Professional Documents
Culture Documents
International University
Email: bhthuy@hcmiu.edu.vn
1
OUTLINES
2
OUTLINES
3
Evidence that DNA is the genetic material
ØA model of genetic
inheritance was in place
in the early 1900s:
• Mendel’s “laws” of genetics
– inherit one copy of each
gene from each parent
• Chromosomes as
locations/carriers of genes
• Distribution of chromosomes
in making sex cells explains
Mendel’s laws
4
Evidence that DNA is the genetic material:
DNA is required for genetic
transformation of bacteria
Ø Studies by Griffith in the
1920s of pneumococcus
in mice
• Smooth (S) strain killed mice,
rough (R) strain did not
• Heat-killed S strain did not
kill mice, but heat-killed S +
R strain killed mice
• Some “transforming principle”
from the heat-killed S strain
changed the R strain to
make it deadly
5
The search for the genetic material
• 1928, Fred Griffith worked with virulent S and
nonvirulent R strain Pneumoccocus bacteria
• 1944, Avery and colleagues announced that the
transforming agent was DNA.
• 1952, Hershey and Chase experiments on
bacteriophage
6
Evidence that DNA is the genetic material
7
EXPERIMENT
Is protein or DNA the genetic material of phage T2?
Alfred Hershey and Martha Chase used radioactive sulfur and phosphorus to trace the
fates of the protein and DNA, respectively, of T2 phages that infected bacterial cells.
1 2 3 4
Mixed radioactively Agitated in a blender to Centrifuged the mixture Measured the
labeled phages with separate phages outside so that bacteria formed radioactivity in
bacteria. The phages the bacteria from the a pellet at the bottom of the pellet and
infected the bacterial cells. bacterial cells. the test tube. the liquid
10
• Maurice Wilkins and Rosalind Franklin
– Were using a technique called X-ray
crystallography to study molecular structure
• Rosalind Franklin
– Produced a picture of the DNA molecule using this
technique
1 nm
G C
3.4 nm
C G
A T
C G
T A
T A
A T
A T
G C
0.34 nm
A T
Figure 16.7a, c (a) Key features of DNA structure (c) Space-filling model
12
Structure of DNA: the double helix
(a) The parent molecule has two (b) The first step in replication is (c) Each parental strand now (d) The nucleotides are connected
complementary strands of DNA. separation of the two DNA serves as a template that to form the sugar-phosphate
Each base is paired by hydrogen strands. determines the order of backbones of the new strands.
bonding with its specific partner, nucleotides along a new, Each “daughter” DNA
A with T and G with C. complementary strand. molecule consists of one parental
strand and one new strand.
17
DNA replication
Origins of replication
• DNA replication begins at specific sites
– Synthesis generally proceeds in both directions
from an origin, creating a “replication bubble”
– There is usually only one origin of replication in
the circular bacterial DNA
– Eukaryotic chromosomes usually have several
origins of replication each
• Both strands are replicated at the same time on
both sides of the replication bubble, producing Y-
shaped replication forks that move as synthesis
proceeds
18
DNA replication
19
Elongating a New DNA Strand
• Elongation of new DNA at a replication fork
– Is catalyzed by enzymes called DNA
polymerases, which add nucleotides to the 3
end of a growing strand
New strand Template strand
5 end 3 end 5 end 3 end
Sugar A T A T
Phosphate Base
C G C G
G C G C
A T A
T OH
P P P
P
P C Pyrophosphate 3 end C
OH
2 P
Nucleoside
Figure 16.13 triphosphate 5 end 5 end
20
DNA replication
Ø Unwinding and opening DNA
• The twisted double helix must be unwound and the basepair
bonds broken (“opening” the DNA molecule)
• DNA helicase does the unwinding and opening
• Single-strand DNA binding proteins keep it open
• Topoisomerases break and rejoin strands, resolving knots
and strains that occur
21
DNA replication
Ø Direction of synthesis
• DNA polymerases direct synthesis of new strands
• synthesis proceeds by adding nucleotides onto the 3’ end
of a strand
• Thus, synthesis can only proceed in the 5’ 3’ direction
• The nucleotide added is from a deoxynucleotide
triphosphate; two phosphates are released in the process
– energy to drive the reaction comes from these
22
DNA replication
ØPriming new strands
– DNA polymerase can only add onto an existing strand,
so it can’t start the strand
– Primase starts the strand by making an RNA primer
that is a few (usually ~10) ribonucleotides long
– DNA polymerase can then add nucleotides starting at
the end of the RNA primer
– The RNA primer is later degraded and (usually)
replaced with DNA
23
DNA replication
Ø Leading and lagging strands
– The 5’ 3’ directionality of synthesis complicates the
replication activity
– One strand being synthesized, the leading strand,
has its 3’ end at the fork; thus, its synthesis can
proceed continuously, in the direction that the fork
moves
– The other, lagging strand has its 5’ end at the fork; it
must be synthesized in the “opposite direction” from
the leading strand
24
• the lagging strand is thus made in
short (100-1000 nt) Okazaki
fragments
Figure 16.15
Overall direction of replication 26
DNA replication
• DNA proofreading and DNA
repair
– DNA polymerase proofreads:
initial error rate about 1 in
100,000; final rate about 1 in
100,000,000 (1 in 108)
– cells have DNA repair
mechanisms to fix most
mistakes that get through as
well as to fix most damaged
DNA
27
DNA replication
ØThe dead end: problem
at the telomeres
– The ends of chromosomes
are called telomeres
– They present special
problems for DNA
replication: the 5’ end RNA
primer cannot be replaced
with DNA, creating 5’ end
gaps
– This leads to shorting of
chromosomes at the ends
with each cell generation
28
DNA replication
ØThe dead end: problem at the telomeres
v In some cells, special telomerase enzymes can
generate longer telomeres
• Telomerase is required in germ-line cells
• Telomerase is active in cancer cells as well
1 µm
Eukaryotes have repetitive, noncoding sequences called
telomeres at the ends of their DNA
29
A Chromosome consists of a DNA molecule
packed together with proteins
DNA packaging
The DNA molecule is too long if not folded
30
DNA packaging
Ø Nucleosomes are the main
packaging mechanism for
eukaryotic DNA
Ø The nucleosome is made up of
8 protein subunits, acting like
a “spool” for the DNA “thread”
Ø The proteins are called
histones
Ø Histones are positively
charged, and thus able to
associate with the negatively
charged phosphates of the
DNA backbone
Ø The 8 proteins in a
nucleosomes are 2 each of 4
different histones
31
DNA packaging
• further packaging: histone
H1 and scaffolding
proteins
– 30 nm fibers form looped
domains that are ~300
nm wide and attached to
non-histone scaffolding
proteins
• this level of packing is
found only for some
regions of DNA, except
when chromosomes are
condensed for cell
division
33
Genes generally are information for
making specific proteins
Ø In connection with the rediscovery of Mendel’s work
around the dawn of the 20th century, the idea that
genes are responsible for making enzymes was
advanced
Ø This view was summarized in the classic work Inborn
Errors of Metabolism (Garrod 1908)
34
Genes generally are information for
making specific proteins
35
Genes generally are information for
making specific proteins
36
RNA
ØRNA has some structural
distinctions from DNA
• Typically single-stranded
(although often with folds and
complex 3D structure)
• Sugar is ribose; thus, RNA
polymers are built from
ribonucleotides
ü -OH at the #2 C on the ribose, vs.
deoxyribose in DNA
• Uracil (U) functions in place of T
37
RNA (ribonucleic acid)
Ø Three main forms of RNA are used: mRNA,
tRNA, and rRNA
• mRNA or messenger RNA: copies the actual
instructions from the gene
• tRNA or transfer RNA: links with amino acids and bring
them to the appropriate sites for incorporation in
proteins
• rRNA or ribosomal RNA: main structural and catalytic
components of ribosomes, where proteins are actually
produced
• All are synthesized from DNA templates (thus, some
genes code for tRNA and rRNA, not protein)
38
• DNA RNA is transcription
– making RNA using directions from a
DNA template
– transcribe = copy in the same language
(language used here is base sequence)
39
Srb and Horowitz further characterize the mutant surviving
arginine suplemented medium to investigate the arginine
synthesis pathway
40
Conclusions
44
45
Central Dogma of Gene Expression
DNA RNA protein
46
Transcription (DNA RNA)
ØRNA is synthesized as a complementary strand
using DNA-dependent RNA polymerases
– Process is somewhat similar to DNA synthesis, but
no primer is needed
– Bacterial cells each only have one type of RNA
polymerase
– Eukaryotic cells have three major types of RNA
polymerase
• RNA polymerase I is used in making rRNA
• RNA polymerase II is used in making mRNA and
some small RNA molecules
• RNA polymerase III is used in making tRNA and
some small RNA molecules
47
Transcription (DNA RNA)
Ø Only one strand is
transcribed, with RNA
polymerase using
ribonucleotide
triphosphates (NTPs) to
build a strand in the 5’3’
direction
– Thus, the DNA is
transcribed (copied or
read) in the 3’ 5’
direction
– The DNA strand that is
read is called the
template strand
48
Transcription (DNA RNA)
Ø Upstream means toward the 5’ end of the RNA
strand, or toward the 3’ end of the template strand
(away from the direction of synthesis)
Ø Downstream means toward the 3’ end of the RNA
strand, or toward the 5’ end of the template strand
Upstream Downstream
50
Ø Transcription
has three stages
Initiation
Elongation
Termination
51
Initiation
Ø Requires a promoter – site where RNA polymerase
initially binds to DNA
– promoters are important because they are needed
to allow RNA synthesis to begin
– promoter sequence is upstream of where RNA
strand production actually begins
– promoters vary between genes; this is the main
means for controlling which genes are transcribed
at a given time
promoter Transcribed DNA sense strand
3’
3’
mRNA transcript
downstream
52
Transcription (DNA RNA)
Initiation
ØBacterial promoters
– about 40 nucleotides long
– positioned just before the point
where transcription begins
– recognized directly by RNA
polymerase
53
Initiation
ØEukaryotic promoters (for
genes that use RNA
polymerase II)
– Initially, transcription factors bind
to the promoter; these proteins
facilitate binding of RNA
polymerase to the site
– Transcription initiation complex
• Completed assembly of
transcription factors and RNA
polymerase at the promoter
region
– Allows initiation of transcription (the
actual production of an RNA strand
complementary to the DNA
template)
54
Initiation
Ø Regardless of promoter
specifics, initiation begins
when RNA polymerase is
associated with the DNA
– RNA polymerase opens
and unwinds the DNA
– RNA polymerase
begins building an RNA
strand in the 5’3’
direction,
complementary to the
template strand
– Only one RNA strand is
produced 55
Elongation
Ø Transcription continues in a
linear fashion, with DNA
unwinding and opening
along the way
Ø The newly synthesized RNA
strand easily separates from
the DNA and the DNA
molecule “zips up” behind
RNA polymerase, reforming
the double helix
56
Termination
Ø Termination: the end of RNA transcription
– In prokaryotes,
transcription continues
until a terminator
sequence is transcribed
– usually a GC hairpin or
something similar
– That terminator
sequence (now in RNA)
causes RNA polymerase
to release the RNA
strand and release from
the DNA
57
Termination
– Termination in eukaryotes is more
complicated and differs for different RNA
polymerases
– Still always requires some specific
sequence to be transcribed
– For RNA pol II the specific sequence is
usually hundreds of bases before the
actual ending site
58
RNA processing
59
Split Genes and RNA Splicing
60
Role of snRNPs and spliceosomes in mRNA splicing
Translation is
the RNA-
directed
synthesis of a
polypeptide
63
Translation (RNA protein)
Ø tRNAs bring amino acids to
the site of translation
• tRNAs are synthesized at
special tRNA genes
• tRNA molecules are strands
about 70-80 bases long that
form complicated, folded 3-
dimensional structures
• tRNAs have attachment sites
for amino acids
• Each tRNA has an anticodon
sequence region that will form
a proper complementary
basepairing with a codon on
an mRNA molecule
64
Translation (RNA protein)
Ø tRNA is linked to the appropriate
amino acid by enzymes called
aminoacyl-tRNA synthetases
• The carboxyl group of each specific amino
acid is attached to either the 3' OH or 2'
OH group of a specific tRNA
• There is at least one specific aminoacyl-
tRNA synthetase for each of the 20 amino
acids used in proteins
• ATP is used as an energy source for the
reaction
• The resulting complex is an aminoacyl-
tRNA, also called a charged tRNA or
activated tRNA
• The amino acid added must be the proper
one for the anticodon on the tRNA
65
Translation
(RNA protein)
Initiation
Elongation
Termination
66
Translation Initiation
67
Translation
Elongation
68
Translation Termination
Ø A stop codon signals the end for translation (UAA,
UGA, and UAG are universal stop codons)
Ø No tRNA matches the stop codon; instead, it a
termination factor (AKA release factor) binds there
Ø The termination factor causes everything to dissociate,
freeing the polypeptide, mRNA, last tRNA, and
ribosomal subunits all from each other (think of the
termination factor as a little molecular bomb)
69
OUTLINES
70
Gene Expression
translation
DNAtranscription mRNA Protein
71
71
Genes can be expressed with different
efficiencies
identical DNA
Gene available
for transcription
differential gene
Intron
RNA processing
expression, the
Tail
Cap mRNA in nucleus
Ø Gene expression is
of protein
Transport to cellular
destination
73
Signa
l
CYTOPLASM
NUCLEUS mRNA in cytoplasm
Chromatin
Translation
Chromatin Degradation
modification of mRNA
DNA
Gene available
for Polypeptide
Gene transcription
Transcription Protein processing
RNA Exon
Primary transcript
Intron Active
Degradation protein
RNA processing of protein
Tail Transport to cellular
destination
Cap mRNA in
nucleus
Transport to Cellular
cytoplasm function
CYTOPLAS
M
74
Chromatin Structure and DNA Packing
7575
Regulation of
Chromatin Histone
tails
Structure
Amino
acids
available
Ø Histone acetylation, DNA for chemical
double helix modification
acetyl groups are
attached to positively
charged lysines in (a) Histone tails protrude outward from a
histone tails nucleosome
Ø This process loosens
chromatin structure,
thereby promoting the
initiation of
transcription
Unacetylated histones Acetylated histones
NH3+
-K9 Ac Me
Nucleosome P S10-
DNA
-K14 Ac
-K18 Ac
H2B H2A
-K27 Me
H4 H3 P S28-
DNA
H3
Octameric
histone core
77
Epigenetic Inheritance
78
Organization of Eukaryotic Gene
Ø Associated with most eukaryotic genes are
control elements, segments of noncoding DNA
that help regulate transcription by binding
certain proteins
Poly-A signal
sequence
Enhancer Proximal
(distal control elements)
Termination
control elements region
Exon Intron Exon Intron Exon
DNA
Upstream Downstream
Promoter Transcription
80
Activators Promoter
Gene
DNA
Enhancer Distal control TATA
element box
General
transcription
• Proximal control elements are factors
located close to the promoter DNA-bending
protein
• Distal control elements,
groups of which are called Group of
enhancers, may be far away mediator proteins
from a gene or even located in
an intron
RNA
• An activator is a protein that polymerase II
binds to an enhancer and
stimulates transcription of a
gene
• Bound activators cause
RNA
mediator proteins to interact polymerase II
with proteins at the promoter
Transcription
initiation complex RNA synthesis
81
Enhancer Promoter
Combinatorial
Albumin gene
Control of Gene Control
elements
Activation Crystallin gene
v A particular
combination of LIVER CELL LENS CELL
control elements NUCLEUS NUCLEUS
when the
appropriate
activator proteins Albumin gene
are present Albumin gene
not expressed
expressed
Crystallin gene
not expressed
Crystallin gene
expressed
82
(a) Liver cell (b) Lens cell
1. Explain how Preimplantation Genomic
Dianosis (PGD) and Fetal Testing can be used
in genetic screening and counseling?
2. Explain why lethal dominant genes are much
rarer than lethal recessive genes
3. Describe replicating at the ends of eukaryotic
chromosomal DNA. How telomerase enzymes
lengthens telomeres?
83
1. What is the difference between transcription
and translation. Describe the events of
initiation, elongation, and termination of
transcription and translation.
2. Describe the method of germline gene
therapy to prevent inherited mitochondrial
diseases passed from mother to child.
84
1. What is epigenetic Inheritance? Explain how
histone acetylation affect chromatin structure
and the regulation of transcription.
2. Explain the role of promoters, enhancers,
activators, and repressors in transcription
control
3. Why is regulation of gene expression important?
How can, for example, a cell in the retina of
your eye make different proteins from a cell in
your liver when both cells have exactly the
same DNA?
85