• Semiconservative
Replication: Each
daughter strands acts as
a template for the new
strand of DNA.
6.3: Replication of DNA
• DNA Replication:
Process of producing
two identical replicas
from one original DNA
molecule.
• Occurs during S phase.
6.3: Replication of DNA
•Topoisomerase:
Enzyme that helps
unwind DNA. Relaxes
the twist.
6.3: Replication of DNA
• Origin of Replication:
Location where
replication begins.
• Replication Fork:
Location where
helicase breaks bonds.
6.3: Replication of DNA
•Ligase: Enzymes
that bonds new
strands together
on lagging.
6.3: Replication of DNA
• DNA polymerase III is very
accurate.
• Around 1 error per
100,000-1,000,000 bp
• DNA polymerase II
proofreads the DNA code to
check for errors.
6.3: Replication of DNA
• Nucleotide Excision Repair:
Nuclease cuts out incorrect pairing
of nucleotides. DNA polymerase fills
in with correct nucleotides.
• This reduces error to 1 in 100 million-
1 billion base pairs.
Xeroderma pigmentosum
• Genetic Disorder
• UV radiation from sun
can cause Thymine-
Thymine dimers.
• Mutation in DNA
enzymes that repair UV
damage in skin cells
• Can’t go out in sunlight
• Increased skin
cancers/cataracts
• 1 in 1,000,000 million
6.4: Central Dogma
1. Replication: DNA copies
itself.
2. Transcription: Sequence
of DNA is copied into
mRNA.
3. Translation: mRNA is read
by a ribosome and
converted into a
sequence of amino acids.
6.4: Central Dogma
• RNA
• Ribose sugar.
• Uracil, no thymine.
• Single stranded
instead of double*
Ribose vs. Deoxyribose
DNA RNA
AU
TA
GC
CG
6.4: Central Dogma
• mRNA = Messenger
RNA: Copy of DNA
that is transferred to
ribosomes.
6.4: Central Dogma
Ingredients =
amino acids
Finished cake
= Protein
Kitchen Counter
= Ribosome
Transcription Translation
DNA mRNA Protein
https://www.youtube.com/watch?v=YlOqI3PQwjo
6.5: Transcription
• RNA Polymerase unzips the DNA at specific
location called a promoter.
6.5: Transcription
• RNA Polymerase makes
complimentary strand of
RNA in a 5’ to 3’ direction.
6.5: Transcription
• Template Strand: Side
that is used by RNA
Polymerase.
• Coding Strand:
Sequence is the same
as mRNA.
DNA has two strands:
• The template strand is the one that RNA polymerase reads to make mRNA.
• The mRNA is complementary to the template strand and has the same sequence as the coding strand
(except U instead of T).
• Think of the template strand as the one being copied, and the coding strand as the final product's twin!
Transcription Practice
DNA: G C A T T A G G C A T G G C C A
RNA: C G U A A U C C G U A C C G G U
6.5: Transcription
• RNA polymerase stops transcribing gene when it
comes to termination site.
• Section of mRNA detaches from RNA polymerase.
6.6: Translation
• Repressible Operon:
Operon is usually on
unless the product is
present which turns
it off.
• Trp operon Model
• On → Off
6.10: Prokaryotic Regulation
• Trp = Tryptophan
• Tryptophan is an
essential amino acid.
• Trp genes make
proteins that make
tryptophan.
6.10: Prokaryotic Regulation
• Low Tryptophan
• RNA polymerase binds
with promoter, produces
mRNA sequence.
• mRNA translates into
protein that make
tryptophan.
6.10: Prokaryotic Regulation
• High Tryptophan
• Trp will bind with repressor,
changing its
structure/function.
• Repressor binds with operator
sequence stopping
transcription.
• When trp is used up, repressor
changes back allowing for RNA
polymerase to work again.
6.11: Eukaryotic Regulation
• Chromosome Structure
• Transcriptional Control
• Post transcriptional Control
• Translational Control
• Post translational Control
6.11: Eukaryotic Regulation
• Chromosome Structure: Regulation of
RNA polymerase’s access to genes.
• Methyl groups condense DNA around
histones.
• Acetyl groups loosen DNA around
histones.
• Epigenetics: Controlling which genes
are expressed through environmental
factors without changing DNA
sequence.
6.11: Eukaryotic Regulation
• Transcriptional Control: Regulation of
how much mRNA is produced. Most
critical, most control.
• Transcriptional Factors: Proteins
that influence the ability of RNA
Polymerase to bind. Create a
hairpin loop. TATA box promotes TF
to help transcription to start.
• Enhancer = Activators
• Silencer = Repressors
6.11: Eukaryotic Regulation
• Post Transcriptional Control:
Processing of mRNA for protein
synthesis.
• mRNA is checked and edited in nucleus.
• Exons = Protein coding regions, Introns =
Non-protein coding regions
• Alternative Splicing: Different cells can
regulate which exons will be translated
which will alter protein structure and
function. Spliceosome cuts out Introns.
• Size of mRNA affects speed at which it
leaves the nuclear pores.
• 5’ cap on mRNA helps mRNA attach to
ribosome. Poly-A tail: makes the RNA
molecule more stable and prevents its
degradation
6.11: Eukaryotic Regulation
• Translational Control:
Regulation of protein synthesis.
• RNAi (interference): Enzymes
and RNA interferer/degrade
RNA.
• Lifespan of mRNA: Shorter in
prokaryotes, longer in
eukaryotes.
6.11: Eukaryotic Regulation
• Post Translational: Regulation
after protein has been produced.
• Proteins modify the structure and
function of protein. (Ex: Chaperone
proteins, phosphorylation, etc.)
• Ubiquitin: Marker protein that
targets proteins for degradation.
• Proteasome: Massive structure that
breaks down marked proteins. Uses
enzyme called protease.
Genomics
• Humans
• 46 Chromosomes
• Genome: 3.2 billion
base pairs.
• Between 20,000-
25,000 genes.
Genomics
•2% is protein
producing.
•98% non-protein
coding DNA.
Restriction Enzymes
• Restriction Enzyme: Enzyme
that binds with a specific
sequence of DNA and
cleaves the DNA in a specific
manner.
Restriction Enzymes
• Sticky End: One strand is
longer than the other.
Allows for ends to easily
rebind.
• Blunt End: Both strands are
of equal length, difficult to
rebind.
Plasmids
• Plasmids: Small circular DNA found in
prokaryotes.
Recombinant DNA
• Beneficial gene from one
organism is cut out using
restriction enzymes.
• Plasmid is cut, gene is
inserted.
Bacterial Transformation
• Process of taking a
gene/plasmid from one
bacteria and transferring
it to another bacteria.
New protein is produced
in bacteria.
Polymerase Chain Reaction
• Small amounts of DNA are
copied multiple times.
• Mimics DNA Replication.
• DNA samples are heated and
cooled along with enzymes
for replication.
• Billions of copies can be
made within a few hours.
• First created in 1985.
Gel Electrophoresis
• Gel electrophoresis is a
laboratory method used
to separate mixtures of
DNA, RNA, or proteins
according to molecular
size.
Gel Electrophoresis
• DNA is cut using restriction
enzymes.
• DNA fragments are added
to wells in plate.
• Electrical current separates
DNA.
• DNA is negatively charged.
←Well
Gel Electrophoresis Largest
→
• Shorter fragments travel
further.
• Longer fragments don’t travel Least →
as far.
• More DNA = Thicker Band Most →
• Less DNA = Thinner Band
Smallest
→
Gel Electrophoresis
• Size Standard or
ladder shows pre-
known fragment
lengths.
DNA Fingerprinting
• Short Tandem Repeat
(STR): Short sequences
(2 to 9 bases) of DNA
that repeat several
times.
• Example: TCGTCGTCG
DNA Fingerprinting
• Variable Number
Tandem Repeats (VNTR):
Longer repeats, around
10 to 100 bases long.
DNA Fingerprinting
• Discovered in 1984.
• Major tool in forensics, will be
replaced with genome sequencing.
• STRs and VNTRs between genes
are different between each person.
• Comparison of repeats can
statistically link two samples
together.
DNA Fingerprinting Problem