Download AP Biology

From Gene
to Protein
SLIDE SHOW BY KIM FOGLIA (modified)
All Blue edged slides are Kim’s
(hyperlinks may have been added)
How Genes
Work
AP Biology
2007-2008
What do genes code for?

How does DNA code for cells & bodies?

how are cells and bodies made from the
instructions in DNA
DNA
AP Biology
proteins
cells
bodies
The “Central Dogma”

Flow of genetic information in a cell

How do we move information from DNA to proteins?
DNA
replication
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RNA
protein
DNA gets
all the glory,
but proteins do
all the work!
trait
Section 17.1
Genes specify proteins via transcription and transaltion
AP Biology
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
PKU (phenylketonuria)
 lack of an enzyme
 Dysfunctional enzyme
Tay-Sachs
Albinism
metabolic pathway
A

AP Biology enzyme 1
disease
disease
disease
disease
B
C
D
E

enzyme 2

enzyme 3

enzyme 4
ARCHIBALD GARROD
1902





1st to suggest genes dictate phenotypes through enzymes that catalyze specific chemical
reactions
Postulated that the symptoms of an inherited disease are due to inability to
make a
specific enzyme
Coined term “inborn errors of metabolism” to describe such diseases
Beginning of “One gene-one enzyme” hypothesis
ALCAPTONURIA- “black urine” disease- defect in enzyme that breaks down amino acid
tyrosine
http://www.personal.psu.edu/faculty/w/x/wxm15/Online/Molecular%20Biology/media/phenylalanine.gif
http://www.nature.com/bjp/journal/v147/n1s/images/0706466f5.jpg
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"

George Beadle and Edward Tatum
exposed bread mold to X-rays, creating
mutants that were unable to survive on
minimal medium as a result of inability
to synthesize certain molecules
AP Biology
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
Minimal media supplemented only with…
experimentals
Choline
Pyridoxine
Riboflavin
Minimal
Nucleic
Arginine
control
amino acid p-Amino
Niacin
Inositol acid Folic
supplements
acid
Thiamine
benzoic acid
AP Biology
Fig. 17-2
EXPERIMENT
No growth:
Mutant cells
cannot grow
and divide
Growth:
Wild-type
cells growing
and dividing
Minimal medium
RESULTS
Classes of Neurospora crassa
Wild type
Class I mutants Class II mutants Class III mutants
Condition
Minimal
medium
(MM)
(control)
MM +
ornithine
MM +
citrulline
MM +
arginine
(control)
CONCLUSION
Wild type
Gene A
Precursor
Precursor
Precursor
Precursor
Enzyme A
Enzyme A
Enzyme A
Enzyme A
Ornithine
Gene B
Gene C
AP Biology
Class I mutants Class II mutants Class III mutants
(mutation in
(mutation in
(mutation in
gene B)
gene A)
gene C)
Ornithine
Ornithine
Ornithine
Enzyme B
Enzyme B
Enzyme B
Enzyme B
Citrulline
Citrulline
Citrulline
Citrulline
Enzyme C
Enzyme C
Enzyme C
Enzyme C
Arginine
Arginine
Arginine
Arginine
The Products of Gene Expression: A Developing Story

Some proteins aren’t enzymes, so researchers later revised
the hypothesis: one gene–one protein

Many proteins are composed of several polypeptides, each of
which has its own gene

Therefore, Beadle and Tatum’s hypothesis is now restated as
the one gene–one polypeptide hypothesis

Note that it is common to refer to gene products as proteins
rather than polypeptides
AP Biology
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings
a
a
From gene to protein
nucleus
cytoplasm
transcription
DNA
a
a
translation
mRNA
a
a
a
a
a
a
a
a
a
a
a
protein
a
a
a
a
a
a
a
ribosome
trait
AP Biology
Basic Principles of Transcription and Translation

RNA is the intermediate between genes and the proteins for
which they code

Transcription is the synthesis of RNA under the direction of
DNA

Transcription produces messenger RNA (mRNA)

Translation is the synthesis of a polypeptide, which occurs
under the direction of mRNA

Ribosomes are the sites of translation
AP Biology
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings
Transcription
from
DNA nucleic acid language
to
RNA nucleic acid language
AP Biology
2007-2008
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
3 KINDS OF RNA HELP WITH INFO TRANSFER FOR PROTEIN
SYNTHESIS
RIBOSOMAL RNA (rRNA):
 Most abundant type
 Made in nucleolus
 2 subunits (large & small)
 Combine with proteins to
form ribosomes
 Bacterial ribosomes different
size than eukaryotic ribosomes
 Medically significant-some antibiotics target
bacterial ribosomes w/o harming host
rRNA and t-RNA images from Image from: Biology; Miller and Levine; Pearson Education publishing as Prentice Hall; 2006
mRNA image from http://wps.prenhall.com/wps/media/tmp/labeling/1140654_dyn.gif
3 KINDS OF RNA HELP WITH INFO TRANSFER FOR
PROTEIN SYNTHESIS
TRANSFER RNA (tRNA):
Interpretor between nucleic acids
And proteins
ANTICODON sequence
matches CODON on mRNA
to add correct
amino acids during
protein synthesis
http://www-math.mit.edu/~lippert/18.417/lectures/01_Intro/
AMINOACYL-tRNA SYNTHETASE
Enzyme attaches a specific
amino acid using energy from ATP
3 KINDS OF RNA HELP WITH INFO TRANSFER FOR
PROTEIN SYNTHESIS
MESSENGER RNA (mRNA):
carries code from DNA to ribosomes
•Transcription
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

RNA polymerase
5
C
DNA
G
3
AP Biology
build
RNA
coding strand
A
G
T
A T C
T A
A G C
A
T
C G T
A
C
T
3
G C A U C G U
C
G T A G C A
T
T
A
C
A G
C T
G
A
T
A
T
3
5
unwinding
rewinding
mRNA
53
G
5
RNA polymerase
template strand

During transcription, one of the two DNA strands called the
template strand provides a template for ordering the sequence of
nucleotides in an RNA transcript

During translation, the mRNA base triplets, called codons, are read
in the 5 to 3 direction

Each codon specifies the amino acid to be placed at the
corresponding position along a polypeptide
AP Biology
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings
Cracking the Code

All 64 codons were deciphered by the mid-1960s

Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to
end translation

The genetic code is redundant but not ambiguous; no codon specifies
more than one amino acid

Codons must be read in the correct reading frame (correct groupings) in
order for the specified polypeptide to be produced
AP Biology
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings
Concept 17.2
Transcription is the DNA-directed synthesis of RNA: a
closer look
AP Biology
RNA polymerases

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
AP Biology
Molecular Components of Transcription

RNA synthesis is catalyzed by RNA polymerase, which pries the
DNA strands apart and hooks together the RNA nucleotides

RNA synthesis follows the same base-pairing rules as DNA, except
uracil substitutes for thymine
AP Biology
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings
Which gene is read?


Promoter region
 binding site before beginning of gene
 TATA box binding site
 binding site for RNA polymerase
& transcription
factors
Enhancer region
 binding site far
upstream of gene
 turns transcription
on HIGH
AP Biology
Transcription Factors

•Transcription
Initiation complex

transcription factors bind to promoter region



AP Biology
suite of proteins which bind to DNA
turn on or off transcription
trigger the binding of RNA polymerase to DNA
Matching bases of DNA & RNA

A
Match RNA bases to DNA bases on one of
the DNA strands
G
C
U
A
G
G
U
U
C
A
AG
C
G
A
U
A
C
5'
RNA
A C C polymerase G
A
U
3'
T G G T A C A G C T A G T C A T CG T A C CG T
AP Biology
U
C

Transcription animation
AP Biology
Section 17.3
Eukaryotic cells modify RNA after transcription
AP Biology
Eukaryotic genes have junk!

Eukaryotic genes are not continuous
 exons = the real gene
 expressed / coding DNA
 introns = the junk
 inbetween sequence
introns
come out!
intron = noncoding (inbetween) sequence
eukaryotic DNA
exon = coding (expressed) sequence
AP Biology
mRNA’s require EDITING before use


Message in NOT CONTINUOUS
INTRONS are removed
Image by Riedell
mRNA splicing

Post-transcriptional processing




eukaryotic mRNA needs work after transcription
primary transcript = pre-mRNA
mRNA splicing
 edit out introns
make mature mRNA transcript
intron = noncoding (inbetween) sequence
~10,000 base
eukaryotic DNA
exon = coding (expressed) sequence
pre-mRNA
primary mRNA
transcript
AP Biology
mature mRNA
transcript
~1,000 base
spliced mRNA
Discovery of exons/introns
Richard
Roberts
CSHL
Philip
Sharp
MIT
beta-thalassemia
AP Biology
1977 | 1993
adenovirus
common cold
Splicing must be accurate

No room for mistakes!

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
AP Biology
Met|Arg|Val|Arg|STOP|
RNA splicing enzymes


snRNPs (small
ribonucleoproteins)
 small nuclear RNA plus
exon
Proteins
5'
 Recognize splicing sites
Spliceosome
 several snRNPs plus
proteins joined together
 recognize splice site
sequence
 cut & paste gene
AP Biology
mature mRNA
snRNPs
snRNA
intron
exon
3'
spliceosome
5'
3'
lariat
5'
exon
5'
3'
exon
3'
excised
intron
RIBOZYMES-RNA molecules
that function as enzymes
(In some organisms pre-RNA
can remove its own introns)
More post-transcriptional processing

Need to protect mRNA on its trip from
nucleus to cytoplasm

enzymes in cytoplasm attack mRNA



protect the ends of the molecule
add 5 GTP cap
add poly-A tail
 longer tail, mRNA lasts longer: produces more protein
3'
mRNA
5'
AP Biology
P
G P
P
A
Section 17.4
Translation is the RNA-directed synthesis of a
polypeptide: a closer look
AP Biology
Translation
from
nucleic acid language
to
amino acid language
AP Biology
2007-2008
How does mRNA code for proteins?
DNA
4 ATCG
TACGCACATTTACGTACGCGG
mRNA
AUGCGUGUAAAUGCAUGCGCC
4 AUCG
protein
?
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 mRNA–amino 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
Marshall Nirenberg
1960 | 1968
Har Khorana
•Determining the code
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”
Why is the
wobble good?

Start codon



AP Biology
AUG
methionine
Stop codons

UGA, UAA, UAG
How are the codons matched to
amino acids?
DNA
3
5
5
3
TACGCACATTTACGTACGCGG
mRNA
AUGCGUGUAAAUGCAUGCGCC
3
codon
5
UAC
tRNA
amino
acid
AP Biology
GCA
anti-codon
CAU
Met
Arg
Val
a
a
From gene to protein
nucleus
cytoplasm
transcription
DNA
a
a
translation
mRNA
a
a
a
a
a
a
a
a
a
a
a
protein
a
a
a
a
a
a
a
ribosome
aa
trait
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
bond is unstable
so it can release amino acid at ribosome easily
Trp C=O
OH
OH
Trp C=O
O
Trp
H2O
O
activating
enzyme
tRNATrp
anticodon
AP Biology
tryptophan attached
to tRNATrp
AC C
UGG
mRNA
tRNATrp binds to UGG
condon of mRNA
Protein synthesis/quiz
Ribosomes

Facilitate coupling of
tRNA anticodon to
mRNA codon


organelle or enzyme?
Structure
ribosomal RNA (rRNA) & proteins
 2 subunits



AP Biology
large
small
E P A
Ribosomes

A site (aminoacyl-tRNA site)


holds tRNA carrying next amino acid to
be added to chain
P site (peptidyl-tRNA site)


Protein synthesis 2
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'
E
P
A
3'
How translation works
Building a polypeptide

Initiation


Elongation


brings together mRNA, ribosome
subunits, initiator tRNA
adding amino acids based on
codon sequence
Termination

3 2 1
end codon
Leu
Val
Met
Met
Met
Met Leu
Ala
Leu
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'
UAC GAC
A U G C U GA A U
5'
3'
U A C GA C
A U G C U G AAU
5'
3'
U AC G A C
AA U
AU G C UG
3'
A CC
U GG U A A
3'

Translation animation
AP Biology
Destinations:
Protein targeting



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' GTP cap
mature mRNA
aminoacyl tRNA
synthetase
poly-A tail
large ribosomal subunit
polypeptide
5'
small ribosomal subunit
AP Biology
tRNA
E P A
ribosome
3'

Bioflix: Protein Synthesis
AP Biology
The Transcriptional unit (gene?)
enhancer
1000+b
20-30b
3'
RNA
TATA
polymerase
translation
start
TAC
translation
stop
exons
transcriptional unit (gene)
5'
DNA
ACT
DNA
UTR
promoter
UTR
introns
transcription
start
transcription
stop
5'
pre-mRNA
AP Biology
5'
GTP mature mRNA
3'
3'
AAAAAAAA
Bacterial chromosome
Protein
Synthesis in
Prokaryotes
Transcription
mRNA
Psssst…
no nucleus!
Cell
membrane
Cell wall
AP Biology
2007-2008
Prokaryote vs. Eukaryote genes

Prokaryotes

Eukaryotes


DNA in cytoplasm
circular
chromosome
naked DNA

no introns





DNA in nucleus
linear
chromosomes
DNA wound on
histone proteins
introns vs. exons
introns
come out!
intron = noncoding (inbetween) sequence
eukaryotic
DNA
exon = coding (expressed) sequence
AP Biology
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
SEE PROCESSING VIDEO
Translation: prokaryotes vs. eukaryotes

Differences between prokaryotes &
eukaryotes

time & physical separation between
processes


AP Biology
takes eukaryote ~1 hour
from DNA to protein
no RNA processing
COMPLETING PROTEINS

POLYRIBOSOMES (POLYSOMES)
Numerous ribosomes translate same mRNA
at same time
 3-D folding (1’, 2’, 3’ structure)
 Chaparonins

POST-TRANSLATIONAL MODIFICATIONS


Some amino acids modified by addition of
sugars, lipids, phosphate groups, etc
Enzymes can modify ends, cleave into pieces
join polypeptide strands (4’ structure)
Ex: Made as proinsulin
then cut
Final insulin hormone
made of two chains
connected by
disulfide bridges
http://www.vivo.colostate.edu/hbooks/pathphys/endocrine/pancreas/insulin.html
Section 17.5
Point mutations can affect protein structure and function
AP Biology
Mutations

Point mutations
single base change
 base-pair
substitution


silent mutation
 no amino acid change
 redundancy in code

missense
 change amino acid

nonsense
 change to stop codon
Slide from Explore Biology by Kim Foglia
Point mutation leads to Sickle cell anemia
What kind of mutation?
Slide from Explore Biology by Kim Foglia
Sickle cell anemia
Slide from Explore Biology by Kim Foglia
Mutations

Frameshift

shift in the reading
frame


insertions


adding base(s)
deletions


changes everything
“downstream”
losing base(s)
More damaging at
beginning of gene than
at end
Slide modified from: Explore Biology by Kim Foglia
DNA → DNA ____________
DNA → RNA
____________
RNA→ Protein ___________
WHAT IS A “GENE”?

Mendel’s factors determine phenotype

T.H. Morgan- genes located on specific chromosomes

Beadle and Tatum’s “one gene-one enzyme”

Became “One gene-one polypeptide”
- Some proteins made of more than one polypeptide chain
Ex: hemoglobin has 4 polypeptide chains

Now: “one gene – one polypeptide or RNA”
- Not all genes code for proteins
Can you tell
the story?
AP Biology
Any Questions??
What color would a smurf turn
if he held his breath?
AP Biology
2007-2008