Sintesis

Protein Sel
peni.indrayudha@gmail.com

AP Biology
 From Gene
to Protein

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

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

DNA RNA protein trait

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

AP Biology
 a
a
From gene to protein 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
 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
A G C A T C G T
A A
3
A
5 G
T C
T C
T 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 RNA polymerase template strand

AP Biology 5
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
 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 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
 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
 a
a
From gene to protein 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

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)?
 mRNA codes for proteins in triplets

DNA TACGCACATTTACGTACGCGG
codon

mRNA AUGCGUGUAAAUGCAUGCGCC
?
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

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 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
mRNA AUGCGUGUAAAUGCAUGCGCC
3 5 codon
UAC
tRNA GCA
Met
CAU anti-codon
amino Arg
acid Val
AP Biology
 a
a
From gene to protein 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
O
activating
enzyme

tRNATrp AC C
anticodon
UGG mRNA
tryptophan attached
AP Biology to tRNATrp tRNATrp binds to UGG
codon of mRNA
 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)
 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
 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

U AC UAC GAC U A C GA C U AC G A C
5' C UGAA U 5'
A U G C U GAA U
5' A U G C U G 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
 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
 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
 Terima kasih

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