RNAbfhscollings.weebly.com/.../chapter_13_notes_-_rna.pdfThe genetic code •Step one - copy DNA to produce RNA •RNA contains instructions on how to make proteins •Proteins are

RNASection 3.1

What is RNA?

•Another type of nucleic acid

•A working copy of DNA• Does not matter if it is damaged or

destroyed

•Used to direct the production of proteins that determines an organisms characteristics

What are the differences between RNA and DNA?

•There are 3 key differences

•1) sugar is Ribose rather than De-oxy ribose

•2) RNA is generally single stranded

•3) RNA contains Uracil rather than Thymine

•Chemical differences make it easier for a cell to distinguish between RNA and DNA

Functions of RNA

•Main function – protein synthesis• Controls assembly of amino acids

into proteins

• 3 types of RNA

•Messenger RNA• Carry information from the DNA to

other parts of the cell

• Ribosomal RNA• Ribosomes are made of ribosomal

RNA and proteins

• Transfer RNA• Transfers amino acids to the

ribosome as/when they are needed

RNA synthesis

• Transcription• Segments of DNA serve as template to

produce complementary RNA molecules

• Prokaryotes• RNA synthesis and Protein synthesis

occurs in the cytoplasm

• Eukaryotes• RNA produced in the nucleus• Transcription occurs in the cytoplasm

• The enzyme RNA polymerase controls transcription

• One gene can produce hundreds or thousands of RNA molecules

Promoters

•RNA polymerase will only bind to areas of DNA where a promoter is present

•Promoter = region of RNA that has specific base sequences

• Similar signals cause transcription to stop

RNA editing

•RNA needs a bit of tweaking before it can be put into action

•Chunks are cut out of them and discarded – introns

• In eukaryotes, introns are taken out of pre-mRNA molecules whilst they are in the nucleus

•What is left – exons, are spliced back together to form the final mRNA

Why does RNA polymerase make more than it needs?• Scientists still aren’t sure

• Some pre-mRNA molecules may be cut/spliced in different ways in different tissues – so a single gene can produce several forms of RNA

• Intron and Exons may play a role in evolution• Small changes in DNA sequences can have a large effect on how genes affect

cellular function

Summary

• RNA is a working copy of the DNA

•Made from small sections of DNA (transcription)• RNA polymerase

• Promoters indicate which part of DNA to use

• Three key types of RNA• Messenger• Ribosomal • Transfer

•More is made than needed• Introns discarded• Exons kept

Ribosomes and protein synthesis

Section 13.2

The genetic code• Step one - copy DNA to produce

RNA• RNA contains instructions on how

to make proteins• Proteins are chains of amino acids

called polypeptides• Up to 20 different amino acids are

commonly found in polypeptides• Specific amino acids and their

arrangement determine properties of different proteins

• Amino acid arrangement influences shape, which determines proteins function

The genetic code continued…•RNA contains four different bases

• Essentially a language with 4 letters

•Genetic code is read three letters at a time• Each ’word’ is three bases long and corresponds to an amino acid• In mRNA, each ‘three letter’ word is a codon

• Three consecutive bases that specify a single amino acid

Reading codons

•There are 64 possible three base combinations in RNA • Due to the 4 different bases

•Most amino acids can be specified by more than one codon

• Leucine is coded by 6 different codons..

•Genetic code table makes decoding codons easy

Start and Stop codons

•These are essentially punctuation marks in the genetic code

•Methionine codon serves as the initiation or start codon for protein synthesis • After this point, the mRNA is

read three bases at a time

•There are 3 different stop codons which mark the end of polypeptide formation

Translation

•Why are ribosomes so important? • mRNA = instruction manual • Ribosome reads the

instruction manual and assembles the parts together

•The assembly process performed by ribosomes is called translation

Translation overview

Steps of translation

• Step 1: Ribosome attaches to mRNA molecule in the cytoplasm

• Step 2: As each codon passes through the ribosome, tRNA brings the proper amino acids into the ribosome. The ribosome attaches amino acids together into a growing chain• Each tRNA molecule is three unpaired bases, called the anticodon• Each tRNA molecule anticodon is complementary to one mRNA codon

• Step 3: Ribosomes help to form peptide bonds between amino acids and build the protein, like a production line

• Step 4: Polypeptide chain grows until it reaches a stop codon• Here the newly formed polypeptide and mRNA molecule are released.

Roles of tRNA and rRNA in translation

•All three types of RNA come together during translation• mRNA carries coded message• tRNA molecules carry the amino acids called for by each codon• Ribosomes are made of about 80 proteins and 3 or 4 different rRNA

molecules

• rRNA helps keep ribosomal proteins in place, and help locate start of mRNA message• They may also help in formation of peptide bonds

Molecular basis of heredity

•Most genes simply contain instructions for making proteins

•Proteins are key in controlling what traits are exhibited

•Many proteins are enzymes, which catalyze and regulate chemical reactions• Skin colour can be controlled by a gene that codes for an enzyme to prdouce

a specific pigment

•Proteins act as microscopic tools, each specifically designed to build or operate a component of a cell

Central Dogma

• Information is transferred from DNA to RNA to protein• There are however many exceptions – e.g. viruses transfer information in the

opposite direction, from RNA to DNA

• Acts as a useful generalization to show how genes work

•Genetic code operates virtually the same way in all living organisms • Some organisms may vary which amino acid applies to specific codons• Code is always read three bases at a time• Code is always read in the same direction• There is remarkable unity between all living organism with the molecular

biology of the gene.

MutationsSection 13.3

In today’s class…..

•We will look at:

•Types of mutations• Gene• Point vs frameshift mutations • Chromosomal

•Effects of mutations• Positive, neutral and negative

•Causes of mutations• Mutagens

What is a mutation?

•Mutations are heritable changes in genetic information

What is a mutation?

•There are two types of mutations• Those that produce changes in a single gene• Those that produce changes in entire chromosomes

Gene mutations

• Gene mutations that involve changes in one or a few nucleotides are point mutations• They occur at a single

point in the DNA sequence

• Occur during replication

• If a gene in one cell is altered, the alteration can be passed on to every cell

Point mutations

• Types of gene mutation• Substitution

• One base is changed to a different base• Only affect one amino acid• Sometime no effect (multiple codons code for the same amino acid)

• Insertions and deletions• Effects are more dramatic - bases are still read in groups of three – everything is thrown off• Also known as frameshift mutations• Can alter proteins so much that they no longer can perform their function

Chromosomal mutations

• Involve changes in the number or structure of chromosomes

• Can change gene location, or the number of copies of some genes

• 4 types• Deletion• Duplication• Inversion• Translocation

Effects of mutations• Genes can be altered naturally or artificially

• Resultant mutations may or may not affect an organism

• Many are caused by errors in the genetic process• DNA replication for example

• An incorrect base is roughly inserted 1 in 10 million times

• Small changes can gradually accumulate

• Environmental conditions can effect mutations • Can help organisms

• Mutations can give new traits

• For example ability consume a new food source, or resist a poison

Mutagens• Some mutations arise from mutagens -

chemical or physical agents in the environment• Examples – some pesticides, tobacco

smoke, environmental pollutants. Physical mutagens – Electromagnetic radiation (X-rays, UV light). • Some interfere with base pairing• Some weaken the DNA strand, causing

breaks and inversions

• If DNA interacts with these mutagens, mutations can be produced at a high rate• Cells can sometimes repair the damage.

If they can’t, the DNA base sequence changes permanently

Harmful vs helpful mutagens

• Effects of mutagens can vary widely

• Some have no effect, some can be beneficial, some negatively disrupt gene function

•Most are neutral - little to no effect on expression of gene

•Mutations often thought of negative, but have lead to evolution

• The organisms' situation will determine whether a mutation is helpful or harmful

Harmful effects

• The most harmful mutations often change protein structure or gene activity• Defective proteins disrupt normal

biological activities• Some cancers are the effect or

mutations that cause the uncontrolled growth of cells • Sickle Cell disease changes the shape of

bloods cells• Caused by point mutations in one of the

polypeptides in hemoglobin• Can lead to anaemia, pain, infections and

stunted growth

Beneficial effects

• Some effects can be very beneficial • Mutations often produce proteins with new or

altered functions• This can be useful to organisms in different or

changing environments• Examples – insects and chemical pesticides

• Mosquitos in Africa are now resistant to many of the chemicals used to control them

• In humans, beneficial mutations can lead to increases in bine strength and density

• Breeders often make use of good mutations

• In plants, a mutation can cause offspring to have 3 or 4 sets of genetic information in the gametes – Polyploidy• These plants are often larger and stronger than diploid

plant – lime and bananas have been successfully produced this way.

Writing assignment

•How does the Central Dogma of molecular biology relate to processes that occur in the cell ? What does the central dogma imply about the role of RNA in a cell? Are there any limitations to this principle?

Gene regulation and expression

Section 13.4

Gene regulation and expression

•Why is gene regulation important?

•Why do cells regulate which genes are used at a given time?

Prokaryotic gene regulation

•Bacteria and prokaryotes do not need all of their genetic information transcribed at once

•They only want to use the genes necessary for the cells to function

•This allows bacteria to respond to changes in their environment

•This is done through DNA binding protein, which regulate genes by controlling transcription

• Some switch genes on, some turn them off

Operons

•An operon is a group of genes that are regulated together

•Genes will have related functions

•E-coli for example has 4238 genes

•3 genes are clustered together, which allow the bacterium to use the sugar lactose as food

•These 3 lactose genes are called the lac operon.

Promoters and operators

•On one side of the operon’s three genes are two regulatory regions

•Promoter: Site where RNA polymerase can bind

•Operator: When a DNA binding protein called a repressor binds to DNA

The lac operon in e-coli

Lactose turns the operon on

Eukaryotic gene regulation•Most of the principles of gene regulation in prokaryotes also apply to

eukaryotes

•Most eukaryotic genes are however controlled individually, and have more complex regulatory sequences than with e-coli.

•TATA box helps with DNA transcription• Made of 25 – 30 base pairs containing the sequence TATATA or TATAAA• Bind a protein that helps position RNA polymerase

Transcription factors

• Transcription factors bind to DNA sequences in the regulatory regions of eukaryotic genes, and control the expression of the gene

• Some enhance transcription by:• Open up tightly packed chromatin• Attract RNA polymerase• Others block access to genes, much like

repressor proteins

• Normally multiple transcription factors are required before RNA polymerase can bind to the DNA

Promoters in Eukaryotes

•Promoters have multiple binding sites for transcription factors

•Certain factors can activate scores of genes at once, changing patterns of gene expression

•Other factors only respond to chemical signals

• Steroid hormones are chemical messengers that enter the cell and bind to receptor proteins• These receptor complexes act as transcription factors, so one single chemical

signal can activate multiple genes

•The exit of mRNA from the nucleus, the stability of mRNA and the breakdown of a gene’s protein s can all also act as a regulating factor

Cell specialization

• Everything is more complicated in Eukaryotes – why? •Our DNA contains the information for

every cell in our body•Would liver enzymes need to be produced

in your bone marrow? Keratin, a protein in hair follicles is not produced in blood cells, or your heart, lungs…• Cell specialization requires genetic

specialization• Complex gene regulation makes this

possible

RNA interference •Cells contain a lot of small RNA molecules that are unrelated to the

three major groups of RNA• These small RNA molecules help regulate gene expression• They interfere with mRNA

• Interference RNA molecule produce by transcription, produces double stranded hairpin loop

•Dicer enzyme make small fragments of miRNA

•miRNA attaches to proteins and forms silencing complex

RNA interference continued

•RNA interference has made it possible for researchers to switch genes on and off at will

•All they had to do was insert double stranded RNA

•Can be used to study gene expression in the lab.

•Holds the potential to cures for cancer and viruses, allowing us to treat currently incurable diseases

Genetic control of development

•What controls the development of cells and tissues?

• In a multicellular organism, all of the specialized cell types came from the same fertilized egg cell

•How do the cells know which cell to become?

•Cells undergo differentiation, and become specialized in structure and function as they develop

• Studying genes that control development and differentiation is an exciting area of Biology

Homeotic genes

•Edward B Lewis showed that specific groups of genes control the identity of body parts in the embryo of fruit fly

•By mutating one of these genes, it was possible to have a fly with a leg growing out of it’s head

•His work showed that there are a set of master control genes (Homeotic genes) that regulate organ development in specific parts of the body

Homeobox and Hox genes

•Homeotic genes share a very similar 180 base DNA sequence – a homeobox

•Homeobox genes code for transcription factors that activate other genes important for cell development and differentiation

•Homeobox genes are expressed in certain regions

• In flies, a group of homeobox genes, called HOX genes are located side by side in a cluster

•These determine the identity of each segment of a flie’s body

•Arranged in the exact order they ate expressed in the body

Hox genes• This does not apply just to flies

• Nearly all animals fit this rule

•Master control genes are like switches that trigger particular patterns of development and differentiation in cells and tissues

• Evidence that genes have descended from common ancestors

Environmental influences • Environment can play a role in cell gene

expression• Temperature, nutrients, salinity for example

can all effect gene expression•Metamorphosis of tadpoles to frogs – great

example•Mixture of environmental and hormonal

factors• Speed of metamorphosis can be influenced

by environmental factors, which translate into hormonal changes. • Hormones function at molecular level