Master's Degree curriculum in "Food and Beverage Innovation and Management" (FABIAM)

Course
Genetic Resources and Food Traceability

Overview of GENETICS: NUCLEIC ACIDS (DNA and RNA)

Lecturer
Dr. Elena Bitocchi
e.bitocchi@univpm.it
Ancona, 20 february 2020
What is DNA?
DNA is a molecule that contains the
instructions an organism needs to develop,
live and reproduce. These instructions are
found inside every cell, and are passed down
from parents to their children.

The book of life!

https://www.ted.com/
https://www.ted.com/about/our-organization
TED TALKS: Riccardo Sabatini
https://www.ted.com/talks/riccardo_sabatini_how_to_read_the_genome_and_buil
d_a_human_being
 DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)
belong to a class of macromolecules called NUCLEIC ACIDS;
they present different level of complexity.
1. They are made up of monomers of Nucleotides
NUCLEOTIDES

2. Nucleotides are linked to form a Single strand

STRAND of DNA (or RNA)

3. Two strands of DNA form a DOUBLE

HELIX Double helix

4. The double helix interact with

proteins to build the 3-dimensional
structure of CHROMOSOMES

3-dimensional structure
• Nucleotides are the basic structural unit and building block
for DNA and RNA

• Nucleotides consist of 3 components

– One or more phosphate groups

– 5-carbon sugar
– Nitrogenous base
The nitrogen bases form a bond between their 1' nitrogen and the 1' -OH group
of the deoxyribose. This type of bond is called a glycosidic bond.

The phosphate group forms a bond with the deoxyribose sugar through an ester
bond between one of its negatively charged oxygen groups and the 5' -OH of the
sugar
Nucleotides join together through phosphodiester linkages between the 5' and 3' carbon
atoms to form nucleic acids. The 3' -OH of the sugar group forms a bond with one of the
negatively charged oxygens of the phosphate group attached to the 5' carbon of another
sugar. When many of these nucleotide subunits combine, the result is the large single-
stranded polynucleotide or nucleic acid.
 5’ end 3’ end

3’ end 5’ end

The two strands are ANTIPARALLEL, the chains run in opposite directions:
One strand 5’  3’ orientation and the other 3’  5’
3’ 5’
3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’

T T A G C G
A A T C G C

5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’

5’ 3’

Polynucleotide chain
Exercise

Which is the complementary sequence of the following?

5’ - A T G C G G G T T A C A T C G T C G T A - 3’

a) 5’ - T A C G A C G A T G T A A C C C G C A T - 3’
b) 5’ - T A C G C C C A A T G T A G C A G C A T - 3’
c) 5’ - A T G C G G G T T A C A T C G T C G T A - 3’
d) a) and b)
e) b) and c)
Exercise

Which is the complementary sequence of the following?

5’ - A T G C G G G T T A C A T C G T C G T A - 3’

a) 5’ - T A C G A C G A T G T A A C C C G C A T - 3’
b) 5’ - T A C G C C C A A T G T A G C A G C A T - 3’
c) 5’ - A T G C G G G T T A C A T C G T C G T A - 3’
d) a) and b)
e) b) and c)
 The double helix of DNA

– The two helical polynucleotide chains are coiled around a

common axis

– The sugar-phosphate backbones are on the outside and,

therefore, the purine and pyrimidine bases lie on the inside of
the helix

– The bases are nearly perpendicular to the helix axis, and

adjacent bases are separated by 3.4 Å. The helical structure
repeats every 34 Å, so there are 10 bases (= 34 Å per repeat/3.4
Å per base) per turn of helix. There is a rotation of 36 degrees
per base (360 degrees per full turn/10 bases per turn). The
diameter of the helix is 20 Å

– The helix is right-handed

– A major and minor groove
result from the unequal
spacing of the phosphate-
sugar backbone

– Proteins can link in

correspondence of these
grooves, interacting with a
particular sequence of DNA
DNA polymers can be very large molecules
containing millions to hundreds of millions of
nucleotides

The size of an individual gene or an organism's

entire genome is often measured in base pairs
bp, or kb (kilo bases, that is 1,000 bp)
 …… and what about RNA
• The primary structure of an RNA strand is much
like that of a DNA strand

• RNA strands are typically several hundred to

several thousand nucleotides in length, usually
single-stranded

• RNA typically copied from DNA by the process

called transcription; a single strand of DNA (the
template strand) is used to synthesize RNA
Although usually single-stranded, RNA molecules can form short
double-stranded helical regions. This secondary structure is due to
complementary base-pairing, A to U and C to G.
The structure of DNA: https://www.youtube.com/watch?v=o_-6JXLYS-k
Where is DNA located?
There are two basic types of cells,
prokaryotic cells and eukaryotic cells. The
main difference between eukaryotic and
prokaryotic cells is that eukaryotic cells
have a nucleus. The nucleus is where cells
store their DNA, which is the genetic
material. The nucleus is surrounded by a
membrane. Prokaryotic cells do not have a
nucleus. Instead, their DNA floats around
inside the cell.
Prokaryotes
Prokaryotic cells are defined by their lack of membrane bound organelles; thus the DNA
floats around inside the cell, the cytoplasm, and occupies an irregular sub-region called the
NUCLEOID.
Nucleoid is not a 'true' nucleus because the DNA is not surrounded by a membrane

Nucleoid
 Eukaryotes
The eukaryotic cells are more complex than prokaryotic ones because of specialized
organelles. The DNA is mainly localized in the NUCLEUS (nuclear DNA)

DNA is present also in organelles in cytoplasm, in particular in MITOCHONDRIA

(mitochondrial DNA) and, only in plants, in CHLOROPLASTS (plastidial DNA)
 GENOME
The genome is all the genetic material contained in a cell

 25kb per page

 1,500 pages per
volume
 C value
The total amount of DNA of an aploid genome is the C VALUE; it can be measured in
weight or in basepairs

Saccharomyces cerevisiae Phaseolus vulgaris

17 million of bp (17Mb) 550 million of bp
(650Mb)

Drosophila
melanogaster Zea mais
180 million of bp 6,6 billion of bp
(6600Mb)
(180Mb) HUMAN 3,0 billion of bp (3000Mb)

You might expect more complex organisms to have

progressively larger genomes, but eukaryotic genome size Value C parodox
fails to correlate well with apparent complexity
 3.4 X 109 bp 1.5 x 1010 bp 6.8 x 1011 bp Amoeba
Homo sapiens Allium cepa dubia
Some phila have a rather costant genome size (es. birds, reptiles and mammals); in other
cases, the C value within philum can vary up to 100 folds.
Phylogenetically closely related species can have very different C value

758 Mbp

1,540 Mbp 1,125 Mbp

758 Mbp 1,491 Mbp 562 Mbp

 Eukaryotic genomes have a very low gene density: on average, the
proteincoding genes occupy only 24% of the entire genome

Example, HUMAN GENOME

 How can we explain this excess of DNA in the eukaryotic
genomes
- presence of promoters, introns and transcription terminators (parts of the genes that
are transcribed but not translated);
- high number of repetitive sequences (not coding proteins);

Are these not coding

regions ‘Junk’ DNA?

NO, they
aren’t
 Repetitive DNA

• Repeated sequences are patterns of nucleic acids (DNA or RNA)

that occur in multiple copies throughout the genome

• Sequence complexity refers to the number of times a particular

base sequence appears in the genome

• There are three main types of repetitive sequences

 Unique or non-repetitive
 Moderately repetitive
 Highly repetitive
• Unique sequences
– Found once or a few times in the genome
– Includes structural genes (genes that control the production of a protein that
performs a structural role in cell) as well as intergenic areas
– In the human species they represent about 40% of the genome
• Moderately repetitive DNA sequences
– Found a few hundred to a few thousand times
– They include
• Genes for ribosomal RNA (rRNA) synthesis and genes coding for histones
• Origins of replication
• Transposable elements (also known as "jumping genes," are DNA sequences
that move from one location on the genome to another)

• Highly repetitive DNA sequences

– Found tens of thousand to millions of times
– They are relatively short sequences (a few nucleotides to several hundred in length)
– Some sequences are interspersed in throughout the genome
– Other sequences are clustered together in tandem arrays
How is DNA packaged?
• If stretched end to end, a single set of human
chromosomes will be over 1 meter long!
 Yet the cell’s nucleus is only 2 to 4 µm in diameter
 Therefore, the DNA must be tightly compacted to fit

• The compaction of linear DNA in eukaryotic chromosomes

involves interactions between DNA and various proteins
 Proteins bound to DNA are subject to change during the life of
the cell
 These changes affect the degree of chromatin compaction
DNA of VIRUS and BACTERIA

DNA molecules are organized within cells into CHROMOSOMES

VIRUS Prokaryotes

Unique chromosome

Unique chromosome, Circular chromosome, double stranded DNA

circular, single or double
DNA strand
NUCLEOID occupies about 1/3 of the total cell volume
Linear double-stranded
Plasmids: DNA molecules physically separated from
or the chromosomal DNA and which can replicate
independently
Linear, single or double
RNA strand
 Viral genome
• Viruses are small infectious particles containing nucleic acid
surrounded by a capsid of proteins

• For replication, viruses rely on their host cells (i.e. the cells they
infect)

• A viral genome is a term used as in whole of the genetic

material. Also termed the viral chromosome

• The genome can be:

DNA or RNA
Single stranded or double stranded
Circular or linear

• Viral genomes vary in size from a few thousand to more than a

hundred thousand nucleotides
 Bacterial genome
• Bacterial chromosomal DNA is usually a circular
molecule that is a few million nucleotides in length (i.e.
Escherichia coli: ~4.6 million bp; Haemophilus influenzae: ~1.8 million bp)

• A typical bacterial chromosome contains a few

thousand different genes;
Structural gene sequences (encoding proteins) account for the majority of
bacterial DNA;
The no transcribed DNA between adjacent genes are termed intergenic regions
 A few hundred Key features:
nucleotides in
length - Most, but not all, bacterial
species contain circular
Origin of chromosomal DNA;
replication
- A typical chromosome is a few
million base pairs in length;

- Several thousand different

genes are interspersed
throughout the chromosome;

- One origin of replication is

required to initiate DNA
replication;
Genes
-Short repetitive sequences
Intergenic regions
Repetitive sequences may be interspersed
throughout the chromosome
These play roles in DNA
folding, DNA replication,
and gene expression
• To fit within the bacterial cell, the chromosomal DNA must be
compacted about a 1,000-fold. This involves the formation of
loop domains.
• The number or loops varies according to the size of the bacterial
chromosome and the species. (i.e. E. coli has 50-100 with 40,000 to
80,000 bp of DNA in each)
• DNA super coiling is a second important way to compact the
bacterial chromosome
 Eukaryotic chromosomes

- A variable number of chromosomes is present in the nucleus; they constitute the

nuclear genome (the number of chromosomes is a feature characteristic of each species);
- Chromosomes are visible only during specific phases of the cell cycle: they reach the
highest degree of condensation during MITOSIS;
- During the interval between two cell divisions chromosomes are not individually
distinguishable.
• Eukaryotic species contain one or more sets of
chromosomes
Each set is composed of several different linear chromosomes

• The total amount of DNA in eukaryotic species is

typically greater than that in bacterial cells

• Chromosomes in eukaryotes are located in the nucleus

To fit in there, they must be highly compacted
This is accomplished by the binding of many proteins
The DNA-protein complex is termed chromatin
 HISTONES
Highly alkaline proteins found in eukaryotic cell nuclei that
package and order the DNA into structural units called
nucleosomes. Alkalinity depends by the high content of
basic aminoacids (Lysine and Arginine);
Histones can be divided in 5 classes on the basis of Lys and
Arg content: H3; H4; H2A; H2B, H1;

H2A H3-H4 H2B

H3 and H4 are rich in Arg and H2A and H2B have an

represent mostly conserved intermediate content of Lys
proteins and show interspecific
variability

These proteins interact with DNA to form NUCLEOSOMES; a

nucleosome is composed of double-stranded DNA wrapped
around an octamer of histone proteins (An octamer is
composed two copies each of four different histones)
 Vary in length between 20 to 100 bp,
depending on species and cell type
Diameter of the
nucleosome

Overall structure of connected nucleosomes resembles “beads on a string”

This structure shortens the DNA length about seven-fold
H1 is the linker histone - Binds to linker DNA and also binds to
nucleosomes, BUT not as tightly as are the core histones

Play a role in the

organization and compaction
of the chromosome
Nucleosomes associate with each other to form a more compact
structure termed the 30 nm fiber

The 30 nm fiber shortens the total length of DNA another seven-

fold

Its structure has proven difficult to determine (the DNA

conformation may be substantially altered when extracted from
living cells)

Two models have been proposed

Solenoid model
Three-dimensional zigzag model
 Heterochromatin vs Euchromatin
The compaction level of interphase chromosomes is not
completely uniform
Euchromatin
Less condensed regions of chromosomes
Transcriptionally active
Regions where 30 nm fiber forms radial loop domains

Heterochromatin
Tightly compacted regions of chromosomes
Transcriptionally inactive (in general)
Radial loop domains compacted even further
There are two types of heterochromatin
Constitutive heterochromatin
Regions that are always heterochromatic
Permanently inactive with regard to transcription
Facultative heterochromatin
Regions that can interconvert between euchromatin and
heterochromatin
 Compaction level
in euchromatin

During interphase
most chromosomal Compaction level
regions are in heterochromatin
euchromatic
 Eucaryotic chromosome
The number and morphology of chromosomes constitute the KARYOTYPE
and are constant for each species;

A karyotype reveals how many chromosomes

are found within an actively dividing cell

Chromosomes are analysed by organising them into a KARYOGRAM

Image (taken during metaphase) of an individual’s complement of chromosomes
arranged by size, length, shape, and centromere location

Pairs of homologous chromosomes are ordered length;

Cytogenetics, is the field of genetics that involves the microscopic examination of

chromosomes.
 Eukaryotic chromosomes occur in sets
Each set is composed of several different types of chromosomes (By convention,
the chromosomes are numbered according to size, with the largest chromosomes having
the smallest numbers)
A second feature of many eukaryotic species is that an individual has two sets
of chromosomes. When the cells of an organism carry two sets of
chromosomes, that organism is said to be DIPLOID

Geneticists use the letter n to represent a set of chromosomes, so diploid organisms are
referred to as 2n (CHROMOSOME NUMBER or SOMATIC CHROMOSOME NUMBER, that is
the number of chromosomes characteristic of somatic cells); the somatic chromosome
number includes 2 complete sets of chromosomes, one of each of these pairs comes from
an organism’s mother, and one comes from the father; these are referred to as maternal and
paternal chromosomes, respectively.

n indicates the GAMETIC CHROMOSOME NUMBER, that is the number of chromosomes

present in gametes of a diploid organism, namely sperm and egg cells, which are HAPLOID
or 1n (which means they contain one set of chromosomes)

x indicates the BASIC CHROMOSOME NUMBER, that is a set of chromosomes

Examples

HUMAN genome 2x=2n=46 chromosomes

BASIC CHROMOSOME NUMBER, x = 23

SOMATIC CHROMOSOME NUMBER, 2n = 46
GAMETIC CHROMOSOME NUMBER, n = 23

Common bean genome 2x=2n=22 chromosomes

BASIC CHROMOSOME NUMBER, x = 11

SOMATIC CHROMOSOME NUMBER, 2n = 22
GAMETIC CHROMOSOME NUMBER, n = 11
When a species is diploid, the members of a pair
of chromosomes are called homologues.

Homologous chromosomes are very similar to

each other. Each of the two chromosomes in a
homologous pair is nearly identical in size and
shape and contains a similar composition of
genetic material (same genes in the same
position/locus).

Homologous chromosomes are not identical; they

can have different alleles of genes
CHROMOSOME’S STRUCTURE
 Centromere
So called primary constrinction ;
Their main function is during cell divisions (mitosis and meiosis);
indeed it is in centromeres, where spindle fibers attach–Pulling
chromatids apart, thus playing a fundamental role in the
chromosome distribution between two daughter cells.

Centromere divides chromosomes

in two arms, and on the basis of
chromosome position we can
observe different types of
Centromere chromosomes
Chromosome types
 Nucleolar organizer
Nucleolar organizers are secondary constrictions. The nucleolar
organizer genetic locus contains tandemly repeated genes that
encode the ribosomal RNA.

The r(RNA) will be associated to proteins to form the

subunits of ribosomes
 Telomers

A telomere is a region of repetitive nucleotide sequences at

each end of a chromosome, which protects the end of the
chromosome from deterioration or from fusion with
neighboring chromosomes.
Short arm
Secondary
constrinction

Primary Centromere
constriction

Long arm
Some traits are inherited only from maternal or paternal parent, they are conditioned
by cytoplasmc factors

Along with nuclear DNA, there is DNA located in MITHOCONDRIA (mt DNA), and in
CHLOROSPLASTS (cp DNA)

MITHOCONDRIAL GENOME

Mitochondria are
organelles which are
responsible for cellular
respiration (ATP
production)
 Mithocondrial DNA (mtDNA) can be organized in one or several copies of the single
circular mtDNA molecule;
(size: ~20kb in animals - 2,500 kb in plants)

Some of the proteins coded by mtDNA are essential for the correct working of the cell.

Mitochondrial DNA are mainly maternally inherited, with exception of some

gymnosperms (male inheritance) - Cytoplasm of the zygote is inherited by one parents.
 PLASTIDIAL GENOME

Mitocondrio

Plastidial genome (cpDNA or plastoma) is organized in circular molecules

Size varies from 50kb to 400kb

cpDNA contains about 120-140 genes, coding for about 60 proteins (mostly
ribosomal proteins and components of photosynthetic apparatus)
How is DNA packaged?
https://www.dnalc.org/resources/3d/07-how-dna-is-packaged-basic.html