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From DNA to Protein ...
Chapters 10 & 11
Overview
• Review of DNA & RNA
• Transcription & Translation
• Gene Mutations
• Controls over Genes
DNA: A Review
Holds:
Genetic information
Protein-building instructions
Double-helix of nucleotide bases with
sugar-phosphate backbone
Bases held together by H-bonds:
– A always pairs with T
– G always pairs with C
So what is a gene?
Segment of DNA molecule
Carries instructions for 1 polypeptide chain
Bases grouped in triplets that code for
specific amino acid
Variations in arrangement of bases lets cells
make all proteins needed
Exons
= protein-coding base sequences
Introns
= non-coding, repetitive sequences
(genome scrapyard of ready-to-use DNA
segments & small RNA molecules)
Both transcribed but introns removed
before mRNA reaches cytoplasm
RNA: A Review
Similar to DNA, except:
– Single-stranded
– Uracil replaces thymine
• Adenine pairs with uracil
Decodes DNA & acts as messenger
Types of RNA: mRNA
Messenger RNA
Carries protein-building
instructions from gene to
ribosome
“Half-DNA”
Types of RNA: rRNA
Ribosomal RNA
One of components of ribosomes
With tRNA, translate protein-building
instructions carried by mRNA
Ribosomes
2 subunits of rRNA & structural proteins
Have 2 tRNA binding sites
Come together as whole functional
ribosome during translation
Ribosomes of prokaryotes and
eukaryotes are similar in function but
different in composition
Certain antibiotics (e.g. tetracycline,
streptomycin) inactivate prokaryotic
ribosomes but don’t affect eukaryotic
ribosomes
Types of RNA: tRNA
Transfer RNA
45 different types
With rRNA, translate proteinbuilding instructions carried by
mRNA
Has anti-codon head:
= 3-base sequence complementary to codon
on mRNA transcript
Anti-codon head is complementary to
amino acid it carries
45 tRNAs exist in eukaryotic cells
Codon-anticodon pairing has “wiggle room”
for 3rd base of codon
e.g. AUU, AUC, AUA (isoleucine) use same tRNA
The Genetic Code
The rules that link codons in RNA with the
corresponding amino acids in proteins
Bases read 3 at a time = codon
64 codons that code for 20 amino acids
Some amino acids have ≥ 1 codon
(↓ transcription & translation errors)
AUG = methionine = START
UAA, UAG, UGA = STOP
Transcription & Translation
Process that turns sequence of nucleotide
bases in genes into sequence of amino
acids in proteins
transcription
DNA
translation
RNA
protein
DNA base sequence acts
as template to make RNA
Occurs in eukaryotic
nucleus
RNA moves into
cytoplasm
Amino acids join to
become
polypeptides
(proteins)
Transcription
DNA gene’s base sequence →
complementary mRNA base sequence
First step in protein synthesis
Sequence of nucleotides bases on DNA
strand exposed
Becomes template for RNA to be built
from A, C, G, T
Transcription factor binds to promoter
(START) base sequence on DNA
Promoter determines where mRNA
synthesis begins & which DNA strand is
template
RNA polymerase binds to
promoter
(unwinds 16-18 bps of DNA
helix)
RNA polymerase moves
along protein-coding gene
region
RNA polymerase unwinds
DNA in front & rewinds
behind as mRNA elongates
Incoming RNA nucleotides bind with
complementary bases on template
strand
e.g. (AGC) on DNA → (UCG) on mRNA
Creates complementary sequence from
DNA base sequence  template
mRNA is released at end of gene region
(STOP)
Is actually pre-mRNA because has
intron junk
mRNA modified before leaving nucleus
= introns cut out & exons respliced to form
functional mRNA
mRNA associates with proteins &
leaves nucleus
= is now ready for protein synthesis
mRNA enters cytoplasm
= location of pool of tRNA & free amino acids
Protein synthesis (translation) begins
Translation
mRNA base sequence → amino acids →
proteins
mRNA transcript enters ribosome
Codons translated into polypeptide chain
Initiation of Translation
mRNA binds to small
ribosomal unit
Initiator tRNA binds to start
codon (AUG)
(this tRNA carries Met & has anticodon UAC)
Large ribosomal subunit binds
to small subunit to form
functional ribosome
Initiator tRNA fits into P site of ribosome
(P site holds growing polypeptide)
A site lies vacant for the next amino-acidcarrying tRNA
Elongation of Translation
Chain of polypeptides is
synthesized as mRNA passes
between ribosomal subunits
tRNAs transfers amino acids
from cytosol to ribosome
Elongation is a 3-step process
1. Codon recognition:
Anti-codon of incoming amino-acidcarrying tRNA pairs with mRNA codon
in A site
Amino acids bind to mRNA in order
dictated by template of codons
2. Peptide bond formation:
Polypeptide separates from tRNA in P site
& attaches to amino acid carried by
tRNA in A site
Peptide bond catalyzed by rRNA in large
ribosomal subunit
3. Translocation:
P site tRNA leaves ribosome
Ribosome moves tRNA in A site (with
attached polypeptide) to P site
(mRNA moves along too)
Next mRNA codon is brought into A site
Elongation begins over again for next
addition
Polyribosomes
Once mRNA passes through ribosome, may
become attached to multiple other ribosomes
in row
Allows many copies of same protein to be
made quickly & simultaneously
Termination of Translation
mRNA STOP codon enters ribosome
(no tRNA has complementary anticodon)
Release factors bind to ribosome & detach
mRNA & polypeptide chain
Ribosome separates back into 2 subunits
Proteins either:
– Join pool of free proteins in cytoplasm
– Enter RER to be modified for transport
Summary of
Transcription &
Translation
Genetic info → protein synthesis
Via info transfer of
complementary base pairing
Phe
Gly
Arg
Phe
Gene Mutations
Most mutations are spontaneous & occur
during DNA replication
DNA polymerases & ligases (proofreaders)
catch most errors but not all
Bases can be substituted, inserted, deleted
Effects on protein structure & function depend
on how mRNA sequence is changed
Point Mutations
a.k.a. base substitution
Single nucleotide replaced with different
nucleotide
Can be harmless if still codes for same
amino acid
Can be harmful or even fatal
(wrong amino acid can alter protein function or
even code for STOP)
a. Missense mutation
Substitution alters codon so that it codes for
different amino acid
Usually changes protein function
(good / bad / neutral effects)
GCA-UUC-GUC
ala - phe - val
GCA-UUA-GUC
ala - leu - val
b. Nonsense mutation
Substitution alters codon so that it codes for
STOP signal
Results in premature termination of translation
Shortened protein is usually non-functional
GCA-UAU-GUC
ala - tyr - val
GCA-UAG-GUC
ala - STOP
c. Silent mutation
Substitution occurs in 3rd base of mRNA codon
New codon codes for same amino acid
(does not affect protein function)
GCA-UUC-GUC
ala - phe - val
GCA-UUU-GUC
ala - phe - val
Frameshift Mutations
1 or more base inserted or deleted
Deletion or insertion shifts 3-base
reading window
Protein is generally useless
= extensive missense & eventually
nonsense
Mutagens
Some mutations are not spontaneous
Ionizing radiation (e.g. x-rays)
= break up chromosomes & deposit free
radicals in cells
Non-ionizing radiation (e.g. UV radiation)
= changes base-pairing properties due to
thymine sensitivity
When are mutations good?
If occur in somatic (body) cells, only
affects individual
(not heritable)
If occur in gametes (sex cells), may be
heritable
– Can result in harmful, beneficial, or neutral
effects on individual’s survival
– Adaptation or elimination?
Cell Differentiation
Body cells differ in composition, structure,
& function
Each cell type undergoes selective gene
expression
= determines which tissues & organs
develop
How Are Genes Regulated?
Differentiated cells contain all genes
BUT
Cells only express genes necessary for their
specialized functions
Human genome = 25,000 – 30,000 genes
Most transcribed only in certain cells at
certain times
(default state = off)
Some transcribed in all cells because
encode proteins / RNA that are
essential for life
= housekeeping genes
Animal development is directed
by cascades of gene
expression & cell-to-cell
signalling
Homeotic gene
= master control gene that
regulates all other genes
Gene Control
How fast & when genes will be
transcribed & translated
Whether gene products are switched on or
silenced
= Controls over what kinds & how much of
each protein are in a cell
Regulatory elements respond to
concentration changes & chemical
signals in environment
e.g. DNAs, RNAs, polypeptide chains,
proteins
Both negative & positive controls exist
Promoters & Enhancers
Promoters:
– Short base sequences in DNA
– Regulatory proteins control transcription of
specific genes
Enhancers:
– Binding sites where promoters increase
transcription rates
Controls Before Transcription
Access to genes
– Blocked vs. open
How genes are transcribed
– Sequences can be rearranged or multiplied
• Allows rapid & simultaneous production of
gene products
Control of Transcript Processing
Frequency of transcription
How genes are transcribed
– Sequences can be rearranged or multiplied
• Allows rapid & simultaneous production of
gene products
Control of Translation
Rate of translation
How many times translation can occur on a
particular mRNA
Controls After Translation
Proteins & protein synthesis molecules
can be:
Activated
Inhibited
Stabilized
Modified
Degraded
Animal Gene Controls:
X Chromosome Inactivation
1 of 2 copies of X chromosome in female
mammals is inactivated
Condenses so can’t be transcribed = Barr body
So that female (XX) doesn’t have twice as
many X chromosome gene products as
male (XY)
= Dosage compensation
Which X chromosome is inactivated is
random in any given cell
– Some cells & descendants will express genes from
maternal X chromosome
– Other cells & descendants will express genes from
paternal X chromosome
Plant Gene Controls: ABC Model
3 sets of genes determine how
specialized parts of flower develop
in predictable pattern
In cells at tip of forming flower,
different sets of genes activated to
form sepals, petals, sexual
structures
Up to now, we have been largely focused on
eukaryotic cells.
What about prokaryotic cells?
Prokaryotic Gene Control
Primarily by changes in transcription rate
(depends on environmental conditions e.g. nutrient
availability, etc.)
When growth & reproduction conditions are
optimum, cells rapidly transcribe growth
enzymes & nutrient-absorbing genes
e.g. E. coli & the lactose operon
Gut of human mammals
Set of 3 genes produces lactosemetabolizing enzymes
In front of genes is promoter & operator
= operon
(controls expression of > 1 gene at a time)
Negative Control of the Lactose Operon in E. coli
Without lactose:
– Repressor binds to operators
– Twists DNA region so that RNA polymerase can’t bind
= no transcription occurs
With lactose:
– E. coli converts lactose to allolactose
– Binds to repressor & changes its shape so can’t bind to
operators
– Twisted DNA unwinds, RNA polymerase binds, & protein
synthesis of lactose-metabolizing enzymes begins
Bacteria divide via binary fission
= genetically-identical offspring
Can increase genetic variation by transferring
DNA between different bacterial cells
= 3 mechanisms
a. Transformation
Take up DNA from surroundings
e.g. from dead cells in the environment
b. Transduction
Transfer genes via phage
(DNA stowaway)
Phage
= virus that infects bacteria
c. Conjugation
Mating & DNA transfer between 2
bacterial cells
Conjugation is enabled by the
F factor
F factor can exist as a plasmid
= small, circular DNA
R plasmids carry genes that destroy
antibiotics
= confers antibiotic resistance
Widespread use of antibiotics has
resulted in antibiotic-resistant strains of
“superbugs”
Regardless of how DNA is transferred:
When new DNA enters bacterial cell, parts
integrate into existing chromosome
Part of donated DNA replaces part of
original DNA
= recombinant chromosome
Viruses
“Genes in a box”
Nucleic acid contained within a capsid
Not living
= can only reproduce within host cells
Some viruses contain RNA
= flu, cold, measles, mumps, AIDS, polio
Some viruses contain DNA
= hepatitis, chicken pox, herpes
Vaccines may prevent these viruses, but
very few effective anti-viral drugs
(kill both host & viral cells)
Amount of damage caused by virus
depends on:
• Immune response
• Self-repair capabilities of affected tissue
e.g. recover from colds quickly because of
rapid regeneration of respiratory tract
tissues
e.g. poliovirus causes permanent damage
because affects non-dividing nerve cells
Viruses arise from:
Mutations
e.g. new strains of flu viruses
Contact between species
e.g. HIV transmitted from chimps to
humans
Spread from isolated populations
e.g. HIV spread from small region of
Africa to worldwide distribution
Some viruses carry cancer-causing genes
= oncogenes
Proto-oncogene
= normal gene that has potential to
mutate into oncogene
Tumor-suppressor genes
= inhibit cell division
(if mutate, cell may end up dividing multiple
times & forming cancerous tumour)
Carcinogen
= cancer-causing agent that alters DNA
e.g. X-rays, UV radiation, tobacco, etc.
Prolonged exposure to carcinogens can cause
activation of oncogenes & inactivation of
tumor-suppressor genes
Carcinogens also promote cell division
= can lead to cancerous tumors
Combo of virus & carcinogen may increase risk
of cancer
Animation of transcription:
http://vcell.ndsu.nodak.edu/animations/transcription/movie.htm
Animation of translation:
http://vcell.ndsu.nodak.edu/animations/translation/movie.htm