GENETIC MATERIAL

(DNA and RNA)

PATRICK JUMAR S. BUENAFLOR, RMT, MSMT(c)

DNA as the GENETIC MATERIAL

“A genetic material must carry out two jobs:

duplicate itself and control the development of
the rest of the cell in a specific way.”

- Francis Crick, 1953

Origin of DNA
An Overview
• DNA, the substance of
inheritance, is the most
celebrated molecule of our time
• Hereditary information is
encoded in DNA and reproduced
in all cells of the body
• This DNA program directs the
development of biochemical,
anatomical, physiological, and (to
some extent) behavioral traits
Discovering DNA

• The key factor in determining the

genetic material was choosing
appropriate experimental organisms
• The role of DNA in heredity was first
discovered by studying bacteria and the
viruses that infect them
 Discovering DNA
Frederick Griffiths
• English microbiologist
• Worked with Streptococcus
pneumoniae bacteria, which exists
in two types
– Type S (Smooth) = Enclosed in a
polysaccharide capsule
– Type R (Rough) = No capsule
• Termed the conversion of one
bacterial type into another as
transformation
 Discovering DNA
Avery, MacLeod, and McCarty
• Treated lysed S bacteria with
protease and DNase
• Only DNase prevented
transformation
• Thus, DNA is the transforming
principle
– Can convert Type R bacteria
into S
Discovering DNA
Griffith,Avery, MacLeod, and McCarty’s
Conclusion

DNA
 Discovering DNA
Alfred Hershey and Martha
Chase
• Used E.coli bacteria infected with a
virus that consisted of a protein
head surrounding DNA
• Grew a batch of virus in a medium
containing 35S and 32P
• Blender experiments showed that
the virus transfers DNA, not protein,
into a bacterial cell
• Thus, DNA is the genetic material
Discovering DNA
Discovering DNA
Phoebus Levine
• Identified the 5-carbon
sugars ribose in 1909 and
deoxyribose in 1929
• Revealed chemical distinction
between RNA and DNA
– RNA has ribose
– DNA has deoxyribose
Discovering DNA
Phoebus Levine
• Discovered that the three parts
of a nucleotide are found in
equal proportions
– Sugar
– Phosphate
– Base
• Deduced that a nucleic acid
building block must contain one
of each component
Discovering DNA
Erwin Chargaff
• Analyzed base composition of
DNA from various species and
observed regular
relationships:
– Adenine (A) + Guanine (G)
– Thymine (T)+ Cytosine (C)
– A = T and C = G
 Discovering DNA
Rosalind Franklin and Maurice Wilkins
• Used a technique called X-ray diffraction
• Deduced the overall structure of the
molecule from the patterns in which the X
rays were deflected
• Distinguished two forms of DNA
– “A” form, which is dry and crystalline
– “B” form, which is wet and cellular
• It took Franklin 100 hours to obtain “photo
51” of the B-form of DNA
Discovering DNA
James Watson and
Francis Crick
• Did not perform any
experiments
• Rather, they used the
earlier research and
inferences from model
building with cardboard
cutouts to solve the
structure of DNA
DNA Structure
• DNA contains genetic information
that is unique to the organism from
which it was isolated
– Gene is a section of a DNA
molecule
• Sequence of building blocks specifies
the sequence of amino acids in a
particular protein
• A single building block is a nucleotide
– Each nucleotide is composed of:
• A deoxyribose sugar
• A phosphate group
• A nitrogenous base
DNA Structure
• Nucleotides are joined
into chains
– Phosphodiester bonds
form between the
deoxyribose sugars and
the phosphates
• This creates a
continuous sugar-
phosphate backbone
 DNA Structure
• The key to the constant width of the double helix is the specific pairing of
purines and pyrimidines via hydrogen bonds
• The complementary base pairs are:
– Adenine and guanine (Purines) DNA ONLY
– Cytosine and thymine (Pyrimidines)
• Hydrogen bonds hold the base pairs together

BOTH DNA
& RNA RNA ONLY
DNA Structure
DNA Structure
• Adenine (A) pairs with Thymine (T)
– 2 hydrogen bond
• Guanine (G) pairs with Cytosine (C)
– 3 hydrogen bond
• The base pairs lie 3.4 Armstrong apart
and the helical turns repeat every 34
Armstrong.
– Therefore, there are 10
complimentary sets of base pairs to
every helical turn
DNA Structure
• DNA Consists of Two
Chains of Nucleotides in
an Antiparallel
Configuration
• Two polynucleotide chains
align forming a double
helix
– The opposing
orientation (head-to-
toe) is called anti-
parallelism
DNA Structure
• Antiparallel nature of the
DNA double helix becomes
apparent when the carbons
in the sugar are numbered
– Carbons are numbered
from 1 to 5
• Note that one strand of the
double-helix runs in a 5’ to 3’
direction, and the other
strand runs in a 3’ to 5’
direction
 DNA Replication
• Since the two strands of DNA are complementary, each strand acts as a template for
building a new strand in replication
• In DNA replication, the parent molecule unwinds, and two new daughter strands are
built based on base-pairing rules
DNA Replication
• Three Models of DNA
replication
– Semiconservative
• each daughter molecule will have one
old strand (derived or “conserved”
from the parent molecule) and one
newly made strand
– Conservative model
• the two parent strands rejoin
– Dispersive model
• each strand is a mix of old and new)
 DNA Replication
OVERVIEW
• DNA replication occurs during the S phase of the
cell cycle, prior to cell division
• When DNA is replicated, it separates and
hydrogen bonds holding the base pairs together
break
– Two identical nucleotide chains are built from
one, as the bases form pairs
• A site where DNA is locally opened is called a
replication fork
DNA Replication
Three Stages of the Replication Process
1. Initiation
2. Elongation
3. Termination
DNA Replication
DNA Replication
DNA Replication
DNA Replication
DNA Replication
DNA Replication
Replication begins at particular sites called origins of replication, where the two DNA
strands are separated, opening up a replication “bubble”
DNA Packing
• Scaffold proteins form frameworks that
guide DNA strands
• The DNA coils around proteins called
histones, forming a bead-on-a-string-like
structure
– The bead part is called the nucleosome
• DNA wraps at several levels, until it is
compacted into a chromatid
• Chromosome substance is called chromatin
DNA v.s. RNA
RNA Structure
• RNA is the bridge between
gene and protein
• Bases of an RNA sequence
are complementary to those
of one strand of the double
helix, called the template
strand
• RNA polymerase builds an
RNA molecule
• Non-template strand of the
DNA double helix is called
the coding strand
RNA Structure
RNA Structure
 Gene Expression
• DNA stores information in the form of a code that we call the genetic
code
– Genetic code is based on the order of the base pairs that make up the
DNA molecule
– The sequence of nucleotide determines the sequence of amino acids
within a protein
• DNA of the human genome which encodes protein is called the exome
– However, this represents only a small part of the genome
• Much of the human genome controls protein synthesis
– Including the time, speed, and location
• Genes encode 20,325 types of proteins
Gene Expression

Proteins Have
Diverse Functions
in the Body
 Gene Expression
• Transfer of genetic information from DNA to protein is called genetic
expression which occurs in two stages:
1. Transcription
– Synthesizes an RNA molecule
– Information is copied from DNA onto an RNA molecule (inside the nucleus of the
cell)
2. Translation
– Uses the information in the RNA to manufacture a protein by aligning and joining
specified amino acids
– RNA moves from the nucleus to the cytoplasm where it helps to make a
polypeptide (protein)
3. Folding of the protein into specific 3-D form
 Gene Expression
1. Redundancy
– More than one codon can code for the
same amino acid – lots of repetition
2. Continuous
– Code reads as a series of 3-letter codons
without spaces, punctuation or overlap
3. Universal
– Code is virtually the same in all
organisms making is possible to transfer
information
Central Dogma of
Molecular Biology
Central Dogma of
Molecular Biology

• The directional
flow of genetic
information
Transcription
Transcription Factors
• Interact and form an apparatus that
binds DNA at certain sequences
• Initiates transcription at specific sites on
chromosomes
• Respond to signals from outside the cell
• Link the genome to the environment
• Mutations in transcription factors may
cause a wide range of effects
Transcription (STEPS)
• Transcription is described in three steps:
– Initiation
– Elongation
– Termination
• In transcription initiation, transcription
factors and RNA polymerase are
attracted to a promoter
• RNA polymerase joins the complex,
binding in front of the start of the gene
sequence
 Transcription (STEPS)
• In transcription elongation, enzymes
unwind the DNA double helix
– Free RNA nucleotides bond with
exposed complementary bases on
the DNA template strand
– RNA polymerase adds the RNA
nucleotides, in the sequence the
DNA specifies
• A terminator sequence in the DNA
indicates where the gene’s RNA-
encoding region ends
Transcription (STEPS)

• Several mRNAs
may be
transcribed from
the same
template DNA
strand at a time
Transcription (STEPS)
• In eukaryotes, mRNA must exit the
nucleus to enter the cytoplasm
• Several steps process pre-mRNA into
mature mRNA
– A methylated cap is added to the 5’
end
• Recognition site for protein
synthesis
– A poly-A tail is added to the 3’ end
• Necessary for protein synthesis to
begin and stabilizes the mRNA
Transcription (STEPS)
– Splicing occurs
• Introns (“intervening sequences”)
are removed
• Ends of the remaining molecule are
spliced together
• Exons are parts of mRNA that
remain, translated into amino acid
sequences
• Note that introns may outnumber
and outsize exons
– mRNA is proofread and the mature
mRNA is sent out of the nucleus
 Translation
• Assembles a protein
using the information in
the mRNA sequence
• Particular mRNA
codons correspond to
particular amino acids
• Occurs on the ribosome
Genetic Code
• The correspondence
between the chemical
languages of mRNA
and proteins
• In the1960s,
researchers used logic
and clever experiments
on simple genetic
systems to decipher
the genetic code
 Genetic Code
• It is a triplet code
– Using combinations of three
nucleotides, the DNA molecule creates
code words that represent the 20
amino acids
– Each set of three bases is called a codon
• Some amino acids (AA) are coded for by more than
one codon, while others, only by one
• Each set of 3 amino acids is called a reading frame
– Codons are represented by the RNA
base sequences
 Genetic Code
• It is a triplet code
– There are 64 codons
– Altering the DNA sequence by one or
two bases produced a different amino
acid sequence due to disruption in the
reading frame
• Adding a base at one point and deleting a
base at another point disrupted the
reading frame between the sites
Genetic Code
• It is non-overlapping
– In an overlapping DNA sequence,
certain amino acids would follow
others, constraining protein structure
• It includes controls
– Includes directions for starting and
stopping translation
• An open reading frame does not include
a stop codon
Genetic Code
• It is universal
– Evidence that all life evolved from a
common ancestor
• Different codons that specify the same
amino acid are termed synonymous
codons
• Nonsynonymous codons encode different
amino acids
Gene Expression
Example
DNA sequence: T-A-C-A-G-T-A-T-C
1. Find the complimentary RNA sequence
• RNA sequence: A-U-G-U-C-A-U-A-G
2. Match each codon with the amino acid to
get the sequence
• RNA sequence: A-U-G-U-C-A-U-A-G
• AA sequence: Met Ser Stop
methionine(start) – serine – stop
Translation
Building a Protein
• Translation Initiation
– The leader sequence of
the mRNA forms H-
bonds with the small
ribosomal subunit
– The start codon (AUG)
attracts an initiator tRNA
that carries methionine
– This completes the
initiation complex
Translation
Building a Protein
• Translation Elongation
– The large ribosomal subunit joins
GGA bonds to its complementary
anticodon, which is part of a free
tRNA that carries the amino acid
glycine
– Two amino acids attached to their
tRNAs align
Translation
Building a Protein
• Translation Elongation
– Positions of the sites on the ribosome
remain the same, cover different parts of
the mRNA as the ribosome moves
– The P site bears growing amino acid chain
– The A site holds the next amino acid to be
added to the chain
– Amino acids link by a peptide bond, with
the help of rRNA that functions as a
ribozyme
Translation
Building a Protein
• Translation Elongation
– The polypeptide builds one amino acid at
a time
– Each piece is brought in by a tRNA whose
anticodon corresponds to a consecutive
mRNA codon as the ribosome moves
down the mRNA
Translation
Building a Protein
• Translation Termination
– Occurs when a stop codon enters the A
site of the ribosome
– A protein release factor frees the
polypeptide
– The ribosomal subunits separate and are
recycled
– New polypeptide is released
 Translation
Building a Protein
The closer to the end of the gene, the longer the
polypeptide
Multiple
Copies of a
Protein Can be
Made
Simultaneously
 Protein Structure
• Proteins fold into one or more 3-D shapes or
conformations
– Based on attraction and repulsion between
atoms of proteins, and interactions of
proteins with chemicals in the environment
• There are four levels for protein structure
– Primary (1O) structure
– Secondary (2O) structure
– Tertiary (3O) structure
– Quaternary (4O) structure
 Protein Folding
• Proteins begin to fold after the amino
acid chain winds away from the ribosome
– First few amino acids in a protein
secreted in a membrane form a “signal
sequence”
• Leads it and the ribosome into a pore in
the ER membrane
• Not found on proteins synthesized on free
ribosomes
 Protein Folding
• Chaperone proteins
– Stabilize partially folded regions in their correct form
– Prevent a protein from getting stuck in an intermediate form
– Developed into drugs to treat diseases that result from misfolded
proteins
 Protein Misfolding
• Misfolded proteins are tagged with
ubiquitin
• Protein with more than one tag is
taken to a proteasome, a tunnel-
like multiprotein structure
– As the protein moves through
the tunnel, it is straightened and
dismantled
– Proteasomes also destroy
properly-folded proteins that are
in excess or no longer needed
 Protein Misfolding
• Proteins misfold from a mutation,
or by having more than one
conformation
– A mutation alters the attractions
and repulsions between parts of
the protein
– Prion protein can fold into any of
several conformations
• Moreover, it can be passed on to
other proteins upon contact,
propagating like an infectious agent
 Protein Misfolding
• In several disorders that
affect the brain, the
misfolded proteins
aggregate
– The protein masses
that form clog the
proteasomes and
inhibit their function
• Different proteins are
affected in different
disorders
Reference:

• Lewis, Ricki (2015), Human Genetics, Concepts and Applications 11th

Edition