Chapter 2 An Introduction to Genes and Genomes. Central Dogma.

Chapter 2

An Introduction to Genes and Genomes

Central Dogma

DNA RNA Protein

Central Idea of Genetics!

DNA RNA PROTEINTranscription Translation

DNA Replication Animations

• http://www.johnkyrk.com/DNAreplication.html• http://www.bioteach.ubc.ca/TeachingResources/MolecularBiology/DNARepli

cation.swf

• http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html

• http://www.mcb.harvard.edu/Losick/images/TromboneFINALd.swf • http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/dna-rna2.swf

• http://207.207.4.198/pub/flash/24/menu.swf• http://www.dnatutorial.com/

DNA Replication

• When a cell divides, it is essential that newly created cells contain exact copies of the DNA

• Somatic cells divide by mitosis – one cell divides to produce daughter cells with an identical copy of the DNA

• Gametes divide by meiosis – a parent cell divides to create four daughter cells with half the number of chromosomes (haploid cells)

Semiconservative Replication

Prior to cell division, DNA replicates itself by semiconservative replication

Semiconservative Replication

1. Two complementary strands of the double helix are pulled apart

2. Two strands become templates for copying new strand

3. Two new strands of DNA are formed

4. Each new double helix contains one original parent strand and one newly synthesized strand

Steps of DNA Replication (p. 34)

1. DNA Helicase

2. Replication Fork

3. Single-strand binding proteins

4. Origin of replication

5. RNA primers and RNA primase

6. DNA polymerase

7. 5’ to 3’

Figure 2.9 – Semiconservative Replication of DNA

Steps of DNA Replication (p. 34)1. DNA Helicase – enzyme that separates the two

strands of nucleotides by breaking the hydrogen bonds2. Replication Fork – two strands separate and form a

replication fork3. Single-strand binding proteins – attach to each strand

and prevent them from reforming double helix4. Origin of replication – place where separation of

strands occur5. RNA primers and RNA primase – the enzyme primase

create short sections of RNA called RNA primers to bond to parent strand

6. DNA polymerase – enzyme that binds to RNA primer and begins to copy new strand. DNA uses the parent strand as a template

7. 5’ to 3’ – DNA polymerase creates new strand in the 5’ to 3’ direction, always adding nucleotides to the 3’ end

Leading and Lagging Strands in DNA Replication

• DNA can only proceed in a 5’ to 3’ direction – Leading strand – continuous replication towards

the replication fork– Lagging strand – discontinuous replication away

from the replication fork• Short pieces of DNA are made called Okazaki

fragments• DNA ligase – the enzyme that bonds the Okazaki

fragments

Protein Synthesis

DNA

(Transcription)

Messenger RNA

(Translation)

Protein

Protein Synthesis

1. Genes within DNA are copied into messenger RNA molecules (mRNA) in a process called transcription

2. mRNA molecules, which are exact copies of DNA, are deciphered into instructions for making a protein in a process called translation

Transcription

Transcription

http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/transcription.swfhttp://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.htmlhttp://www.johnkyrk.com/DNAtranscription.htmlhttp://www.biostudio.com/d_%20Transcription.htmhttp://207.207.4.198/pub/flash/26/transmenu_s.swfhttp://learn.genetics.utah.edu/units/basics/transcribe/

TranscriptionCopying the Code1. Transcription occurs in the section of DNA containing the gene. Adjacent

to most genes is a promoter region, specific sequence of nucleotides that allow RNA polymerase to bind at a specific location next to the genes.

2. The enzyme RNA polymerase unwinds the DNA double helix and copies one strand of DNA into RNA. RNA polymerase separates the DNA strand and proceeds in a 5’ to 3’ direction along the DNA template to copy a complementary strand of RNA.

3. When RNA polymerase reaches the end of the gene, it encounters a termination sequence. The newly formed mRNA is released from the RNA polymerase and DNA.

• Multiple copies of mRNA can be transcribed from each gene during transcription

• Besides mRNA, Two other types of RNA are produced by transcription, transfer RNA (tRNA), ribosomal RNA (rRNA), and microRNA (miRNA).

Transcription

• The process of making RNA by copying part of the DNA sequence into a complementary RNA sequence

Transcription

• Requires enzyme RNA polymerase

1. RNA Polymerase binds to DNA and separates strands

2. RNA Polymerase uses DNA as template and assembles complementary RNA strands

Transcription

Transcription Animations• http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.html• http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/transcription.swf

mRNA Processing

• Initial mRNA copied from a gene is a primary transcript (pre-mRNA) – it is not fully functional

• There are genes that contain stretches of DNA that do not code for proteins –these stretches of DNA are still transcribed into mRNA. These non-coding sections are called introns

• Exons are the protein coding sequences of a gene.• Introns and exons are copied during transcription of mRNA• Before mRNA can be used to make a protein, the introns must

be removed and the exons must be spliced together

mRNA Processing• Alternative splicing can join together certain exons

and cut out others. Alternative splicing allows several different proteins products to be produced from the same gene sequence

• A gene contains several exons and splicing doesn’t always occur in the same way. As a result, multiple proteins can be produced from a single gene.

• This process creates multiple mRNAs of different sizes from the same gene. Each mRNA can then be used to produce different proteins with different functions.

Two other types of mRNA processing:1. At the 5’ end of the mRNA, a guanine base containing a methyl

group is added. Known as the 5’ cap Plays a role in ribosome recognition of the 5’ end of mRNA during

translation

2. In a process called polyadenylation, a string of adenine nucleotides around 100 to 300 nucleotides in length is added to the 3’ end of the mRNA Known as the poly(A) tail. Protects the mRNA from degradation in the cytoplasm, increasing its

stability and availability for translation

• Following processing, a mature mRNA leaves the nucleus and enters the cytoplasm where it is now ready for translation

RNA Editing

• The introns are cut out of RNA molecules.

• The exons are the spliced together to form mRNA.

Exon IntronDNA

Pre-mRNA

mRNA

Cap Tail

RNA Editing

• RNA Editing– The DNA of eukaryotic genes contains sequences

of nucleotides, called introns, that are not involved in coding for proteins.

– The DNA sequences that code for proteins are called exons.

– When RNA molecules are formed, introns and exons are copied from DNA.

Translation

• The ultimate function of a gene is to produce a protein.

• Translation is using the information in mRNA to synthesize a protein from amino acids.

Protein Review• Proteins are made by joining

– AMINO ACIDS• Each protein contains a combination of the 20

amino acids• The function of the protein is determined by

number and sequence of amino acids• (A polypeptide is a protein!)

Protein 1

Protein 2

Genetic Code• The genetic code is the “language” of mRNA instructions.• A codon consists of three consecutive nucleotides on

mRNA that specify a particular amino acid.

Each codon specifies a particular amino acid that is to be placed on the polypeptide chain.

http://cluelessaboutdna.blogspot.com/2008/01/more-about-genetic-code-start-codons.html

Genetic Code

RNA Sequence -

U C G C A C G G U

Codon Sequence – U C G – C A C – G G U

Use the Amino Acid Guide to determine amino acid –

U C G – C A C – G G U

Amino acid sequence –

U C G – C A C – G G U

Serine – Histidine – Glycine

Translation

• Translation is the decoding of an mRNA message into a polypeptide chain (protein).

• Translation takes place on ribosomes.

• During translation, the cell uses information from messenger RNA to produce proteins.

Translation

1. Messenger RNA is transcribed in the nucleus, and then enters the cytoplasm where it attaches to a ribosome.

Translation2. The ribosome “reads” the mRNA codon and

the corresponding amino acid is brought to the ribosome by the tRNA

codon

Amino Acid

Amino Acid

Translation3. The ribosome forms bonds between the

amino acids to form the proteinBond formed

Translation 4. Translation

continues until the ribosome reaches a stop codon on the mRNA and releases the protein (polypeptide)

The BIG Picture!

Translation Animation

• http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a3.html

• http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/translation.swf

Translation

The genetic code• Ribosomes read the code and produce

proteins. Proteins are formed by joining the building blocks called amino acids.

• A chain of amino acids linked together by covalent bonds is a polypeptide. Some proteins consist of a single polypeptide chain, while others contain several polypeptide chain that must wrap and fold around each other to form complicated three-dimensional structures.

• Proteins can contain combinations of up to 20 different amino acids.

Genetic Code• The genetic code is a universal language of

genetics used by all living organisms. • The code works in three-nucleotide units

called codons which are contained within mRNA molecules.

• Each codon codes for a single amino acid. • There are 64 different potential codons

corresponding to all possible combinations of the four possible bases assembled into three nucleotide codons.

http://www.cbs.dtu.dk/staff/dave/roanoke/genetics-finalex-spr98.htm

http://scienceblogs.com/oscillator/2010/02/expanding_the_genetic_code.php

Translation

What amino acid is coded by the following codons?

ACC Threonine

CGC Arginine

AGC Serine

UUA Leucine

GUA Valine

Translation

• Also contained in the genetic code are codons which tell ribosomes where to begin translation and end translation.

• The start codon, AUG, codes for the amino acid methionine and signals the starting point for mRNA translation.

• Stop codons terminate translation. UGA is a commonly used stop codon in many mRNA, but UAA and UAG are other stop codons. Stop codons do not code for amino acids; they simple signal the end of translation.

Translation

Ribsomes

• Each ribosome contains two subunits, the large and small subunit.

• There are specific sites, called the A site and the P site, into which tRNA molecules can bind.

TranslationtRNA molecules• At one end of each tRNA is an amino acid attachment site.

– tRNA molecules carry their amino acids to the ribosome– Bind with the ribosomes at the A site.

• At the opposite end of each tRNA molecule is three-nucleotide sequence called an anticodon. – Different amino acids have different anticodon. – Anticodons are designed to complementary base pair with codons

in mRNA.

Stages of translation

• The three major stages of translation in eukaryotes: – Initiation– Elongation

– Termination.

Intiation• During initiation, the small ribosomal subunit recognizes and binds

to the 5’ end of the mRNA• The small subunit moves along the mRNA until it encounters the

start codon, AUG.

• The small subunit waits for the correct tRNA, called the initiator tRNA to come along. This tRNA has the amino acid methionine (met) attached to it and the anticodon UAC. The UAC binds to the start codon by complementary base pairing.

• Then the large ribosomal subunit binds and the ribosome can start translating a protein.

Elongation• During this phase additional tRNAs enter the ribosome, one at a time, and a growing

polypeptide chain is elongated. • The second tRNA enters the A site of the ribosome and the anticodon base pairs with

the codon.• After two tRNAs are attached to the ribosome, an enzyme catalyzes the formation of

a peptide bond between amino acids. Peptide bonds join together amino acids to form a polypeptide chain.

• After the amino acids are attached to each other, the initiator tRNA, without methionine attached, is released from the ribosome. The newly formed polypeptide remains attached to the tRNA in the A site.

• During a phase called translocation, the ribosome shifts so that the tRNA and growing protein move into the P site of the ribosome. The A site is now aligned with the third codon in sequence and the ribosome waits for the proper tRNA to enter. The cycle continues to attach the next amino acid to the growing protein and repeats itself as the ribosome moves along the mRNA.

• Elongation continue to form a new protein until the ribosome encounters a stop codon.

Termination• The third stage of translation is called

termination. • Proteins called releasing factors interact with

the stop codon to terminate translation.• The ribosomal units come apart and release

from the mRNA, and the newly synthesized protein is released into the cell.

Translation Animations• http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/translati

on.swf • http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene

_a3.html

• http://www.tvdsb.on.ca/westmin/science/sbioac/genetics/translat.htm • http://www.sciencenetlinks.com/interactives/protein.html • http://vcell.ndsu.edu/animations/translation/movie.htm

TranslationTranslation occurs in the cytoplasm of cells as a multi-stepprocess that involves several different of RNA molecules:

• Messenger RNA (mRNA) – an exact copy of a gene. Acts as a messenger by carrying the genetic code, from the nucleus to the cytoplasm where this information can be read to produce a protein.

• Ribosomal RNA (rRNA) – short molecules that make up ribosomes, organelles that are essential for protein synthesis. Ribosomes recognize and bind to mRNA and read the mRNA during translation.

• Transfer RNA (tRNA) – molecules that transport amino acids to the ribosomes during protein synthesis.