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Biology 1 Al-Ahlya Amman University
Prof. Dr. Samih Tamimi
Chapter 16 and 17 Notes
Biology 1 Al-Ahlya Amman University
Chapter 16 People:
1. Griffith - studied bacteria- heat killed cells (bacteria) were able to take in material from living cells that were not harmful (bacteria)- mixture would kill the mice- bacteria cells were transformed
2. Avery - announced transformation agent was DNA
4. Chargaff - identified 4 nitrogen bases: adenine, thymine, guanine, cytosine- base pairing rules: A-T, C-G- % of A = % of T, % of C = % of G
6. Watson and Crick – model for DNA molecule
Biology 1 Al-Ahlya Amman University
Sugar–phosphate backbone
5 end
Nitrogenous bases
Thymine (T)
Adenine (A)
Cytosine (C)
Guanine (G)
DNA nucleotide
Sugar (deoxyribose)
3 end
Phosphate
one side of DNA withbases
5’ carbon attachedto phosphategroup
3’ carbon attachedto hydroxyl group
Structure of the double helix
Biology 1 Al-Ahlya Amman University
The double helixMonomer of nucleic acid:
3 parts to a nucleotide:
1.
2.
3.
nucleotide
phosphate
sugar-DNA (deoxyribose)
base - purines - pyrimidines
Biology 1 Al-Ahlya Amman University
Purines -
-
-
Pyrimidines -
-
-
Bonds that connect bases:
double ringed bases
adenine
guanine
single ringed bases
cytosine
thymine
hydrogen bonds
Biology 1 Al-Ahlya Amman University
A T
GC
T A
TA
G C
(a) Parent molecule
A T
GC
T A
TA
G C
(c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand
(b) Separation of strands
A T
GC
T A
TA
G C
A T
GC
T A
TA
G C
complementary base pairing
A - T C - G
Biology 1 Al-Ahlya Amman University
Parent cellFirst replication
Second replication
(a) Conservative model
(b) Semiconserva- tive
model
(c) Dispersive model
Semiconservative model:
the old strand makes a new strand
Biology 1 Al-Ahlya Amman University
Origin of replication Parental (template) strand
Daughter (new) strand
Replication fork
Replication bubble
Two daughter DNA molecules
(a) Origins of replication in E. coli
Origin of replication Double-stranded DNA molecule
Parental (template) strandDaughter (new) strand
Bubble Replication fork
Two daughter DNA molecules
(b) Origins of replication in eukaryotes
0.5 µm
0.25 µm
Double-strandedDNA molecule
bacterial DNA
Biology 1 Al-Ahlya Amman University
A
C
T
G
G
G
GC
C C
C
C
A
A
AT
T
T
New strand 5 end
Template strand 3 end 5 end 3 end
3 end
5 end5 end
3 end
Base
Sugar
Phosphate
Nucleoside triphosphate
Pyrophosphate
DNA polymerase
Antiparallel - side chains of DNA run in DNA elongates only in the5’ 3’3’ 5’ 5’ 3’ direction
oppositedirections
Biology 1 Al-Ahlya Amman University
OverviewOrigin of replication
Leading strand
Leading strand
Lagging strand
Lagging strandOverall directions
of replication
Leading strand
Lagging strand
Helicase
Parental DNA
DNA pol III
Primer Primase
DNA ligase
DNA pol III
DNA pol I
Single-strand binding protein
5
3
5
5
5
5
3
3
3
313 2
4
helicase - unwinds double helix
ssbp’s – stabilize unwound DNA
primase – synthesizes RNA primer
DNA polymerase III – synthesizes new DNA on 3’ endDNA polymerase I – removes primers and brings in DNA nucleotides
ligase – covalently connectsDNA nucleotides
Biology 1 Al-Ahlya Amman University
Biology 1 Al-Ahlya Amman University
TRANSCRIPTION
TRANSLATION
DNA
mRNARibosome
Polypeptide
DNA
Pre-mRNA
Prokaryotic cell
Nuclearenvelope
mRNA
TRANSLATION
TRANSCRIPTION
RNA PROCESSING
Ribosome
Polypeptide
Eukaryotic cell
Transcription – synthesis of
makes
Translation – synthesis of a polypeptide
-
-
CHAPTER 17
RNA from DNA
mRNA (messenger)
occurs on ribosome
from mRNA
uses tRNA
Compartmentalization oftranscription and translation
-provides an opportunity to
*bacteria
-
modify mRNA beforeit leaves the nucleus
do not havethis
no nucleus
Biology 1 Al-Ahlya Amman University
DNAmolecule
Gene 1
Gene 2
Gene 3
DNA strand(template)
3
TRANSCRIPTION
Codon
mRNA
TRANSLATION
Protein
Amino acid
35
5**
-
-codon-
-start codon:
1 gene codes for oneprotein (polypeptide)
gene/protein results inthe organisms
3 consecutive baseson mRNA
AUG (methaionine)
20 different amino acids
phenotype
Biology 1 Al-Ahlya Amman University
Second mRNA base
Firs
t mR
NA
base
(5 e
nd o
f cod
on)
Third
mR
NA
base
(3 e
nd o
f cod
on)
Biology 1 Al-Ahlya Amman University
Promoter Transcription unit
Start point DNA
RNA polymerase
5533
Initiation1
2
3
5533
UnwoundDNA
RNAtranscript
Template strandof DNA
Elongation
RewoundDNA
5
55
5
5
333
3
RNAtranscript
Termination
5533
35Completed RNA transcript
Newly madeRNA
Templatestrand of DNA
Direction oftranscription(“downstream”)
3 end
RNApolymerase
RNA nucleotides
Nontemplatestrand of DNA
Elongation
Promotor region: a start point for RNA polymerase
also determines which strand will be copied
Biology 1 Al-Ahlya Amman University
Amino acidattachment site
3
5
Hydrogenbonds
Anticodon
(a) Two-dimensional structure
Amino acidattachment site
5
3
Hydrogenbonds
3 5AnticodonAnticodon
(c) Symbol used in this book(b) Three-dimensional structure
anticodon – complementary to the
tRNA – transfers amino acids
from the cytoplasms pool to
a ribosome
codon on mRNA
Biology 1 Al-Ahlya Amman University
Amino acid Aminoacyl-tRNAsynthetase (enzyme)
ATP
AdenosineP P P
AdenosineP
PP i
PPi
i
tRNA
tRNA
Aminoacyl-tRNAsynthetase
Computer modelAMPAdenosineP
Aminoacyl-tRNA(“charged tRNA”)
connecting an aminoacid to tRNA
Biology 1 Al-Ahlya Amman University
Polypeptide
tRNA withamino acidattached
Ribosome
tRNA
Anticodon
35
mRNA
Aminoacids
Codons
Synthesis of proteins:
A site –
P site –
E site –
incoming
growing polypeptide
exit site
Biology 1 Al-Ahlya Amman University
Ribosome
-
-
Functional ribosome:
- small
- add
- large
Growingpolypeptide Exit tunnel
Largesubunit
Smallsubunit
tRNAmolecules
E PA
mRNA5 3
(a) Computer model of functioning ribosome
P site (Peptidyl-tRNAbinding site)
E site(Exit site)
A site (Aminoacyl-tRNA binding site)
E P A Largesubunit
mRNAbinding site Small
subunit
(b) Schematic model showing binding sites
Amino end Growing polypeptide
Next amino acidto be added topolypeptide chain
mRNAtRNAE
3
5 Codons
(c) Schematic model with mRNA and tRNA
2 subunits
rRNA and protein
ribosomal unit
mRNA and tRNA
unit binds
-uses energy
Biology 1 Al-Ahlya Amman University
3355U
UA
ACGMet
GTP GDPInitiator
tRNA
mRNA5 3
Start codon
mRNA binding siteSmallribosomalsubunit
5
P site
Translation initiation complex
3
E A
Met
Largeribosomalsubunit
1. Initiation
3 stages for building a polypeptide:
Binding of mRNA to small subunit and initiator tRNA carrying met to P site with initiation codon (AUG)
Then large subunit attaches
Biology 1 Al-Ahlya Amman University
Amino endof polypeptide
mRNA
5
3E
Psite
Asite
GTP
GDP
E
P A
E
P A
GDPGTP
Ribosome ready fornext aminoacyl tRNA
E
P A
2. Elongation Cycle
peptide bonds are formedbetween amino acids
Codon recognition
Peptide bond formation
Translocation
Biology 1 Al-Ahlya Amman University
Releasefactor
3
5Stop codon(UAG, UAA, or UGA)
5
32
Freepolypeptide
2 GDP
GTP
5
3
3. Termination release factor attaches to stop codon, everythingreleases