DNA Gregor Mendel – 1840’s - PowerPoint Presentation

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DNASlide2

Gregor Mendel – 1840’s

Conclusion:

Heredity material was packaged in discrete transferable units; came up with law of segregation and law of independent assortment.Slide3

Thomas Morgan – early 1900’sDiscovered that fruit flies’ genes were associated with chromosome inheritance.

Conclusion:

Chromosomes were known to be composed of proteins and DNA, so genes must be one of these two macromoleculesSlide4

Experiment

If dead (heat-killed) pathogenic bacteria was mixed in a culture with living harmless bacteria, the harmless bacteria would become deadly.

Conclusion

Transformation

in bacteria allows a change in genotype and phenotype due to the assimilation of external DNA by the cell.

FREDRICK GRIFFITH -1928Slide5

He separated the components of the heat-killed, deadly bacteria & divided it into smaller samples (proteins, lipids, carbohydrates, or nucleic acids) & left the other molecules intact. He then mixed each sample of the treated lethal strain with living samples of the non-lethal strain.

AVERY’S EXPERIMENT -1944

Only the DNA extract from the deadly bacteria would allow the live harmless bacteria to become deadly.

AVERY’S CONCLUSIONSlide6

HERSHEY AND CHASE - 1952

Conclusion:

The DNA molecule entered the bacteria cell & not the protein. This showed that DNA and not protein controls traits that are passed on.Slide7

CHARGAFF - 1947

Experiment:

Studied the composition of DNA and the concentration of each of the nitrogenous bases.

Conclusion:

DNA base composition varies from one species to another; bases are not present in equal amounts in any one species but they are found in a predictable ratio; concentration of T=A and concentration of C=G.Slide8

Franklin and Wilkins

Experiment:

Took x-ray diffraction pictures of DNA in its different forms

Conclusion:Discovered that the B form of DNA was double helix in structure.Slide9

Watson and Crick

Experiment:

Built a 3-D model that reflected the base pairing rules determined by

Chargraff & the distance between bases suggested by Franklin’s X-ray photos.

Conclusion:DNA was a double helix that made one full turn every 3.4nm with bases 0.34nm apart & sugar/phosphate molecules on the outside of the ladder.Slide10

So what are the various parts of DNA?Nitrogen basesAdenineCytosine

Guanine

Thymine

PhosphatesDeoxyribose

Hydrogen bondsSlide11

DNA Molecule

Sugar and phosphate backbones are

antiparallel

(their subunits run in opposite directions)

Adenine and guanine are purines

(both have 2 organic rings)Cytosine and thymine are pyrimidines (both have 1 organic ring)Adenine forms 2 hydrogen bonds with thymineCytosine forms 3 hydrogen bonds with guanineSlide12

WHY 5’ AND 3’?Slide13

Let’s make some DNA Red = phosphateWhite =

deoxyribose

Yellow = adenine

Blue = thymineOrange = cytosine

Green = guaninePink = uracilPlastic connectors = hydrogen bonds

Minimum of 10 pairsSlide14

DNA ReplicationSlide15

What is the purpose of DNA Replication?To produce a copy of DNA identical to the original in preparation for mitosis or meiosis.Slide16
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Meselson and Stahl experiment

Conclusion:

DNA replication follows the semiconservative model.

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st replication in the 14 N medium produced a band of hybrid. This eliminated the conservative model.2nd replication produced both light and hybrid DNA this eliminated the dispersive model & supported the semiconservative model.Slide18

E. coli vs Human DNA ReplicationE. coli

Has a single chromosome

4.6 million nucleotide pairs

Can replicate its chromosome in less than an hour.

Human46 DNA molecules; each in a chromosome6 billion nucleotide pairsCan replicate all chromosomes in a few hours

Replication process is similar in prokaryotes and eukaryotes.Slide19

Some of the “players” involved…

DNA Polymerase-

adds nucleotides to a preexisting chain.

Ligase

- joins the sugar phosphate backbones of all Okazaki fragments.Primase- synthesizes the primer that’s 5-10 nucleotides long.

Helicase- unzips the DNA Topoisomerase-relieves the strain of overtwisting DNA by braking, swiveling, & rejoining DNA strands.Slide20

DNA unwinds & unzips with the help of helicaseSlide21

In order for replication to begin a primer is needed & it is an RNA primer

The primer is about 5-10 nucleotides long

The new DNA strand starts from the 3’ end of the RNA primer

DNA Polymerase adds nucleotides to the preexisting strandSlide22

Replication occurs from 5’ to 3’

In eukaryotes Okazaki fragments are 100-200 nucleotides long.

Leading strand- is made going towards the replication fork and is continuous

Lagging strand- is made going away from the replication fork and is synthesized discontinuously, as a series of segments called Okazaki fragments.

Leading strand needs only one primer & lagging strand needs a primer for each Okazaki fragment.Slide23

Ligase

-

joins sugar-phosphate backbone.

DNA polymerase I –

removes the primer and replaces it with DNA nucleotides; one by oneDNA polymerase III-Continuously synthesizes the leading strand

LET’S WATCH A VIDEOSlide24

How is replication of one side of each double strand different than the other?Because bases can only be added in the 5’ to 3’ direction, the 3’ to 5’ strand must be assembled in fragments that are later annealed together by a ligase protein.Slide25

Proofreading and Repairing DNA

Errors amount to 1 in 10 billion nucleotides in the final DNA product

Initial pairing error amount to 1 in 100,000 more common.Slide26

How is the new strand ensured to be identical?The bases are matched in a consistent patternThe daughter strands are half new, half old

There is a proofreading mechanism that checks for errors in both strands.Slide27

Why are mistakes made?Spontaneous chemical changes under normal conditions.Exposure to mutagens

EX: cigarette smoke and X-rays

There are many different DNA repair enzymes.

-E. coli has 100 known repair enzymes

-Humans have 130 identified repair enzymesSlide28

Teams of enzymes detect & repair damaged DNA, such as this thymine

dimer

(often caused by UV radiation), which distorts the DNA molecule.

A nuclease enzyme cuts the damaged DNA strand at 2 points, & the damaged section is removed.

Repair synthesis by a DNA polymerase fills in the missing nucleotides.

DNA

ligase

seals the free end of the new DNA to the old DNA, making the strand complete.Slide29

If your body is unable to repair the thymine dimer…Slide30

Replicating the ends of DNA molecules

This kind of thing does not occur prokaryotes with a circular chromosome

The primer on the end is removed but can’t be replaced with DNA because DNA polymerase can only add nucleotides to the 3’ end of a preexisting polynucleotide

The strand will get shorterSlide31

What is done to compensate for this problem?Telomeres (located at the ends of DNA molecules) are made of repeated units that are non-coding so that, as they get shorter, no genes are lost.

The enzyme

telomerase

lengthens telomeres in germ cells

Cells can only go through a limited number of replications before they are put to death.plus

alsoSlide32
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Let’s Replicate!!!

with narrative Slide34

How Does a Gene Become a Protein?With a lot of help, I’ll tell you that!!!Slide35

Let’s start with the 2 nucleic acids involvedDNA and RNA

These molecules have structural similarities and differences that define function.Slide36

Compare DNA to RNASlide37

Made of nucleotides

Connected by covalent bonds to form a linear molecule from 5’ to 3’

Contains

deoxyribose

Nitrogen bases A,T,G, & CDouble strandedRestricted to the nucleus (eukaryotes)Made of nucleotidesConnected by covalent bonds to form a linear molecule from 5’ to 3’Contains riboseNitrogen bases A,U,C, & GSingle strandedAble to travel out of the nucleus (eukaryotes)

Comparison of DNA to RNADNA

RNASlide38

Is Uracil a purine or a pyrimidine?Since thymine is a

pyrimidine

and in essence

uracil replaces thymine in RNA it would make

sence that uracil is also a pyrimidine. Wouldn’t it?Slide39

The sequence of the RNA bases, together with the structure of the RNA molecule, determines RNA function.

mRNA:

carries information from the DNA to the ribosome.

tRNA:

are molecules that bind specific amino acids and allow information in the mRNA to be translated to a linear peptide sequence.rRNA: are molecules that are functional building blocks of ribosomes.RNAi: plays a role in regulation of gene expression at the level of mRNA transcription.To be discussed laterSlide40

Genetic information flows from a sequence of nucleotides in a gene to a sequence of amino acids in a protein

This occurs in two partsSlide41

What signals the cell to make a specific protein?Cell signalingCell receptorCell hormonesSlide42

Transcription

Is the synthesis of RNA using one side of a segment of a DNA strand.

The DNA segment serves as a template.

The RNA made is mRNA.

It is antiparallel to the DNA templatemRNA is made from 5’ to 3’ (reading the DNA in a 3’ to 5’ direction).This is all completed in the nucleus.Slide43

RNA Polymerase opens the DNA strands & joins the RNA nucleotides that are complimentary to the DNA template.Needs promoter to begin

Bacteria have a single type of RNA polymerase that synthesizes all types of RNA.

Eukaryotes have at least 3 types of RNA polymerase.Slide44
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An example of a promoter is the TATA boxSlide46

Termination of Transcription

Differs between bacteria and eukaryotes

In bacteria

Go through a terminator sequence in DNA.

Once RNA polymerase hits the terminator signal it releases from the DNA and the mRNA that was being made.In eukaryotesRNA Polymerase II transcribes a sequence on the DNA which codes for a polyadenylation signal (AAUAAA) in the pre-mRNA.About 10-35 nucleotides later proteins cut the pre-mRNA from the polymerase & undergoes processing…Slide47

Modifying of the pre-mRNA in EukaryotesBoth ends of the mRNA transcript are altered.

In most cases, certain interior sections are cut out and the remaining pieces are spliced together.

These actions produce a mRNA molecule that is ready for action!!!Slide48

RNA Processing

The cap and tail:

help facilitate the mRNA leaving the nucleus & help protect the

mRNA strand from degradation by hydrolytic enzymes.

help the ribosomes attach to the 5’ end of the mRNA

For ribosome bindingSlide49

More RNA ProcessingRNA splicing:

Removing portions of the RNA molecule & putting the other ends together.

The parts to be “edited out” are interspersed between the coding segments.

The segments that intervene with the coding segments are called:

intronsThe segments that will eventually be expressed & exit the nucleus are called: exonsAverage length of transcription unit = 8000 nucleotides, but average size protein is 400 amino acids so only about 1,200 nucleotides long. This indicates long noncoding stretches of nucleotides which happen to be interspersed in the coding segments.Slide50

HOW IS PRE-mRNA SPLICING CARRIED OUT?

A small nuclear

ribonucleoproteins

(

snRNPs) recognize the splice sites. These are located at the end of introns

.Composed of RNA & proteinSeveral snRNPs and additional proteins form a larger assembly: spliceosome

These molecules release introns & join the exonsSlide51

Why have introns?One idea is that introns play regulatory roles in the cell.

Splicing process is necessary for mRNA to leave the nucleus.

Consequence for having introns & exons

Genes are known to give rise to 2 or more different polypeptides, depending on which segments are treated as exons during RNA processing =

alternative RNA splicing.Slide52

TranslationDivided into 3 stages: initiation, elongation, & terminationSlide53

TranslationMolecular components of translationmRNA: has nucleotide triplets called:

codons

Written in the 5’ to 3’ direction

tRNA

: has nucleotide triplets called: anticodonsThey are complimentary to the codonsMain function is to transport amino acids to the ribosome & drop off the amino acid to add to the polypeptide chain.Ribosomes: made of rRNA and proteinsAdds each amino acid brought by the tRNA

to the growing end of the polypeptide chain.Slide54

How do you know the code from the mRNA to the amino acid?Slide55

Stage 1: InitiationmRNA interacts with the rRNA of the ribosome to initiate translation at the (start) codon & travels from the 5’ to 3’ end.

The sequence of nucleotides on the mRNA is read in triplets called

codons

.Each

codon encodes a specific amino acid, which can be deduced by using a genetic code chart. Many amino acids have more than one codon.Slide56

tRNA

brings the correct amino acid to the correct place on the mRNA.

The amino acid is transferred to the growing peptide chain, with the help of ATP.

The process continues along the mRNA until a “stop” codon is reached

Stage 2 : ElongationSlide57

Stage 3: TerminationA release factor (protein) binds directly to the stop codon.This causes an addition of a water molecule instead of an amino acid to the polypeptide chain.

This breaks the bond between the chain & the

tRNA

.

The process terminates by the ribosome falling off the mRNA strand releasing the newly synthesized peptide chain.Slide58

The polypeptide chain folds and becomes activeSlide59

What happens to the mRNA strand?They eventually degrade in the cytoplasm and become free floating nucleotides once again.Slide60

Transcription and translation can happen simultaneously.

In other words, translation of an mRNA molecule begins while still being transcribed.Slide61

Picture summary of transcription and translation in a eukaryotic cell.

Each amino acid attaches to its proper

tRNA

with the help of a specific enzyme & ATP.Slide62

Questions

Transcription

Translation

Where?

NucleusCytosol/CytoplasmWhat is used as a template?DNA

mRNAWhat is used to synthesize the new strand?RNA PolymeraseRibosomes

What is the new strand made

of?

RNA

Amino acidsSlide63

LET’S MAKE SOME PROTEIN!

I need 4 volunteers

Slide64

Which parts played what in transcription & translation?

Master Chef

= RNA Polymerase

Prep-chef

= ribosome

Cookbook

=DNA

Scrap paper

= mRNA

Ingredients

= amino acids

Customer 1

= receptor mediated cell signal

Customer 2

= cell signal- hormone

Tabs on cookbook

= TATA boxes (telling chef where to find the

recipe

=geneSlide65

Now it’s your turn You will get together with 4-5 people in class.

You will now create a completely different analogy for the transcription & translation process.

You have 20 minutes to come up with your analogy & then we will present themSlide66

How Genes Influence Traits

Genes specify the amino acid sequence of proteins

The amino acid sequence determines the shape and activity of proteins

Proteins determine a majority of what the body looks like and how it functionsSlide67

Fig. 8.11 The journey from DNA to phenotypeSlide68

Fig. 8.11 The journey from DNA to phenotypeSlide69

HIV

- HIV is a unique virus in that its genetic material is a single-stranded RNA.

The flow of genetic information travels from RNA to DNA.

Once the HIV virus enters the white blood cells, it activates an enzyme called reverse transcriptase.

This enzyme uses the RNA of the virus to synthesize complimentary double stranded DNA. The process of reverse transcription is very error-prone, hence there is a large degree of mutation which is why finding a cure for AIDS is so difficult

.This new DNA integrates itself into the host genome & becomes transcribed and translated for the assembly of new viral progeny.

RETROVIRUSSlide70

Targeting polypeptides to specific locationsTwo populations of ribosomes

Free and bound

Free are in the

cytosol

Make proteins that stay and function hereBound ribosomesUsually attached to the cytosolic side of the endoplasmic reticulum (ER) or the nuclear envelope.Make proteins of the endomembrane system as well as proteins secreted from the cell (ex: insulin)Slide71

One gene/one polypeptide hypothesisIn the 1940’s experimental work led to the hypothesis:

Every one gene of DNA produce one enzyme

This was amended to include all proteins.

It was later discovered that many proteins are actually composed of more than one polypeptide.

This led to the proposal that each individual polypeptide required one gene.Slide72

In the last few years…Researchers have discovered that at least some genes aren’t quite that straightforward.For Example:

One gene may lead to a single mRNA molecule, but the mRNA molecule may then be modified in many different ways.

Each modification may result in a different polypeptide.Slide73

So…what is a gene?A region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule.Slide74

Point MutationsWhat can affect protein structure and function?Slide75

Types of Small-Scale MutationsSubstitutions:Nucleotide-pair substitutionReplacement of one nucleotide & its partner with another pair of nucleotides.

Results in one of the following: silent mutation,

missense

mutation, or nonsense mutation.

Insertions & deletionsAdditions or loses of nucleotide pairs in a geneDisastrous effect on the resulting proteinWhenever the number of insertions or deletions aren’t a multiple of three = frameshift mutation. Slide76
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EX: Point mutation: Sickle-cell disease