From Gene

to Protein

How Genes
Work
AP Biology

2007-2008

Nucleus & Nucleolus

AP Biology

large
subunit

Ribosomes

Function

small
subunit

protein production

Structure

rRNA & protein

2 subunits combine

0.08m

Ribosomes
Rough
ER

Smooth
ER
AP Biology

Types of Ribosomes

Free ribosomes

suspended in cytosol
synthesize proteins that
function in cytosol

Bound ribosomes

AP Biology

attached to endoplasmic
reticulum
synthesize proteins
for export or
for membranes

membrane proteins

TO:

endoplasmic
reticulum

nucleus

protein
on its way!

DNA
RNA

vesicle

TO:

TO:

TO:

vesicle

ribosomes

TO:

Making Proteins
AP Biology

finished
protein

protein
Golgi
apparatus

Metabolism taught us about genes

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

metabolic pathway

disease

AP Biologyenzyme 1

Am I just the
sum of my proteins?

disease

enzyme 2

disease

enzyme 3

disease

enzyme 4

1 gene 1 enzyme hypothesis

Beadle & Tatum

Compared mutants of bread mold,

Neurospora fungus

created mutations by X-ray treatments

X-rays break DNA
damage a gene

wild type grows on minimal media

sugars + required nutrients allows fungus to
synthesize essential amino acids

mutants require added amino acids

each type of mutant lacks a certain enzyme needed

AP Biology

to produce a certain amino acid

non-functional enzyme from damaged gene

Beadle & Tatum

X rays or ultraviolet light

Wild-type
Neurospora

create mutations
asexual
spores

Minimal
medium
spores

Growth on
complete
medium
positive control

Select one of
the spores
Test on minimal
medium to confirm
presence of mutation
negative control

Grow on
complete medium

de
i
on
i
t
a

ed
i
f
i
nt

t
Minimal media supplemented only with
mu
experimentals

Choline
Pyridoxine
Minimal
Nucleic
Arginine Riboflavin
amino acid
Niacin
control
Inositol acid
Folic
p-Amino
supplements
AP Biology
Thiamine
acid
benzoic acid

One gene / one enzyme hypothesis

Damage to specific gene, mapped to

nutritional mutations

chromosome

gene
cluster 1

gene
cluster 2

arg-E
encoded
enzyme

arg-G arg-H

arg-F

enzyme E

glutamate

gene
cluster 3

enzyme F

ornithine

substrate in
AP biochemical
Biology
pathway

enzyme G

citruline

enzyme H

arginine
arginosuccinate
gene that
was damaged

1941 | 1958

Beadle & Tatum

one gene : one enzyme hypothesis

George Beadle
Edward Tatum
AP Biology

"for their discovery that genes act by

regulating definite chemical events"

The Central Dogma

Flow of genetic information in a cell

How do we move information from DNA to proteins?

DNA

n
o
i
t
p
i
r
c
s
n
tra

replication

AP Biology

RNA

tr

on
i
t
a
l
ans

protein

DNA gets
all the glory,
but proteins do
all the work!

trait

RNA

ribose sugar
N-bases

uracil instead of thymine

U:A
C:G

single stranded
lots of RNAs

mRNA, tRNA, rRNA, siRNA

DNA
AP Biology

transcription

RNA

Transcription
from
DNA nucleic acid language
to
RNA nucleic acid language

AP Biology

2007-2008

Transcription

Making mRNA

transcribed DNA strand = template strand

untranscribed DNA strand = coding strand

synthesis of complementary RNA strand

same sequence as RNA

transcription bubble

enzyme

coding strand

RNA polymerase
5

DNA

C
G

3
AP Biology
build
RNA 53

A
G
T
A T C
T A

rewinding

mRNA 5

G
C

A G C

C G T

3
G C A U C G U
C
G T A G C A

RNA polymerase

T
A

A
C
T
A G
C T
G

A
T

3
5

unwinding

template strand

Bacterial chromosome

Transcription in
Prokaryotes

Transcription
mRNA

Psssst
no nucleus!

Cell
membrane
Cell wall
AP Biology

2007-2008

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 35!
build RNA 53
APBiology

Transcription in Prokaryotes

Promoter sequences

enzyme
subunit

RNA polymerase

read DNA 35

bacterial DNA
Promoter
TTGACA TATAAT
35 sequence
10 sequence
RNA polymerase
molecules bound to
bacterial DNA
RNA polymerase
AP Biology

strong vs. weak promoters

Transcription in Prokaryotes

Elongation

RNA polymerase copies

DNA as it unwinds

~20 base pairs at a time

300-500 bases in gene
builds RNA 53

Simple proofreading
1 error/105 bases
make many mRNAs
mRNA has short life
not worth editing!
AP Biology

reads DNA 35

Transcription in Prokaryotes

Termination

RNA polymerase stops at termination

sequence

RNA GC
hairpin turn

AP Biology

Transcription in Eukaryotes

Transcription
Psssst
DNA cant
leave nucleus!

RNA Processing

Translation
Protein

AP Biology

2007-2008

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

intron = noncoding (inbetween) sequence

eukaryotic
DNA
exon = coding (expressed) sequence
AP Biology

introns
come out!

Transcription in Eukaryotes

3 RNA polymerase enzymes

RNA polymerase 1

RNA polymerase 2!

AP Biology

transcribes genes into mRNA

RNA polymerase 3!

only transcribes rRNA genes

makes ribosomes

only transcribes tRNA genes

each has a specific promoter sequence

it recognizes

Transcription in Eukaryotes

Initiation complex

transcription factors bind

to promoter region
upstream 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

Post-transcriptional processing

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
mRNA
p
a
c
add polyA tail
5' PPP
5' G

ail
t
A
ly3'
o
p
3'
AA
AAA

5
50-2

s
0 A

intron = noncoding (inbetween) sequence

~10,000 bases

ryotic DNA
exon = coding (expressed) sequence

ary mRNA
transcript
mature
mRNA
AP Biology
transcrip

pre-mRNA

~1,000 bases
spliced mRNA

Splicing must be accurate

No room for mistakes!

AP Biology

splicing must be exactly accurate

a single base added or lost throws off the
reading frame
AUGCGGCTATGGGUCCGAUAAGGGCCAU
AUGCGGUCCGAUAAGGGCCAU
AUG|CGG|UCC|GAU|AAG|GGC|CAU
Met|Arg|Ser|Asp|Lys|Gly|His
AUGCGGCTATGGGUCCGAUAAGGGCCAU
AUGCGGGUCCGAUAAGGGCCAU
AUG|CGG|GUC|CGA|UAA|GGG|CCA|U
Met|Arg|Val|Arg|STOP|

Whoa! I think
we just broke
a biological rule!

Splicing enzymes

snRNPs

small nuclear RNA

exon
proteins

Spliceosome

cut & paste

No,
not smurfs!
snurps

AP Biology

intron

exon

5'

several snRNPs
recognize splice
site sequence

snRNPs

snRNA

mature mRNA

3'

spliceosome
5'

3'
lariat

5'

exon
5'

3'

exon
3'

excised

Ribozyme

1982 | 1989

RNA as ribozyme

some mRNA can even splice itself

RNA as enzyme

Sidney Altman
AP Biology
Yale

Thomas Cech
U of Colorado

Translation
from
nucleic acid language
to
amino acid language

AP Biology

2007-2008

Bacterial chromosome

Translation in
Prokaryotes

Transcription
mRNA
Translation

Psssst
no nucleus!

protein

Cell
membrane
Cell wall
AP Biology

2007-2008

Translation in Prokaryotes

Transcription & translation are simultaneous

in bacteria

DNA is in
cytoplasm
no mRNA
editing
ribosomes
read mRNA
as it is being
transcribed

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

AP Biology

Translation in Eukaryotes

AP Biology

2007-2008

From gene to protein

aa
aa
aa

DNA

transcription

mRNA

mRNA leaves
nucleus through
nuclear pores

nucleus

AP Biology

aa

translation

protein

aa

aa

aa

aa

ribosome

cytoplasm

proteins synthesized
by ribosomes using
instructions on mRNA

How does mRNA code for proteins?

DNA
4 ATCG

mRNA
4 AUCG

protein

TACGCACATTTACGTACGCGG
AUGCGUGUAAAUGCAUGCGCC

?
Met Arg Val Asn Ala Cys Ala

20
AP Biology

How can you code for 20 amino acids

with only 4 nucleotide bases (A,U,G,C)?

mRNA codes for proteins in triplets

DNA

TACGCACATTTACGTACGCGG
codon

mRNA

AUGCGUGUAAAUGCAUGCGCC

?
protein

AP Biology

Met Arg Val Asn Ala Cys Ala

Cracking the code

1960 | 1968
Nirenberg & Khorana

Crick

determined 3-letter (triplet) codon system

WHYDIDTHEREDBATEATTHEFATRAT

Nirenberg (47) & Khorana (17)

determined mRNAamino acid match

added fabricated mRNA to test tube of
ribosomes, tRNA & amino acids

AP Biology

created artificial UUUUU mRNA

found that UUU coded for phenylalanine (phe)

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

Why is the
wobble good?

Start codon

AP Biology

AUG
methionine

Stop codons

UGA, UAA, UAG

From gene to protein

aa
aa
aa

DNA

transcription

mRNA

aa

translation

protein

aa

aa

aa

aa

ribosome
aa

nucleus

AP Biology

cytoplasm

Transfer RNA structure

Clover leaf structure

anticodon on clover leaf end

amino acid attached on 3 end

AP Biology

Ribosomes

Facilitate coupling of
tRNA anticodon to
mRNA codon

organelle or enzyme?

Structure

ribosomal RNA (rRNA) & proteins

2 subunits

large
small
E P A

AP Biology

Ribosomes

A site (aminoacyl-tRNA site)

P site (peptidyl-tRNA site)

holds tRNA carrying next amino acid to

be added to chain
holds tRNA carrying growing
polypeptide chain

Met

E site (exit site)

AP Biology

empty tRNA
leaves ribosome
from exit site

U A C
A U G

5'

3'

Building a polypeptide

Initiation
brings together mRNA, ribosome
subunits, initiator tRNA

Elongation
adding amino acids based on
codon sequence

Termination
3 2 1

end codon

Leu

Val

Met

Met

Met

Met Leu

Leu

Ala

Leu

release
factor

Ser
Trp

tRNA

U AC
5'
C U GA A U
mRNA A U G
3'
E P A

AP Biology

5'

U A C G A C AA
U
A U G CU G

5'
3'

U A C GA C
A U G C UG AAU

3'

5'

U A C G A C AA U
AU G C U G

3'

A CC
U GG U A A

3'

Protein targeting

Destinations:

Signal peptide

address label

start of a secretory pathway

AP Biology

secretion
nucleus
mitochondria
chloroplasts
cell membrane
cytoplasm
etc

RNA polymerase
DNA

Can you tell the

story?

amino
acids

exon

intron
tRNA

pre-mRNA

5' cap
mature mRNA
polyA tail

large ribosomal subunit

aminoacyl tRNA
synthetase
3'
polypeptide

5'
small ribosomal subunit

AP Biology

tRNA
E P A

ribosome

Any Questions??

What color would a smurf turn

if he held his breath?

AP Biology

2007-2008