Transcript • In 1909- Archibald _______ suggested that CHAPTER 17 FROM GENE TO PROTEIN

CHAPTER 17
FROM GENE TO PROTEIN
• DNA makes ______ makes __________.
• Proteins are the links between ________ and_________.
• In 1909- Archibald _______ suggested that
1. genes dictate phenotype through enzymes that catalyze
specific chemical reactions in the cell.
2. the symptoms of an inherited disease reflect a person’s
inability to synthesize a particular ___________.
• Gerrod speculated that alkaptonuria, a hereditary disease,
was caused by the absence of an enzyme in a pathway
1. The study of metabolic defects provided
evidence that genes specify proteins
• The idea of __________ pathways was suggested
• 1930s- George Beadle and Boris Ephrussi
speculated that each mutation affecting ________
in Drosophila blocks pigment synthesis at a
specific step by preventing production of the
___________ that catalyzes that step.
Actual evidence for metabolic pathways came from Beadle and
Tatum in the 1930s
Beadle and Tatum Experiment
• Organism used- -bread mold, Neurospora crassa.
Experiment
1. Mutate Neurospora with __________
2. Screened the survivors for mutants that differed in their
nutritional needs.
•____________ Neurospora can grow on a
____________ medium
Minimal medium = agar, inorganic salts, glucose, and the
vitamin biotin.
• Most nutritional mutants can survive on a complete growth
medium which includes all 20 amino acids.
3. If mutant failed to grow on minimal medium, add amino
acid ____________ until growth is evident
Results
1. Identify a number of mutants that did not grow on arginine, but
would grow if supply arginine pathways intermediates
Their results provided strong evidence for the one
gene - one __________ hypothesis.
Later modified to the one gene-one __________ hypothesis
Why? Not all proteins are _____________
Gene A
Gene A
mutants
Gene B
mutants
Gene C
mutants
Fig. 17.2
Gene B
Gene C
2. Transcription and translation are the two
main processes linking gene to protein
• The bridge between DNA and
__________synthesis is RNA.
• RNA differs from DNA
1. RNA contains ________ as its
sugar (not deoxyribose)
2. _________ replaces thymine.
AGTCAT becomes AGUCAU
3. An RNA molecule almost
always consists of a ________
strand.
This is an H in DNA
• In DNA or RNA, only four nucleotides produce
life
• The specific _________ of hundreds or thousands
of nucleotides in each gene carries the information
for the primary structure of a protein, the linear
order of the ____ possible amino acids.
• To get from DNA, written in one chemical
language, to protein, written in another, requires
two major stages, ____________
and____________ .
• ____________ - DNA is the template for RNA,
usually __________ RNA (mRNA).
•____________________ - the
information contained in the
order of nucleotides in mRNA is
used to determine the
__________ sequence of a
polypeptide.
-Translation occurs at
____________.
• The basic mechanics of transcription and translation are
________ in eukaryotes and prokaryotes.
Fig. 17.3a
Major differences between prokaryotes and eukaryotes1. Transcription and translation are __________in bacteria (which
lack________ ), but occur at separate locations in eukaryotes.
Protein
RNA
DNA
- In bacteria, ___________attach to the leading end of a
mRNA molecule while transcription is still in progress.
-In a eukaryotic cells, almost all transcription occurs in
the nucleus and translation occurs mainly at ribosomes
in the cytoplasm.
2. Eukaryotes- Before the ________
can leave the nucleus it is
modified in various ways during
__________________ before the
finished mRNA is exported to the
cytoplasm.
Fig. 17.3b
3. In the genetic code, nucleotide triplets
specify amino acids
• A single or doublet code can not provide enough
____________ (4 and 16 respectively) to code for all
20 amino acids.
• Triplets of nucleotide bases are the smallest units of
uniform length that can code for all the amino acids.
• In the__________, three consecutive bases specify
an amino acid, creating 43 (64) possible__________.
• The genetic instructions for a polypeptide chain are
written in DNA as a series of three-_________
words.
• During transcription, one DNA strand,
the_____________, provides a template for ordering
the sequence of nucleotides in an RNA transcript.
• The _____________RNA
molecule is synthesized
according to base-pairing
rules, except that _______ is
the complementary base Template
strand
to adenine.
• During translation, blocks
of three nucleotides,
_______, are decoded into
a sequence of amino acids.
mRNA
Protein
Fig. 17.4
• During translation
• _________ are read in the 5’->3’ direction
• Each codon specifies _____ of the 20 amino acids
• It is a triplet code: three bases for one amino acid
• It would take at least ____ nucleotides to code for a
polypeptide that is 100 amino acids long.
Problem: We have 64 possible combinations of the nucleotides
Why 64 possibilities? How many ways can you arrange
4 bases in sets of three?
Answer = _____ =________________
Thus, predict that _______________ combination must
specify a given amino acid
• 1960s-Marshall Nirenberg determined the first
match, that UUU coded for the amino acid
_______________.
• Experiment - Add poly-U (uracil-only) RNA _______
• plus amino acids, ribosomes, other components.
• Result- This poly(U translated into a long chain of
phenyalanine.
UUUUUUUUUUUUUUU
• Other more elaborate techniques were required to decode
mixed triplets such a AUA and CGA.
• By the mid-1960s the entire code was _________________.
The genetic code
1. ___ of 64 triplets code
for amino acids.
• AUG codes for the
methionine and
_______ of translation.
•Three codons –UAA, UAG and
______ do not code amino acids
but signal the termination of
translation.
2. The genetic code is ___________ but
not______________ .
• Typically several different codons
specify a given amino acid
Fig. 17.5
• Any one codon indicates
___________ amino acid.
•If you know a specific codon, you know the amino acid
•If you know only the amino acid, there may be several possible codons
•Example- Both GAA and GAG specify glutamate, but no other amino acid.
The genetic code (cont.)
Fig. 17.5
• Codons synonymous for
the same amino acid often
differ only in the _______
codon position.
Example:
GUU, GUC, GUA and
GUG all encode ________
A ________________ is
established at the translation start
RNA 5’ UUACGAUGGAUUCAAACGUCAGGGCCUAAGGCUAG3’
Met Asp Ser Asn Val Arg Ala
Stop
Start
codon
codon
Summary- The genetic code uses__________________________, or
codons, each of which is translated into a specific amino acid.
• The genetic code is nearly__________ , from
bacteria to mammals
Thus, we can synthesize bacterial proteins in_________
Exceptions do exist- they use slightly
altered genetic codes:
1.single-celled eukaryotes like
Paramecium.
2. certain mitochondria and chloroplast_______
4. Transcription is the DNA-directed synthesis of RNA
• Transcription
can be
separated
into three
stages:
1. _________
2. elongation
3. __________
Fig. 17.7
What actually makes the RNA?
• Messenger RNA is transcribed from the template
strand of a gene by _____________________.
• ___________________:
• separates the DNA strands
• bonds the RNA nucleotides as they base-pair along the
DNA template.
• can add nucleotides ______ to the ________ of the
growing polymer.
• Genes are read _______ creating a ______RNA molecule.
5’
3’
RNA
3’
5’
DNA
Compare prok and euk polymerases
• Bacteria -________ type of RNA polymerase that
synthesizes all RNA molecules.
• Eukaryotes -_________ RNA polymerases (I, II,
and III) in their _________ .
• ___________________ is used for ________synthesis.
What marks the start of transcription??
•Answer- Specific sequences of nucleotides called the
_________ mark where gene transcription begins
•In prokaryotes, RNA polymerase can recognize and bind
__________ to the promotor region.
•In eukaryotes, proteins called ________________ first
bind the promotor region, especially a_________ , then RNA
polymerase II binds
1. Initiation
• Eukaryotes- The
complex including RNA
polymerase II plus
transcription factors is
called the
_________________.
Fig. 17.8
2. Elongation
• As RNA polymerase ________ the double helix,10
to 20 bases at time.
• The enzyme adds
nucleotides to the
___ end of the
growing strand.
• Behind the point
of RNA synthesis,
the double helix
_______ and the
RNA molecule
peels away.
Fig. 17.7
2. Elongation (cont.)
• A single gene can be transcribed simultaneously by
_____________ RNA polymerases at a time.
• A growing strand of RNA trails off from
each______________.
5’
3’
RNA
5’ DNA
TATAA
5’
3. Termination
• Prokaryotes- RNA polymerase stops transcription at
the end of the______________ .
• Both the RNA and DNA is then released.
• ______________- the polymerase continues for
hundreds of nucleotides past the terminator
sequence,_____________ .
• At a point about _____________ nucleotides past this
sequence, the pre-mRNA is cut.
5’
3’
TATAA
AAUAAA
10-35
nucleotides
5’
5. Eukaryotic cells modify RNA after transcription
• Modifications include:
1. A ________at the 5’ end of the pre-mRNA molecule
The cap is a modified form of guanine
Function: a. Protect mRNA from __________enzymes.
b. “Attach here” signal for____________
2. _____________50 to 250 adenine nucleotides at the 3’ end
Function- a. inhibiting hydrolysis, b. facilitating ribosome
___________c. facilitate the export of mRNA from the nucleus.
3’ tail
5’ cap
Fig. 17.9
•The mRNA molecule also includes ____________leader and trailer segments.
RNA modification in eukaryotes (cont.)
3. ______________ - Most eukaryotic genes and their RNA
transcripts have long ____________ stretches of nucleotides.
• The noncoding segments are called ________
• The coding regions (final mRNA transcript) are
called__________
•What is a coding region??
•RNA sequences that are translated into amino acid sequences
Leader
Coding region
Trailer
3’ tail
5’ cap
Fig. 17.9
Fig. 17.10
• RNA splicing removes ______ and joins ______
to create an mRNA molecule with a
_____________ coding sequence.
This splicing is accomplished
by a________________.
Contains small nuclear
ribonucleoproteins (snRNPs).
and small nuclear RNA
molecules (snRNA). Each is
about 150 nucleotides long.
Fig. 17.11
Splicing steps
(1) Pre-mRNA combines with
_________ and other proteins to
form a spliceosome.
(2) Within the spliceosome,
________ base-pairs with
nucleotides at the ends of the
intron.
(3) The RNA transcript is cut to
release the________ , and the
exons are spliced together;
Here the snRNA acts as a____________ ,
an RNA molecule that functions as an enzyme.
15.3
15.2
15.1
Overview of eukaryotic transcription/translation
14
13.2
13.3
13.1
12
11
11.1
11.2
Chromosome- 1.5 x 108 base pairs containing about 3000 genes
12
13.1
13.2
13.3
14
15
21
22
23.1
23.2
23.3
31.1
31.2
31.3
0.4% of a chromosome, containing 10 genes
32
33.2 33.1
33.3
34
35.2
35.1
35.3
= exon
= intron
5’
3’
ATG B
C
+1
D
E
F
TAA
3’
5’
DNA
Transcription AAUAAA Template strand
AUG
hnRNA
Promoter
RNA Splicing
UAA
polyA tail,cap
Transport to cytoplasm
Cap
AB
7mG
AUG
CD
Poly-A tail
E
F
AAAAAA…..
UAA
mRNA
Translation
NH2
COO-
Protein
6. Translation is the RNA-directed synthesis
of a polypeptide
How do proteins read the RNA molecule??
Answer-the tRNA molecule
• ______________(tRNA) transfers amino acids from the
cytoplasm’s pool to a
______________ .
• The ribosome adds each
amino acid carried by tRNA
to the growing end of the
______________ chain.
Fig. 17.13
A tRNA molecule
Fig. 17.14
• Is about ___ nucleotides long
• Contains attachment site at the
3’ end for an amino acid.
• Contains a loop with the
___________
The anticodon base-pairs with a
complementary codon on mRNA.
3’
5’
If the codon on mRNA is UUU, a tRNA with a
______ anticodon and a tRNA carrying phenylalanine
will bind to it.
•The anticodons of some tRNAs recognize more than one________.
•Why? Because the rules for base pairing between the third base of
the codon and anticodon are ________ (called______________).
How do we explain this “wobble”??
• If each anticodon had to be a perfect match to each
codon, we would expect to find ___ types of
tRNA, but the actual number is about____ .
• At the wobble position, U on the _____________can
bind with A or G in the third position of a codon.
• Some tRNA anticodons include a modified form of
adenine, inosine, which can hydrogen bond with U, C,
or A on the codon.
“Wobble” base pairing
Fig. 17.5
Leu
“Wobble”
AAU
AAU
UGGCGAUGUUAGUAUUGCAUGAGUUAGGUGACCAAGAU
Start Leu
Leu
How the is the tRNA linked to the amino acid??
• Each amino acid is joined
to the correct tRNA by
____________________________
The 20 different synthetases match
the 20 different________________.
• The synthetase catalyzes a
covalent bond between them,
forming _______________ or
activated amino acid.
•______________ (protein +
rRNA) facilitate the specific
coupling of the tRNA anticodons
with mRNA codons.
phetRNA
Protein
RNA
Ribosomal subunits
1. Large
2. Small
Fig. 17.15
• Each ribosome has a binding site for mRNA and
three binding sites for tRNA molecules.
• The ________ holds the tRNA carrying the growing
polypeptide chain.
• The ______carries the tRNA with the next__________.
• Discharged tRNAs leave the ribosome at the_________.
Fig. 17.16
Translation
• Translation can be divided into three _________ :
1. initiation
2. ____________
3. termination
• Both initiation and chain elongation require energy provided by
the hydrolysis of________.
1. Initiation
a.
Small ribosomal
subunit binds mRNA
b.
Initiator tRNA (with
methionine) is attached
to start codon
•
Initiation factors
bring in the large
subunit such that the
initiator tRNA
occupies the P site.
Fig. 17.17
2. Elongation - ________ steps per amino acid added Translation
a. Codon recognition- an elongation factor assists hydrogen
bonding between the mRNA codon under the A site with the
corresponding anticodon of tRNA carrying the appropriate
amino acid.
• This step requires the ____________ of two GTP.
b. _____________________- a
________ molecule catalyzes the
formation of a peptide bond between
the polypeptide in the P site with the
new amino acid in the A site
Fig. 17.18
c. ____________ - the ribosome
moves the tRNA with the attached
polypeptide from the A site to the P
site.
Note: mRNA is “read” 5’ -> 3’, codon by codon.
Translation
3. Termination occurs when one of the three ______ codons
reaches the ___ site.
• A ____________ binds to the stop codon and hydrolyzes the
bond between the polypeptide and its tRNA in the P site.
Fig. 17.19
Other translation facts
• Multiple ribosomes, polyribosomes, may
trail along the same mRNA.
• A ribosome requires less than a minute to
translate an average-sized mRNA into a
polypeptide.
Fig. 17.20
Post-translational modifications• Additions of________ , lipids, or phosphate groups to
amino acids.
• Enzymes may remove some amino acids or cleave
whole polypeptide chains.
• Two or more ______________ may join to form a
protein.
7. Signal peptides target some eukaryotic
polypeptides to specific destinations in the cell
• Recall that some ribosomes reside in two locations• Free ribosomes are suspended in the ________ and
synthesize proteins that reside in the__________ .
• __________ ribosomes are attached to the cytosolic side
of the_______________________.
• They synthesize proteins of the endomembrane system
as well as proteins secreted from the cell.
• Translation in all ribosomes begins in the cytosol
• A polypeptide destined for the ________________ system
or for export has a specific ________________ (approx
20 amino acids) region at or near the leading end.
• A _________________________(SRP) binds to the signal
peptide and attaches it and its ribosome to a receptor
protein in the ER membrane.
Fig. 17.21
The SRP leaves
and protein
synthesis resumes
with the growing
polypeptide
snaking across
the membrane
into the cisternal
space
8. RNA plays multiple roles in the cell: a
review
• RNA is versatile
• ________ - carries info for protein production
• _______-transport amino acids in translation
• _______- part of ribosome, has role in translation
• ________ - splicing mRNA
9. Comparing protein synthesis in
prokaryotes and eukaryotes: a review
Euks
DNA polymerase
Requires
Transcription and
translation coupled?
RNA processing?
Protein targeting?
Proks
10. Point mutations can affect protein
structure and function
• __________ are changes
in the genetic material of
a cell (or virus).
Fig. 17.23
• include large-scale
mutations in which ______
segments of DNA are
affected (translocations,
duplications, and
inversions).
• A chemical change in just
one base pair of a gene
causes a_______________
In sickle cell, a single T to A
mutation changes amino
acid from glu to val
•______________________ - alterations of nucleotides still indicate the
same amino acids because of redundancy in the genetic code.
•Many other mutations cause no effect in function
• Other base-pair
substitutions cause a
readily detectable
change in a protein.
• ____________mutations
are those that still code
for an amino acid but
change the indicated
amino acid.
• ____________mutations
change an amino acid
codon into a _____
codon, nearly always
leading to a nonfunctional
protein.
Fig. 17.24
• Insertions and ____________
are additions or losses of
nucleotide pairs in a gene.
• These have a __________
effect on the resulting protein
more often than substitutions
do.
• Unless these mutations occur in
multiples of three, they cause a
___________ mutation.
• All the nucleotides
downstream of the deletion
or insertion will be
improperly grouped into
codons.
• The result will be extensive
missense, ending sooner or
later in nonsense - premature
termination.
Fig. 17.24
• ______________ are chemical or physical agents
that interact with DNA to cause mutations.
• ___________ agents include high-energy radiation like
X-rays and ultraviolet light.
• _________ mutagens may operate in several ways.
• As base ________ ___that may be substituted into
DNA, but that pair incorrectly during DNA
replication.
• Interfere with DNA replication by inserting into DNA
and distorting the____________________.
• Cause chemical changes in bases that change their
pairing properties.
11. What is a gene? revisiting the question
• ___________ concept - a discrete unit of inheritance
that affects phenotype.
or
• Morgan and his colleagues assigned genes to specific loci
on chromosomes.
• A specific nucleotide sequence along a region of a
DNA molecule.
or
• A DNA sequence that codes for a specific
polypeptide chain.
or
• A region of DNA whose final product is either a
polypeptide or an RNA molecule.
Fig. 17.26