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 proteins cells bodies

AP Biology
 The “Central Dogma”
 Flow of genetic information in a cell
 How do we move information from DNA to proteins?

p ti on ti on
c ri l a
trans trans
DNA RNA protein trait

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

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

 lack of an enzyme Am I just the
sum of my proteins?
 Tay sachs
 PKU (phenylketonuria)
 albinism

metabolic pathway
disease disease disease disease
A 
AP Biology enzyme 1
B 
enzyme 2
C 
enzyme 3
D 
enzyme 4
E
 1941 | 1958
Beadle & Tatum
one gene : one enzyme hypothesis

George Beadle

Edward Tatum
"for their discovery that genes act by
AP Biology regulating definite chemical events"
Beadle & Tatum X rays or ultraviolet light
Wild-type
Neurospora create mutations

Minimal asexual
spores Growth on
medium complete
medium
positive control
spores
Select one of
the spores

Test on minimal Grow on

medium to confirm complete medium
presence of mutation
negative control
d
t ifie
Minimal media supplemented only with… n
n ide
tatio
experimentals
mu
Pyridoxine Choline Nucleic Arginine Riboflavin Minimal
amino acid p-Amino Inositol acid Folic Niacin control
supplements
benzoic acid
AP Biology acid Thiamine
 a
From gene to protein a a
a
nucleus cytoplasm a
a
a
a
a
a
a
transcription translation a a
DNA mRNA protein
a
a
a

a
a a
a a
a
ribosome

trait
AP Biology
 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…

transcription
DNA
AP Biology RNA
3 KINDS OF RNA HELP WITH INFO TRANSFER FOR
PROTEIN SYNTHESIS

RIBOSOMAL RNA (rRNA)

Made in nucleolus
2 subunits (large & small)
Combine with proteins to
form ribosomes
Bacterial ribosomes different
size than eukaryotic ribosomes
 Evidence for ENDOSYMBIOTIC THEORY
 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)

ANTICODON sequence
matches CODON on mRNA
to add correct
amino acids during
protein synthesis

AMINOACYL-tRNA SYNTHETASE http://www-math.mit.edu/~lippert/18.417/lectures/01_Intro/

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
 same sequence as RNA
 synthesis of complementary RNA strand
 transcription bubble
 enzyme coding strand
 RNA polymerase
A G C A T C G T A
3
5 G
A
T
G
C
A
T C
T
A
T
C A T C A G
T
DNA G T A 3 A
C T
G C A U C G U T
G 5
C unwinding
3 G T A G C A
rewinding

mRNA 5 RNA polymerase template strand

AP Biology
build RNA 53
 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
 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
AP Biology
on HIGH
 •Transcription
Transcription Factors
 Initiation complex
 transcription factors bind to promoter region
 suite of proteins which bind to DNA
 hormones?
 turn on or off transcription
 trigger the binding of RNA polymerase to DNA

AP Biology
 Matching bases of DNA & RNA
A
 Match RNA bases to DNA C U
G
bases on one of the DNA G A

strands U G
C
U U
C G
A
A C
U
A
AG
C
U
5' RNA
A 3'
A C C polymerase G

T G G T A C A G C T A G T C A T CG T A C CG T

AP Biology
 Eukaryotic genes have junk!
 Eukaryotic genes are not continuous
 exons = the real gene introns
 expressed / coding DNA come out!
 introns = the junk
 inbetween sequence

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
~1,000 base
AP Biology mature mRNA spliced mRNA
transcript
 1977 | 1993
Discovery of exons/introns

Richard
Roberts Philip
Sharp adenovirus
CSHL
MIT common cold

beta-thalassemia
AP Biology
 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|
 Whoa! I think
we just broke
RNA splicing enzymes a biological “rule”!

 snRNPs
snRNPs
 small nuclear RNA snRNA
 proteins exon intron exon

 Spliceosome 5' 3'

 several snRNPs
 recognize splice spliceosome
site sequence 5' 3'
 cut & paste gene
lariat
No,
not smurfs! 5' 3'
“snurps”

exon exon
mature mRNA excised
AP Biology 5' 3' intron
PROCESSING RNA mRNA EDITING
SPLICEOSOMES

ALL ENZYMES ARE PROTEINS?

RIBOZYMES-RNA molecules
that function as enzymes
(In some organisms pre-RNA
can remove its own introns)
 Alternative splicing
 Alternative mRNAs produced from same gene
 when is an intron not an intron…
 different segments treated as exons

Starting to get
hard to
define a gene!

AP Biology
 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

A tai l
-
' p oly 3'
3 A
A
A
A A
mRNA A’s
cap 250
50-
5' P P
5' G P

AP Biology
 a
From gene to protein a a
a
nucleus cytoplasm a
a
a
a
a
a
a
transcription translation a a
DNA mRNA protein
a
a
a

a
a a
a a
a
ribosome

trait
AP Biology
 Translation
from
nucleic acid language
to
amino acid language

AP Biology 2007-2008
 How does mRNA code for proteins?
DNA TACGCACATTTACGTACGCGG
4 ATCG

AUGCGUGUAAAUGCAUGCGCC
mRNA
4 AUCG
?
protein Met Arg Val Asn Ala Cys Ala
20
How can you code for 20 amino acids
AP Biology with only 4 nucleotide bases (A,U,G,C)?
 mRNA codes for proteins in triplets

DNA TACGCACATTTACGTACGCGG

codon

AUGCGUGUAAAUGCAUGCGCC
mRNA

?
protein
AP Biology
Met Arg Val Asn Ala Cys Ala
 1960 | 1968
Cracking the code 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

 created artificial UUUUU… mRNA
 found that UUU coded for phenylalanine
AP Biology
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
 AUG
 methionine
 Stop codons
AP Biology  UGA, UAA, UAG
 How are the codons matched to
amino acids?
3 5
DNA TACGCACATTTACGTACGCGG

5 3
AUGCGUGUAAAUGCAUGCGCC
mRNA
3 5 codon
UAC
tRNA GCA
Met
CAU anti-codon
amino Arg
acid Val
AP Biology
 a
From gene to protein a a
a
nucleus cytoplasm a
a
a
a
a
a
a
transcription translation a a
DNA mRNA protein
a
a
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 Trp C=O Trp

OH H2O
OH O

C
=O
O
activating
enzyme

tRNATrp AC C
anticodon
UGG mRNA
tryptophan attached
AP Biology to tRNATrp 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

 large
 small E P A

AP Biology
 Protein synthesis 2
Ribosomes
 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 Met

 E site (exit site)

 empty tRNA
leaves ribosome 5' U A C
A U G
from exit site 3'
E P A
AP Biology
 How translation works

Building a polypeptide
 Initiation
 brings together mRNA, ribosome
subunits, initiator tRNA
 Elongation
 adding amino acids based on
codon sequence
 Termination
 end codon 3 2 1
Leu Val release
Ser factor
Met Met
Met Met Leu Leu Leu Ala
Trp
tRNA
C
A

U AC UAC GAC A U A C GA C U AC G A C
5' CUGAA U 5'
A U G CU G AU 5' A U G C UG AAU 5'
AU G C U G
AA U 3'
mRNA A U G 3' 3' 3' A CC
U GG U A A
E P A 3'
AP Biology
 Destinations:
Protein targeting 
secretion

nucleus
 Signal peptide  mitochondria

chloroplasts
 address label 
cell membrane

cytoplasm
start of a secretory pathway

etc…

AP Biology
 RNA polymerase
DNA

Can you tell amino

acids
the story? exon intron
tRNA
pre-mRNA 5' GTP cap

mature mRNA
aminoacyl tRNA
poly-A tail synthetase

large ribosomal subunit 3'

polypeptide

5'
tRNA
small ribosomal subunit
E P A

AP Biology ribosome
 The Transcriptional unit (gene?)
enhancer translation translation
1000+b
start exons stop
20-30b

3' TAC
transcriptional unit (gene) ACT 5'
RNA
TATA
polymerase DNA

DNA
UTR UTR
introns
promoter transcription transcription
start stop

5' 3'
pre-mRNA

5' 3'
AP Biology GTP mature mRNA AAAAAAAA
 Bacterial chromosome

Protein
Transcription
Synthesis in mRNA

Prokaryotes
Psssst…
no nucleus!

Cell
membrane

Cell wall
AP Biology 2007-2008
 Prokaryote vs. Eukaryote genes
 Prokaryotes  Eukaryotes
 DNA in cytoplasm  DNA in nucleus
 circular  linear
chromosome chromosomes
 naked DNA  DNA wound on
histone proteins
 no introns  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
 takes eukaryote ~1 hour
from DNA to protein
 no RNA processing

AP Biology
 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
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
 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
 changes everything
“downstream”
 insertions
 adding base(s)
 deletions
 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