1. From Gene
to Protein
How Genes
Work
AP Biology 2007-2008

2. 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

3. The “Central Dogma”
 Flow of genetic information in a cell
 How do we move information from DNA to proteins?
n n
iptio latio
transcr trans
DNA RNA protein trait
DNA gets
all the glory,
replication but proteins do
all the work!
AP Biology

4. 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

5. 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"

6. 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
Minimal media supplemented only with… ntifie
i de
n
ta tio
experimentals
mu
Pyridoxine Choline Nucleic Arginine Riboflavin Minimal
amino acid p-Amino Inositol acid Folic Niacin control
supplements
benzoic acid
AP Biology acid Thiamine

7. 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

8. Transcription
from
DNA nucleic acid language
to
RNA nucleic acid language
AP Biology 2007-2008

9. 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

10. 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
G
A G C A T C G T
A A
3′
5′ G
A
T C
T C
T
A
T
A G
C A T C 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′

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 1977 | 1993
Discovery of exons/introns
Richard
Roberts Philip
Sharp adenovirus
CSHL
MIT common cold
beta-thalassemia
AP Biology

18. 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|

19. 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

20. 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

21. 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
il
ly-A ta 3'
3' po A
A
A
A A
mRNA A’s
5' cap 50-250
P P
5' G P
AP Biology

22. 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

23. Translation
from
nucleic acid language
to
amino acid language
AP Biology 2007-2008

24. How does mRNA code for proteins?
DNA TACGCACATTTACGTACGCGG
4 ATCG
mRNA AUGCGUGUAAAUGCAUGCGCC
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)?

25. mRNA codes for proteins in triplets
DNA TACGCACATTTACGTACGCGG
codon
mRNA AUGCGUGUAAAUGCAUGCGCC
?
protein
AP Biology
Met Arg Val Asn Ala Cys Ala

26. 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

27. Marshall Nirenberg 1960 | 1968
Har Khorana
AP Biology

28. 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

29. How are the codons matched to
amino acids?
3′ 5′
DNA TACGCACATTTACGTACGCGG
5′ 3′
mRNA AUGCGUGUAAAUGCAUGCGCC
3′ 5′ codon
UAC
tRNA GCA
CAU anti-codon
amino Met
acid Arg
Val
AP Biology

30. 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

31. Transfer RNA structure
 “Clover leaf” structure
 anticodon on “clover leaf” end
 amino acid attached on 3′ end
AP Biology

32. 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

33. 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

34. 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 AC
A U G
from exit site 3'
E P A
AP Biology

35. 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
G
U AC U A C G A C AA U A C GA C AA U AC G A C A A U
5' CUGAA U 5'
A U G CU G U 5' A U G C UG U 5'
AU G C U G 3'
mRNA A U G 3' 3' 3' A CC
U GG U A A
E P A 3'
AP Biology

36. Destinations:
Protein targeting secretion
nucleus
 Signal peptide mitochondria
chloroplasts
 address label cell membrane
cytoplasm
start of a secretory pathway etc…
AP Biology

37. 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

38. 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

39. Bacterial chromosome
Protein
Transcription
Synthesis in mRNA
Prokaryotes
Psssst…
no nucleus!
Cell
membrane
Cell wall
AP Biology 2007-2008

40. 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

41. 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

42. 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

43. Any Questions??
What color would a smurf turn
if he held his breath?
AP Biology 2007-2008

44. Substitute Slides
for Student Print version
AP Biology 2007-2008

45. Can you tell
the story?
AP Biology

46. The Transcriptional unit
enhancer
1000+b exons
20-30b
3' TAC
transcriptional unit ACT 5'
RNA
TATA
polymerase DNA
introns
5' 3'
5' 3'
AP Biology