Introduction

• Molecular Genetics: The subfield of biology that studies the molecular structure and function of genes

• Molecular genetics is largely defined by the interplay between three classes of macromolecule: the nucleic
acid molecules, DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), and proteins.
• In organisms and cells, DNA is the genetic (hereditary) material that is transmitted to daughter cells when
cells replicate, and from one generation to the next when organisms reproduce.
Introduction
• Organisms are built according to information encoded in a collection of genes, which are constructed of
DNA.

• Genes are more than storage lockers for information: they constitute the blueprints for constructing
cellular structures, the directions for running cellular activities, and the program or making more of
themselves.

• The human genome consists of large amounts of the chemical deoxyribonucleic acid (DNA) that contains
within its structure the genetic information needed to specify all aspects of embryogenesis, development,
growth, metabolism, and reproduction— essentially all aspects of what makes a human being a
functional organism.

• The human genome is around 3 billion base pair long.

• Remarkably, this vast amount of information is packaged into a set of chromosomes that occupies the space
of a cell nucleus—hundreds of times smaller.
Introduction
• Discovering the mechanisms by which cells use and transmit their genetic information has been one of the
greatest achievements of science in recent decades.

• Appreciation of the importance of genetics to medicine requires an understanding of the nature of the
hereditary material, how it is packaged into the human genome, and how it is transmitted from cell to cell
during cell division and from generation to generation during reproduction.

• The human genome contains approximately 3 billion of these base pairs, which reside in the 23 pairs of
chromosomes within the nucleus of all our cells.
• Each chromosome contains hundreds to thousands of genes, which carry the instructions for making
proteins.
• The Human Genome Project, which worked to determine the sequence of the human genome and identify
the genes that it contains, estimated that humans have between 20,000 and 25,000 genes.
• The estimated genes in the human genome makes an average of three proteins i.e every nucleated cell in the
body carries its own copy of the human genome, which contains, by current estimates, about 25,000 genes.
• But not all genes are used or expressed by these cells.
What is Life Made of?
• Genes which at this point we define simply as units of genetic information, that instruct the cell as to how to
function, consist of DNA organized into a number of rod-shaped organelles called chromosomes in the
nucleus of each cell.

• Organization of life
• Almost every cell in an organism contains the same libraries and the same sets of books.

• Books represent all the information (DNA) that every cell in the body needs so it can grow and carry out its
various functions.
• Nucleus = library
• Chromosomes = bookshelves
• Genes = books
DNA (The Genetic Material) – A Basic Review
• Before the organization of the human genome and it’s chromosomes is considered in detail, it is necessary to
review the nature of the DNA that makes up the genome.

• DNA is a polymeric nucleic acid macromolecule composed nucleotides.

• Nucleotides, each composed of three types of units: a five-carbon sugar - deoxyribose; a nitrogen-
containing base; and a phosphate group polymerize into long polynucleotide chains by 5′-3′
phosphodiester bonds formed between adjacent deoxyribose units.

• The bases are of two types, purines and pyrimidines.

• In DNA, there are two purine bases, adenine (A) and guanine (G), and two pyrimidine bases, thymine (T)
and cytosine (C).

• In the human genome, these polynucleotide chains (in the form of a double helix) are hundreds of
millions of nucleotides long, ranging in size from approximately 50 million base pairs (for the smallest
chromosome, chromosome 21) to 250 million base pairs (for the largest chromosome, chromosome 1).
DNA STRUCTURE (A Basic Review)
DNA STRUCTURE (A Basic Review)
DNA STRUCTURE (A Basic Review)
DNA (The Genetic Material) – A Basic Review
• The helical structure resembles a right-handed spiral staircase in which its two polynucleotide chains run in
opposite directions, held together by hydrogen bonds between pairs of bases: A of one chain paired with T
of the other, and G with C.

• The specific nature of the genetic information encoded in the human genome lies in the sequence of
C’s, A’s, G’s, and T’s on the two strands of the double helix along each of the chromosomes, both in
the nucleus and in mitochondria.

• Because of the complementary nature of the two strands of DNA, knowledge of the sequence of nucleotide
bases on one strand automatically allows one to determine the sequence of bases on the other strand.

• The double stranded structure of DNA molecules allows them to replicate precisely by separation of the two
strands, followed by synthesis of two new complementary strands, in accordance with the sequence of the
original template strands.
DNA (The Genetic Material) – A Basic Review
• Two single nucleic acid strands that can form a double helix with perfect base matching (according to the
base pairing rules given above) are said to have complementary sequences.
• As a result of base pairing rules, the sequence of one DNA strand in a double helix can immediately be used
to predict the base sequence of the complementary strand.
DNA STRUCTURE (A Basic Review)
DNA STRUCTURE (A Basic Review)
DNA Replication – A Basic Review
• Base pairing rules also explain the mechanism of DNA replication.
• In preparation for new DNA synthesis before cell division, each DNA double helix must be unwound using
a helicase.
• During the unwinding process the two individual single DNA strands become available as templates for
making complementary DNA strands that are synthesized in the 5ʹ→3ʹ direction.
• DNA replication therefore uses one double helix to make two double helices, each containing one strand
from the parental double helix and one newly synthesized one (semi-conservative DNA replication).

• Because DNA synthesis occurs only in the 5ʹ→3ʹ direction, one new strand (the leading strand) can be
synthesized continuously; the other strand (the lagging strand) needs to be synthesized in pieces, known as
Okazaki fragments.
• Mammalian cells have very many kinds of DNA-directed DNA polymerases that serve a variety of different
roles, including DNA replication initiation, synthesis of the leading and lagging strands, and also, multiple
roles in DNA repair.
• Our cells also contain specialized DNA polymerases that use RNA as a template to synthesize a
complementary DNA
DNA Replication – A Basic Review
DNA Replication – A Basic Review
Molecular Basis of Genes – A Basic Review
• As a repository of genetic information, DNA must be stably transmitted from mother cell to daughter cells,
and from individuals to their progeny; DNA replication provides the necessary mechanism.
• But within the context of individual cells, the genetic information must also be interpreted to dictate how
cells work.

• Genes are discrete segments of the DNA whose sequences are selected for this purpose, and gene
expression is the mechanism whereby genes are used to direct the synthesis of two kinds of product: RNA
and proteins.

• The first step of gene expression is to use one of the two DNA strands as a template for synthesizing an
RNA copy whose sequence is complementary to the selected template DNA strand.
• This process is called transcription, and the initial RNA copy is known as the primary transcript.
Molecular Basis of Genes – A Basic Review
Molecular Basis of Genes – A Basic Review
• Subsequently, the primary transcript undergoes different processing steps, eventually giving a mature RNA
that belongs to one of two broad RNA classes:
• Coding RNA: RNAs in this class contain a coding sequence that is used to direct the synthesis of
polypeptides (the major component of proteins) in a process called translation.
• This type of RNA has traditionally been called a messenger RNA (mRNA) because it must transport
genetic instructions to be decoded by the protein synthesis machinery.

• Noncoding RNA: All other mature functional RNAs fall into this class, and here the RNAs, not proteins,
are the functional endpoint of gene expression.
• Noncoding RNAs have a variety of different roles in cells.
Molecular Basis of Genes – A Basic Review
• In all forms of life, genetic information is interpreted in what initially seemed to be one direction only:
DNA→RNA→protein, a principle that became known as the central dogma of molecular biology.
• However, certain DNA polymerases, known as reverse transcriptases, were found initially in certain types
of viruses, and as their name suggests they reverse the flow of genetic information by making a DNA copy
of an RNA molecule.
• Cells, too, have their reverse transcriptases.
• In addition, RNA can sometimes also be used as a template to make a complementary RNA copy.
• So, although genetic information in cells mostly flows from DNA to RNA to protein, the central dogma is
no longer strictly valid.

• We will explore gene expression (including protein synthesis) in greater detail in later lessons.
Molecular Basis of Genes – A Basic Review
DNA becomes Chromosomes
• Each chromosome in the cells of complex multicellular organisms normally contains a single, immensely
long DNA double helix.

• For example, an average-sized human chromosome contains a single DNA double helix that is about 4.8
cm long with 140 million nucleotides on each strand; that is, 140 million base pairs (140 megabases
(Mb)) of DNA.
• To appreciate the difficulty in dealing with molecules this long in a cell that is only about 10 μm across,
imagine a model of a human cell 1 meter across (a 105-fold increase in diameter).
• Now imagine the problem of fitting into this 1-meter-wide cell 46 DNA double helices that when scaled
up by the same factor would each be just 0.2 mm thick but on average 4.8 km (about 3 miles) long.

• Then there is the challenge of replicating each of the DNA molecules and arranging for the cell to divide in
such a way that the replicated DNA molecules are segregated equally into the two daughter cells.
• All this must be done in a way that avoids any tangling of the long DNA molecules.
DNA becomes Chromosomes
• To manage nuclear DNA molecules efficiently and avoid any tangling, they are complexed with various
proteins and sometimes RNAs to form chromatin that undergoes different levels of coiling and compaction,
forming chromosomes.

• In interphase—the stages of the cell cycle other than mitosis—the nuclear DNA molecules are still in a very
highly extended form and normally the very long slender interphase chromosomes remain invisible under
the light microscope.

• But even in interphase cells, the 2-nm-thick double helix is subject to at least two levels of coiling.

• First, the double helix is periodically wound round a specialized complex of positively charged histone
proteins to form a 10 nm nucleosome filament.

• The nucleosome filament is then coiled into a 30 nm chromatin fiber that undergoes looping and is
supported by a scaffold of non-histone proteins
DNA becomes Chromosomes
DNA becomes Chromosomes
• During interphase most chromatin exists in an extended state (euchromatin) that is dispersed through the
nucleus.
• Euchromatin is not uniform, however—some euchromatic regions are more condensed than others, and
genes may or may not be expressed, depending on the cell type and its functional requirements.

• Some chromatin, however, remains highly condensed throughout the cell cycle and is generally genetically
inactive (heterochromatin).
• As cells prepare to divide, the chromosomes need to be compacted much further to maximize the chances of
correct pairing and segregation of chromosomes into daughter cells.

• Packaging of DNA into nucleosomes and then the 30 nm chromatin fiber results in a linear condensation
of about fifty fold.
• During the M (mitosis) phase, higher-order coiling occurs, so that DNA in a human metaphase chromosome
is compacted to about 1/10,000 of its stretched-out length. As a result, the short, stubby metaphase
chromosomes are readily visible under light microscopes.
Organization of the Human Chromosome
• Except during cell division, chromatin is distributed throughout the nucleus and is relatively homogeneous
in appearance under the microscope; when diffuse, chromatin is referred to as euchromatin.
• When a cell divides, however, its genome condenses to appear as microscopically visible chromosomes;
when condensed and readily visible, as heterochromatin.
Organization of the Human Chromosome
• Chromosomes are not naked DNA double helices, within each cell, the genome is packaged as chromatin,
in which genomic DNA is complexed with several classes of chromosomal proteins (histone).
• Any protein that is structurally associated with nucleic acid is referred to as nucleoprotein.

• Chromosomes are thus visible as discrete structures only in dividing cells, although they retain their
integrity between cell divisions.
Organization of the Human Chromosome
• The DNA molecule of a chromosome exists in chromatin as a complex with a family of basic
chromosomal proteins called histones and with a heterogeneous group of non-histone proteins that are
much less well characterized but that appear to be critical for establishing a proper environment to ensure
normal chromosome behavior and appropriate gene expression.

• Five major types of histones play a critical role in the proper packaging of chromatin.
• Two copies each of the four core histones H2A, H2B, H3, and H4 constitute an octamer, around which a
segment of DNA double helix winds, like thread around a spool (Fig. 2-6) and H1.
• Approximately 140 base pairs of DNA are associated with each histone core, making just under two turns
around the octamer.
• After a short (20- to 60–base pair) “spacer” segment of DNA, the next core DNA complex forms, and so
on, giving chromatin the appearance of beads on a string.
Organization of the Human Chromosome
 Organization of the Human Chromosome
• Each complex of DNA with core histones is called a nucleosome, which is the basic structural unit of
chromatin, and each of the 46 human chromosomes contains several hundred thousand to well over a
million nucleosomes.
• The fifth histone, H1, appears to bind to DNA at the edge of each nucleosome, in the internucleosomal
spacer region.
• The amount of DNA associated with a core nucleosome, together with the spacer region, is about 200 base
pairs.
• During the cell cycle, as we will see later in this chapter, chromosomes pass through orderly stages of
condensation and decondensation.

• However, even when chromosomes are in their most decondensed state, in a stage of the cell cycle called
interphase. The long strings of nucleosomes are themselves compacted into a secondary helical chromatin
structure that appears under the electron microscope as a thick, 30-nm-diameter fiber (about three times
thicker than the nucleosomal fiber).
 Organization of the Human Chromosome
• This cylindrical “solenoid” fiber (from the Greek solenoeides, “pipe shaped”) appears to be the
fundamental unit of chromatin organization.
• The enormous amount of genomic DNA packaged into a chromosome can be appreciated when
chromosomes are treated to release the DNA from the underlying protein scaffold.
• When DNA is released in this manner, long loops of DNA can be visualized, and the residual scaffolding
can be seen to reproduce the outline of a typical chromosome.
Organization of the Human Chromosome
Organization of the Human Chromosome
Organization of the Human Chromosome
 Organization of the Human Genome
• The overall significance of this functional organization is that chromosomes are not just a random
collection of different types of genes and other DNA sequences.
• Some chromosome regions, or even whole chromosomes, are high in gene content (“gene rich”), whereas
others are low (“gene poor”).
• Certain types of sequence are characteristic of the different structural features of human chromosomes.
• The clinical consequences of abnormalities of genome structure reflect the specific nature of the genes
and sequences involved.
• Thus, abnormalities of gene rich chromosomes or chromosomal regions tend to be much more severe
clinically than similar-sized defects involving gene-poor parts of the genome.
• As a result of knowledge gained from the Human Genome Project, it is apparent that the organization of
DNA in the human genome is far more varied than was once widely appreciated.
Organization of the Human Genome
• Of the 3 billion base pairs of DNA in the genome, less than 1.5% actually encodes proteins and only about
5% is thought to contain regulatory elements that influence or determine patterns of gene expression
during development or in different tissues.

• Only about half of the total linear length of the genome consists of so-called single copy or unique DNA,
that is, DNA whose nucleotide sequence is represented only once (or at most a few times).
• The rest of the genome consists of several classes of repetitive DNA and includes DNA whose nucleotide
sequence is repeated, either perfectly or with some variation, hundreds to millions of times in the genome.

• Whereas most (but not all) of the estimated 25,000 genes in the genome are represented in single copy
DNA, sequences in the repetitive DNA fraction contribute to maintaining chromosome structure and are
an important source of variation between different individuals; some of this variation can predispose to
pathological events in the genome.
What is Life Made of?
• Each species has a characteristic chromosome complement in terms of the number and the morphology of
the chromosomes that make up its genome (karyotype).

• The number of chromosomes has nothing to do with what or how complicated something is. And neither
does the number of genes or the number of base pairs of DNA.
• What matters is what those genes are and how the cells and the organism use its set of genes.
• This is what makes a dog a dog and a dove a dove even though they both have 78 chromosomes. Which
of course is way more than we do!
What is Life Made of?
• The genes are in linear order along the chromosomes, each gene having
a precise position or locus.
• A gene map is the map of the chromosomal location of the genes and is
characteristic of each species.

• The study of chromosomes, their structure, and their inheritance is

called cytogenetics.
• Except for cells that develop into gametes (the germline), all cells that
contribute to one’s body are called somatic cells (soma, body).

• The genome contained in the nucleus of human somatic cells consists

of 46 chromosomes, arranged in 23 pairs.
• Of those 23 pairs, 22 are alike in males and females and are called
autosomes, numbered from the largest to the smallest.

• The remaining pair comprises the sex chromosomes: two X

chromosomes in females and an X and a Y chromosome in males.
• Each chromosome carries a different subset of genes that are arranged
linearly along its DNA.
Chromosomes
• At the submicroscopic level, chromosomes consist of an extremely
elaborate complex, made up of supercoils of DNA.
• Members of a pair of chromosomes (referred to as homologous
chromosomes or homologues) carry matching genetic information; that
is, they have the same genes in the same sequence.
• At any specific locus, however, they may have either identical or slightly
different forms of the same gene, called alleles.

• One member of each pair of chromosomes is inherited from the father,

the other from the mother.
• Normally, the members of a pair of autosomes are microscopically
indistinguishable from each other.

• In females, the sex chromosomes, the two X chromosomes, are likewise

largely indistinguishable. In males, however, the sex chromosomes
differ.
• One is an X, identical to the X’s of the female, inherited by a male from
his mother and transmitted to his daughters; the other, the Y
chromosome, is inherited from his father and transmitted to his sons.
Chromosomes
• In addition to the nuclear genome, a small but important part of the human genome resides in mitochondria
in the cytoplasm.
• The mitochondrial chromosome, to be described later, has a number of unusual features that distinguish it
from the rest of the human genome.
• The Mitochondrial Chromosome a small but important subset of genes encoded in the human genome
resides in the cytoplasm in the mitochondria.

• Mitochondrial genes exhibit exclusively maternal inheritance.

• Human cells can have hundreds to thousands of mitochondria, each containing a number of copies of a
small circular molecule, the mitochondrial chromosome.
• The mitochondrial DNA molecule is only 16 kb in length (less than 0.03% of the length of the smallest
nuclear chromosome!) and encodes only 37 genes.

• The products of these genes function in mitochondria, although the majority of proteins within the
mitochondria are, in fact, the products of nuclear genes.
• Mutations in mitochondrial genes have been demonstrated in several maternally inherited as well as
sporadic disorders.
Organization of the Human Chromosome
Chromosomes
• The composition of genes in the human genome, as well as the determinants of their expression, is specified
in the DNA of the 46 human chromosomes in the nucleus plus the mitochondrial chromosome.

• Each human chromosome consists of a single, continuous DNA double helix; that is, each chromosome
in the nucleus is a long, linear double-stranded DNA molecule, and the nuclear genome consists, therefore,
of 46 DNA molecules (i.e for the 46 chromosomes), totaling more than 6 billion nucleotides.

• At this time each chromosome can be seen to consist of two identical strands known as chromatids, or sister
chromatids, which are the result of DNA replication having taken place during the S (synthesis) phase of the
cell cycle.
• These sister chromatids can be seen to be joined at a primary constriction known as the centromere.
Centromeres consist of several hundred kilobases of repetitive DNA and are responsible for the movement
of chromosomes at cell division.

• Each centromere divides the chromosome into short and long arms, designated p (= petite) and q (‘g’ =
grande), respectively
Chromosomes
p-arm

q-arm
Monads

Dyads Tetrad
Chromosomes
• Although all eukaryotes have chromosomes, in the interphase between divisions, they are spread out or
diffused throughout the nucleus and are usually not identifiable.
• Each chromosome, with very few exceptions, has a distinct attachment point for fibers (microtubules) that
make up the mitotic and meiotic spindle apparatuses.

• The attachment point occurs at a constriction in the chromosome termed the centromere, which is
composed of several specific DNA sequences.
• The kinetochore is the proteinaceous structure on the surface of the centromere to which microtubules of
the spindle attach.
Chromosomes
Chromosomes
Chromosomes
• Chromosomes can be classified according to whether the centromere is in the middle of the chromosome
(metacentric), at the end of the chromosome (telocentric), very near the end of the chromosome
(acrocentric), or somewhere in between (subtelocentric or submetacentric).

• For any chromosome, the position of the centromere is fixed. In various types of preparations, dark bands
(chromomeres) are visible.

• Most higher eukaryotic cells are diploid; that is, all their chromosomes occur in pairs. One member of each
pair came from each parent.
• Haploid cells, which include the reproductive cells (gametes), have only one copy of each chromosome.

• In the diploid state, members of the same chromosome pair are referred to as homologous chromosomes
(homologues); the two make up a homologous pair.

• The total chromosomal complement of a cell, the karyotype, can be photographed during mitosis and
rearranged in pairs to take a picture called a karyotype or idiogram .
Chromosomes
Chromosomes
Chromosomes
• From the idiogram it is possible to see whether the chromosomes have any abnormalities and to identify the
sex of the organism.

• As you can see below, all of the homologous pairs are made up of identical partners, and are thus referred to
as homomorphic chromosome pairs.
• A potential exception is the sex chromosomes, which in some species are of unequal size and are therefore
called a heteromorphic chromosome pair.
• The number of chromosomes individuals of a particular species possess is constant.

• Some species exist mostly in the haploid state or have long haploid intervals in their life cycle.
• For example, pink bread mold, Neurospora crassa, a fungus, has a chromosome number of seven (n=7) in
the haploid state.
• Its diploid number is, of course, fourteen (2n=14). The diploid chromosome numbers of several species
appear in the figure below.
Chromosomes
Cells
Cells
Cells
Cells
Key Fundamental Concepts
• Cells are of two basic types: eukaryotic and prokaryotic.
• Structurally, cells consist of two basic types, although, evolutionarily, the story is more complex.
• Prokaryotic cells lack a nuclear membrane and possess no membrane-bounded cell organelles, whereas
eukaryotic cells are more complex, possessing a nucleus and membrane-bounded organelles such as
chloroplasts and mitochondria.

• The gene is the fundamental unit of heredity.

• The precise way in which a gene is defined often varies, depending on the biological context. At the
simplest level, we can think of a gene as a unit of information that encodes a genetic characteristic.
• We will enlarge this definition as we learn more about what genes are and how they function.

• Genes come in multiple forms called alleles.

• A gene that specifies a characteristic may exist in several forms, called alleles.
• For example, a gene for coat color in cats may exist in an allele that encodes black fur or an allele that
encodes orange fur.
Key Fundamental Concepts
• Genes confer phenotypes.
• One of the most important concepts in genetics is the distinction between traits and genes.
• Traits are not inherited directly. Rather, genes are inherited and, along with environmental factors, determine
the expression of traits.
• The genetic information that an individual organism possesses is its genotype; the trait is its phenotype. For
example, the A blood type is a phenotype; the genetic information that encodes the blood-type-A antigen is
the genotype.
• Genetic information is carried in DNA and RNA.
• Genetic information is encoded in the molecular structure of nucleic acids, which come in two types:
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
• Nucleic acids are polymers consisting of repeating units called nucleotides; each nucleotide consists of a
sugar, a phosphate, and a nitrogenous base.
• The nitrogenous bases in DNA are of four types (abbreviated A, C, G, and T), and the sequence of these
bases encodes genetic information.
• DNA consists of two complementary nucleotide strands. Most organisms carry their genetic information in
DNA, but a few viruses carry it in RNA.
• The four nitrogenous bases of RNA are abbreviated A, C, G, and U.
Key Fundamental Concepts
• Genes are located on chromosomes.
• The vehicles of genetic information within a cell are chromosomes, which consist of DNA and associated
proteins.
• The cells of each species have a characteristic number of chromosomes; for example, bacterial cells
normally possess a single chromosome; human cells possess 46; pigeon cells possess 80.
• Each chromosome carries a large number of genes.

• Chromosomes separate through the processes of mitosis and meiosis.

• The processes of mitosis and meiosis ensure that each daughter cell receives a complete set of an organism’s
chromosomes.
• Mitosis is the separation of replicated chromosomes in the division of somatic (nonsex) cells.Meiosis is the
pairing and separation of replicated chromosomes in the division of sex cells to produce gametes
(reproductive cells).
Key Fundamental Concepts
• Genetic information is transferred from DNA to RNA to protein.
• Many genes encode traits by specifying the structure of proteins. Genetic information is first transcribed
from DNA into RNA, and then RNA is translated into the amino acid sequence of a protein.

• Mutations are permanent, heritable changes in genetic information.

• Gene mutations affect the genetic information of only a single gene; chromosome mutations alter the
number or the structure of chromosomes and therefore usually affect many genes.

• Some traits are affected by multiple factors.

• Some traits are influenced by multiple genes that interact in complex ways with environmental factors.
• Human height, for example, is affected by hundreds of genes as well as environmental factors such as
nutrition.

• Evolution is genetic change.

• Evolution can be viewed as a two-step process: first, genetic variation arises and, second, some genetic
variants increase in frequency, whereas other variants decrease in frequency.
Key Fundamental Concepts