Chapter 8Chapter 8From DNA to ProteinsFrom DNA to Proteins

DNA rap

Look at the image of the mice below. Notice anything that seems odd?

These mice have had a jellyfish gene (Green Fluorescent protein) inserted into their DNA DNA by way of a virus. The virus inserted the GFP gene into the DNADNA of the mice.

What is DNA?

In your own words, write down what DNA is

What is DNA? How does it transmit genetic information?

What is the structure of DNA?

These were all questions scientists raced to figure out from 1923 – the 1960’s.

It was The Race for the Double Helix

There were a number of scientist who worked on trying to figure out what was the genetic material in a cell.

Was it the proteins or the nucleic acids?

They worked with bacteriabacteria and virusesviruses as models and figured out that it was the nucleic acids nucleic acids that were responsible for passing on traits.

Therefore, the DNA is the Therefore, the DNA is the heredity materialheredity material

Conclusion: Nonpathogenic mice were transformed

by nucleic acid

Used S35 Used P32

*Conclusion:

DNA DNA is the genetic material which is transmitted from one generation to the next

Found that the S35 stayed outside the cell &

P32 ended up in the bacteria and then in new viruses

Erwin Chargaff – 1950

Noticed a pattern in the amounts of the four bases: Adenine, Guanine, Cytosine, and Thymine

• Found the # of Guanine = # of Cytosine nitrogen bases in DNA

• The # of Thymine = # of Adenine

• Didn’t know why though!

What else did they know?Knew that:

• DNA was a polymer made up of repeating units (monomers) called nucleotidesnucleotides

• NucleotidesNucleotides are made up of:– a 5 carbon sugar 5 carbon sugar (called Deoxyribose)– a phosphate groupphosphate group– 4 different nitrogen basesnitrogen bases P

S

4 Nitrogen Bases4 Nitrogen Bases

• Thymine (T)

• Adenine (A)

• Cytosine (C)

• Guanine (G)

Remember that the amount of Guanine = Cytosine and the amount of Thymine = Adenine

Label the diagram of the nucleotide nucleotide below

Identify the 4 nitrogen Identify the 4 nitrogen bases in bases in DNADNA1. _________________1. _________________2. _________________2. _________________3. _________________3. _________________4. _________________4. _________________

Phosphate group

Nitrogen base

Deoxyribose sugar

CytosineAdenine

Guanine

Thymine

The Main Characters in Cracking the Genetic Code

Watson & Crick

Rosalind Franklin

Maurice Wilkins

Putting all the evidence together

1.1. Rosalind Franklin Rosalind Franklin worked in Maurice Wilkins’ lab.

– Purified, then crystallized DNADNA and then shot X-Rays through the crystal.

– Took Photo 51 Photo 51 (100 hr exposure!!)– Showed that DNADNA was a double helix a double helix with the

bases in a regular pattern inside the 2 twisting strands.

2. James Watson and Francis Crick – Model builders trying to figure

out the structure of DNA.– Somehow, they saw Franklin’s

Photo 51 – Immediately figured out the

same thing that Franklin did but published faster than she did.

– DNA was a double helix double helix • Two twisting strands of

alternating sugars and phosphates with the nitrogen bases inside

– Win Nobel Prize along with Wilkins. (Franklin dies prior to the award).

Structure of DNA DNADeoxyribonucleic acidDeoxyribonucleic acid

It is a polymer of Nucleotides (monomer)

Single nucleotide

5 carbon sugar – deoxyribose

A phosphate group

A nitrogen baseS

P

N-base

Nucleotide

DNA is a double helix double helix with the sugarssugars and phosphate groups phosphate groups alternating along the sides rungs

The nitrogen bases are paired together (following the base pairing rules)

Guanine – Cytosine

Adenine - Thymine

What holds DNA together?• The alternating SugarsSugars and

PhosphatePhosphate groups are held together by covalent bonds covalent bonds

• The nitrogen bases nitrogen bases are attached to the sugar molecules by covalent covalent bondsbonds

• The bond between the two nitrogen bases is a weak hydrogen bondhydrogen bond.

Covalent Covalent bondsbonds

S

S

SS

SS

S

S

Label the DNA strand shown to your right. 1. Put a PP on each of the Phosphate groups 2. Put an SS on each of the Sugars 3. Using the base pairing rules, fill in the base pairsbase pairs4. Label the bond bond indicated by the arrow

DNA Model LabDNA Model LabYou will need to cut

out and label:

24 Phosphates - P24 Deoxyribose – S

6 Adenine – A6 Thymine – T6 Cytosine – C6 Guanine - G

Need for more DNAWe have over 100 billion cells. Each cell has

exactly the same DNA in its nucleus except for the gametes (sex cells)

DNA needs to be replicated EXACTLYEXACTLY each time a new cell is produced during Interphase of Mitosis

Watson and Crick looked at the structure of DNA and figured out how it could make a copy of itself

“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material”.

Why would a zipper be a good analogy to DNA?

1. DNA and a zipper have two strands

2. The teeth of the zipper are like the nitrogen bases of DNA

3. The teeth are held together by a bond like the Hydrogen bonds holding the bases together

If you wanted to make an exact copy of DNA, how would you do it precisely and quickly?

The process of making an exact copy of DNA is called DNA DNA ReplicationReplication

As a result of Replication, there will be two identical strands of DNA

The two strands of DNA act as templates for the new strands.

Original DNA strand

Hydrogen bonds are broken

between the bases exposing

the base

New DNA nucleotides bind with the exposed bases, following the base pairing

rules

Two identical strands of DNA are produced with the old

strand on the outside of each

new strand

DNA ReplicationDNA Replication

How does DNA Replication DNA Replication occur?

1. The DNA helix needs to flatten out– No one likes a twisted zipper

2. In order to expose the nitrogen bases, the helix needs to be unzipped by Helicase Helicase. The hydrogen bonds are broken, exposing the bases.

– Just like the slide on a zipper exposes the teeth

3. An enzyme called DNA polymerase DNA polymerase “re-zips” the two strands by allowing free DNA nucleotides in the nucleus to bond to the exposed bases on both sides of the helix

The helix is being flattened

The hydrogen bonds are being

broken by Helicase

In the space below, write out the 3 steps in DNA Replication

1.

2.

3.

Animation

Glenn

Here is a song

Maybe you will like this one better

It’s your turn to Replicate DNA

C – GA – TT – AG – CC – GC – GT – AT – AA – TG – C

C – GA – TT – AG – CC – GC G

T-__ __-AT-__ __-A

A-__ __-TG-__ __-C

C – __A – __T – __G – __C – __C – __T – __T – __A – __G – __

__ – G__ – T__ – A__ – C__ – G__ – G__ – A__ – A__ – T__ – C

Original DNA strand DNA being replicated New DNA strands following replication

Listen to the song and then explain what DNA’s real job is?Central Dogma Song

What is DNA’s job?

Francis Crick figured out that the role of the role of DNA in the DNA in the production of proteinsproduction of proteins.

He called this the Central DogmaCentral Dogma.

DNADNA to to RNARNA, , RNARNA to to ProteinsProteins

The Production of Proteins is called Protein SynthesisProtein Synthesis

Remembering back to the cell, where in a cell does Protein Synthesis Protein Synthesis take place?

Occurs in the RibosomesRibosomes of all cells, both prokaryotic (bacterial) and eukaryotic

Protein

mRNA

Amino acid

Ribosome

Ribosome

tRNA

Big problem with DNA and Protein Synthesis

We have always referred to DNADNA as the Boss

The DNADNA (Boss) stays in its office – the nucleus nucleus. Only problem is that the DNADNA is too large to get out of the nucleus.

DNADNA has the message (genegene) to produce a particular protein. Since it can’t deliver the message itself, it needs a messenger to deliver the message to the ribosomesribosomes.

It also can’t make the protein itself from available amino acids amino acids in the cytoplasm so it needs some molecule to transfer the amino acids to the ribosomesribosomes to make the proteinprotein.

RNA Ribonucleic acid

The other Nucleic Acid Acts as a messenger between DNADNA and the

ribosomesribosomes and carries out protein synthesis by delivering the amino acids to the ribosomeribosome

How DNA & RNA Differ

1. RNA is single stranded. DNA is double stranded

2. Has Ribose sugar instead of Deoxyribose

3. Can be found in the nucleus, cytoplasm or at the ribosomesDNA is only in the nucleus

1. Contains UracilUracil in place of Thymine so AdenineAdenine bonds with UracilUracil

Three different kinds of RNA

• Messenger RNA (mRNA)Messenger RNA (mRNA)

Is produced in the nucleus of eukaryotes and gets DNADNA’s message. Then goes to the ribosomes

• Transfer RNA (tRNA)Transfer RNA (tRNA)

Found in the cytoplasm & transfers amino acids to the mRNAmRNA in the ribosomes

• Ribosomal RNA (rRNA)Ribosomal RNA (rRNA)

Makes up the ribosomes

Label the three types of RNA and tell what each of them does

mRNAmRNA

tRNAtRNA

rRNArRNA

Steps in Protein Synthesis1.1. TranscriptionTranscription

DNADNA’s message on the genegene gets “read” (in reverse) by messenger RNA (mRNA).messenger RNA (mRNA).– RNA polymerase RNA polymerase enzyme will allow free RNA

nucleotides to temporarily bind to DNADNA– This message on mRNAmRNA will go to the

ribosomesribosomes.

2.2. TranslationTranslation

mRNAmRNA will attach into the ribosomesribosomes and amino acids will be transferred in the proper order according to the gene by transfer RNA (tRNA)transfer RNA (tRNA)– The The amino acids amino acids will string together to form a will string together to form a

protein (polypeptide)protein (polypeptide)

TranscriptionTranscription

Occurs in the nucleusnucleus: •If DNADNA is: ATG CCG TTA GAC CGT TGA TACTAC GGC AAT CTG GCA ACT mRNA mRNA is: AUG CCG UUA GAC CGU UGA

(Remember, U substitutes for T in RNA)•This is called Transcription. Animation Another one

mRNAmRNA

What happens in transcription?

TranslationTranslation

Process that converts an mRNAmRNA message into a polypeptidepolypeptide

mRNAmRNA will now go to the ribosomesribosomes

mRNA mRNA has the reverse code forhas the reverse code for DNA’s DNA’s gene.gene.

Remember that Remember that DNADNA’s ’s genesgenes code for code for proteinsproteins and and proteinsproteins are made up of are made up of amino amino acidsacids

Now we must consult the Genetic Code Now we must consult the Genetic Code decoding wheeldecoding wheel

Start codon

Stop Codons

Going off of the mRNAmRNA’s codonscodons, we use this to figure out which amino acid amino acid is needed (according to DNADNA’s message)

Try:

GGG: ____________

CAU: ____________

AUG: ____________

UUU: ____________

GAC: ____________

UAG:____________

mRNAmRNA is: AUG CCG UUA GAC CGU UGA

tRNAtRNA will bind with specific amino acids amino acids and transfer them to the codoncodon (3 bases in a row on mRNAmRNA)

mRNAmRNA is: AUG CCG UUA GAC CGU UGA

Amino acidAmino acid: Methionine (start codon)

Proline

Leucine

Aspartic Acid

Arginine

Stop codon means to stop translation

Every 3 consecutive bases on mRNA on mRNA is a codoncodon. CUA AAU GAU

• tRNAtRNA with the anticodonanticodon (complimentary to mRNAmRNA) links to mRNA mRNA. It carries a specific Amino Acid (specified by mRNAmRNA).

If DNADNA reads:T A C G T C G A T T G G CAA…

mRNAmRNA: A U G C A G C U A A CC GUU…

tRNAtRNA: U A C G U C G A U U GG CAA…

TranslationTranslation:Amino Acids: Methionine - Glutamine – Leucine -Threonine – Valine

Please note that DNADNA’s code and tRNAtRNA match!! TranslationTranslation!!!!!

• When adjacent Amino Acids link together, they link together with a peptide bond peptide bond and form a and form a Polypeptide Polypeptide (protein). (protein).

Animation

Peptide bonds

Amino Amino acidacid

Growing PolypeptideGrowing Polypeptide

DNA mRNA Protein

Transcription Translation

Protein Synthesis

Protein Synthesis • Animation Protein Synthesis - Learning • You tube animation – really good!• McGraw animation

• http://www.youtube.com/watch?v=41_Ne5mS2ls – HHMI one

• Replication & Protein synthesis – song with only typed words but good

• Does this process ever make a mistake?

• Have you ever had to copy a large amount of information?

• What is the likelihood of you making a mistake or more?

Changes in genetic material

Gene Mutations:

Change in the nucleotide sequence which alters one or more genes

Chromosomal Mutations:

Change in the chromosome structure which could alter the entire chromosome or a portion of it.

Gene MutationsGene Mutations

Point MutationsPoint Mutations – usually affect only one amino acid

Frameshift mutations – May affect an entire amino acid sequence.

Point mutation

• Involves a change in one or a few nucleotides.

• Influences a single amino acid in the polypeptide chain.

• Caused by a substitution of a Nitrogen base.

• THE FAT CAT ATE THE RAT

• Take out “C” in Cat & substitute a “B”

• THE FAT BAT ATE THE RAT

• Does not really change the meaning to the sentence or the protein formed except for the bat but the rat is still gone!

• If DNA reads: A T G G T C G A T T G G CAA• mRNA: U A C C A G C U A AC C GUU• Amino Acid: Tyrosine - Glutamine – Leucine -Threonine – Valine

• But if mRNA: U A C C A G C A A AC C GUU• The AA: Tyrosine – Glutamine – Glutamine – Threonine – Valine

Only 1 Amino acid in the sequence was altered.

Frameshift mutation

• Involves a change in the entire protein formed or a large portion of it.

• Caused by insertions (additions) or deletions of Nitrogen bases.

• THE FAT CAT ATE THE RAT

• Take out “E” in THE & group into 3’s

• THF ATC ATA TET HER AT_

This makes no sense at all!!

• If DNA reads: A T G G T C G A T T G G CAA• mRNA: U A C C A G C U A AC C GUU• AA: Tyrosine - Glutamine – Leucine -Threonine –

Valine• BUT if mRNA: U A C C A G U A A C C G U U _• THEN Amino Acid: Tyrosine - Glutamine – STOP!!!!• The entire sentence makes no sense. The protein formed

would be totally different

So which form of a mutation would be more severe?

• Frameshift mutation …

since an entirely new protein would be formed

Blame it on the DNA

CHROMOSOMAL MUTATIONS

• involve changes in number and structure of the chromosomes.

• Could change location of genes on the chromosomes or the number of copies of some of the genes.

• Deletions – part of a chromosome is missing

• Duplications – Extra copies of genes are inserted

• Inversions – Reverse direction of parts of the chromosome

Parts of one non-homologous chromosome breaks off and attached onto another non-homologous chromosome

TranslocationsTranslocations

5. tRNA carries ___________________ to the mRNA in the ______________________6. tRNA complementing mRNA at the ribosome occurs during (transcription/translation).7. The codon is made up of 3 nitrogenous bases on _______ while the anticodon is on the ______8. The bond that connects the amino acids together to form the polypeptide is a ___________ bond.