division ave. high school ms. foglia ap biology17+-+gene+to... · division ave. high school ms....

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Division Ave. High School Ms. FogliaAP Biology

2007-2008AP Biology

From Geneto Protein

How Genes Work

AP Biology

� Organelles� nucleus� ribosomes� endoplasmic reticulum

(ER)� Golgi apparatus� vesicles

Making proteins

smallribosomal

subunit

largeribosomal

subunit

cytoplasm

mRNA

nuclear pore

AP Biology

Nucleus & Nucleolus

AP Biology

Nucleolus� Function

� ribosome production� build ribosome subunits from rRNA & proteins� exit through nuclear pores to cytoplasm &

combine to form functional ribosomes

smallsubunit

large subunit

ribosome

rRNA &proteins

nucleolus

AP Biology

smallsubunit

largesubunitRibosomes

� Function� protein production

� Structure� rRNA & protein� 2 subunits combine 0.08µµµµm

RibosomesRough

ER

SmoothER

AP Biology membrane proteins

Types of Ribosomes� Free ribosomes

� suspended in cytosol� synthesize proteins that

function in cytosol

� Bound ribosomes� attached to endoplasmic

reticulum� synthesize proteins

for export orfor membranes

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AP Biology

DNA

RNA

ribosomes

endoplasmicreticulum

vesicle

Golgi apparatus

vesicle

proteinon its way!

protein finishedprotein

Making Proteins

TO:

TO:

TO:

TO:nucleus

TO:

AP Biology

End of the Tour

AP Biology

TACGCACATTTACGTACGCGGATGCCGCGACTATGATCACATAGACATGCTGTCAGCTCTAGTAGACTAGCTGACTCGACTAGCATGATCGATCAGCTACATGCTAGCACACYCGTACATCGATCCTGACATCGACCTGCTCGTACATGCTACTAGCTACTGACTCATGATCCAGATCACTGAAACCCTAGATCGGGTACCTATTACAGTACGATCATCCGATCAGATCATGCTAGTACATCGATCGATACTGCTACTGATCTAGCTCAATCAAA

What happens in the cellwhen a gene is read?

Where are the genes?

Where does a gene start?Where does the gene end?

How do cells make proteinsfrom DNA?

How is one gene read and another one not?

How do proteinscreate phenotype?

AP Biology

� Inheritance of metabolic diseases� suggested that genes coded for enzymes� each disease (phenotype) is caused by

non-functional gene product � lack of an enzyme� Tay sachs� PKU (phenylketonuria)� albinism

Am I just thesum of my proteins?

Metabolism taught us about genes

A B C D Edisease disease disease disease

� � � �enzyme 1 enzyme 2 enzyme 3 enzyme 4

metabolic pathway

AP Biology

Beadle & Tatum 1941 | 1958

George Beadle

Edward Tatum

"for their discovery that genes act by regulating definite chemical events"

one gene : one enzyme hypothesis

AP Biology

One gene / one enzyme hypothesis

chromosome

genecluster 1

enzyme E

glutamate ornithine citruline argino-succinate

arginine

enzyme F enzyme G enzyme H

encodedenzyme

substrate inbiochemical pathway

genecluster 2

genecluster 3

arg-Harg-Garg-Farg-E

� Damage to specific gene, mapped to nutritional mutations

gene thatwas damaged


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AP Biology

The “Central Dogma”� Flow of genetic information in a cell

� How do we move information from DNA to proteins?

transcriptiontranslation

replication

proteinRNADNA trait

DNA getsall the glory,

but proteins do all the work!

AP Biology

RNA� ribose sugar � N-bases

� uracil instead of thymine� U : A� C : G

� single stranded� lots of RNAs

� mRNA, tRNA, rRNA, siRNA…

RNADNAtranscription

2007-2008AP Biology

Transcription

fromDNA nucleic acid language

toRNA nucleic acid language

AP Biology

Transcription� Making mRNA

� transcribed DNA strand = template strand� untranscribed DNA strand = coding strand

� same sequence as RNA

� synthesis of complementary RNA strand� transcription bubble

� enzyme� RNA polymerase

template strand

rewinding

mRNA RNA polymerase

unwinding

coding strand

DNAC C

C

C

C

C

C

C

C CC

G

GG

G

G G

G G

G

G

GAA

AA A

A

A

A

A

A A

A

AT

T T

T

T

T

T

T

T T

T

T

U U

5′′′′

3′′′′5′′′′

3′′′′

3′′′′

5′′′′build RNA 5 ′′′′→→→→3′′′′

2007-2008AP Biology

Transcription in Prokaryotes

Bacterial chromosome

mRNA

Cell wall

Cellmembrane

Transcription

Psssst…no nucleus!

AP Biology

Transcription in Prokaryotes� Initiation

� RNA polymerase binds to promoter sequence on DNA

Role of promoter� Starting point

� where to start reading� start of gene

� Template strand� which strand to read

� Direction on DNA� always read DNA 3 ′′′′→→→→5′′′′� build RNA 5 ′′′′→→→→3′′′′


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AP Biology

Transcription in Prokaryotes� Promoter sequences

RNA polymerase molecules bound to bacterial DNA

TATAAT

RNA polymerase

Promoter

enzymesubunit

bacterial DNA

–35 sequence –10 sequenceTTGACA

RNA polymerasestrong vs. weak promoters

read DNA 3 ′′′′→→→→5′′′′

AP Biology

Transcription in Prokaryotes

Simple proofreading� 1 error/10 5 bases� make many mRNAs� mRNA has short life� not worth editing !

� Elongation� RNA polymerase

copies DNA as it unwinds� ~20 base pairs at a time

� 300-500 bases in gene

� builds RNA 5 ′′′′→→→→3′′′′

reads DNA 3 ′′′′ →→→→5′′′′

AP Biology

Transcription in Prokaryotes� Termination

� RNA polymerase stops at termination sequence

RNA GChairpin turn

2007-2008AP Biology

Transcription in Eukaryotes

Protein

RNA Processing

Translation

Transcription

Psssst…DNA can’t

leave nucleus!

AP Biology

Prokaryote vs. Eukaryote genes� Prokaryotes

� DNA in cytoplasm� circular

chromosome� naked DNA

� no introns

� Eukaryotes� DNA in nucleus� linear

chromosomes� DNA wound on

histone proteins� introns vs. exons

eukaryoticDNA

exon = coding (expressed) sequence

intron = noncoding (inbetween) sequence

intronscome out!

AP Biology

Transcription in Eukaryotes� 3 RNA polymerase enzymes

� RNA polymerase 1� only transcribes rRNA genes� makes ribosomes

� RNA polymerase 2� transcribes genes into mRNA

� RNA polymerase 3� only transcribes tRNA genes

� each has a specific promoter sequence it recognizes


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AP Biology

Transcription in Eukaryotes� Initiation complex

� transcription factors bind to promoter regionupstream of gene� suite of proteins which bind

to DNA� turn on or off transcription

� TATA box binding site� recognition site for

transcription factors

� transcription factors trigger the binding of RNA polymerase to DNA

AP Biology

A A A A A3' poly-A tail

mRNA

5'5' cap

3'

G P PP50-250 A’s

Post-transcriptional processing

eukaryotic DNA

exon = coding (expressed) sequence

intron = noncoding (inbetween) sequence

primary mRNAtranscript

mature mRNAtranscript

pre-mRNA

spliced mRNA

� Primary transcript (pre-mRNA )� eukaryotic mRNA needs work after transcription

� mRNA processing (making mature mRNA )� mRNA splicing = edit out introns� protect mRNA from enzymes in cytoplasm

� add 5′′′′ cap� add polyA tail

~10,000 bases

~1,000 bases

2007-2008AP Biology

Translation

fromnucleic acid language

toamino acid language

2007-2008AP Biology

Translation in Prokaryotes

Bacterial chromosome

mRNA

Cell wall

Cellmembrane

Transcription

Translation

proteinPsssst…no nucleus!

AP Biology

� Transcription & translation are simultaneous in bacteria � DNA is in

cytoplasm� no mRNA

editing� ribosomes

read mRNAas it is beingtranscribed

Translation in Prokaryotes

AP Biology

Translation: prokaryotes vs. eukaryotes

� Differences between prokaryotes & eukaryotes� time & physical separation between

processes� takes eukaryote ~1 hour

from DNA to protein� RNA processing


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2007-2008AP Biology

Translation in Eukaryotes

AP Biology

mRNA

From gene to protein

DNAtranscription

nucleus cytoplasm

mRNA leaves nucleus through nuclear pores

proteins synthesized by ribosomes using instructions on mRNA

aa

aa

aaaa

aa

aaaa

aa

ribosome

proteintranslation

AP Biology

How does mRNA code for proteins?

TACGCACATTTACGTACGCGGDNA

AUGCGUGUAAAUGCAUGCGCCmRNA

MetArgValAsnAlaCysAlaprotein

?

How can you code for 20 amino acids with only 4 nucleotide bases (A,U,G,C)?

4

4

20

ATCG

AUCG

AP Biology


mRNA codes for proteins in triplets



MetArgValAsnAlaCysAlaprotein

?

codon

AP Biology

Cracking the code1960 | 1968

� Crick� determined 3-letter (triplet) codon system

Nirenberg & Khorana

W HYDIDTHEREDBATEATTHEFATRATW HYDIDTHEREDBATEATTHEFATRAT

� Nirenberg (47) & Khorana (17)

� determined mRNA–amino acid match� added fabricated mRNA to test tube of

ribosomes, tRNA & amino acids� created artificial UUUUU… mRNA � found that UUU coded for phenylalanine (phe)

AP Biology

1960 | 1968Marshall Nirenberg

Har Khorana


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AP Biology

The code� Code for ALL life!

� strongest support for a common origin for all life

� Code is redundant� several codons for

each amino acid� 3rd base “wobble”

� Start codon� AUG� methionine

� Stop codons� UGA, UAA, UAG

Why is thewobble good?

AP Biology

How are the codons matched to amino acids?



aminoacid

tRNA

anti-codon

codon

5′′′′ 3′′′′

3′′′′ 5′′′′

3′′′′ 5′′′′

UAC

MetGCA

ArgCAU

Val

AP Biology

mRNA

From gene to protein

DNAtranscription

nucleuscytoplasm

aa

aa

aaaa

aa

aaaa

aa

ribosome

proteintranslation

aa

AP Biology

Transfer RNA structure� “Clover leaf” structure

� anticodon on “clover leaf” end� amino acid attached on 3 ′′′′ end

AP Biology

Loading tRNA � Aminoacyl tRNA synthetase

� enzyme which bonds amino acid to tRNA� bond requires energy

� ATP →→→→ AMP

� energy stored in tRNA-amino acid bond� unstable� so it can release amino acid at ribosome easily

activatingenzyme

anticodontRNATrp binds to UGG

condon of mRNA

Trp Trp Trp

mRNAA C CU G G

C=O

OHOH

H2OO

tRNATrp

tryptophan attached to tRNA Trp

C=O

O

C=O

AP Biology

Ribosomes � Facilitate coupling of

tRNA anticodon tomRNA codon� organelle or enzyme?

� Structure� ribosomal RNA ( rRNA) & proteins� 2 subunits

� large� small E P A


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AP Biology

Ribosomes

Met

5'

3'

UUA C

A G

APE

� A site (aminoacyl-tRNA site)� holds tRNA carrying next amino acid to

be added to chain

� P site (peptidyl-tRNA site)� holds tRNA carrying growing

polypeptide chain

� E site (exit site)� empty tRNA

leaves ribosome from exit site

AP Biology

Building a polypeptide� Initiation

� brings together mRNA, ribosome subunits, initiator tRNA

� Elongation� adding amino acids based on

codon sequence

� Termination� end codon 123

Leu

Leu Leu Leu

tRNA

Met MetMet Met

PE AmRNA5' 5' 5' 5'

3' 3' 3' 3'U UA AAAC

CC

AU UG GGU

UA AA

ACC

CAU UG G

GUU

A AAAC

CC

AU UG GGU U

A AACCA U UG G

G A C

ValSer

AlaTrp

releasefactor

AA A

CCU UGG 3'

AP Biology

Protein targeting � Signal peptide

� address label

Destinations:� secretion� nucleus� mitochondria� chloroplasts� cell membrane� cytoplasm� etc…start of a secretory pathway

AP Biology

Can you tell the story?

DNA

pre-mRNA

ribosome

tRNA

aminoacids

polypeptide

mature mRNA

5' cap

polyA tail

large ribosomal subunit

small ribosomal subunit

aminoacyl tRNAsynthetase

E P A

5'

3'

RNA polymerase

exon introntRNA

2007-2008AP Biology

Got Questions?Can I translate that for you?

2007-2008AP Biology

Substitute Slidesfor Student Print version


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AP Biology

Can you tell the story?

2007-2008AP Biology

Extra Slides(used some years & not others)

AP Biology

Translation � Codons

� blocks of 3 nucleotides decoded into the sequence of amino acids

AP Biology

Building Proteins� Organelles involved

� nucleus� ribosomes� endoplasmic reticulum

(ER)� Golgi apparatus� vesicles

nucleus ribosome ERGolgi

apparatusvesicles

The Protein Assembly Line

AP Biology

From nucleus to cytoplasm…� Where are the genes?

� genes are on chromosomes in nucleus

� Where are proteins synthesized?� proteins made in cytoplasm by ribosomes

� How does the information get from DNA in nucleus to cytoplasm?� messenger RNA

nucleus AP Biology

Alternative splicing� Alternative mRNAs produced from same gene

� when is an intron not an intron…� different segments treated as exons

Starting to gethard to

define a gene!


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AP Biology

Domains

� Modular architectureof many proteins� exons may represent

functional units of protein

� easier to mix and match in the production of new proteins?

AP Biology

So… What is a gene?� One gene – one enzyme?

� but not all proteins are enzymes� but all proteins are coded by genes

� One gene – one protein?� but many proteins are composed of several polypepti des� but each polypeptide has its own gene

� One gene – one polypeptide?� but many genes only code for RNA (tRNA, rRNA…)

� One gene – one product?� but many genes code for

more than one product …So…

Where doesthat leave

us?!

AP Biology

Defining a gene…““““Defining a gene is problematic becauseDefining a gene is problematic becauseDefining a gene is problematic becauseDefining a gene is problematic because…………one gene can code for several protein products, one gene can code for several protein products, one gene can code for several protein products, one gene can code for several protein products, some genes code only for RNA, two genes can some genes code only for RNA, two genes can some genes code only for RNA, two genes can some genes code only for RNA, two genes can overlap, and there are many other complications.overlap, and there are many other complications.overlap, and there are many other complications.overlap, and there are many other complications.””””

– Elizabeth Pennisi, Science 2003

gene

polypeptide 1

polypeptide 2

polypeptide 3

RNAgeneIt’s hard to

hunt for wabbits,if you don’t knowwhat a wabbit

looks like.

AP Biology

TACGCACATTTACGTACGCGGATGCCGCGACTATGATCACATAGACATGCTGTCAGCTCTAGTAGACTAGCTGACTCGACTAGCATGATCGATCAGCTACATGCTAGCACACYCGTACATCGATCCTGACATCGACCTGCTCGTACATGCTACTAGCTACTGACTCATGATCCAGATCACTGAAACCCTAGATCGGGTACCTATTACAGTACGATCATCCGATCAGATCATGCTAGTACATCGATCGATACTGCTACTGATCTAGCTCAATCAAACTCTTTTTGCATCATGATACTAGACTAGCTGACTGATCATGACTCTGATCCCGTAGATCGGGTACCTATTACAGTACGATCATCCGATCAGATCATGCTAGTACATCGATCGATACTGCTACTGATCTAGCTCAATCAAACTCTTTTTGCATCATGATACTAGACTAGCTGACTGATCATGACTCTGATCCCGTAGATCGGGTACC

human genome3.2 billion bases

AP Biology AAAAAAAAGTP

20-30b

3'

promoter transcriptionstop

transcriptionstart

introns

The Transcriptional unit (gene?)

transcriptional unitTAC ACT

DNA

DNATATA5'RNA

polymerase

pre-mRNA5' 3'

translationstart

translationstop

mature mRNA5' 3'

UTR UTR

exonsenhancer

1000+b

2007-2008AP Biology

Any Questions??

What color would a smurf turnif he held his breath?


11


AP Biology

20-30b

3'

introns

The Transcriptional unit

transcriptional unitTAC ACTDNATATA

5'RNApolymerase

5' 3'

5' 3'

exonsenhancer

1000+b

AP Biology

1977 | 1993

Richard Roberts Philip

SharpCSHL

MITadenovirus

common cold

Discovery of Split genes

beta-thalassemia

AP Biology

Splicing must be accurate� No room for mistakes!

� splicing must be exactly accurate� a single base added or lost throws off the

reading frame

AUG|CGG|UCC|GAU|AAG|GGC|CAU

AUGCGGCTATGGGUCCGAUAAGGGCCAUAUGCGGUCCGAUAAGGGCCAU

AUG|CGG|GUC|CGA|UAA|GGG|CCA|U

AUGCGGCTATGGGUCCGAUAAGGGCCAUAUGCGGGUCCGAUAAGGGCCAU

Met|Arg|Ser|Asp|Lys|Gly|His

Met|Arg|Val|Arg|STOP| AP Biology

Splicing enzymes

snRNPs

exonexon intron

snRNA

5' 3'

spliceosome

exonexcisedintron

5'

5'

3'

3'

3'

lariat

exonmature mRNA

5'

No,not smurfs!“snurps”

� snRNPs� small nuclear RNA� proteins

� Spliceosome� several snRNPs� recognize splice

site sequence� cut & paste

Whoa! I thinkwe just broke

a biological “rule”!

AP Biology

Ribozyme

Sidney Altman Thomas Cech

1982 | 1989

Yale U of Colorado

� RNA as ribozyme� some mRNA can even splice itself� RNA as enzyme


division ave. high school ms. foglia ap biology17+-+gene+to... · division ave. high school ms....

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