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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

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From dna to protein

From DNA to Protein ...

Chapters 10 & 11


Overview
Overview

  • Review of DNA & RNA

  • Transcription & Translation

  • Gene Mutations

  • Controls over Genes


Dna a review
DNA: A Review

Holds:

Genetic information

Protein-building instructions


From dna to protein

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
So what is a gene? backbone

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


From dna to protein

Exons backbone

= 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
RNA: A Review backbone

Similar to DNA, except:

  • Single-stranded

  • Uracil replaces thymine

    • Adenine pairs with uracil

      Decodes DNA & acts as messenger


Types of rna mrna
Types of RNA: mRNA backbone

Messenger RNA

Carries protein-building instructions from gene to ribosome

“Half-DNA”


Types of rna rrna
Types of RNA: rRNA backbone

Ribosomal RNA

One of components of ribosomes

With tRNA, translate protein-building instructions carried by mRNA


Ribosomes
Ribosomes backbone

2 subunits of rRNA & structural proteins

Have 2 tRNA binding sites

Come together as whole functional ribosome during translation


From dna to protein

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
Types of RNA: tRNA function but different in composition

Transfer RNA

45 different types

With rRNA, translate protein-building instructions carried by mRNA


From dna to protein

Has function but different in compositionanti-codon head:

= 3-base sequence complementary to codon on mRNA transcript

Anti-codon head is complementary to amino acid it carries


From dna to protein

45 tRNAs exist in eukaryotic cells function but different in composition

Codon-anticodon pairing has “wiggle room” for 3rd base of codon

e.g. AUU, AUC, AUA (isoleucine) use same tRNA


The genetic code
The Genetic Code function but different in composition

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
Transcription & Translation function but different in composition

Process that turns sequence of nucleotide bases in genes into sequence of amino acids in proteins

transcription translation

DNA RNA protein


From dna to protein

DNA base sequence acts as template to make RNA function but different in composition

Occurs in eukaryotic nucleus

RNA moves into cytoplasm

Amino acids join to become polypeptides (proteins)


Transcription
Transcription function but different in composition

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


From dna to protein

Transcription factor binds to function but different in compositionpromoter (START) base sequence on DNA

Promoter determines where mRNA synthesis begins & which DNA strand is template


From dna to protein

RNA polymerase function but different in composition 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


From dna to protein

Incoming RNA nucleotides bind with function but different in compositioncomplementary 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)


From dna to protein

Is actually pre-mRNA because has intron junk function but different in composition

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


From dna to protein

mRNA enters cytoplasm function but different in composition

= location of pool of tRNA & free amino acids

Protein synthesis (translation) begins


Translation
Translation function but different in composition

mRNA base sequence → amino acids → proteins

mRNA transcript enters ribosome

Codons translated into polypeptide chain


Initiation of translation
Initiation of Translation function but different in composition

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


From dna to protein

Initiator tRNA fits into function but different in compositionP site of ribosome

(P site holds growing polypeptide)

A site lies vacant for the next amino-acid-carrying tRNA


Elongation of translation
Elongation of Translation function but different in composition

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


From dna to protein

1. Codon recognition: function but different in composition

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


From dna to protein

2. Peptide bond formation: function but different in composition

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


From dna to protein

3. Translocation: function but different in composition

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
Polyribosomes function but different in composition

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
Termination of Translation function but different in composition

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

Phe function but different in composition

Gly

Arg

Phe

Summary of Transcription & Translation

Genetic info → protein synthesis

Via info transfer of complementary base pairing


Gene mutations
Gene Mutations function but different in composition

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
Point Mutations function but different in composition

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
a. Missense mutation function but different in composition

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
b. Nonsense mutation function but different in composition

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
c. Silent mutation function but different in composition

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
Frameshift Mutations function but different in composition

1 or more base inserted or deleted

Deletion or insertion shifts 3-base reading window

Protein is generally useless

= extensive missense & eventually nonsense


Mutagens
Mutagens function but different in composition

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
When are mutations good? function but different in composition

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
Cell Differentiation function but different in composition

Body cells differ in composition, structure, & function

Each cell type undergoes selective gene expression

= determines which tissues & organs develop


How are genes regulated
How Are Genes Regulated? function but different in composition

Differentiated cells contain all genes

BUT

Cells only express genes necessary for their specialized functions


From dna to protein

Human genome = 25,000 – 30,000 genes function but different in composition

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


From dna to protein

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
Gene Control expression & cell-to-cell signalling

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


From dna to protein

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 & Enhancers chemical signals in environment

Promoters:

  • Short base sequences in DNA

  • Regulatory proteins control transcription of specific genes

    Enhancers:

  • Binding sites where promoters increase transcription rates


Controls before transcription
Controls Before Transcription chemical signals in environment

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
Control of Transcript Processing chemical signals in environment

Frequency of transcription

How genes are transcribed

  • Sequences can be rearranged or multiplied

    • Allows rapid & simultaneous production of gene products


Control of translation
Control of Translation chemical signals in environment

Rate of translation

How many times translation can occur on a particular mRNA


Controls after translation
Controls After Translation chemical signals in environment

Proteins & protein synthesis molecules can be:

Activated

Inhibited

Stabilized

Modified

Degraded


Animal gene controls x chromosome inactivation
Animal Gene Controls: chemical signals in environmentX Chromosome Inactivation

1 of 2 copies of X chromosome in female mammals is inactivated

Condenses so can’t be transcribed = Barr body


From dna to protein

So that female (XX) doesn’t have twice as many X chromosome gene products as male (XY)

= Dosage compensation


From dna to protein

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
Plant Gene Controls: ABC Model cell

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



Prokaryotic gene control
Prokaryotic Gene Control cell

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
e.g. cellE. 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
Negative Control of the Lactose Operon in cellE. coli

Without lactose:

  • Repressor binds to operators

  • Twists DNA region so that RNA polymerase can’t bind

    = no transcription occurs


From dna to protein

With lactose: cell

  • 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


From dna to protein

Bacteria divide via cellbinary fission

= genetically-identical offspring

Can increase genetic variation by transferring DNA between different bacterial cells

= 3 mechanisms


A transformation
a. Transformation cell

Take up DNA from surroundings

e.g. from dead cells in the environment


B transduction
b. Transduction cell

Transfer genes via phage (DNA stowaway)

Phage

= virus that infects bacteria


C conjugation
c. Conjugation cell

Mating & DNA transfer between 2 bacterial cells


From dna to protein

Conjugation is enabled by the cellF factor

F factor can exist as a plasmid

= small, circular DNA


From dna to protein

R plasmids cell carry genes that destroy antibiotics

= confers antibiotic resistance

Widespread use of antibiotics has resulted in antibiotic-resistant strains of “superbugs”


From dna to protein

Regardless of how DNA is transferred: cell

When new DNA enters bacterial cell, parts integrate into existing chromosome

Part of donated DNA replaces part of original DNA

= recombinant chromosome


Viruses
Viruses cell

“Genes in a box”

Nucleic acid contained within a capsid

Not living

= can only reproduce within host cells


From dna to protein

Some viruses contain RNA cell

= 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)


From dna to protein

Amount of damage caused by virus depends on: cell

  • 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


From dna to protein

Viruses arise from: cell

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


From dna to protein

Some viruses carry cancer-causing genes cell

= oncogenes

Proto-oncogene

= normal gene that has potential to mutate into oncogene


From dna to protein

Tumor-suppressor genes cell

= inhibit cell division

(if mutate, cell may end up dividing multiple times & forming cancerous tumour)


From dna to protein

Carcinogen cell

= 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


From dna to protein

Animation of transcription: cell

http://vcell.ndsu.nodak.edu/animations/transcription/movie.htm

Animation of translation:

http://vcell.ndsu.nodak.edu/animations/translation/movie.htm