BCHOBI 812 Biochemistry for Dental Students

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Stryer Chapter 5 DNA, RNA and the Flow of
Genetic Information
Proteins are the molecular machinery of the
cell Where do they come from ? DNA and RNA The
genetic material
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Nucleic Acids
Deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA) are both composed of a sugar phosphate
backbone with four kinds of bases linked to
it They are linear polymers
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Nucleic Acids Constant Backbone
The sugar phosphate backbones of DNA and RNA
differ - the 2 carbon of ribose has a hydroxyl
group attached in RNA
The backbone is constant - it does not change
from one monomer to the next
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Nucleic Acids Variable Bases
DNA and RNA each have two purines (adenine and
guanine) and two pyrimidines (cytosine and
thymine in DNA, cytosine and uracil in RNA)
The sequence of bases along a strand of DNA
carries the genetic information
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Nucleic Acids Nucleosides
A base attached to a ribose is called a
nucleoside The bond between the ribose and the
base is a b-glycosidic linkage
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Nucleic Acids Nucleotides
Nucleosides attached to one or more phosphate
groups by an ester linkage is called a nucleotide
Nucleic acids consist of nucleotides attached by
5 to 3 link
Nucleic acids have polarity
By convention, sequences are written from 5?3
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DNA Can Form a Two-Strand Double Helix
The covalent structure (sequence) of DNA accounts
for its ability to carry information The
three-dimensional structure of DNA facilitates
the process of replication - the generation of
copies of DNA The three-dimensional structure of
DNA arises from the ability of pairs of bases to
interact in specific manners - base pairing
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The DNA Double Helix Base Pairing
In double-stranded DNA, guanine always pairs with
cytosine (GC) and adenine always pairs with
thymine (AT) These pairings result from
complementary hydrogen bonds
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The DNA Double Helix Base Pairing
The base pairs result in two strands of DNA
interacting in a specific manner, forming a
double helix The bases are inside the helix with
the backbone on the outside
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The DNA Double Helix
The double helix is a regular structure with the
two chains running in opposite directions The
bases are stacked with strong hydrophobic and van
der Waals interactions between layers
There are 10 base pairs per full turn of helix
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The Double Helix and DNA Replication
The double helix structure suggests a replication
(copying) mechanism Each strand can act as a
template for the other strand - the sequences are
complementary due to base pairing Double-stranded
DNA could be separated, with new daughter strands
being synthesized using the parent strands as
templates
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The Double Helix and DNA Replication
Meselson and Stahl decided to test this
replication idea in 1958 They synthesized DNA
using 15N - a heavy isotope of nitrogen The
labeled DNA was generated in E.coli, which was
then switched to a medium that contained 14N
(normal nitrogen) They then looked at the
distribution of 14N and 15N in DNA molecules
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The Double Helix and DNA Replication
The distribution of 14N and 15N could be detected
using density-gradient equilibrium sedimentation
(a centrifugation technique) The heavier
15N-enriched DNA will separate from 14N DNA
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The Double Helix and DNA Replication
Meselson and Stahl collected DNA from their
E.coli at various point in time and looked at the
distributions of DNA After one generation there
is one lighter band - hybrid DNA (half 15N and
half 14N) After two generations, two bands (one
hybrid, one 14N)
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The Double Helix and DNA Replication
DNA replication is semi-conservative - each new
double-stranded DNA consists of one of the parent
strands and one newly-synthesized daughter strand
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The DNA Double Helix Can Be Reversibly Melted
In replication the two strands of DNA must be
separated (at least locally)
In the laboratory, DNA can be separated into
single strands by heating (melting) This can be
followed by monitoring the absorption of light -
stacked bases absorb less light than unstacked
bases (hypochromism)
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The DNA Double Helix Can Be Reversibly Melted
Separated strands will spontaneously reassociate
to form a double helix when cooled -
reannealing This reversible melting is important
for various laboratory techniques
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DNA Can Be Circular and Supercoiled
DNA molecules in human chromosomes are linear DNA
from some other organisms can be circular (the
two ends are attached)
Circular DNA can be twisted like a rubber band,
leading to supercoiling Supercoiled DNA is more
compact
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Single-Stranded Nucleic Acid Structure
Single-stranded DNA and RNA can adopt a variety
of structures These structures all involve
extensive base-pairing Simplest structure is a
stem-loop
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Single-Stranded Nucleic Acid Structure
Structures can be complex and can involve
mismatched base-pairing and other interactions
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DNA Replication
DNA replication requires the coordinated effort
of over twenty proteins The central players are
DNA polymerases - these enzymes synthesize the
new DNA strands DNA polymerases catalyze
phosphodiester-bond formation (DNA)n dNTP ?
(DNA)n1 PPi
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DNA Replication DNA Polymerases
DNA polymerases requires a template - a single
strand or a double strand with one chain
broken DNA polymerase is a template-directed
enzyme If single stranded, a short stretch of
DNA known as a primer must be bound - polymerases
will add nucleotides to the primer Polymerases
also require a supply of all four activated
precursors - dATP, dGTP, dTTP and dCTP, plus
Mg2 Elongation of DNA occurs 5 to 3
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DNA Replication DNA Polymerases
Addition of a nucleotide is efficient only if
incoming nucleotide base-pairs with corresponding
base on template - DNA polymerase has a very low
error rate
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Some Viruses Have No DNA
Some viruses use RNA to store their genes rather
than DNA An important class of RNA viruses are
the retroviruses (including HIV) The flow of
genetic information in retroviruses is from RNA
to DNA (opposite to DNA-based organisms)
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RNA Retroviruses
When such a virus infects a cell, a copy of its
RNA is used as a template to make a corresponding
DNA This is done by a viral enzyme called reverse
transcriptase
The viral DNA can then be incorporated into the
host genome
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Gene Expression

• The information stored as genes in DNA becomes
  useful when it is expressed in the production of
  RNA and proteins
• Expression occurs in two steps
• An RNA copy is made
• The RNA is translated into a functional protein

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Roles of RNA in Expression

• Several types of RNA molecules are involved in
  gene expression
• Messenger RNA (mRNA) - template for protein
  synthesis (translation)
• Transfer RNA (tRNA) - carries amino acids in
  activated form to the ribosome for addition to
  protein chain being synthesized
• Ribosomal RNA (rRNA) - the major component of the
  ribosome (protein synthesis complex)

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Roles of RNA in Expression
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RNA Synthesis
Synthesis of RNA from a DNA is called
transcription All RNA synthesis is performed by
RNA polymerases RNA polymerases are similar to
DNA polymerases in that they require a template,
activated precursors - ATP, GTP, CTP and UTP -
and Mg2 The template is usually double-stranded
DNA, but can be single-strand DNA No primer is
needed - synthesis can start using a single NTP
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RNA Synthesis Transcription
Synthesized RNA will be complementary to DNA
template strand
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Transcription Promoters and Terminators
RNA polymerase requires signals that tell it
where to start and stop synthesis - these are
promoters (start) and terminators (stop)
A promoter site specifically binds RNA polymerase
and determines where synthesis begins
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Transcription Promoters and Terminators
Transcription will continue from the promoter
site until RNA polymerase encounters a
termination signal In bacteria this sequence
forms a b-hairpin structure
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Transcription Promoters and Terminators
Termination in eukaryotes is not well
understood In eukaryotes, after transcription a
cap structure is added to the 5 end of the
RNA, and a polyA tail is added to the 3 end
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Transfer RNA An Adaptor
tRNA acts as an adaptor in protein synthesis Each
tRNA has an amino acid attachment site and a
corresponding template-recognition site Each
amino acid type is attached to a specific tRNA -
there is at least one tRNA for each amino
acid The amino acid is attached by an enzyme
called an aminoacyl-tRNA synthetase The template
recognition site is a set of three bases called
the anticodon
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Transfer RNA An Adaptor
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The Genetic Code

• The genetic code is the relation between the
  sequence of bases in DNA and RNA, and the
  sequence of amino acids in proteins
• The code has the following features
• Three nucleotides encode a single amino acid
• The code is nonoverlapping
• The code has no punctuation
• It is degenerate - some amino acids are encoded
  for by more than one codon

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The Genetic Code
There are 64 possible codons (4x4x4 64) Only
Trp and Met are coded by a single codon The
number of codons coding each amino acid
correlates with their frequency of occurrence in
proteins
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The Genetic Code
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The Genetic Code Start and Stop Signals
mRNA is translated by a large complex called the
ribosome - a protein synthesis factory The
ribosome needs signals to tell it where to start
and stop synthesis There are three stop signals -
UAA, UAG and UGA These are read by proteins known
as release factors, which cause the ribosome to
release the newly synthesized protein
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The Genetic Code Start and Stop Signals
The start codon is AUG (or GUG) - AUG also codes
for Met, and GUG for Val In bacteria, protein
synthesis is started with a modified amino acid
called fMet
In eukaryotes, synthesis starts with Met (not
fMet) The start codon establishes the reading
frame
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The Genetic Code Start and Stop Signals
In bacteria the start codon is preceded by a
purine-rich sequence
In eukaryotes the start codon is the AUG closest
to the 5 end of the mRNA
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The Genetic Code is Nearly Universal
The same genetic code is used by almost all
organisms Those organisms (or organelles) that do
differ have only a few differences
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Eukaryotic Genes
Most eukaryotic genes contain exons and introns -
the genes are discontinuous Introns are stretches
of DNA sequence that do not code for protein that
are interspersed within a gene Exons are the
coding regions
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Eukaryotic Genes RNA Processing
When are introns removed during gene expression
? Introns are transcribed into mRNA mRNA is
processed after synthesis in a process called
splicing carried out by complexes known as
spliceosomes
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Eukaryotic Genes RNA Processing
Specific splice sites are encoded in the
mRNA Introns nearly always start with GU and end
with AG, which is preceded by a pyrimidine-rich
tract
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Eukaryotic Genes Exons
Studies of evolution suggest that introns were
present in ancestral genes They were lost by
organisms that require rapid growth, such as
prokaryotes and lower eukaryotes Many exons
encode for discrete functional and structural
units in proteins (domains) One hypothesis is
that new proteins arose in evolution by the
rearrangement of exons - exon shuffling
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Eukaryotic Genes Exons
Exons can be shuffled by breaking and recombining
DNA
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Eukaryotic Genes Exons
Another advantage of exons is the possibility of
generating a series of related proteins by
splicing nascent mRNA in different ways -
alternative splicing This is used by
antibody-producing cells to generate by membrane
bound and soluble versions of the same antibody