Semifinals

 3.1 Types of nucleic acids

 3.2 Nucleotides
 3.3 Primary nucleic Acids structure
 3.4 DNA
 3.5 DNA replication
 3.6 RNA
 3.7 RNA synthesis (Transcription)
 3.8 The Genetic code
 3.9 Anti codons
 3.10 Protein Synthesis (translation)
 3.11 Mutation
 3.12 Recombinant DNA and Genetic Engineering
3.1 Nucleic Acid & Its types
 Nucleic acids are molecules that store information
for cellular growth and reproduction
 There are two types of nucleic acids:
- deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA)
 These are polymers consisting of long chains of
monomers called nucleotides
 A nucleotide consists of a nitrogenous base, a
pentose sugar and a phosphate group:
 Nitrogen Bases
 The nitrogen bases in nucleotides consist of two general types:
- purines: adenine (A) and guanine (G)
- pyrimidines: cytosine (C), thymine (T) and Uracil (U)
Pentose Sugars
 There are two related pentose sugars:
- RNA contains ribose
- DNA contains deoxyribose
 The sugars have their carbon atoms numbered
with primes to distinguish them from the nitrogen
bases
3.2 Nucleosides and Nucleotides
 A nucleoside consists of a nitrogen base linked by a
glycosidic bond to C1’ of a ribose or deoxyribose
 Nucleosides are named by changing the nitrogen
base ending to -osine for purines and –idine for
pyrimidines
 A nucleotide is a nucleoside that forms a phosphate
ester with the C5’ OH group of ribose or deoxyribose
 Nucleotides are named using the name of the
nucleoside followed by 5’-monophosphate
Names of Nucleosides and Nucleotides
 AMP, ADP and ATP
 Additional phosphate groups can be added to the nucleoside
5’-monophosphates to form diphosphates and
triphosphates
 ATP is the major energy source for cellular activity
3.3 Primary Structure of
Nucleic Acids
The primary structure of a
nucleic acid is the nucleotide
sequence
The nucleotides in nucleic acids are
joined by phosphodiester bonds
The 3’-OH group of the sugar in one
nucleotide forms an ester bond to
the phosphate group on the 5’-
carbon of the sugar of the next
nucleotide
 Reading Primary Structure

A nucleic acid polymer

has a free 5’-phosphate
group at one end and a
free 3’-OH group at the
other end
 The sequence is read

from the free 5’-end using

the letters of the bases
 This example reads

5’—A—C—G—T—3’
Example of RNA Primary Structure
 In RNA, A, C, G, and U are linked by 3’-5’ ester
bonds between ribose and phosphate
3.4. DNA Double Helix
 Example of DNA Primary Structure
 In DNA, A, C, G, and T are linked by 3’-5’ ester
bonds between deoxyribose and phosphate
Base Pairing in the DNA Double Helix
 Storage of DNA
 In eukaryotic cells (animals, plants, fungi) DNA is
stored in the nucleus, which is separated from the
rest of the cell by a semipermeable membrane
 The DNA is only organized into chromosomes
during cell replication
 Between replications, the DNA is stored in a compact
ball called chromatin, and is wrapped around
proteins called histones to form nucleosomes
3.5 DNA Replication
Semi-Conservative DNA Replication
 Direction of Replication
 The enzyme helicase unwinds several sections of parent
DNA
 At each open DNA section, called a replication fork, DNA
polymerase catalyzes the formation of 5’-3’ester bonds of
the leading strand
 The lagging strand, which grows in the 3’-5’ direction, is
synthesized in short sections called Okazaki fragments
 The Okazaki fragments are joined by DNA ligase to give a
single 3’-5’ DNA strand
Enzymes and Proteins Involved in DNA
Replication
3.6 Ribonucleic Acid (RNA)
 RNA is much more abundant than DNA
 There are several important differences between
RNA and DNA:
- the pentose sugar in RNA is ribose, in DNA it’s
deoxyribose
- in RNA, uracil replaces the base thymine (U pairs
with A)
- RNA is single stranded while DNA is double
stranded
- RNA molecules are much smaller than DNA
molecules
 There are three main types of RNA:
- ribosomal (rRNA), messenger (mRNA) and transfer
(tRNA)
Types of RNA
Ribosomal RNA and Messenger RNA
 Ribosomes are the sites of protein synthesis
- they consist of ribosomal DNA (65%) and proteins (35%)
- they have two subunits, a large one and a small one
 Messenger RNA carries the genetic code to the ribosomes
- they are strands of RNA that are complementary to the
DNA of the gene for the protein to be synthesized
 Transfer RNA
 Transfer RNA translates the genetic code from the messenger
RNA and brings specific amino acids to the ribosome for protein
synthesis
 Each amino acid is recognized by one or more specific tRNA
 tRNA has a tertiary structure that is L-shaped
- one end attaches to the amino acid and the other binds to the
mRNA by a 3-base complimentary sequence
3.7. Protein Synthesis
 The two main processes involved in protein synthesis are
- the formation of mRNA from DNA (transcription)
- the conversion by tRNA to protein at the ribosome
(translation)
 Transcription takes place in the nucleus, while translation takes
place in the cytoplasm
 Genetic information is transcribed to form mRNA much the
same way it is replicated during cell division
Transcription
 Several steps occur during transcription:
- a section of DNA containing the gene unwinds
- one strand of DNA is copied starting at the
initiation point, which has the sequence TATAAA
- an mRNA is synthesized using complementary
base pairing with uracil (U) replacing thymine (T)
- the newly formed mRNA moves out of the
nucleus to ribosomes in the cytoplasm and the
DNA re-winds
 RNA Polymerase
 During transcription, RNA polymerase moves
along the DNA template in the 3’-5’direction to
synthesize the corresponding mRNA
 The mRNA is released at the termination point
Processing of mRNA
 Genes in the DNA of eukaryotes contain
exons that code for proteins along with
introns that do not
 Because the initial mRNA, called a pre-RNA,
includes the noncoding introns, it must be
processed before it can be read by the tRNA
 While the mRNA is still in the nucleus, the
introns are removed from the pre-RNA
 The exons that remain are joined to form the
mRNA that leaves the nucleus with the
information for the synthesis of protein
Removing Introns from mRNA
Regulation of Transcription
 A specific mRNA is synthesized when the cell
requires a particular protein
 The synthesis is regulated at the transcription
level:
- feedback control, where the end products
speed up or slow the synthesis of mRNA
- enzyme induction, where a high level of a
reactant induces the transcription process to
provide the necessary enzymes for that reactant
 Regulation of Prokaryotic Transcription
 In prokaryotes (bacteria and archebacteria),
transcription of proteins is regulated by an operon,
which is a DNA sequence preceding the gene
sequence
 The lactose operon consists of a control site and the
genes that produce mRNA for lactose enzymes
Lactose Operon and Repressor
 When there is no lactose in the cell, a regulatory
gene produces a repressor protein that
prevents the synthesis of lactose enzymes
- the repressor turns off mRNA synthesis
 Lactose Operon and Inducer
 When lactose is present in the cell, some lactose
combines with the repressor, which removes the
repressor from the control site
 Without the repressor, RNA polymerase catalyzes the
synthesis of the enzymes by the genes in the operon
 The level of lactose in the cell induces the synthesis of
the enzymes required for its metabolism
RNA Polymerase
3.8. The Genetic Code
 The genetic code is found in the sequence of
nucleotides in mRNA that is translated from the DNA
 A codon is a triplet of bases along the mRNA that
codes for a particular amino acid
 Each of the 20 amino acids needed to build a protein
has at least 2 codons
 There are also codons that signal the “start” and
“end” of a polypeptide chain
 The amino acid sequence of a protein can be
determined by reading the triplets in the DNA
sequence that are complementary to the codons of
the mRNA, or directly from the mRNA sequence
 The entire DNA sequence of several organisms,
including humans, have been determined, however,
- only primary structure can be determined this way
- doesn’t give tertiary structure or protein function
mRNA Codons and Associated Amino Acids
Reading the Genetic Code
 Suppose we want to determine the amino
acids coded for in the following section of a
mRNA

5’—CCU —AGC—GGA—CUU—3’

 According to the genetic code, the amino acids

for these codons are:

CCU = Proline AGC = Serine

GGA = Glycine CUU = Leucine

 The mRNA section codes for the amino acid

sequence of Pro—Ser—Gly—Leu
 Translation and tRNA Activation

 Once the DNA has been

transcribed to mRNA, the
codons must be tranlated
to the amino acid
sequence of the protein
 The first step in
translation is activation
of the tRNA
 Each tRNA has a triplet
called an anticodon that
complements a codon on
mRNA
 A synthetase uses ATP
hydrolysis to attach an
amino acid to a specific
tRNA
 Initiation and Translocation
 Initiation of protein synthesis occurs when a mRNA
attaches to a ribosome
 On the mRNA, the start codon (AUG) binds to a
tRNA with methionine
 The second codon attaches to a tRNA with the
next amino acid
 A peptide bond forms between the adjacent amino
acids at the first and second codons
 The first tRNA detaches from the ribosome and the
ribosome shifts to the adjacent codon on the
mRNA (this process is called translocation)
 A third codon can now attach where the second
one was before translocation
Termination
 After a polypeptide with all the amino acids for
a protein is synthesized, the ribosome reaches
the the “stop” codon: UGA, UAA, or UAG
 There is no tRNA with an anticodon for the
“stop” codons
 Therefore, protein synthesis ends
(termination)
 The polypeptide is released from the ribosome
and the protein can take on it’s 3-D structure
(some proteins begin folding while still being
synthesized, while others do not fold up until
after being released from the ribosome)
3.11. Mutation

Amutation is a change in the sequence of bases in

DNA.
Spontaneous mutations result from errors in base
pairing during replication.
Replication errors are very rare, less than 1 base pair
per 1010, because of the proofreading function of DNA
polymerase as well as the presence of various enzymes
that have repair functions. Superimposed on
spontaneous mutations are those produced by
mutagens (agents that produce mutation).
3.11. Mutation

Mutagens include ultraviolet light (sunlight) various

high-energy radiations (x- and cosmic rays,
radioactivity), and a variety of chemicals.
 An example of a chemical mutagen is sodium
nitrite, which is used as a preservative for bologna
and hot dogs.
Mutagens react with nucleotide base pairs, either
converting them to other bases or to other structures.
Repair enzymes minimize the effects of mutagens;
the overall effects of mutagens depend on their
amounts and the duration of exposure.
3.11. Mutation
Mutations occur by substitution, insertion, or
deletion of bases.
Substitution mutations are the most common
types of mutation. A substitution mutation,
involving the substitution of one base by
another, changes one codon in mRNA. This may
or may not alter the amino acid residue specified
by that codon because of the degeneracy of the
genetic code.
3.11. Mutation
An insertion mutation involves the insertion of a base into the normal
sequence. A deletion mutation involves the deletion of a base from the normal
sequence. Insertion and deletion mutations, referred to as frame shift
mutations, are rarer than substitution mutations but can cause much larger
effects. A frame shift mutation changes all codons that follows an insertion or
deletion in an exon or intron. There is no effect of a mutation (substitution or
frame shift) in an intron. The mutation is constrained within the intron and has
no effect on the codons in the exons because the introns are excised (Fig
21.10). But a frameshift mutation in an exon yields nonfunctional protein
because all codons after the mutation are altered. The polypeptide sequence
generally bears no resemblance to that coded in the original DNA. Mutations
that have negative biological consequences fall into two categories. Such
mutations in somatic cells (cells other than egg and sperm cells) affect the
physiological functioning of an individual organism. The individual may
become ill and even die, depending on the level of the mutation and the
particular physiological functions which are affected. Uncontrolled growth of
cells (cancer) may result from mutation. A mutagen giving rise to cancer is
referred to as a carcinogen. Most mutagens are carcinogens. Mutations in
germ cells (egg and sperm cells) have much greater and far-reaching
significance since they are passed onto offspring and subsequent generations.
Such mutations are referred to as genetic defects or hereditary diseases when
physiological functions are severely affected (Table 21-2).
 THE
CENTRAL
DOGMA
How does DNA work?
 The “Central Dogma”
DNA
 The “Central Dogma”
DNA

RNA
 The “Central Dogma”
DNA

RNA

proteins
 The “Central Dogma”
DNA

RNA

proteins

you
 RNA
Five differences between RNA and DNA
1.Sugar in RNA is ribose instead of deoxyribose
2.RNA is single stranded
3.RNA contains Uracil instead of Thymine
4.RNA is disposable
5.RNA can be outside the nucleus, DNA can’t
If you are going from DNA to RNA – what nitrogenous
base would pair with Adenine?
DNA: C A G T T A
RNA: _ _ _ _ _ _
 ANSWER:
DNA: C A G T T A
RNA: G U C A A U
 Types of RNA
• Key players in Protein Synthesis -
– Messenger RNA (mRNA): carry
instruction copies
– Ribosomal RNA (rRNA): makes
up ribosome along with proteins
– Transfer RNA (tRNA): brings
amino acids to the ribosome
Big picture of protein
synthesis
Transcription
Translation
 Just Like
Construction…
• DNA is the master plan
• mRNA is the everyday blueprint
• rRNA is the builder
• tRNA is the gopher
• Amino Acids are the wood
• Proteins are the building
Translation of
the Genetic
Code -
Protein
Synthesis
 This is a molecule of messenger
RNA.
mRNA is transcribed in the nucleus.

codo
A U GnG G C U U A A A G C A G U G C A C G U U

mRNA molecule
 Transcription
• Several steps occur during transcription:
- a section of DNA containing the gene unwinds
- one strand of DNA is copied starting at the
initiation point, which has the sequence TATAAA
- an mRNA is synthesized using complementary
base pairing with uracil (U) replacing thymine (T)
- the newly formed mRNA moves out of the
nucleus to ribosomes in the cytoplasm and the
DNA re-winds
 RNA Polymerase
• During transcription, RNA polymerase moves
along the DNA template in the 3’-5’direction
to synthesize the corresponding mRNA
• The mRNA is released at the termination point
Processing of mRNA
Removing Introns from mRNA
Regulation of Transcription
Regulation of Prokaryotic Transcription
 Lactose Operon and Repressor
• When there is no lactose in the cell, a
regulatory gene produces a repressor protein
that prevents the synthesis of lactose enzymes
- the repressor turns off mRNA synthesis
 Lactose Operon and Inducer
• When lactose is present in the cell, some lactose
combines with the repressor, which removes the repressor
from the control site
• Without the repressor, RNA polymerase catalyzes the
synthesis of the enzymes by the genes in the operon
• The level of lactose in the cell induces the synthesis of the
enzymes required for its metabolism
RNA Polymerase
TRANSLATION
 A ribosome attaches
to the mRNA
molecule.

ribosome

AUGGGCUUAAAG CAGUGCACGUU
 Amino acid

tRNA molecule

A transfer RNA molecule

arrives.
It brings a specific amino acid to
the first three bases (codon) on
anticodon the mRNA.
The three unpaired bases
(anticodon) on the tRNA link up
UAC with the codon.
AUGGGCUUAAAG CAGUGCACGUU
 Another tRNA molecule comes
into place, bringing a second
amino acid.
Its anticodon links up with the
second codon on the mRNA.
CC
UAC G
AUGGGCUUAAAG CAGUGCACGUU
 Peptide
bond

A peptide bond forms

between the two amino
acids.
U A CC C G
AUGGGCUUAAAG CAGUGCACGUU
 The first tRNA molecule
releases its amino acid
and moves off into the
U A C cytoplasm.
CCG
AUGGGCUUAAAG CAGUGCACGUU
 The ribosome moves
along the mRNA to the
next codon.
CCG
AUGGGCUUAAAG CAGUGCACGUU
 Another tRNA
molecule brings the
AA
next amino acid into
CCG U place.
AUGGGCUUAAAG CAGUGCACGUU
 A peptide bond joins
the second and third
amino acids to form a
polypeptide chain.
CCGCCG
AUGGGCUUAAAG CAGUGCACGUU
The process continues.
The polypeptide chain gets
longer.
This continues until a
termination (stop) codon is
reached.
The polypeptide is then AC
complete. GUC G
AUGGGCUUAAAG CAGUGCACGUU
CODON TABLE
1. What amino acids
would be coded by the
following DNA sequence?

CGGACCGCTAT
C

2. What would be the

mRNA sequence for a
polypeptide chain (protein)
that had the following
amino acids? DNA
sequence?