Molecular Genetic Ppt

8/2/2019 Molecular Genetic Ppt

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MOLECULAR

GENETICS



I. THE CENTRAL DOGMA*http://www.mansfield.ohio-state.edu/~sabedon/biology.htm

*Coined by Francis Crick in 1958 (http://www.euchromatin.org/Crick01.htm#Published)

A. Explains how genetic informationmoves around a cell and from parentto offspring under normalcircumstances

Replication (S.H.)

http://www.euchromatin.org/Crick01.htm#Published

http://www.euchromatin.org/Crick01.htm#Published



B. Exceptions to the Central Dogma

1. retroviruses have RNA, not DNA andthen their RNA is used as a template

to make DNA in the host cell

a. Enzyme called reverse transcriptase

catalyses the production of DNA from RNA



(points b and c are from

http://en.wikibooks.org/wiki/IB_Biology/Nucleic_Acids_and_Proteins)

b. can make DNA from mature mRNA

(eg insulin) which can then bespliced into host's (eg bacteria) DNA without the introns. Then when thehost's DNA is transcribed, proteins

like insulin are made.

http://en.wikibooks.org/wiki/IB_Biology/Nucleic_Acids_and_Proteins





i. important that the DNA created by

reverse transcriptase has nointrons, because the host does nothave the genes (and thereforeproteins) necessary to remove theintrons.

2. prions are misshapen proteins that

have the ability to make normalproteins become misshapen as welland thus cause disease



Let's begin with a specific example of whatwe are trying to learn in this section:

http://learn.genetics.utah.edu/content/begin/dna/firefly/fireflymon8.swf





II. Transcription A. the process of using a section of DNA

(known as a gene) as a template to

make a molecule of messenger RNA (mRNA)

1. each gene has the information forone polypeptide strand











B. only one strand of the two strands is

transcribed

i. Called the template strand ornonsense or anti-sense strand or

non-coding strand

C. the strand that is not transcribed is

called the sense or coding or mRNA-like strand














D. only about 2% of the 3 billion basepairs in human DNA are part of genes

1. in total, there are about 30 000genes

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.htm l






http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html




E. Requirements1. RNA polymerase

a. An enzyme

b. Many forms exist

i. In eukaryotes usually a form

called RNA polymerase II



2. Raw Materials

a. 4 ribonucleoside triphosphates

i. ATP/adenosine triphosphateii. GTP/guanosine triphosphateiii. CTP/cytidine triphosphateiv. UTP/uridine triphosphate



F. Steps (in Prokaryotes)

1. Initiation

a. RNA polymerase binds to thetemplate strand of the DNA at an area called thepromoter site

i. by convention, the promoter isindicated on the sense/coding/non-template strand



b. RNA polymerase opens the DNA

molecule so that about 10 basepairs are separated

2. Elongation

a. Complementary base pairing of free nucleoside triphosphates

occurs with the exposednitrogenous bases of the templatestrand



b. RNA polymerase binds the

nucleosides to each other

i. Two of the phosphates are

released in the process

c. The 5' end of a nucleoside isadded to the 3' end of the RNA molecule being made



i. Means that the RNA is made in a5' to 3' direction

ii. Means that the template isbeing read in a 3' to 5' direction

d. As the RNA polymerase movesalong the DNA, it rewinds the

DNA that has been transcribedand unwinds the DNA that hasnot yet been transcribed



3. Termination

a. RNA polymerase reaches atermination site or terminator

b. RNA polymerase releases themRNA strand

c. DNA rewinds completely



G. Note that more than one RNA polymerase can be transcribing onegene at the same time

H. Other types of RNA are also made by

transcription

Here are 2 animations of transcription:http://bcs.whfreeman.com/thelifewire9e/default.asp#542578__591855 __

http://www.johnkyrk.com/DNAtranscription.html

http://bcs.whfreeman.com/thelifewire9e/default.asp#542578__591855






I. Transcription in Eukaryotes

Here is an animation of transcription in prokaryotes and also in eukaryotes. Pay attentionto the differences.

http://highered.mcgraw-hill.com/olc/dl/120077/bio25.swf

1. initiation requires proteins called

transcription factors that RNA polymerase binds to

2. the promoter region has a sequence

called the TATA box

3. the promoter often includes a CAATsequence





4. product is called pre-mRNA andmust be processed

a. Synthesis of a cap made of amodified guanine attached to the5' end

i. protects the RNA from enzymesthat work from the 5' end

ii. Assembly point for the proteinsneeded to attract the smallsubunit of the ribosome to begin

translation



b. introns (highly repetitive

sequences that code for aminoacids that are not found in theactual polypeptide) are removed

i. Most begin with GU and endwith AG

c. what's left are sequences calledexons (they are expressed)



i. joined together by spliceosomes

(made of 5 types of snRNA anda large number of proteinmolecules) in a process

called splicing

d. Synthesis of a polyA tail, a stretchof adenine nucleotides attachedto the 3' end



e. After processing mRNA can leavethe nucleus

Here is an animation of spliceosomes atwork:


*alternative and trans splicing makes itpossible for a large number of proteins to be

made from a small number of genes formore information see the following:








III. TRANSLATION

A. the process of producing apolypeptide chain using the sequenceof nitrogenous bases in mRNA as a

template

B. Requirements

1. Raw materials: amino acids











2. energy

3. ribosomes consisting of twosubunits (small and large)

a. Are separate when not in use forprotein synthesis

i. Small subunit consists of 1 rRNA molecule and 33 differentprotein molecules in eucaryotes













ii. Large subunit consists of 3different rRNA molecules and

about 45 different proteins ineucaryotes

4. mRNA with nitrogenous bases intriplets called codons

5. transfer RNA (tRNA) with asequence of nitrogenous basescalled an anticodon













a. Will complementary base pair withcodons on the mRNA

b. Each tRNA can bind to one aminoacid

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPROTSYn.html#Table%20of%20Contents










5. Wobble in anticodons

a. Theoretically, there should be 64types of tRNA's based oncomplementary base pairing with

the mRNA codons

b. Most organisms have between 31

and 40 tRNA's

c. One type of tRNA will bind tomore than one codon













d. Third base of a codon is allowedto bind inexactly (this position isknown as the wobble position)

i. G can bind with U in the wobble

position

ii. Inosine (a modified G) can pair

with C, U or A in the wobbleposition












C. The Triplet Code

1. the mRNA nitrogenous bases areread in groups of three calledcodons

2. each codon calls for a particularamino acid










3. the code is degenerate meaning

that more than one codon can codefor the same amino acid

a. there are 64 different codonspossible but only 20 amino acids

b. some codons are stop codons andsignal the end of the polypeptide











https://www.dna20.com/index.php?pageID=251






http://www.accessexcellence.org/RC/VL/GG/genetic.php






D. Steps

1. Initiation

a. Small subunit of ribosome binds

to mRNA and moves along themRNA until it reaches the startcodon AUG

b. Initiator tRNA binds at the P siteon the large subunit












i. In eucaryotes, the start codon is

AUG

ii. Initiator tRNA has the anticodon

UAC and carries the amino acidmethionine

c. Lastly, large subunit of ribosomebinds











http://kentsimmons.uwinnipeg.ca/cm1504/proteinsynth.htm






2. Elongation

a. tRNA's that carry amino acids(charged tRNA's) diffuse to the A site on the ribosome

b. If the anticodon base pairs arecomplementary to the codon base

pairs, the tRNA will stay











c. A peptide bond is formed between

the amino group of the incomingamino acid and the carboxyl groupof the amino acid or peptide heldat the P site

d. The tRNA at the P site is released

e. The growing polypeptide is on thetRNA located at the A site

f The ibosome mo es one codon













f. The ribosome moves one codonforward from the 5' end to the 3'

end

i. The start codon is closer tothe 5' end than is the stop

codon

g. The tRNA with the growingpolypeptide is now at the P siteand the A site is empty

h. The steps from a to g repeat

h //k / 0 / h h






















3. Termination

a. Ribosome's A site reaches a stopcodon

b. A release factor binds to thestop codon on the mRNA

c. Polypeptide is released from thetRNA at the P site











d. Ribosome releases the mRNA

and separates into 2 subunitshttp://kentsimmons.uwinnipeg.ca/cm1504/proteinsynth.htm

l h









E. Polysomes occur when manyribosomes are translating the same

mRNA http://kentsimmons.uwinnipeg.ca/cm1504/proteinsynth.htm

H 2 i ti f t l ti d i t ti









Here are 2 animations of translation and an interactivepractice of trascription and translation:

http://bcs.whfreeman.com/thelifewire9e/default.asp#542578__591858 _ _

http://www.johnkyrk.com/DNAtranslation.html

http://learn.genetics.utah.edu/content/begin/dna/transcribe/

E. Fate of Molecules

1. mRNA: can be translated by other

ribosomes or degraded and thenucleotides made available forreuse

2 tRNA: becomes charged again










2. tRNA: becomes charged again

3. ribosomes: available for reuse

4. polypeptide:

a. Folds and coils into secondary andtertiary structures

b. Associate with other polypeptidesto form quaternary structures

c transported to its final destination



c. transported to its final destinationbased on signal sequences

(sequence of amino acids atterminal end)

d. proteolysis: cutting polypeptideinto smaller fragments

e. glycosylation: addition of sugars

f. phosphorylation: addition of phosphate groups

IV Replication



IV. Replication

A. the synthesis of a new DNA moleculeusing an existing DNA molecule as atemplate

B. semi-conservative because at end of replication, each new molecule is

made of one old strand plus one newstrand

C R i t



C. Requirements

1. Raw materials

a. 4 deoxyribonucleoside triphosphates

i. deoxy-ATP/deoxyadenosine

triphosphateii. deoxy-GTP/deoxyguanosine

triphosphateiii. deoxy-CTP/deoxycytidine

triphosphateiv. deoxy-TTP/deoxythymidine

triphosphate

2 h li th t i d



2. helicase: an enzyme that unwindsthe DNA double helix

3. DNA polymerase III: enzyme that

a. binds to DNA and incomingnucleotides

b. proofreads the growing newstrand

l dd l tid t th 3'



c. can only add nucleotides to the 3'end of the growing chain

d. Two work at the same time, onefor each strand of DNA

3. RNA primase: enzyme that adds ashort strand of RNA that

complementary base pairs witheach strand of DNA



a. initiates DNA replication by

producing a 3' end that DNA polymerase can add nucleotidesto

4. DNA ligase: links together shortchains of DNA called Okazaki

fragments



5. DNA Polymerase I: enzyme that

removes RNA primers and replacesthem with DNA

a. can only add nucleotides to the 3'end of a nucleotide chain

6 telomerase: enzyme that replaces



6. telomerase: enzyme that replacestelomeres

a. telomeres: region of DNA at theends of chromosomes that help to

prevent against DNA erosion

b. telomerase mostly found in

immortal cells and in thedeveloping organism



D. Process

1. helicase unwinds the double helix

a. becomes unstable

b. open area is called a replicationbubble or fork

2 single-strand binding protein



2. single strand binding proteinprevents the two strands from re-

joiningThe following diagram and all similar ones are from:http://www.scq.ubc.ca/breakfast-of-champions-does-replication/

http://kentsimmons.uwinnipeg.ca/cm1504/dnareplication.htm

http://www.scq.ubc.ca/breakfast-of-champions-does-replication/






p // p g / / p

3. RNA primase puts a short strand of







p pRNA that is complementary to each

strand of the separated DNA a. needed because the DNA

polymerase need a 3' end to add

nucleotides to

3 RNA primase puts a short strand of RNA











3. RNA primase puts a short strand of RNA

that is complementary to each strand of

the separated DNA

a. needed because the DNA polymeraseneeds a 3' end to add nucleotides to

3. RNA primase puts a short strand of RNA










p p

that is complementary to each strand of

the separated DNA a. needed because the DNA polymerase

needs a 3' end to add nucleotides to

b. Only 1 primer is needed for the










y pDNA strand that ends with the 3'

end (leading strand)

i. because the primer will end with

a 3' end

c. Problem with the strand that endswith the 5' end (lagging strand) isthat the primer will end with the 5'end













i. DNA polymerase cannot add





nucleotides to the 5' end

ii. Must make short strands of DNA on the 3' end of the primer

iii. results in short strands of DNA called Okazaki fragments

4. DNA sequence is now copied but thenew nucleic acid is in short piecesand has many bits of RNA





















5. DNA polymerase I finds the placesh RNA i d h t






where an RNA primer and a short

strand of DNA are not joinedtogether

a. Begins from the 5' end and

removes the RNA primer

b. Leaves a 3' end at the end of the

DNA freec. Adds nucleotides to the free 3'

end


















6. the strands are still in bits





7. ligase joins all the DNA bits together






8. Now there are two new double-stranded molecules of DNA

9. in eucaryotes, replication occurssimultaneously at many sites on the








simultaneously at many sites on the

DNA molecule


Here are animations of the replication process:









p p

http://bcs.whfreeman.com/thelifewire9e/default.asp#542578__591852__

(there are two parts here)

http://highered.mcgraw-hill.com/olc/dl/120076/bio23.swf http://highered.mcgraw-hill.com/olc/dl/120076/micro04.swf

http://www.johnkyrk.com/DNAreplication.html

V. Mutations

A. mutation: heritable changes in DNA

1. somatic mutations are only passedon to daughter cells





http://highered.mcgraw-hill.com/olc/dl/120076/micro04.swf



http://highered.mcgraw-hill.com/olc/dl/120076/micro04.swf



Documents

Molecular Genetic Ppt