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