Transcript Bio 112 17 sp11

Quiz
• Nucleotide?
• Added to which end?
• Lagging strand?
DNA pol III synthesizes
leading strand continuously
Parental
DNA
3
5
DNA pol III starts DNA
synthesis at 3 end of primer,
continues in 5  3 direction
5
3
5
Primase synthesizes
a short RNA primer
Lagging strand synthesized
in short Okazaki fragments,
later joined by DNA ligase
3
5
Chapter 17
From Gene to Protein
Big Questions
• How does your body produce insulin?
• How does your offspring know how to make insulin?
• Central “Dogma”
DNA > RNA > “Protein”
(Info > Message > Product)
Chapter 17 Study Guide Questions
The Connection between Genes and Proteins
1. Explain how RNA differs from DNA.
2. Briefly explain how information flows from gene to protein. Is the central
dogma ever violated?
3. Distinguish between transcription and translation.
4. Compare where transcription and translation occur in bacteria and in
eukaryotes.
5. Define “codon” and explain the relationship between the linear
sequence of codons on mRNA and the linear sequence of amino acids
in a polypeptide.
6. Explain what it means to say that the genetic code is redundant and
unambiguous.
7. Explain the significance of the reading frame during translation.
Chapter 17 Study Guide Questions
The Synthesis and Processing of RNA
8. Explain how RNA polymerase recognizes where transcription should
begin. Describe the role of the promoter, the terminator, and the
transcription unit.
9. Explain the general process of transcription, including the three major
steps of initiation, elongation, and termination.
10. Explain how RNA is modified after transcription in eukaryotic cells.
11. Define and explain the role of ribozymes. What three properties allow
some RNA molecules to function as ribozymes?
12. Describe the functional and evolutionary significance of introns.
13. Explain why, due to alternative RNA splicing, the number of different
protein products an organism can produce is much greater than its
number of genes.
Chapter 17 Study Guide Questions
The Synthesis of Protein
14. Describe the structure and function of tRNA.
15. Explain how tRNA is joined to the appropriate amino acid.
16. Describe the structure and functions of ribosomes.
17. Describe the process of translation (including initiation, elongation,
and termination) and explain which enzymes, protein factors, and
energy sources are needed for each stage.
18. Describe the significance of polyribosomes.
19. Explain what determines the primary structure of a protein and
describe how a polypeptide must be modified before it becomes fully
functional.
20. Define “point mutations”. Distinguish between base-pair substitutions
and base-pair insertions. Give an example of each and note the
significance of such changes.
Today’s Tip: Ricin will kill you
Georgi Ivanov Markov
Inhibits ribosome translation of mRNA
1. Explain how RNA differs from DNA.
RNA
• Single-stranded
• AUCG
• Ribose
DNA
• Double-stranded
• ATCG
• Deoxyribose
2. Briefly explain how information flows from gene to
protein. Is the central dogma ever violated?
Genes
Specific sequences of
nucleotides
Proteins
Instructions carried in genes
Gene expression
•DNA directs protein
synthesis
Includes two stages:
•transcription and translation
Cellular chain of
command:
DNA RNA protein
3. Distinguish between transcription and translation.
Transcription
• synthesis of RNA under the
direction of DNA
Messenger RNA (mRNA)
Product of transcription
Translation
• synthesis of a polypeptide
• occurs under the direction
of mRNA
•_________are the sites of
translation
4. Compare where transcription and
translation occur in bacteria and in
eukaryotes.
Prokaryotes
Transcription – cytoplasm
Translation – cytoplasm
Eukaryotes
Transcription – Nucleus
Translation – cytoplasm
LE 17-3-1
TRANSCRIPTION
Prokaryotic cell
DNA
LE 17-3-2
TRANSCRIPTION
DNA
mRNA
Ribosome
Prokaryotic cell
Polypeptide
Prokaryotic cell
LE 17-3-3
DNA
TRANSCRIPTION
mRNA
Ribosome
TRANSLATION
Polypeptide
Prokaryotic cell
Nuclear
envelope
TRANSCRIPTION
Eukaryotic cell
DNA
LE 17-3-4
DNA
TRANSCRIPTION
mRNA
Ribosome
TRANSLATION
Polypeptide
Prokaryotic cell
Nuclear
envelope
TRANSCRIPTION
DNA
Pre-mRNA
RNA PROCESSING
mRNA
Eukaryotic cell
LE 17-3-5
DNA
TRANSCRIPTION
mRNA
Ribosome
TRANSLATION
Polypeptide
Prokaryotic cell
Nuclear
envelope
DNA
TRANSCRIPTION
Pre-mRNA
RNA PROCESSING
mRNA
Ribosome
TRANSLATION
Polypeptide
Eukaryotic cell
5. Define “codon” and explain the relationship between the linear
sequence of codons on mRNA and the linear sequence of amino
acids in a polypeptide.
Codons
• mRNA base triplets
• specifies specific amino acid
• amino acid placed at the
corresponding position along a
polypeptide
Template strand
• provides a template for
ordering the sequence of
nucleotides in an RNA
transcript
5. Define “codon” and explain the relationship between the linear
sequence of codons on mRNA and the linear sequence of amino acids
in a polypeptide.
Triplet code
• nonoverlapping
• three-nucleotide words
• code for amino acids
Example:
• AGT on DNA strand
• results in the placement of
the amino acid serine
• at the corresponding
position of the polypeptide to
be produced
6. Explain what it means to say that the genetic code is
redundant and unambiguous.
How many amino acids?
20
How many codons?
64
What does that imply?
6. Explain what it means to say that the genetic code is
redundant and unambiguous.
Redundant but not
ambiguous (?)
1. One amino acid can
have more than one codon
e.g., UCU, UCC, UCA,
etc., all code for Serine
2. No codon specifies more
than one amino acid
7. Explain the significance of the reading frame during
translation.
The fat cat ate the rat
Reading Frame
• Codons must be read in the
correct reading frame
• What happens if you are off
by one letter?
• Frame Shift Error
Practice
What amino acid does
CAC code for?
• AGA?
• CGU?
• Three code for stop
• AUG codes for begin
Evolution of the
Genetic Code
The genetic code is nearly
universal
What does that mean?
• shared by the simplest
bacteria to the most
complex animals
What does that imply?
Luciferase
9. Explain the general process of transcription, including the
three major steps of initiation, elongation, and termination.
The three stages of
transcription:
1) Initiation
2) Elongation
3) Termination
Molecular Components of Transcription
RNA Polymerase
pries the DNA strands
apart and hooks
together the RNA
nucleotides
• RNA synthesis follows
the same base-pairing
rules as DNA
• except __?__
substitutes for thymine
8. Explain how RNA polymerase recognizes where transcription
should begin. Describe the role of the promoter, the terminator,
and the transcription unit.
Initiation
Promoter
• DNA sequence where RNA polymerase attaches
Transcription Unit
• stretch of DNA that is transcribed
Terminator
• DNA sequence found only on prokaryotes
Animation: Transcription
LE 17-7
Promoter
Transcription unit
5
3
Start point
RNA polymerase
3
5
DNA
Initiation
5
3
3
5
RNA Template strand
Unwound tran- of DNA
DNA
script
Elongation
Rewound
DNA
5
3
3
5
RNA
transcript
3
5
LE 17-7
Promoter
Transcription unit
5
3
Start point
RNA polymerase
3
5
DNA
Initiation
5
3
3
5
RNA Template strand
Unwound tran- of DNA
DNA
script
Elongation
Rewound
DNA
5
3
3
5
3
5
RNA
transcript
Termination
5
3
3
5
5
Completed RNA transcript
3
Elongation of the RNA Strand
RNA polymerase
• untwists the double helix
• 10 to 20 bases at a time
• 40 nucleotides per
second (eukaryotes)
• can be transcribed
simultaneously by several
RNA polymerases
Why?
Termination of Transcription
Mechanisms of termination are
different in prokaryotes and
eukaryotes
Prokaryotes
• polymerase stops
transcription at the end of the
terminator sequence
Eukaryotes
• polymerase continues
transcription after the premRNA is cleaved
• Polymerase eventually falls
off the DNA
10. Explain how RNA is modified after transcription in
eukaryotic cells.
• Does the pre-mRNA now leave the nucleus?
• How is the pre-mRNA modified?
Alteration of mRNA Ends
Each end of a pre-mRNA molecule is modified in a particular way:
–
The 5 end receives a modified nucleotide cap
–
The 3 end gets a poly-A tail
These modifications share several functions:
–
They seem to facilitate the export of mRNA
–
They protect mRNA from hydrolytic enzymes
–
They help ribosomes attach to the 5’ end
Split Genes and RNA Splicing
Intervening sequences (Introns)
• long noncoding stretches - removed
Exons
• shorter coding sections – will be expressed
RNA splicing
• removes introns and joins exons
• creating an mRNA molecule with a continuous coding sequence
RNA duplicating RNA, a step closer to the origin of life
By Yun Xie |http://arstechnica.com/science/news/2011/04/investigations-into-the-ancient-rnaworld.ars
NASA JPL
According to the “RNA world” model of life's origin, RNA performed all of the operations
that are essential to life. RNA alone passed on genetic information and catalyzed the
reactions of basic metabolism; DNA and proteins were not in the picture. The RNA
world hypothesis is an appealingly simple model for simple early life forms, since it
allows the complex array of biochemical interactions among proteins, DNA, and RNA
to evolve gradually.
Concept 17.4: Translation is the RNA-directed
synthesis of a polypeptide: a closer look
Transfer RNA (tRNA)
•translates an mRNA message
into protein
•Molecules of tRNA are not
identical:
–
Each carries a specific
amino acid on one end
–
Each has an anticodon
on the other end
14. Describe the structure and function of tRNA.
tRNA molecule
• single RNA strand
• ~ 80 nucleotides long
• cloverleaf shape
• twists and folds into a threedimensional molecule
How?
• hydrogen bonds
A
C
C
“problems”
A. How do you make
sure that the correct
amino acid to connects
to the correct tRNA?
B. How do you make
sure that the correct
tRNA matches up with
the correct codon?
15. Explain how tRNA is joined to the
appropriate amino acid.
Accurate translation requires
two steps:
First step:
– correct match between a
tRNA and an amino acid
– done by the enzyme
aminoacyl-tRNA
synthetase (20 types)
Second step:
- correct match between
the tRNA anticodon and
an mRNA codon
16. Describe the structure and functions of ribosomes.
Ribosomes
facilitate specific coupling
of tRNA anticodons with
mRNA codons in protein
synthesis
Two ribosomal subunits
(large and small)
made of proteins and
ribosomal RNA (rRNA)
You have brucellosis. What do you do?
•
Tetracycline:
•
works by binding specifically to
the 30S ribosome of the
bacteria
•
preventing attachment of the
aminoacyl tRNA to the RNAribosome complex
•A ribosome has three
binding sites for tRNA:
–
The P site
–
holds the growing
polypeptide chain
–
The A site
–
holds the next
amino acid to be
added
–
The E site
–
is the exit site,
where discharged
tRNAs leave the
ribosome
17. Describe the process of translation (including initiation, elongation, and
termination) and explain which enzymes, protein factors, and energy sources
are needed for each stage.
•The three stages of
translation:
– Initiation
– Elongation
– Termination
Ribosome Association and Initiation of Translation
Initiation stage
• brings together mRNA, a tRNA with the
first amino acid, and the two ribosomal
subunits
Ribosome Association and Initiation of Translation
•First, a small ribosomal
subunit binds with mRNA and
a special initiator tRNA
Ribosome Association and Initiation of Translation
Then the small subunit
moves along the mRNA until
it reaches the start codon
(AUG)
Ribosome Association and Initiation of Translation
Proteins called initiation
factors bring in the large
subunit so the initiator tRNA
occupies the P site
Elongation of the Polypeptide Chain
Elongation
• Amino acids added
one by one
• Each addition
involves proteins
called elongation
factors
•Occurs in three steps:
1. codon recognition
2. peptide bond
formation
3. translocation
LE 17-18
Amino end
of polypeptide
E
3
mRNA
Ribosome ready for
next aminoacyl tRNA
P A
site site
5
2
GTP
2 GDP
E
E
P
A
P
A
GDP
GTP
E
P
A
three steps:
1- codon recognition
2 -peptide bond formation
3- translocation
LE 17-19
Termination of Translation
Release
factor
Free
polypeptide
5
3
3
3
5
5
Stop codon
(UAG, UAA, or UGA)
When a ribosome reaches a stop
codon on mRNA, the A site of the
ribosome accepts a protein called
a release factor instead of tRNA.
The release factor hydrolyzes the
bond between the tRNA in the
P site and the last amino acid of the
polypeptide chain. The polypeptide
is thus freed from the ribosome.
The two ribosomal subunits
and the other components
of the assembly dissociate.
Ribosome acts as one large Ribozyme
18. Describe the significance
of polyribosomes.
Polyribosomes
– make many
copies of a
polypeptide very
quickly
19. Explain what determines the primary structure of a protein and
describe how a polypeptide must be modified before it becomes fully
functional.
Primary structure
Amino acid sequence
Polypeptide chains are
modified after translation
Post-translational
modifications
–Removal of amino acids
• AUG
–Splitting of polypeptide
chain
• insulin
Targeting Polypeptides to Specific Locations
Two populations of ribosomes
are evident in cells:
1. free ribsomes (in the
cytosol)
2. bound ribosomes (attached
to the ER)
Free ribosomes mostly
synthesize proteins that function
in the cytosol
Targeting Polypeptides to Specific Locations
Bound ribosomes:
• endomembrane system
• secreted from the cell
Ribosomes are identical and can
switch from free to bound
Concept 17.5: RNA plays multiple roles in the cell:
a review
Type of RNA
Messenger
RNA (mRNA)
Functions
Carries information specifying
amino acid sequences of
proteins from DNA to ribosomes
Transfer RNA Serves as adapter molecule in
(tRNA)
protein synthesis; translates
mRNA codons into amino acids
Ribosomal
Plays catalytic (ribozyme) roles
RNA (rRNA)
and structural roles in ribosomes
Type of RNA
Primary
transcript
Functions
Serves as a precursor to mRNA,
rRNA, or tRNA, before being
processed by splicing or
cleavage
Concept 17.6: Comparing gene expression in prokaryotes
and eukaryotes reveals key differences
Prokaryotic cells:
• lack a nuclear envelope
• allows translation to begin
while transcription
progresses
Eukaryotic cell:
– The nuclear envelope
separates transcription
from translation
– Extensive RNA
processing occurs in
the nucleus
LE 17-22
RNA polymerase
DNA
mRNA
Polyribosome
RNA
polymerase
Direction of
transcription
0.25 mm
DNA
Polyribosome
Polypeptide
(amino end)
Ribosome
mRNA (5 end)
Coupled transcription and translation in bacteria
20. Define “point mutations”. Distinguish between base-pair substitutions and
base-pair insertions. Give an example of each and note the significance of such
changes.
Mutations
• changes in the genetic
material of a cell or virus
Point mutations
• chemical changes in just
one base pair of a gene
The change of a single
nucleotide in a DNA template
strand leads to production of
an abnormal protein
LE 17-23
Wild-type hemoglobin DNA
3
Mutant hemoglobin DNA
5
3
mRNA
5
mRNA
3
Normal hemoglobin
5
5
3
Sickle-cell hemoglobin
Substitutions
Base-pair substitution
• replaces one nucleotide and its
partner with another pair of
nucleotides
• can cause missense or
nonsense mutations
Missense
• mutations still code for an amino
acid, but not necessarily the right
amino acid
Nonsense mutations
• change an amino acid codon
into a stop codon, nearly always
leading to a nonfunctional protein
Missense mutations are more
common
Insertions and Deletions
Insertions and deletions
• additions or losses of
nucleotide pairs in a gene
• have a disastrous effect on
the resulting protein more
often than substitutions do
• may alter the reading
frame, producing a frameshift
mutation
Mutagens
Spontaneous mutations
• may occur during DNA
replication, recombination,
or repair
Mutagens
• physical or chemical
agents that can cause
mutations
– Mutagenic radiation,
ultraviolet light
(physical)
– Cancer-causing
chemicals