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DNA
C
G
T
A
Base
pair
C
Hydrogen bond
T
A
T
G
C
G
A
T
A
C
G
C
G
T
T
C
A
G
A
A
T
A
T
A
G
A
Ribbon model
T
C
T
Partial chemical structure
Computer model
What does the cell use DNA for?
• Gives you traits
What IS a trait?
• Physical structure produced by a protein!
• DNA controls the production of proteins.
What do we know about making
proteins?
DNA is in the NUCLEUS
RIBOSOMES, ER,
and GOLGI are in
the CYTOPLASM
How does that work?
• RNA acts as a messenger to carry information
from the DNA in the nucleus to the ribosomes
in the cytoplasm
What’s RNA?
• Nucleic Acid
• Similar to DNA
• Some differences
Nitrogenous base
(A, G, C, or U)
Phosphate
group
Uracil (U)
Sugar
(ribose)
What’s RNA?
FEATURE
DNA
RNA
Subunits
Nucleotide
Nucleotide
Strands
2 – double helix 1 (mostly)
Sugar
Deoxyribose
Ribose
Bases
A = T; C = G
A = U; C = G
Protein Synthesis Overview
DNA is located in the NUCLEUS
Protein Synthesis Overview
A messenger RNA (mRNA) copy is made of DNA.
Protein Synthesis Overview
mRNA leaves the nucleus and goes to the ribosome
Protein Synthesis Overview
Ribosome uses mRNA to assemble amino acids in the
correct order to make a specific protein
Genes to Polypeptides
• Polypeptides = chains of
AA = proteins
• 20 different AA exist
• specific polypeptide has
specific AA sequence
• Sequence of AA
determines the shape
and function of a
protein
Genes to Polypeptides
• Sequence of bases in
DNA determine AA
sequence
• “Genes” store order of
AA in a code in DNA
• One specific gene will
yield one* specific
polypeptide
– polypeptide = protein
that does a job!
DNA & Genetic Code
• There are 20 amino
acids, and a stop
• How can DNA specify
21 things with only four
bases?
Genetic Code
G
A
T
C
4
• IF: 1 base = 1 amino
acid
• THEN: how many
amino acid possibilities
are there?
Genetic Code
G
A
T
C
G
A
T
C
4 x 4
= 16
• IF: 2 bases = 1 amino
acid
• THEN: how many
amino acid possibilities
are there?
Genetic Code
G
A
T
C
G
A
T
C
4 x 4 x 4 =
G
A
T
C
64
• IF: 3 bases = 1 amino
acid
• THEN: how many
amino acid possibilities
are there?
DNA & Genetic Code
• In a gene, every three
bases code for a specific
amino acid (one of the
20)
• 4 x 4 x 4 = 64 total
possiblities
• One amino acid can be
coded for by more than
one triplet
DNA & Genetic Code
Genetic code is composed of codons made up of
of base triplets
DNA & Genetic Code
• The genetic code is both universal and
degenerate.
– Universal = found in all living organisms
– Degenerate = having more than one base triplet
(codon) to code for one amino acid
Protein Synthesis Overview
• DNA is located in the nucleus
Protein Synthesis Overview
• Ribosomes are located in the cytoplasm
Protein Synthesis Overview
• Messenger RNA carries “message”
from DNA to ribosomes
Transcription
• Genes are made of DNA
• DNA cannot leave the
nucleus
• A copy must be
“transcribed” into RNA
• RNA exits nucleus
http://www.fed.cuhk.edu.hk/~jo
hnson/teaching/genetics/anima
tions/transcription.htm
Transcription
1. INITIATION: RNA
polymerase uncoils
DNA double helix
2. ELONGATION: RNA
polymerase creates a
new mRNA strand using
free RNA nucleotides; a
single DNA template
strand is used
Transcription
3. RNA nucleotides
attached together
(type of reaction?) via
RNA polymerase
4. TERMINATION: New
mRNA strands
separates from DNA
5. DNA reforms
Animation: Campbell Ch
10 – 10_9 Transcription
GENE
Contains the instructions to assemble one
protein
TRANSCRIPTION
The process by which an mRNA copy is made
of a DNA sequence
RNA POLYMERASE
Enzyme that catalyzes synthesis of mRNA
strand
PROMOTER REGION
Sequence of DNA bases within gene where
RNA polymerase binds
CODING REGION
Sequence of DNA bases that codes for the
actual structure of the protein
TERMINATOR
REGION
Sequence of DNA were RNA polymerase stops
transcribing.
CODON
3 bases of DNA or RNA; specifies 1 amino acid
What’s it look like?
So, the new mRNA strand was just made, now what?
Final Steps – Eukaryotes ONLY
1. mRNA Splicing
–
–
–
INTRONS: non-coding
regions of the mRNA
strand
EXONS: coding regions
of the mRNA strand
Introns are spliced out
of final mRNA
Final Steps – Eukaryotes ONLY
2. 5’ Cap
–
–
Modification to 5’ end
of mRNA
Ensures stability of
mRNA
Final Steps – Eukaryotes ONLY
3. 3’ poly-A tail
–
–
Addition of poly-A to 3’ end of mRNA
Protects RNA from nucleases
Exon
Intron
Exon
Intron
Exon
DNA
Cap
RNA
transcript
with cap
and tail
Transcription
Addition of cap and tail
Introns removed
Tail
Exons spliced together
mRNA
Coding sequence
Nucleus
Animation: Cain
Ch13a03 - Transcription
Cytoplasm
Transcription in a cell
• Multiple genes can be transcribed at the same
time
• The same gene can be transcribed at the same
time
Translation
Nucleus
Ribosome (cytoplasm)
DNA mRNA Protein
Transcription
Translation
Where we
are now.
Translation Summary
• Instructions in the mRNA are used by a
ribosome to assemble amino acids in the
correct order
• Order of amino acids gives the protein its
shape
• Shape gives protein its function
Translation Summary
The Key Players
• mRNA
• tRNA
• rRNA
Animation: Cain
Ch13a07 - Translation
The Stages of Translation
• Initiation
• Elongation
• termination
mRNA (messenger RNA)
• copy of the directions to make the product
(protein)
• tells the ribosome the correct sequence of
Amino Acids while putting together the
protein
• each codon (3 bases) directs a specific amino
acid to be added to the growing protein
tRNA (transfer RNA)
• the delivery RNA;
delivers specific Amino
Acids to the ribosome
• composed of RNA
• anticodon binds to a
corresponding codon
on mRNA
• Carries one specific
amino
6.4.1
Translation
rRNA (ribosomal RNA)
• ribosomes are made of
RNA and protein
• composed of two
subunits: the 30s and
50s subunits
• two tRNA binding sites;
one mRNA binding site
Translation INITIATION
• small (30S) ribosome subunit binds to mRNA
at the 5’ end of the mRNA
• 30S moves along mRNA 5’ to 3’ until it hits the
start codon AUG
Translation INITIATION
• large subunit binds
• Methionine tRNA moves into ribosome
Translation INITIATION
• another tRNA, with the anticodon
complementary to the next codon binds to the
ribosome
Translation ELONGATION
• first amino acid added
• ribosome moves down
mRNA to next codon
• next tRNA comes in
• its amino acid is bound
to the polypeptide
chain
• ribosome moves down
mRNA to next codon
Translation TERMINATION
• the ribosome encounters a stop codon
• no tRNA molecule has an anticodon for this
codon
Translation TERMINATION
• polypeptide is released and ribosome
disassociates
Animation: Campbell Ch
10 – 10_14 Translation
Where does translation happen?
• Cytoplasmic (free)
Ribosomes  proteins
for use in cytoplasm
• Rough ER (attached)
Ribosomes  proteins
secreted or used in
lysosomes
DNA molecule
Gene 1
• DNA
Gene 2
– TRANSCRIPTION
• RNA
Gene 3
– TRANSLATION
• PROTEIN
DNA strand
A
A
A
C
C
G
G
C
A
A
A
A
U
U
U G
G
C
C
G
U
U
U
U
Transcription
RNA
Codon
Translation
Polypeptide
Amino acid
Interpreting the Genetic Code
Strand to be transcribed
Second base
T
A
C
T
T
C
A
A
A
A
T
UUU
DNA
A
T
G
A
A
G
T
T
T
T
A
G
C
U
C
U
UUC
UUA
UUG
Phe
Leu
CUU
Transcription
C
A
U
G
A
A
G
U
U
U
U
A
RNA
G
A
CUC
CUA
Stop
codon
Translation
Lys
Phe
UCA
Ser
UAC
U
C
CCU
CAU
CGU
CCC
CCA
Pro
CAC
CAA
AUC lle
ACC
AUA
ACA
GUA
UGC
Cys
UAG Stop
AAU
Val
UGU
UCG
ACU
GUC
Tyr
UGA Stop A
UGG Trp G
AUU
Met or
start
G
UAA Stop
CAG
GUG
Polypeptide Met
UCC
CCG
GUU
G
UAU
UCU
CUG
AUG
Start
codon
Leu
A
Thr
AAC
AAA
ACG
AAG
GCU
GAU
GCC
GCA
GCG
Ala
GAC
GAA
GAG
His
Gln
Asn
Lys
Asp
Glu
CGU
CGA
U
Arg
G
CGG
AGU
AGC
AGA
AGG
C
A
Ser
Arg
U
C
A
G
U
GGC
C
Gly
GGA
A
GGG
G
GGU
Animation: Starr Ch 14 –
Genetic code
Changes in the Genetic Code
• MUTATION = change in the nucleotide sequence of
DNA
Normal hemoglobin DNA
Mutant hemoglobin DNA
C
T
T
mRNA
C
A
T
G
U
A
mRNA
G
A
A
Normal hemoglobin
Glu
Sickle-cell hemoglobin
Val
Changes in the Genetic Code
• MUTATION = change in the nucleotide sequence of
DNA
Normal hemoglobin DNA
Mutant hemoglobin DNA
C
T
T
mRNA
C
A
T
G
U
A
mRNA
G
A
A
Normal hemoglobin
Glu
Sickle-cell hemoglobin
Val
Changes in the Genetic Code
• MUTATION = change in the nucleotide sequence of
DNA
Normal hemoglobin DNA
Mutant hemoglobin DNA
C
T
T
mRNA
C
A
T
G
U
A
mRNA
G
A
A
Normal hemoglobin
Glu
Sickle-cell hemoglobin
Val
What causes mutations?
• Spontaneous
mutations: uncorrected
errors in replication
What causes mutations?
• Spontaneous
mutations: uncorrected
errors in replication
• Harmful environmental
agents: UV light,
radiation, chemicals
Radiation damages DNA
Radiation as a cancer treatment
Why would radiation be a
treatment for cancer?
• What type of cells would
radiation affect most:
rapidly dividing or rarely
dividing cells?
• Cancer cells are very
rapidly dividing cells
• Radiation targets ALL
rapidly dividing cells, not
just cancer cells
What causes mutations?
• Spontaneous
mutations: uncorrected
errors in replication
• Harmful environmental
agents: UV light,
radiation, chemicals
• Transposable elements:
“jumping genes”
Mutations
• Sickle Cell Anemia
– Single-base substitution
Sickle Cell Anemia
Missense mutation = single base
substitution
Changes one
amino acid
Variable effect on protein depending on how much
structure is changed
Missense Mutations
• Tay Sachs Disease
– Single-base substitution
in HexA gene
Missense Mutations
• Cystic Fibrosis
– Single-base substitution
in CFTR gene
Nonsense mutation = single base
substitution that introduces a STOP
Truncates protein
Often more severe
Nonsense
Mutations
• Cystic Fibrosis
– More severe form
• Duchenne Muscular
Dystrophy
– Dystrophin – connects
cytoskeleton to
extracellular matrix
Silent mutation = single base
substitution that doesn’t change an
amino acid
Second base
C
U
UUU
U
UUC
UUA
UUG
Phe
Leu
CUU
C
A
CUC
CUA
Leu
UAU
UCU
UCC
UCA
Ser
UAC
CAU
CGU
CCC
CCA
Pro
CAC
CAA
AAU
AUC lle
ACC
AUA
ACA
GUA
GUG
U
C
CCU
ACU
Val
UGC
Cys
UAG Stop
AUU
GUC
UGU
UCG
CAG
GUU
Tyr
UGA Stop A
UGG Trp G
CCG
Met or
start
G
UAA Stop
CUG
AUG
G
A
Thr
AAC
AAA
ACG
AAG
GCU
GAU
GCC
GCA
GCG
Ala
GAC
GAA
GAG
His
Gln
Asn
Lys
Asp
Glu
CGU
CGA
U
Arg
G
CGG
AGU
AGC
AGA
AGG
C
A
Ser
Arg
U
C
A
G
U
GGC
C
Gly
GGA
A
GGG
G
GGU
Insertion mutation = addition of one
or more nucleotides
Can change
entire protein
after mutation
Deletion mutation = deletion of one or
more nucleotides
Can change
entire protein
after mutation
Frameshift mutation = Change of
“reading frame” in DNA
Can change
entire protein
after mutation
Insertion or
deletion
Cancer
• BRCA1 - increased risk
of developing breast
cancer
• Mutations due to
mutagens
Summary of Mutations
• Base Substitution
– Missense
– Nonsense
– Silent
• Frameshift
– Insertion
– Deletion
• Which kind would be
most likely to cause
disease?
Normal gene
A U G A A G U U U G G C G C A
mRNA
Protein Met
Lys
Phe
Gly
Ala
Base substitution
A U G A A G U U U A G C G C A
Met
Lys
Base deletion
Phe
Ser
Ala
U Missing
A U G A A G U U G G C G C A U
Met
Lys
Leu
Ala
His
Good information about genes and
mutations
• http://ghr.nlm.nih.gov/handbook/basics
Effect of Mutation on Protein Structure
Effect of Mutation on Protein Structure
Transcription
Assembly of RNA on unwound regions
of DNA molecule
mRNA processing
mRNA
mature mRNA
transcripts
Translation
At an intact
ribosome,
synthesis of a
polypeptide
chain at the
binding sites for
mRNA and tRNAs
rRNA
ribosomal
subunits
Convergence of
RNAs
tRNA
mature tRNA
cytoplasmic
pools of amino
acids,
ribosomal
subunits, and
tRNAs
Protein
Animation: Starr Ch
14 - Protein Synthesis
in Prokaryotes vs
Eukaryotes
In-class assignment – Protein Synthesis
• Complete the classwork assignment
Gene Expression
• Every cell in your body came from
1 original egg and sperm
• Every cell has the same DNA and
the same genes
76
Gene Expression
• Every cell in your body came from 1
original egg and sperm
• Every cell has the same DNA and the
same genes
• Each cell is different, specialized
• Differences due to gene expression
– Which genes are turned on
– When the genes are turned on
– How much product they make
77
Genetic Potential
• Embryonic Stem Cells
– Can differentiate to
become any type of cell
in the body
• Adult Stem Cells
– Can differentiate to
become several types of
cell
Genetic Potential
• Plants in Cell Culture
• Plants creating roots
Root of
carrot plant
Single cell
Root cells cultured
in nutrient medium
Cell division
in culture
Plantlet
Adult plant
Genome Size
• Genome: total amount of
DNA
• Prokaryotes
– 0.6 to 30 million base pairs
– Approximately 2,000 genes
• Eukaryotes
– 12 million to 1 trillion base
pairs
– Humans have ~25,000
genes
80
Organization of DNA
• Prokaryotes
– Several million base pairs one circular piece
– Related genes grouped
together
– Mostly coding DNA
81
Organization of DNA
• Eukaryotes
– Billions of base pairs –
several linear
chromosomes
– Genes not grouped
– Mostly non-coding DNA
82
Noncoding DNA
• Spacer DNA
• Transposons – “selfish DNA”
83
DNA Packaging
•
•
•
•
Eukaryotic chromosomes are very large
Must be packaged to fit inside nucleus
Unavailable for transcription
Unpacking must occur before transcription
84
Levels of
Packaging
• Chromosome – fully
condensed
• Tightly packed loops
• 30 nm fibers
• Histone spool
• Double helix
85
Patterns of Gene Expression
• Bacteria directly exposed to environment
• Respond to changes in nutrient availability
directly
– Make enzymes for nutrients when they are
present
– Turn genes off when they are not
86
Patterns of Gene Expression
• Eukaryotic cells
• Tissue specific expression
• Housekeeping
genes
87
Gene Expression: Development
• Embryo development
depends on gene
expression
• Timing of expression
vital
• Controlled by cascades
of gene expression
88
Levels of
Gene Control
1.
2.
3.
4.
5.
6.
7.
89
Packaging
Transcription
mRNA maturation
mRNA breakdown
Translation
Protein Regulation
Protein Degradation
1. Packaging
• If the DNA isn’t
unwrapped from the
histones, it can’t be
transcribed
• DNA Methylation
• HistoneMethylation
Animation: Campbell Ch 11
– DNA Packing
1. Packaging
Methylation
• DNA marked with a
methyl group can be
identified by an enzyme
1. Packaging
• X chromosome
Inactivation
– Females have 2 X
chromosomes
– One gets methylated and
inactivated during
development
1. Packaging
• “Copycat” – first cloned cat
1. Packaging
• Agouti, mottled and yellow mice
1. Packaging
• Methylation is required for development
– Lethal to eliminate methylation in animals
– Not lethal in plants, but profound effects on
development
1. Packaging
• Imprinting – methylate and silence genes on
one parent’s chromosome specifically
– About 1% of total human genes (about 300 genes)
1. Packaging
• Parental DNA contributions to embryo are
marked
1. Packaging
• Normal = maternal
expressed, paternal
silenced
• Prader-Willi = paternal
allele lost, maternal
allele present
• Angelman = maternal
allele lost, paternal
allele present
1. Packaging
• Cancer cells are often aberrantly methylated
1. Packaging
• Cancer cells are often aberrantly methylated
2. Transcription
• Control when and how
much a gene is
transcribed
2. Example of Transcriptional Control: The Lac
Operon in Bacteria
• E. coli lactose sugar
utilization genes
• When lactose is present,
bacteria needs to have the
proteins coded for by these
genes
– Lactase Enzymes
Lac Operon
Animation (online)
2. Example of Transcriptional Control: The Lac
Operon in Bacteria
• Operon: group of
nucleotide sequences
including an operator, a
promoter, and one or more
genes that are controlled as
a unit to produce
messenger RNA (mRNA)
*The Operon model is one
example of gene expression
regulation
6.3.2
Lac Repressor Protein
• NO LACTOSE: repressor
binds to the DNA and
prevents RNA pol from
binding (no
transcription)
• No lactase is produced
6.3.2
Lac Repressor Protein
• LACTOSE: repressor
binds lactose and
changes shape. Now
repressor can’t bind
DNA
• Lactase is produced;
lactose is metabolized
2. Example of Transcriptional Control:
The Trp Operon
Tryptophan AA
genes
 ANIMATION
(Ch14a03)

107
2. Transcriptional Control - Eukaryotic
Gene Expression
•
•
•
•
No operons
More complex than prokaryotic
Many different types of regulatory proteins
Many DNA elements controlling each gene
108
2. Transcriptional Control - Eukaryotic
Gene Expression
• OFF: proteins are
produced that bind to
gene preventing RNA
polymerase from
binding
3. mRNA Maturation
• If 3’ cap, 5’ poly-A tail
are not added, mRNA
cannot be transported
out of the nucleus and
used
• mRNA can be
“alternatively spliced”
to generate different
transcripts
Exons
DNA
RNA
transcript
RNA splicing
mRNA
or
4. mRNA Breakdown
• If mRNA is broken down more quickly, it can be
used fewer times
5. Translational Regulation
• Inhibit any of the steps
of translation and the
mRNA can’t be used
6. Protein Regulation
• Activate or inactivate
the newly made protein
– Phosphorylation
– Acetylation
6. Protein Regulation
• Activate or inactivate
the newly made protein
– Phosphorylation
– Acetylation
– Cleavage
INSULIN
7. Protein Degradation
• If the protein is broken down, obviously it can’t
work anymore