NUCLEIC ACIDS

STRUCTURE
Eukaryotic Cell

Bounded by a nuclear membrane having pores

connecting it with the ER

Contains 1 or more paired, linear

chromosomes composed of DNA associated
with histone proteins

Nucleolus present

Nuclear body is called a nucleus

Prokaryotic Cell

Not bounded by a nuclear membrane

Usually contains 1 circular chromosome

composed of DNA associated with
histone-like proteins

No nucleolus

Nuclear body is called a nucleoid

DNA as Genetic Material
 What is a genome?

• A genome is composed of all the DNA in an

organism.

• includes all the genes which carry the

information for making the proteins required
by the organism
How big is the human genome?
 How big is the human genome?

Nuclear Genome
• about 3 billion bases organized into
chromosomes

• the nucleus of most human cells contains two

sets of chromosomes
= one set given by each parent
= each set : 23 chromosomes
22 autosomes +
an X or Y sex chromosome
Nuclear Genome

Size 3300 Mb
No. of diff. DNA molecules 23 (XX), 24 (XY) linear

Total number DNA molecules 23 in haploid cells

per cell 46 in diploid cells
Number of genes 30,000 – 40,000
Gene density 1/40 kb

Repetitive DNA large fraction

Transcription most genes transcribed

individually
Introns present in most

Inheritance Mendelian on X, autosomes

paternal on Y
Mitochondrial Genome

Size 16.6 kb
No. of diff. DNA molecules 1, circular

Total number DNA molecules thousands

per cell
Number of genes 37
Gene density 1/0.45 kb

Repetitive DNA very little

Transcription continuous,
multiple genes
Introns absent

Inheritance maternal
Mitochondrial
Genome

 Circular

 37 genes
= 13 polypeptides
= 22 tRNAs
= 2 rRNAs
Limited Autonomy of the Mitochondrial Genome

Mitochondrial Genome Nuclear Genome

Components of OP
System 13 subunits > 80 subunits
I NADH dehydrogenase 7 subunits >41 subunits
II Succinate CoQ reductase 0 subunit 4 subunits
III Cytochrome b-c complex 1 subunit 10 subunits
IV Cytochrome c oxidase 3 subunits 10 subunits
complex
V ATP synthase complex 2 subunits 14 subunits
Components of Protein
Synthesis Apparatus 24 About 80
tRNA components 22 tRNAs none
rRNA components 2 rRNAs none
Ribosomal proteins none About 80
Other Mitochondrial None all
Proteins
Mitochondria & Chloroplast Genomes

• Their circular genomes are a notable exception to

the rule that eukaryotic chromosomes are linear.

• However, this nicely fit into the dichotomy that

eukaryotic chromosomes are linear and bacterial
chromosomes are circular because these organelles
seem to have evolved from entrapped bacteria.

• Endosymbiotic theory
Nucleic Acids
• Chromosomes
• Contain genetic information
• Found primarily in nucleus

• Chromatin
• Tightly packed DNA and histones
• Can be seen during cell division
Nucleic Acids
• Deoxyribonucleic Acid (DNA)
• Found in nucleus (in chromosomes)
• Contain genes which contain genetic information

• Ribonucleic Acid (RNA)

• Some found in nucleus (but not in chromosomes)
• Also found in cytoplasm
Nucleic Acid Structure
• DNA has a double helix structure
• Phosphates on outside
• Complementary Base Pairs on inside

• RNA is single stranded

• Messenger RNA (mRNA)

• Transfer RNA (tRNA) has some double stranded

loops
 DNA
• Deoxyribonucleic acid

• Its importance lies in it being the

GENETIC MATERIAL

• Discovered by Johann Friedrich

Miescher in 1869
Evidences: DNA as genetic material

• 1867
• Gregor Mendel noted inheritance of traits in peas

• 1903
• WS Sutton proposed the chromosome theory

• 1928
• Frederick Griffith noted transformation
• 1944
• Oswald Avery, Colin MacLeod and Maclyn McCarty
confirmed that the genetic material was DNA
• 1952
• The “blender” experiment
• Second experiment that proves
DNA is the genetic material

• T2 Phages
• Viruses infecting E. coli
• Protein and DNA
• To replicate, the genetic
material should go inside
the bacteria
• Erwin Chargaff
• Observed the “Chargaff rules”
• 1950s
• The composition of DNA is being known
• Composed of deoxyribonucleotides
• Phosphate group
• Deoxyribose
• Nitrogenous bases
 BUILDING
MOLECULE BLOCK MAJOR FUNCTION

DNA Nucleotides Genetic Material

Template for Protein

RNA Nucleotides
synthesis

Cell Structure and

Protein Amino acids
Function

Membrane
Lipid Fatty acids
Component

Carbohydrate Sugars Energy Production

What Makes Up a Nucleotide?

 Purine and Pyrimidine Bases

Functional Groups
Functional Groups
Properties of free Purines & Pyrimidines

1. Nonpolar

2. Weakly basic

3. Absorb strongly at 250-280nm

4. Easily separated by chromatography &

electrophoresis
 Sugars found in nucleosides/nucleotides
Base + Sugar = NUCLEOSIDE
 Nomenclature:

Base Nucleoside Deoxynucleoside

adenine adenosine deoxyadenosine

guanine guanosine deoxyguanosine

cytosine cytidine deoxycytidine

uracil uridine (not found in DNA)

thymidine (not found in RNA) (deoxy)thymidine*

Properties of Nucleosides

1. More soluble in water

2. Separated chromatographically

3. Relatively stable in alkali

4. Purine nucleosides easily hydrolyzed by acid

5. Pyrimidine nucleosides hydrolysis-resistant to

acids
Base + Sugar + Phosphate= NUCLEOTIDE
Base + Sugar + Phosphate= NUCLEOTIDE
Base + Sugar + Phosphate= NUCLEOTIDE
Nomenclature
Base Nucleoside Nucleotide

Adenine (Ade) Adenosine (A) Adenylic Acid; Adenosine 5’-

phosphate; 5’-AMP;
pA
Guanine (Gua) Guanosine (G) Guanylic Acid; Guanosine 5-
phosphate; 5’-GMP;
pG
Cytosine (Cyt) Cytidine (C) Cytidylic Acid;
Cytidine 5’-phosphate;
5’-CMP;
pC
Thymine (Thy) Thymidine Thymidylic Acid;
Thymidine 5’-phosphate
5’-TMP;
pT

Insert “deoxy-” in names or “d” in abbreviation if sugar is in deoxyribose form.

Reduction of ribonucleotides to
deoxynucleotides

= usually occurs at the diphosphate

level
= requires three proteins
thioredoxin reductase
thioredoxin
ribonucleotide reductase

= NADPH provides reducing power to

the thioredoxin reductase
Reduction of ribonucleotides to
deoxynucleotides
Functions of Nucleotides

1. Source of energy

2. Precursors of DNA and RNA

3. Regulatory signals

4. Components of coenzymes

5. High-energy intermediates
Adenosine Triphosphate (ATP)
Cyclic AMP
Coenzyme A Flavin Adenine Dinucleotide
(FAD)
Nicotinamide Adenine Nicotinamide Adenine
Dinucleotide (NAD+) Dinucleotide Phosphate
(NADP+)
Nucleic Acids are nucleotide polymers
3’ to 5’ Phosphodiester Bond
Genetic Code for sequence
DNA 2° Structure
• Based on two primary
sources of information
• Irwin Chargaff: A = T
and C = G

• X-ray diffraction
picture of DNA taken
by Rosalind Franklin
Secondary Structures of Nucleic Acids
DNA Structure
Watson and Crick Double Helix Model

= two strands, antiparallel

= right-handed helix
= sugar phosphate backbone
= four different bases ( A, C, T, G )
= complementary base pairing

A: T
G: C
DNA Structure
Complementary Base Pairs
• Must be one purine and one pyrimidine to fit
properly
• Two purines too big
• Two pyrimidines too small

• Not every purine-pyrimidine pair forms naturally

Complementary Base Pairs

• 2 H-bonds

• 3 H-bonds
Base pairing is specific and stable
= addition of
deoxyribo-
nucleotide
to 3’ OH end

= “high energy”
phosphate
bond
Double stranded DNA is a dynamic structure

The higher the GC content of a molecule, the higher

the melting temperature
Secondary structures of DNA
• Helical
• The DNA forms a continuous helical 3-dimensional form
• Have 2 grooves - major and minor
• The helix has precise measurements
• Forms
• B-DNA –most common in physiological conditions
• A-form - Preferred when hydration is high
• Z-form –left-handed
Forms of DNA
Characteristics of different forms of nucleic
acid helices
Feature B-DNA A-DNA Z-DNA
Type of helix Right-handed Right-handed Left-handed
Helical diameter 2.37 2.55 1.84
(nm)
Rise per base pair 0.34 0.29 0.37
(nm)
Distance per 3.4 3.2 4.5
complete turn
(pitch) (nm)
Number of base 10 11 12
pairs per
complete turn
Topology of major Wide, deep Narrow, deep Flat
groove
Topology of minor Narrow, shallow Broad, shallow Narrow, deep
groove
Forces stabilizing helix
• Base stacking
• Most important
• Hydrophobic interaction among bases
• Van der Waals forces among bases

• H-bonding among bases

Higher Structure of DNA
• Coiling of DNA around histones

• Nucleosome
• DNA molecules (with – charge) and histones (with +
charge) attract each other
• A core of eight histone molecules around which the
DNA helix is wrapped
• Nucleosomes are condensed into chromatin
Nucleosomes
Higher Structure of DNA
• Chromatin fibers
• Organized into loops and then bands in the
superstructure of chromosomes
Chromatin Fibers
Levels of DNA
Packaging
DNA Structure and Organization

= DNA is long and

unbranched

= Packaged into
chromosomes

total : 1.7 – 8.5 cm

Chromosomes
Nucleic Acids and Heredity
• Chromosomes exist in pairs (23 pairs in humans)

• Inherit one DNA copy from each parent.

• Most cells in our body contain copies of both.

Nucleic Acids and Heredity
• Genetic information is carried in the sequence of
bases along the DNA strands.

• Information is passed to daughter cells when cell

divides.
What is a Gene?

• An inheritable trait associated with a

discrete linear sequence or region of
DNA that codes for a polypeptide
chain or specifies an RNA molecule

• A transcriptional unit

• The smallest unit of heredity

Gene
• A segment of DNA that carries a base sequence
that directs the synthesis of a particular protein,
tRNA or mRNA

• There are many genes in one DNA molecule

• In bacteria the gene is continuous
• In higher organisms the gene is discontinuous
Exons VS. Introns
• Exon: a section of DNA that, when transcribed,
codes for a protein or RNA

• Intron: a section of DNA that does not code for

anything functional
Gene Structure

• Exon

• Intron

• Regulatory Elements
• Promoter
• Enhancer
• DNA-binding site
Bacteria vs. Eukaryotic Gene
Gene Structure
What is a Gene Locus?
DNA and RNA
• The three differences in structure between DNA
and RNA are
• DNA bases are A, G, C, and T; the RNA bases are A, G,
C, and U
• The sugar in DNA is 2-deoxy-D-ribose; in RNA it is D-
ribose
• DNA is always double stranded; there are several kinds
of RNA, all of which are single-stranded
RNA
• RNA molecules are classified according to their
structure and function
RN A type S ize Function
Mess enger 750 bas e pairs directs amino acid
(mRN A ) on average seq uence of protein s
Transfer from 73 to 93 transp orts amino acids
(tRN A) bas e pairs to the site of p rotein
synth esis
Ribosomal very large; combines w ith proteins
(rRNA ) MW up to 106 to form ribosomes

Ribozymes very large catalyze cleavage of part

(catalytic RN A) of th eir ow n seq uences
in mRN A and tRN A
Other RNAs
 RNA molecules are classified according to their
structure and function

 snRNA – small nuclear RNA (100-200 b)

Combine to make snRNPs to help processing of mRNA for
export from nucleus

 miRNA – microRNA
Bind to mRNA in development

 siRNA – small interfering RNA

Knock out mRNA for genes that are undesirable
mRNA
tRNAs

= about 60 - 95 nucleotides long, includes specific

nucleotides (dihydro-uridine, pseudo-uridine)

= cloverleaf-like secondary structure consisting of

a stem and three main loops

= larger loop include a specific nucleotide triplet

(anticodon) bind to complementary codon
in mRNA.

= displays a tertiary L-like structure which interacts

with ribosomes

= pick up free amino acids in cytoplasm

tRNA as Adaptor Molecule
tRNAs

= the stem ends in 3' by the sequence ...CCA

attachment site for an amino acid

= each tRNA is coupled to the amino acid in

accordance with its anticodon

= the coupling between a given tRNA and the

corresponding amino acid is catalyzed by
a specific aminoacyl-tRNA synthetase
rRNAs

= major constituents of ribosomes

= ribosome :
- holds the mRNA in place
- matches the anti-codon of a tRNA carrying
appropriate amino acid to the
complementary codon of the mRNA
- catalyzes formation of peptide bond
- consists of two subunits of different size
containing rRNAs arranged with
specific proteins
- both rRNAs and associated proteins are
slightly different in prokaryotes
vs eukaryotes
Ribosome
Structure
Ribosome Structure