Download Life: The Science of Biology, 8e

12
From DNA to Protein:
Genotype to Phenotype
12.1 What Is the Evidence that Genes Code for Proteins?
The gene-enzyme relationship is one-gene,
one-polypeptide relationship.
Example: In hemoglobin, each polypeptide
chain is specified by a separate gene.
12.2 How Does Information Flow from Genes to Proteins?
Expression of a gene to form a
polypeptide takes 3 main processes:
• Transcription—copies information from
gene to a sequence of pre-mRNA.
• RNA Processing-converts pre-mRNA to
mRNA
• Translation—converts mRNA sequence
to amino acid sequence.
12.2 How Does Information Flow from Genes to Proteins?
RNA, ribonucleic acid differs from DNA:
• Single strand-so what’s that mean?
• The sugar is ribose
• Contains uracil (U) instead of thymine (T)
12.2 How Does Information Flow from Genes to Proteins?
RNA can pair with a single strand of
DNA, except that adenine pairs with
uracil instead of thymine.
Single-strand RNA can fold into much
more unique and differing shapes by
internal base pairing. (This flexibility is
not seen in DNA)
Figure 12.2 The Central Dogma
The central dogma of molecular biology for
eukaryotes: information flows in one direction
when genes are expressed (Francis Crick).
12.2 How Does Information Flow from Genes to Proteins?
ONE Exception to the central dogma:
Viruses: acellular particles that reproduce
inside cells; many have RNA instead of DNA
so reverse the process. Synthesis of DNA
from RNA is called reverse transcription.
Viruses that do this are called retroviruses
12.2 How Does Information Flow from Genes to Proteins?
Messenger RNA (mRNA) forms as a
complementary copy of DNA and
carries information to the cytoplasm.
(WHY use a copy of DNA?)
This process is called transcription and
occurs in the nucleus.
RNA polymerase is the enzyme that runs
the same direction as it’s “cousin”. Will
we have a leading or lagging strand
now? Why or why not?
Figure 12.3 From Gene to Protein
12.3 How Is the Information Content in DNA Transcribed to
Produce RNA?
Transcription occurs in three phases:
• Initiation
• Elongation
• Termination
12.3 How Is the Information Content in DNA Transcribed to
Produce RNA?
Initiation requires a promoter—a special
sequence of DNA.
RNA polymerase binds to the promoter.
Promoter tells RNA polymerase where to
start, which direction to go in, and which
strand of DNA to transcribe. In
eukaryotes it is the “TATA” region called
the initiation site.
Figure 12.5 DNA Is Transcribed to Form RNA (A)
12.3 How Is the Information Content in DNA Transcribed to
Produce RNA?
Elongation: RNA polymerase copies
base pairs of DNA into pre-mRNA.
RNA polymerase also runs in a 5-3
direction. (So what DNA template will
we use? Why? What about the other
one?)
Figure 12.5 DNA Is Transcribed to Form RNA (B)
12.3 How Is the Information Content in DNA Transcribed to
Produce RNA?
Termination: specified by a specific DNA
base sequence.
Mechanisms of termination are complex
and varied.
Figure 12.5 DNA Is Transcribed to Form RNA (C)
Eukaryotes—first product is a premRNA that is longer than the final
mRNA and must undergo processing.
The Pre mRNA must be readied for
travel so 5’ caps and poly A tails (3’)
are added to the strand. Non coding
regions called introns are also
removed leaving only exons. Once
RNA processing is complete, we
have mRNA
• Please get a book and turn to page
262
Before we begin, we need to understand that RNA is extremely
flexible!
• There are 4 types of RNA, each encoded by its own type of gene:
• mRNA - Messenger RNA: Encodes amino acid sequence of a
polypeptide.
• tRNA - Transfer RNA: Brings amino acids to ribosomes during
translation.
• rRNA - Ribosomal RNA: With ribosomal proteins, makes up
the ribosomes, the organelles that translate the mRNA.
• snRNA - Small nuclear RNA: With proteins, forms complexes that
are used in RNA processing in eukaryotes. (Not found in
prokaryotes.) (This is what splices out introns!)
12.3 How Is the Information Content in DNA Transcribed to
Produce RNA?
The genetic code: specifies which amino
acids will be used to build a protein
Codon: a sequence of three bases. Each
codon specifies a particular amino acid.
Start codon: AUG—initiation signal for
translation
Stop codons: stops translation and
polypeptide is released-UAA, UGA or
UAG
Figure 12.6 The Genetic Code
12.3 How Is the Information Content in DNA Transcribed to
Produce RNA?
How do we keep from having too many
mutations?
For most amino acids, there is more than
one codon; the genetic code is
redundant.
How does that protect the integrity of
proteins?
12.3 How Is the Information Content in DNA Transcribed to
Produce RNA?
The genetic code is nearly universal: the
codons that specify amino acids are the
same in all organisms.
That means we get uniqueness because
of the sequence of amino acids
Even in all that diversity, all life uses the
same start and stop codons!
12.4 How Is RNA Translated into Proteins?
Let’s look at each type of RNA now….
Functions of tRNA:
• Carries an inactive amino acid
• Carries an active amino acid
• Interacts with ribosomes by providing
the anticodon
Figure 12.8 Transfer RNA
12.4 How Is RNA Translated into Proteins?
The conformation (three-dimensional
shape) of tRNA results from base
pairing (H bonds) within the molecule.
Anticodon: site of base pairing with
mRNA. Unique for each species of
tRNA.
Formula for building a protein is
Codon + anticodon + inactive aa=
specific aa in polypeptide chain
12.4 How Is RNA Translated into Proteins?
Example:
DNA codon for alanine: GCC
Complementary mRNA: CGG
Anticodon on the tRNA: GCC
Active amino acid would be: alanine
12.4 How Is RNA Translated into Proteins?
Wobble: specificity for the base on tRNA
so one tRNA can decode up to 3
different codons.
Example: codons for alanine—GCA,
GCC, and GCU—are recognized by the
same tRNA.
Allows cells to produce fewer tRNA.
12.4 How Is RNA Translated into Proteins?
Ribosome: the workbench—holds
mRNA and tRNA in the correct positions
to allow assembly of polypeptide chain.
Ribosomes are not specific, they can
make any type of protein.
12.4 How Is RNA Translated into Proteins?
rRNA:
AKA the Ribosomes have two subunits,
large and small.
The subunits are made of rRNA or
ribosomal RNA.
Figure 12.10 Ribosome Structure
12.4 How Is RNA Translated into Proteins?
Large subunit has three tRNA binding
sites:
• A site binds with anticodon of charged
tRNA. Activation
• P site is where tRNA adds its amino
acid to the growing chain. Polypeptide
chain is held and built
• E site is where tRNA sits before being
released. Exit
12.4 How Is RNA Translated into Proteins?
Translation also occurs in three steps:
• *Initiation-start codon (AUG) first amino
acid is always methionine
• Elongation of the polypeptide chain
• Termination- stop codon enters the A
site.
Methionine (AUG) hits the P site of the small
ribosomal sub-unit
that action initiates the process.
One of the first things that happens is the large
ribosomal sub-unit
joins with the small unit and makes an rRNA
Figure 12.11 The Initiation of Translation (Part 1)
Figure 12.11 The Initiation of Translation (Part 2)
Figure 12.12 The Elongation of Translation (Part 1)
Figure 12.12 The Elongation of Translation (Part 2)
Figure 12.13 The Termination of Translation (Part 1)
Figure 12.13 The Termination of Translation (Part 2)
Figure 12.13 The Termination of Translation (Part 3)
Table 12.1
Figure 12.14 A Polysome (Part 1)
Figure 12.14 A Polysome (Part 2)
• http://highered.mheducation.com/sites/
0072507470/student_view0/chapter3/a
nimation__how_translation_works.html
• http://www.stolaf.edu/people/giannini/fla
shanimat/molgenetics/translation.swf
• http://www.phschool.com/science/biolog
y_place/biocoach/transcription/difgns.ht
ml
Figure 12.15 Destinations for Newly Translated Polypeptides in a Eukaryotic Cell
12.6 What Are Mutations?
Somatic mutations occur in somatic
(body) cells. Mutation is passed to
daughter cells, but not to sexually
produced offspring.
Germ line mutations occur in cells that
produce gametes. Can be passed to
next generation. This is the key to
evolution and are available to occur in
transcription.
12.6 What Are Mutations?
All mutations are alterations of the
nucleotide sequence. 2 levels of
mutation….
Point mutations: change in a single
base pair—loss, gain, or substitution
of a base.
Chromosomal mutations: change in
segments of DNA—loss, duplication, or
rearrangement.
12.6 What Are Mutations?
Point mutations can result from
replication and proofreading errors, or
from environmental mutagens.
Silent mutations have no effect on the
protein because of the redundancy of
the genetic code.
Silent mutations result in genetic diversity
not expressed as phenotype
differences.
12.6 What Are Mutations?
12.6 What Are Mutations?
KEY! These CAN be beneficial!
Missense mutations: base substitution
results in amino acid substitution.
12.6 What Are Mutations?
Sickle allele for human β-globin is a
missense mutation.
Sickle allele differs from normal by only
one base—the polypeptide differs by
only one amino acid.
Individuals that are homozygous have
sickle-cell disease.
Figure 12.18 Sickled and Normal Red Blood Cells
12.6 What Are Mutations?
Nonsense mutations: base substitution
results in a stop codon.
12.6 What Are Mutations?
Frame-shift mutations: single bases
inserted or deleted—usually leads to
nonfunctional proteins.
12.6 What Are Mutations?
Chromosomal mutations:
Deletions—severe consequences unless
it affects unnecessary genes or is
masked by normal alleles.
Duplications—if homologous
chromosomes break in different places
and recombine with the wrong partners.
Figure 12.19 Chromosomal Mutations (A, B)
12.6 What Are Mutations?
Chromosomal mutations:
Inversions—breaking and rejoining, but
segment is “flipped.”
Translocations—segment of DNA
breaks off and is inserted into another
chromosome. Can cause duplications
and deletions. Meiosis can be
prevented if chromosome pairing is
impossible.
Figure 12.19 Chromosomal Mutations (C, D)
12.6 What Are Mutations?
• Replication errors—some escape
detection and repair.
• Nondisjunction in meiosis.
12.6 What Are Mutations?
Mutation provides the raw material for
evolution in the form of genetic diversity.
Mutations can harm the organism, or be
neutral.
Occasionally, a mutation can improve an
organism’s adaptation to its
environment, or become favorable as
conditions change.
Eukaryotic gene regulationTATA REGION=3'-TATAAT-5’
RNA PROCESSING
12.6 What Are Mutations?
Induced mutation—due to an outside
agent, a mutagen.
Chemicals can alter bases
Prokaryotic gene regulation much simpler!
Operons are repeating regions that make up the prokaryote’s
genome
They include 3 main regions; promoter, operator and
structural genes
The 2 main operon examples are the inducible (lac for lactose)
or repressible (trp for tryptophan) models
What do you think regulatory genes code for?
Lac operon structural genes, produce enzymes that can digest lactose.
So, when would you want to transcribe and translate those enzymes?
In the lac (lactose) model, we call this method of gene regulation
“inducible” as the substance (lactose) causes the genes to be on or off.
(Lactose induces the operon to be on)
Let’s try it!
Open notebook
Since lactose is a factor in the operating of this enzyme in that it
Changes the repressor protein’s shape so it can not fit into the operator
region, we call it “allolactose”.
But what about if the mRNA we make creates proteins that make
A substance we need?
Tryptophan is an essential substance for bacterial metabolism.
Therefore when would you want the operon “ON” and the creation
Of tryptophan to occur?
Let’s try it…
Open notebook
What happens to levels of trp as we go on and on?
Yes! As more and more trp is made, enough already! So,
Some of the trp made binds to the inactive repressor to change it’s
shape and allow it to bind to the promoter!
The product (trp) is a co-repressor when levels get high enough!
Complete this table:
Lac on when:
Lac off when:
So what determines?
Trp on when:
Trp off when:
So what determines?