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: tRNATransfer RNA
45 different types
With rRNA, translate protein-building 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 translation
DNA 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
strande.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 anti-codon 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-acid-carrying 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-acid-carrying 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
PolyribosomesOnce 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
Phe PheGly Arg
Genetic info → protein synthesis
Via info transfer of complementary base pairing
Summary of Transcription &
Translation
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 mutationSubstitution 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 mutationSubstitution 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 mutationSubstitution 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 DifferentiationBody 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 environmente.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 lactose-metabolizing 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:
Mutationse.g. new strains of flu viruses
Contact between speciese.g. HIV transmitted from chimps to
humans
Spread from isolated populationse.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 DNAe.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
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