DNA

DNA

Deoxyribonucleic Acid-

In eukaryotes the DNA is stored inside the Nucleolus In prokaryotes the DNA is stored in the Cytosol

DNA or Proteins?

DNA or Proteins?

• The discovery of the genetic role of DNA began with research by Frederick Griffith in 1928

• Griffith worked with two strains of a bacterium, one pathogenic and one harmless.

• When he mixed heat-killed remains of the pathogenic strain with living cells of the harmless strain, some

living cells became pathogenic

• He called this phenomenon transformation, now

• More evidence for DNA as the genetic material came from studies of viruses that infect bacteria.

• Such viruses, called bacteriophages (or phages), are widely used in molecular genetics research.

• A virus is DNA (or RNA) enclosed by a protective protein coat.

• In 1952, Alfred Hershey and Martha

Chase showed that DNA is the genetic

material of a phage known as T2

• To determine this, they designed an

experiment showing that only the DNA of

the T2 phage, and not the protein, enters

an

E. coli

cell during infection

• They concluded that the injected DNA of

the phage provides the genetic information

Hershey-Chase Experiment

Hershey-Chase Experiment

Important DNA Scientists

In 1869 he discovered a substance

containing phosphorus and nitrogen in the

nuclei of white blood cells – this substance

became known as

nucleic acids.

Nucleic acids- complex molecules that make up DNA and RNA

Nucleic Acids

• DNA has 4 types of nucleic acids:

2. Guanine

Both of these are purines

3. Thymine 4. Cytosine

• Erwin Chargaff- (Austrian Biochemist that moved to the U.S. during the Nazi era)

In 1950 he discovered that the amounts of adenine and thymine in DNA were the

same, and the same with cytosine and guanine. He concluded that these bases pair up with each other or …..

BASE PAIR RULES

• Cytosine and

Guanine form a

triple bond with

one another.

• Wilkins and Franklin-

Maurice Wilkins and Rosalind Franklin took x-ray diffraction images of DNA. In 1951 Rosalind took the famous “photo 51”that lead to the discovery of the complete structure of DNA.

• Watson and Crick- In 1953 these two scientists

took Wilkins and Franklin’s data and

constructed the first 3-D model of DNA.

In 1962, they were awarded the Nobel Prize for their discovery.

Watson and Crick concluded that the

shape of DNA was like a winding staircase. They called it a….

DNA PARTS

• Nucleic acids- (the steps of the winding staircase) the base pairs are connected together by a hydrogen bond.

• Deoxyribose- this 5 carbon sugar “glues” the base pairs (steps) to the railings of the double helix.

• Phosphate group- this substance “glues” each step together – creating a full double helix.

• Nucleotide- One complete set of a nucleic acid

• The smallest known genome belongs to bacteria. It has 600,000 base pairs.

• The human genome has over 3,000,000,000 base pairs packed into 23 chromosomes. All

human cells contain a complete genome (except red blood cells and gametes)

• Each human chromosome has 50 million to 250 million base pairs.

• Chromosomal abnormalities (that cause

disease, retardation, or even death) occur when chromosomes are missing or have extra copies, when the break, or when they receive extra

information.

• Gene- the basic physical and functional structure of heredity. They are specific

sequences of bases that are instructions to make proteins. These proteins express an organisms traits.

• The human genome contains 20,000 to 25,000 genes.

• 99.9% of the nucleotides in humans are exactly the same in all people.

The Human

Genome Project

The Human Genome Project

• The project took 13 years and was completed in 2003

• Scientists decoded the entire human genome and identified were all of the genes were located • Scientists are using this information to detect

genetic diseases

DNA Replication

The copying of genetic material

This occurs during the S phase of the cell cycle.

Step 1:

The DNA double helix unwinds and DNA HELICASE (an enzyme) breaks the hydrogen bonds and splits the base pairs apart.

Step 2:

Replication Fork- the site on DNA where the double helix is separating.

•

DNA Polymerase-

this enzyme moves

along the split DNA chain (starting at the

RNA Primase

signal)by the

Replication

Fork

and adds matching base pairs.

== This makes 2 new identical DNA chains

DNA Polymerase also “proofreads” as it

goes to prevent mutations

STEP 3…

In humans- approximately 80 nucleotides are added per second.

Antiparallel Elogation

Antiparallel Elogation

• DNA polymerases add nucleotides only to the free 3end of a

growing strand; therefore, a new DNA strand can elongate only in the 3todirection.

• Along one template strand of DNA, the DNA polymerase

synthesizes a leading strand continuously, moving toward the replication fork

• To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direction away from the replication fork • The lagging strand is synthesized as a series of segments called

Where do the new nitrogen base

pairs come from?

They are made and brought to the site of replication with the help of RNA.

Transcription- RNA reads the DNA strand and makes the instructions to make the needed nucleotides and proteins.

_{Translation- Another RNA reads the}

RNA vs. DNA

• RNA- ribonucleic acid. The sugar in RNA is RIBOSE

•

RNA

DOESN’T

have

thymine- instead it has

Uracil

.

Therefore in RNA adenine

pairs with uracil.

•

RNA is

SINGLE

stranded.

RNA’s job is to read the DNA,

create instructions to make proteins

Transcription

STEP 1….

RNA Polymerase (enzyme) binds to a gene promoter on the split apart DNA strand.

gene promoter- a sequence of DNA that acts as a start signal.

Transfer of genetic information from DNA to RNA

Step 2…

RNA Polymerase

adds RNA complementary

base pairs to the strand of DNA in the 5



to 3



Step 3…

separates from the DNA

strand and begins a life of its own. It moves out of the

nucleus and on to translation.

This strand of RNA is called Messenger RNA

or mRNA

mRNA likes to write the instructions

(or reads) three nucleotides at a time. This group of three nucleotides is

Eukaryotic RNA Processing

Eukaryotic RNA Processing

• Enzymes in the eukaryotic nucleus modify

pre-mRNA (

RNA processing

) before the

genetic messages are dispatched to the

cytoplasm

• During RNA processing, both ends of the

primary transcript are altered

• Each end of a pre-mRNA molecule is modified in a particular way

– The 5 end receives a modified G nucleotide 5 cap

– The 3 end gets a poly-A tail

• These modifications share several functions

– Facilitating the export of mRNA to the cytoplasm – Protecting mRNA from hydrolytic enzymes

Translation

Step 1….

mRNA leaves the nucleus and enters the

cytoplasm. This is where protein synthesis

will occur.

Step 2…

Transfer RNA

or

tRNA

binds to

the mRNA. It reads the

mRNA instructions and

puts the correct amino acids

into a chain.

• Three nucleotides make up the instructions for one amino acid.

This group of three nucleotides is called an anticodon.

There are 20 standard amino acids.

Tryptophan- helps make serotonin. This helps regulate sleep, anger, body temperature and appetite.

Glycine- helps our body make heme. Heme is the iron in our blood that carries oxygen.

Carnitine- helps transport lipids around the cell.

Split Genes and RNA Splicing

Split Genes and RNA Splicing

• Most eukaryotic mRNAs have long noncoding stretches of nucleotides that lie between coding regions

• The noncoding regions are called intervening sequences, or introns

• The other regions are called exons and are usually translated into amino acid sequences

• Many genes can give rise to two or more different polypeptides, depending on which segments are used as exons

• This process is called alternative RNA splicing

• RNA splicing is carried out by spliceosomes • Spliceosomes consist of proteins and small

RNA Interference

RNA Interference

• MicroRNAs (miRNAs) are small single-stranded RNA molecules that can bind to complementary mRNA

sequences

• These can degrade the mRNA or block its translation • Another class of small RNAs are called small

interfering RNAs (siRNAs)

• siRNAs and miRNAs are similar but form from different RNA precursors

Gene Expression

Gene Expression

• Prokaryotes and eukaryotes alter gene

expression in response to their changing

environment

• Multicellular eukaryotes also develop and

maintain multiple cell types

• Gene expression is often regulated at the

transcription stage, but control at other

Gene Regulation

Gene Regulation

• Natural selection has favored bacteria that

produce only the gene products needed by

the cell

• A cell can regulate the production of

enzymes by feedback inhibition or by gene

regulation

• A group of functionally related genes can

be coordinately controlled by a single

“on-off switch”

• The regulatory “switch” is a segment of

DNA called an

operator

usually positioned

within the promoter

• An

operon

is the entire stretch of DNA

• The operon can be switched off by a protein repressor

• The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase

• The repressor is the product of a separate regulatory gene.

• The repressor can be in an active or inactive form, depending on the presence of other molecules

• For example,

E. coli

can synthesize the

amino acid tryptophan

– By default the trp operon is on and the genes for tryptophan synthesis are transcribed

– When tryptophan is present, it binds to the trp

repressor protein, which then turns the operon off

– The repressor is active only in the presence of its corepressor tryptophan; thus the trp operon is

turned off (repressed) if tryptophan levels are high

Negative Feedback

• An inducible operon is one that is usually off; a

molecule called an inducer inactivates the

repressor and turns on transcription

– The lac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose

– By itself, the lac repressor is active and switches the lac operon off

• The lac operon is an inducible operon and contains

genes that code for enzymes used in the hydrolysis and metabolism of lactose

• By itself, the lac repressor is active and switches the lac

operon off

Gene Expression Overview

Gene Expression Overview

• Inducible enzymes usually function in catabolic pathways; their synthesis is induced by a

chemical signal (positive feedback)

• Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high

levels of the end product (negative feedback) • Regulation of the trp operons involves negative

• The greater complexity of eukaryotic cell structure and function provides opportunities for regulating gene expression at many additional stages.

• The structural organization of chromatin packs DNA into a compact form and also helps regulate gene expression in several ways

Eukaryotic Gene Expression

• In

histone acetylation

, acetyl groups are

attached to positively charged lysines in

histone tails

• DNA methylation is the addition of methyl

groups to certain bases in DNA, usually cytosine • Individual genes are usually more heavily

methylated in cells where they are not expressed

• Once methylated, genes usually remain so through successive cell divisions

Epigenetic Inheritance

Epigenetic Inheritance

• Though chromatin modifications do not

alter DNA sequence, they may be passed

to future generations of cells

• The inheritance of traits transmitted by

mechanisms not directly involving the

nucleotide sequence is called

epigenetic

inheritance

• Associated with most eukaryotic genes are multiple

control elements, segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription

• Control elements and the transcription factors they bind are critical for the precise regulation of gene expression in different cell types.

– To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors

– General transcription factors are essential for the transcription of all protein-coding genes

– In eukaryotes, high levels of transcription of particular genes depend on interaction between control elements

More on Eukaryotic Gene

More on Eukaryotic Gene

Expression

• Proximal control elements are located close to the promoter

• Distal control elements, groupings of which are called enhancers, may be far away from a gene or even located in an intron

• An activator is a protein that binds to an

enhancer and stimulates transcription of a gene • Activators have two domains, one that binds

DNA and a second that activates transcription

• Bound activators are brought into contact with a group of mediator proteins through DNA bending

• The mediator proteins in turn interact with proteins at the promoter

• During DNA replication, transcription, and

translation there are opportunities for

mistakes.

• These mistakes lead to mutations.

• Sometimes these mutations are positive

and sometimes they are negative.

OOPS!

Mutations create variation in the gene pool, and the less favorable mutations are removed from the

gene pool by natural selection, while more

• Point mutation- a mutation that happens when a single nucleotide is changed.

Ex: Sickle Cell Anemia- Red Blood cells (oxygen carriers)are sickle shape, they block small blood vessels, and they don’t last long leaving

blood short of red blood cells

Types of Mutations

•

added to the DNA chain.

• Deletions- the removal of one or more

nucleotides.

Ex: Tay-Sachs disease is when fatty acids build up in the nerves of the brain.

Children with this disease die before age 5.

• Silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code

•

Missense mutations

still code for an

amino acid, but not the correct amino acid

•

Nonsense mutations

change an amino

acid codon into a stop codon, nearly