Download chapter 24 lecture (ppt file)

Power Point to Accompany
Principles and Applications of
Inorganic, Organic, and
Biological Chemistry
Denniston, Topping, and Caret
4th ed
Chapter 24
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
24-1
24.1Structure of the Nucleotide
DNA and RNA are polymers whose
monomer units are called nucleotides
A nucleotide itself consists of:
1. a nitrogen containing
heterocyclic base
2. a ribose or deoxyribose sugar
ring
3. a phosphoric acid unit
24-2
Major Purine Bases
NH2
C
N1
HC
2
6
C
5
O
N
7
9
3 4C
N
8 CH
N
H
adenine
in DNA and RNA
C
HN
C
C
C
H2N
N
N
CH
N
H
guanine
in DNA and RNA
24-3
Major Pyrimidine Bases
O
O
NH2
C
CH
C
C
3 HN
CH
N3 4 5CH HN C
C CH
C2 1 6CH C CH
O N
O N
O N
H
H
H
cytosine
in DNA
and RNA
thymine
in DNA
and some RNA
uracil
in RNA
24-4
Nucleotides-1
A nucloetide is the
NH2
base
repeating unit of the
C
DNA or RNA
N
phosphate N
C
polymer. The
CH
ester
nitrogen base is
C N
HC
attached b to the
N
2ribose (RNA) or
O3PO CH2
O
deoxyribose (DNA)
ring. The sugar is
H
H
phosphorylated at
H
H
carbon 5’
OH H
deoxyribose sugar
24-5
Nucleotides-2: Names
Begin with the name of the nitrogenous base.
• Remove –ine ending and replace with:
– -osine for purines or –idine for
pyramidines. Uracil: -acil with –idine.
• ribose then ribonucleotide
– deoxyribose then deoxyribonucleotide
– deoxy before base name for
deoxyribonucleotide
• Add prefix for number of phosphoryl groups
– Monophosphate, diphosphate,
24-6
triphosphate
Nucleotides-3
NH2
C CH3
C
HN
C
N
O
2O3PO CH2
O
H
H
H
H
OH H
C
Deoxythymidine
5’-monophosphate
dTMP
24-7
Nucleotides-4
NH2
NH2
N
C
C
N
C N
N
O P O CH2
O
O
H
H
H
H
OH H
O
N
CH
HC
O
O
O P O CH2
O
H
2-deoxy
Deoxyadenosine
5’-monophosphate
dAMP
C
C
N
CH
CH
O
H
H
H
OH
H
Deoxycytidine
5’-monophosphate
24-8
dCMP
Nucleotides-5
Uridine
O
5’-monophosphate
C
UMP
HN
CH
O
2O3PO CH2
H
C
N
O
H
2-
H
H
OH
CH
H
HN
H2N
C
O
C
CH
C N
N
O3PO CH2
H
C
N
O
H
H
H
OH
H
Guanosine 5’-monophosphate, GMP
24-9
24.2 DNA/RNA Chains
When nucleotides polymerize, the 5’
phosphate on one unit esterifies to the 3’ OH
on another unit. The terminal 5’ unit retains
the phosphate. An example of a three
nucleotide DNA product is shown on the
next slide .
24-10
Segment of One DNA Chain
5’-end
N
O
C
C N
C N
C
H2N
N
-2
O3PO CH2
O
H
H
H
H
H
O
guanine
CH
N
C
O
C
O
N
O P O CH2
O
O
H
H
H
H
H
O
3’-5’
link
CH3
C
CH
NH2
C
N
CH
C
CH
O
N
O P O CH2
O
O
H
H
H
H
OH H
3’-end
thymine
cytosine
24-11
DNA-Secondary Structure
The most common form of DNA is the B form .
Its structure was determined by Watson and
Crick in 1953.
This DNA consists of two chains of
nucleotides coiled around one another in a
right handed double helix.
The chains run antiparallel and are held
together by hydrogen bonding between
complimentary base pairs: A=T, G=C.
24-12
Insert Fig 24.4
24-13
DNA-Secondary Structure, cont.
H
Hydrogen
CH3
N H||||||||||| O
N
HC
bonding
C C
C C
N C
CH between A and T
N|||||||||||H N
C N
or
G
and
C
helps
N CH
A
TO
to
hold
the
H
chains
in
the
O
|||||||||||
N
N
H
HC C C
C CH double helix
N C
N H ||||||||||| N
CH
The
strands
are
N C
C N
said to be
N H ||||||||||| O
G
C
complimentary
24-14
H
B DNA segment
Chain 2
Sugar-phosphate
backbone
Chain 1
Hydrogen bonded
base pairs in the
core of the helix24-15
B DNA: 2
Major groove
Outside diameter, 2 nm
Interior diameter, 1.1 nm
Minor groove
Length of one turn of helix
is 3.4 nm and contains 10
base pairs.
24-16
Chromosomes
Chromosomes are pieces of DNA that contain
the genetic instructions, or genes, of an
organism.
Prokaryotes (single chromosome)
No true nucleus. Chromosome is a circular
DNA molecule that is supercoiled, that is,
the helix is coiled on itself.
At approximately 40 sites a complex of
proteins is attached, forming a series of
loops.
This structure is the nucleoid.
24-17
Chromosomes, cont.
Eukaryotes (Number and size of
chromosomes vary.)
True nucleus. Membrane bound organelles
that separate cellular functions.
Nucleosome which consists of a strand of
DNA wrapped around a disk of histone
proteins.
Larger structure is the 30 nm fiber.
Coiled in to a 200 nm fiber
24-18
RNA Structure
Sugar-phosphate backbone for
ribonucleotides linked by 3’-5’
phosphodiester bonds.
RNA molelcules usually single stranded.
Ribose replaces deoxyribose.
Uracil replaces thymine.
Base pairing between U and A and G and C
results in portions of the single strand that
become double stranded.
24-19
24.4 Information Flow
DNA
RNA
Protein
Replication: DNA duplicates itself
Transcription: RNA is made on a DNA
template
Translation: Protein is synthesized
from AAs and the three RNAs.
Reverse Transcription: RNA directs
synthesis of DNA
24-20
Classes of RNA Structure
transfer RNA (tRNA)
Transfers amino acids to the site of protein
synthesis (ribosomes). Has the
anticoden.
ribosomal RNA (rRNA)
rRNA forms ribosomes by reacting with
proteins
messenger RNA (mRNA)
mRNA directs the AA sequence of proteins
and is a complimentary copy of a gene. It
has the codon for an AA in a protein,
24-21
tRNA
There is at least one tRNA (and often several)
for each AA to be incorporated into a
protein.
tRNA is single stranded with typically about
80 nucleotides.
Intrachain hydrogen bonding (A=U and G=C)
occurs to gives regions called stems with an
a-helix
The overall structure is called a cloverleaf in a
L-shaped conformation.
24-22
tRNA
Transfer RNA (tRNA) transfers AA to the site
of protein synthesis. Has the anticoden
Attachment to
mRNA here
AA
attaches
here
24-23
Transcription
Transcription is catalyzed by RNA polymerase. Initiation binds RNA polymerase to
the promoter region at the beginning of the
gene. Cain elongation then occurs forming
a 3’-5’ phosphodiester bond. Termination is
the final step of transcription.
Will Fig 24.12 fit here??
24-24
Post Transcription Processing, mRNA
Prokaryote mRNA is continuous.
Eukaryote mRNA must be processed:
A 5’ cap structure is added
A 3’ poly A tail (100 to 200 units) is added
The introns (noncoding base sequences)
are cut out and the introns (coding
sequences) are spliced together.
Splicosomes help recognize intron-exon
boundaries. They are composed of small
nuclear ribonucleoproteins (snRNPs,
“snurps”).
24-25
24.5 The Genetic Code (DNA)
The message on DNA translated to mRNA:
1. Degenerate: more than one three base
codon can code for the same AA.
2. Specific: each codon specifies one AA
3. Nonoverlapping and commaless : none of
the bases are shared between consecutive
codons and no noncoding bases appear in
the base sequence.
4. Universal: except in a few instances, all
organisms use the same code.
24-26
The Genetic Code-2
All 64 codons have meaning; 61 code for an
AA and three code for the “stop” signal.
Multiple codes for an AA tend to have two
bases in common.
E. g. CUU, CUC, CUA, CUG code for leu
(codons are written: 5’-> 3’ sequence.)
A partial table for the genetic code follows on
the next slide. See your text for a complete
table.
24-27
The Genetic Code-3
5’ end
U
C
Middle base
U
C
A
phe ser tyr
phe ser tyr
leu ser end
leu ser end
leu pro his
leu pro his
leu pro gln
leu pro gln
3’ end
G
cys
cys
end
trp
arg
arg
arg
arg
U
C
A
G
U
C
A
G
24-28
The Genetic Code-4
Use the table in slide 6 to answer the
questions. Click for the answer.
1. CCU codes for: ?
pro
arg
2. CGA codes for: ?
ser
3. UCA codes for: ?
24-29
24.6 Protein Synthesis
Protein synthesis is called translation. It is
carried out on ribosomes, complexes of
rRNA and proteins.
Protein synthesis occurs in multiple places on
one mRNA. The mRNA plus the multiple
ribosomes are called a polysome,
tRNA binds a specific AA aided by aminoacyl
tRNA synthethase and recognizes the
appropriate codon on the mRNA.
24-30
Translation Process-1
Initiation
Initiation factors (proteins), mRNA, initiator
tRNA, and small and large ribosomes
come together.
Ribosome has two sites to bind tRNA
P-site binds to the growing peptide
A-site binds the aminoacyl tRNA
Chain Elongation
An aminoacyl tRNA binds to A site
Peptide bond formation occurs
Translocation (movement) of ribosome
down the mRNA chain to next codon. 24-31
Translation Process-2
Termination
Upon finding a “stop” codon a release
factor binds a the empty A site.
The bond between the last AA and peptidyl
tRNA is hydrolyzed releasing the protein.
The protein released may not be in its final
form. Cleavage, association with other
proteins, and bonding to carbohydrate or
lipid groups may occur before a protein is
fully functional.
24-32
Insert Fig 24.19
24-33
24.7 Mutation and Repair
Mutations are mistakes introduced into the
DNA sequence of an organism.
They can be classified as:
Point: substitution of a single nucleotide for
another.
Deletion: one or more nucleotides are lost.
Insertion: one or more nucleotides are
added.
Many mutagens (chemicals causing a change
in the DNA sequence) are also carcinogens
and cause cancer.
24-34
UV Damage and DNA Repair
UV light causes formation of a pyrimidine
dimer on a DNA strand. Failure to repair
this defect can lead to xeroderma
pigmentosum.
People who suffer from this genetic skin
disorder are very sensitive to UV light and
develop multiple skin cancers.
Insert Fig 24.20
24-35
24.8 Recombinent DNA
Restriction enzymes are bacterial enzymes
that cut the backbone of DNA at specific
nucleotide sequences.
Donor and plasmid (bacteria) DNA are cleaved
by the same restriction enzyme.
Donor and plasmid DNA are mixed and donor
fragment joins to a complimentary plasmid
fragment due to hydrogen bonding.
Plasmid ring is restored using using DNA
ligase.
Engineered plasmid (recombinent DNA) is
introduced to a bacterium to be reproduced.
24-36
24.9 Polymerase Chain Reaction
DNA is mixed with Taq polymerase (a heat
stable DNA polymerase), a primer DNA
sequence for a specific gene, and the four
nucleotide triphosphates.
A thermocycler raises the temperature to 9496 oC to separate the DNA strands, lowers
the temperature to 50-56 oC to the primers to
hybridize to the DNA, and raises the
temperature to 72 oC to allow the Taq
polymerase to act.
Repeating the cycle doubles the new DNA
strands each cycle. (12481632
etc)
24-37
24.10 Human Genome Project
The DNA to be sequenced is placed in four
test tubes (tt) with all the enzymes and
nucleotides necessary for DNA synthesis.
In addition, each tt contains a small amount
of one species of dideoxynucleotide with an
H at the 3’ position. Once this is incorporated in the growing chain, chain
synthesis stops.
The DNA fragments are separated by gel
electrophoresis in four wells side by side.
The sequence is read from the gel as shown
in the figure on the next slide.
24-38
Insert Fig 24.26
24-39
The End
Introduction to
Molecular Genetics
24-40