THE CENTRAL

DOGMA
of LIFE
BRIEF HISTORY
NUCLEIC ACID STRUCTURE
CENTRAL DOGMA
BRIEF HISTORY
 Timeline, People and Their
Accomplishments
• Gregor Mendel (heredity)
• Thomas Hunt Morgan (flies, linkage)
• Frederick Griffith (1928: transformation and mice)
• Oswald Theodore Avery, Colin MacLeod and Maclyn
McCarty (1944: DNA as the transforming agent)
• Erwin Chargaff (late 40’s-early 50’s: base pairing=AT CG)
• Alfred Hershey-Martha Chase (1952: DNA is not a protein)
• Watson and Crick (1953: chemical structure of DNA)
• Meselson-Stahl (mid 1950’s: DNA Replication details)
Watson and Crick
STRUCTURE
 CHROMOSOMES AND GENES
• Chromosome
– Structure in the cell nucleus thought to be the
carrier of genetic information-(vector of heredity)

• Gene
– Portion of a chromosome that controlled a
specific inheritable trait
 COMPOSITION OF NUCLEIC ACIDS
• Nucleic Acids
– Polymers
– Polynucleotides

• Part of Nucleotide
– A five-member ring monosaccharide
– A nitrogen-containing cyclic compound
– A phosphate group
 COMPOSITION OF NUCLEIC ACIDS
• Types of Nucleic Acids
– DNA
– RNA

• SUGARS
– DNA – 2-deoxyribose
– RNA – ribose
COMPOSITION OF NUCLEIC ACIDS
 COMPOSITION OF NUCLEIC ACIDS
• BASES
– Purine (2)-bicyclic w/ fused 5&6
• Contains two-fused N-containing ring
• Adenine
• Guanine
– Pyrimidine (3)-monocyclic w/6
• Has one nitrogen-containing ring
• Cytosine
• Thymine
• Uracil
 Phosphate-3rd component
• Derived from phosphoric acid( H3PO4)
• Under cellular conditions, the phosphoric acid
loses 2 of its hydrogen atom to give a
hydrogen phosphate ion(HPO42-)
COMPOSITION OF NUCLEIC ACIDS
COMPOSITION OF NUCLEIC ACIDS
 COMPOSITION OF NUCLEIC ACIDS
• SUGAR + BASE = NUCLEOSIDE
 COMPOSITION OF NUCLEIC ACIDS
• SUGAR + BASE = NUCLEOSIDE
 COMPOSITION OF NUCLEIC ACIDS
• NUCLEOSIDE + PHOSPHATE = NUCLEOTIDE
– are the building blocks of nucleic acids
– Monomers of the DNA and RNA polymers
– is a 5’-monophosphate ester of a nucleoside
– Are named by adding 5’-monophosphate at the
end of the name of the nucleoside
 RIBONUCLEOTIDE VS.
DEOXYRIBONUCLEOTIDE
 COMPOSITION OF NUCLEIC ACIDS
• Nucleotides
– Can add additional phosphate groups to form
diphosphate or triphosphate esters
 DNA
BASES DEOXYRIBONUCLEOSIDES DEOXYRIBONUCLEOTIDES

ADENINE (A) Deoxyadenosine 5’-Monophosphate

Deoxyadenosine (dAMP)

GUANINE (G) Deoxyguanosine 5’-Monophosphate

Deoxyguanosine (dGMP)

CYTOSINE (C) Deoxycytidine 5’-Monophosphate

Deoxycytidine (dCMP)

THYMINE (T) Deoxythymidine 5’-Monophosphate

Deoxythymidine (dAMP)
 RNA
BASES RIBONUCLEOSIDES RIBONUCLEOTIDES

ADENINE (A) Adenosine 5’-Monophosphate (AMP)

Adenosine

GUANINE (G) Guanosine 5’-Monophosphate

Guanosine (GMP)

CYTOSINE (C) Cytidine 5’-Monophosphate (CMP)

Cytidine

URACIL (T) Uridine 5’-Monophosphate (AMP)

Uridine
 STRUCTURE OF DNA AND RNA
• Primary Structure
– Alternating deoxyribose and
phosphate group
• backbone of the molecule
• Provides structural stability

– The bases that are the side-

chain groups
• Carry all the information necessary
for protein synthesis
 STRUCTURE OF DNA AND RNA
• Secondary Structure
– Based on the following:
• Chargaff Rule that (A and T) and
(G and C) are present in
equimolar quantities

• X-ray diffraction photographs

obtained by Rosalind Franklin and
Maurice Wilkins

James Watson and Francis Crick

 STRUCTURE OF DNA AND RNA
• Secondary Structure
– Double Helix
• The 2 polynucleotide chains run
in opposite directions
• One 5’ – OH and one 3’ – OH
terminal
• Bases are hydrophobic
• Sugar-phosphate backbone is
exposed to the aqueous
environment
 STRUCTURE OF DNA AND RNA
• Secondary Structure
STRUCTURE OF DNA AND RNA
STRUCTURE OF DNA AND RNA
 STRUCTURE OF DNA AND RNA
• Higher Structure
– HISTONES
• Basic protein to w/c the DNA
is coiled around

– NUCLEOSOMES
• acidic DNA + basic histones
• attract each other by
electrostatic (ionic) forces
 STRUCTURE OF DNA AND RNA
• DNA
– Is almost always double-stranded (helical
structure)
– 2’-deoxyribose

• RNA
– Single-stranded
– Ribose
 STRUCTURE OF DNA AND RNA
• Types of RNA
– Messenger RNA (mRNA)
• Carry the genetic information from the DNA in the
nucleus directly to the cytoplasm
• Consists of a chain of nucleotides whose sequence is
exactly complementary to one of the strands of DNA
 STRUCTURE OF DNA AND RNA
• Types of RNA
– Transfer RNA (tRNA)
• Containing from 73 to 93
nucleotides per chain
• There is at least one different
tRNA for each of the 20 AAs
• Transports amino acids to the
site of protein synthesis in the
ribosomes
 STRUCTURE OF DNA AND RNA
• Types of RNA
– Ribosomal RNA (rRNA)
• RNA in complexed with proteins in ribosomes
 STRUCTURE OF DNA AND RNA
• Types of RNA
– Ribozymes
• Catalytic RNA
• Catalyze the splicing of
mRNA
 STRUCTURE OF DNA AND RNA
• Exons
– Coding sequences
– “expressed sequences”

• Introns
– Noncoding sequences
– “Intervening sequences”
 T H E
D O G M A
• This dogma forms the backbone of
molecular biology and is represented
by four major stages.
– 1. Replication
– 2. Transcription
– 3. Processing (in eukaryotes)
– 4. Translation
 THE FOUR MAJOR STAGES
• REPLICATION
– DNA replicates its information in a
process that involves many enzymes
(a.k.a DNA synthesis)

• TRANSCRIPTION
– DNA codes for the production of
messenger RNA (mRNA)
 THE FOUR MAJOR STAGES
• PROCESSING
– in eukaryotic cells, the mRNA is
processed (essentially by splicing) and
migrates from the nucleus to the cytoplasm

• TRANSLATION
– mRNA carries coded information to
ribosomes
– ribosomes "read" the information (a.k.a.
protein synthesis)
 Energy of DNA Replication
Where does energy for bonding usually come from?
We come
You with our own
remember energy! energy
ATP! energy
Are there
other ways
Are there
to getenergy
other energy
out of it?
nucleotides?
You bet!

And we
leave behind a
ATP
CTP
TTP
GTP CMP
TMP
GMP
AMP
ADP
nucleotide!
modified nucleotide
DNA REPLICATION
 DNA REPLICATION MODELS
• 1) Semiconservative Replication
– DNA Replication would create two molecules
– Each of them would be a complex of an old
(parental) and a daughter strand.

• 2) Conservative Replication
– DNA Replication process would create a
brand new DNA double helix made of two
daughter strands while the parental chains
would stay together.
 DNA REPLICATION MODELS
• 3) Dispersive Replication
– Replication Process would create two DNA
double-chains, each of them with parts of both
parent and daughter molecules.

The correct model is the Semiconservative

DNA Replication as was proven by the
experimentation of Meselson - Stahl.
 Let’s meet
the team…
DNA Replication
• Large team of enzymes coordinates replication
 Enzymes/Proteins of DNA
Replication
• Helicase:
– Unwind a portion of the DNA Double Helix

• RNA Primase:
– Attaches RNA primers to the replicating
strands

• Exonuclease (DNA Pol I):

– Finds and removes the RNA Primers
 Enzymes/Proteins of DNA
Replication
• DNA Polymerase delta(δ) (DNA pol III)
– Reads the DNA strand in a 3' - 5‘ direction
• Going towards the direction of the replication fork:
leading strand that runs 5' - 3';
• Away from the direction of the replication fork:
lagging strand that runs 5' - 3
– has a 3' - 5‘ exonuclease activity
 Enzymes/Proteins of DNA
Replication
• DNA Ligase:
– Adds phosphate in the remaining gaps (phosphate -
sugar backbone)

• DNA gyrase:
– Relaxes the possible supercoiling of the
unwounded DNA strand

• Nucleases: (DNA pol II, IV, V)

– Remove wrong nucleotides from the daughter
strand
 Enzymes/Proteins of DNA
Replication
• Sliding clamp:
– Stabilizes the attachment of the DNA
polymerase to the DNA strand to be copied

• SSB proteins:
– Prevents the re-annealing of the unwounded
DNA strand
Steps of DNA Replication
• 1) The first step: breaking of hydrogen bonds
– splitting happens in places which are rich in A-T

– Helicase is the enzyme that splits the two strands

– structure created is known as "Replication Fork"

Steps of DNA Replication
• 1) The first step: breaking of hydrogen bonds
Steps of DNA Replication
• 2) Binding of RNA Primase in the initiation point
of the 3'-5' parent chain
– RNA Primase attracts RNA nucleotides to the DNA

– RNA nucleotides are the primers (starters) for the

binding of DNA nucleotides

– DNA Pol α forms the RNA-DNA complex to help DNA

Pol δ copy the parent strand
Steps of DNA Replication
• 2) Binding of RNA Primase in the initiation point
of the 3'-5' parent chain
Steps of DNA Replication
• 3) Elongation process
– A) LEADING STRAND:
• Uses the 3'-5' parent strand (towards replication fork)
• It is the continuous 5'-3' proceeding daughter strand
• DNA Polymerase delta "reads" the template with ease and
continuously adds nucleotides
Steps of DNA Replication
• 3) Elongation process
– A) LEADING STRAND:
Steps of DNA Replication
• 3) Elongation process
– B)LAGGING STRAND:
• Uses the 3'-5' parent strand (away the replication fork)
• It is the interrupted 5'-3' proceeding daughter strand
• the 5'-3' parent strand cannot be directly "read" by DNA
Polymerase delta
• the RNA Primase adds more RNA Primers to prompt
eleongation by DNA Pol delta
• "Okazaki Fragments" (gap between two RNA primers)
Steps of DNA Replication
• 3) Elongation process
– B)LAGGING STRAND:
Steps of DNA Replication
• 4) Sealing the gap in Lagging strand:
– DNA Pol I -exonuclease- reads the fragments and
removes the RNA Primers

– DNA Ligase adds phosphate in the remaining gaps of

the phosphate - sugar backbone
5 3 5 need “primer” bases to add on to 3

energy
no energy


to bond
energy
energy

energy
energy

ligase
energy

energy

3 5 3 5
Steps of DNA Replication
• 5) The last step is Termination
– the end of the parental strand where the last primer
binds isn't replicated

– these ends of linear (chromosomal) DNA consists of

noncoding DNA that contains repeated sequences
and are called telomeres
• Part of the telomere is removed in every cycle of DNA Replication.
Steps of DNA Replication
• 6) The DNA Replication is not completed before
a mechanism of repair that fixes possible
errors caused during the replication.

– Enzymes like nucleases remove the wrong nucleotides and the

DNA Polymerase fills the gaps.
 DNA Repair
• For the rare mutations occurring during
replication that isn’t caught by DNA
polymerase proofreading
• For mutations occurring with daily assault
• If no repair
– In germ (sex) cells  inherited diseases
– In somatic (regular) cells  cancer
CONSEQUENCES OF GENETIC ERRORS :SOURCES OF
GENETIC VARIATION

• Mutation - any novel genetic change in the gene

complement or genotype relative to the parental
genotypes, beyond that achieved by genetic
recombination during meiosis.

• Mutations are changes in DNA structure, and

therefore changes in protein and phenotype.
 CONSEQUENCES OF GENETIC ERRORS SOURCES OF
GENETIC VARIATION

• Mutations are rare! For every 100 million

nucleotides added to a developing DNA strand only
one mistake occurs on average.

• Mutations are heritable; and may be beneficial,

neutral, lethal, detrimental or harmful to the
organism.
 ASSIGNMENT:
• Enumerate the different repair mechanism in
eukaryotes:
– Name the process
– Brief description of mechanism
– Example disease if it does occur

• Long bond paper, hand written. Submit on

Saturday.
• STUDY the Flash Presentation of
DNA synthesis…

• http://www.wiley.com/college/pratt/047139
3878/student/animations/dna_replication/i
ndex.html
 Eukaryotic Transcription

• Transcription occurs in the nucleus in eukaryotes, nucleoid

in bacteria
• Translation occurs on ribosomes in the cytoplasm
• mRNA is transported out of nucleus through the nuclear
pores
How does the process of transcription
begin?
• The DNA serves as the template for producing
an RNA transcript or copy of information
stored on the DNA molecule.

• The DNA molecule must open up and allow an

enzyme called RNA polymerase read and
connect together the sequence of nucleotides
in the proper order.
How does the process of transcription
begin?
• After the RNA transcript is made, it is not yet
ready to leave the nucleus.
• Regions called introns (noncoding) are
snipped out with enzymes and degraded,
leaving behind exons (coding regions of RNA)
which are spliced together.
How does the process of transcription
begin?
• A sequence of nucleotides (AAAA to 3’ end of
RNA transcript are added, polyadenylation,
which allows the product to leave the nucleus
 Mature RNA transcript.
• If the mature RNA transcript carries the
“message” for producing proteins, then it
becomes mRNA.
 RNA Processing
• Eukaryotic cells process the RNA in the
nucleus before it is moved to the cytoplasm
for protein synthesis
• The RNA that is the direct copy of the DNA is
the primary transcript
• 2 methods used to process primary transcripts
to increase the stability of mRNA being
exported to the cytoplasm
– RNA capping
– Polyadenylation
 RNA Processing

• RNA capping happens at the 5’ end of the RNA, usually

adds a methylgaunosine shortly after RNA polymerase
makes the 5’ end of the primary transcript
• Polyadenylation modifies the 3’ end of the primary
transcript by the addition of a string of A’s
 Coding and Non-coding Sequences

• In bacteria, the RNA made is translated to a protein

• In eukaryotic cells, the primary transcript is made of
coding sequences called exons and non-coding sequences
called introns
• It is the exons that make up the mRNA that gets translated
to a protein
 RNA Splicing
• Responsible for the removal of the introns to create the
mRNA
• Introns contain sequences that act as cues for their removal
• Carried out by small nuclear riboprotein particles (snRNPs)
 snRNPs
• snRNPs come together
and cut out the intron
and rejoin the ends of
the RNA
• Intron is removed as a
lariat – loop of RNA
like a cowboy rope
 Benefits of Splicing
• Allows for genetic recombination
– Link exons from different genes together to create a new
mRNA
• Also allows for 1 primary transcript to encode for
multiple proteins by rearrangement of the exons
Summary