Sugar: Deoxyribose Nucleic Acid DNA

DNA
Deoxyribose nucleic acid, DNA, is the information storage medium found in all of
your cells. It contains information in a code containing only four different letters that
spells out how and when to make proteins. These proteins make up everything about
you, your genetic information is the cause of your physical and chemical
characteristics. The small units that make up DNA are called a nucleotides with three
parts: a sugar, a phosphate, and a nitrogenous base.
Sugar
The sugar in DNA is called deoxyribose. It is a five-carbon sugar molecule with one
less oxygen atom in the 2 position compared to the closely related ribose(found
in RNA)
Phosphate
Phosphate groups(PO43–) link the deoxyribose molecules together through links
called phosphodiester bonds. The phosphate groups cause DNA molecules to be
acidic.
Nitrogenous bases
Nitrogenous bases are the key to information storage in genetic material. DNA
nucleotides contain either guanine, cytosine, adenine or thymine attached to the
sugar. These bases link together in a process called complimentary base pairing and
hold two strands of DNA together in a double helix.
guanine pairs with cytosine adenine pairs with thymine

G≡C A=T
Nucleotides
Sugars are the core of nucleotides. The nitrogenous base is attached to the side of
the sugar, the phosphate group is attached to the top. The chemical structure of a
nucleotide is quite complex and is often represented by a cartoon structure with a
circle for the phosphate, a pentagon for the sugar and another shape for the
nitrogenous base.
nucleotide structure cartoon structure

Chromosomes
DNA is a long polymer of nucleotides joined together one after the other to create
large chains called chromosomes. The chromosomes inside your nuclei containing
between 45 and 248 million nucleotides joined together. Each of the chromosomes
in your cells are between 1.5 and 8.5 cm long. For comparison, width of a double
helix of DNA is approximately 2.5 nm, meaning chromosomes are about 30 million
times longer than they are wide.
Strands of DNA are formed by bonding between the sugars and phosphates of
nucleotides, forming the sugar-phosphate backbone. The start of a DNA strand is the
5′(five-prime) end (the end of the nucleotide with the phosphate) and ends at the 3′
(three-prime) end (the end of the nucleotide with the sugar). The start of DNA
sequences is shown by convention with the 5′ at the left or top, and then the
sequence continuing to the 3′ at the right or bottom.
The diagram right shows the sequence GTAC(5′→3′). You can see that the top of the
strand begins with a phosphate group, followed by the first deoxyribose, then the
second nucleotide, all the way down the sugar-phosphate backbone to the cytosine
at the end.
DNA in chromosomes is normally found as a double strand with each nitrogenous

base bound by hydrogen bonds to its complimentary base. This strand is aligned in
the opposite direction, with its 5′ end found near the 3′ end of the other strand. This
means that not only do the strands have complimentary bases at each position, but
the directions of the strands are opposite. You can see this represented in the
diagrams left and below.
5′ G → T → A → C 3′
3′ C ← A ← T ← G 5′
In this example the base strand and the complimentary strands are actually the same
sequence, GTAC. Small interesting things like this have led to many interesting
discoveries and applications within molecular biology, for example the use
of restriction enzymes to insert short segments of DNA into large sequences. You
can read more about these technologies in section 2.12 of Year 10 Science on
JacPlus.
Biological sex
In biology, the sex of an organism is strictly defined as the trait that determines the
type of gametes (reproductive cells) produced. In animals, individuals that produce
small, mobile gametes (sperm) are called male, while those that produce larger, non-
mobile gametes (ova) are called female. In humans and many other complex
multicellular organisms this trait is genetically determined at fertilisation. Learn more
about sex determination in other species with the TedEd
video: https://youtu.be/kMWxuF9YW38
Organism System Female Male Determining factor

genetics genetics
Mammals X-Y genetic determination at XX XY chromosome in
fertilisation sperm cell
Birds
Ants
Complicated sex genetics in humans

The Y chromosome carries the SRY gene which codes for the sex-determining region
Y protein. Presence of this gene in an individual results in the initiation of male sex
determination in a developing fetus and the formation of testes. When the SRY gene
is not expressed a fetus develops female sex characteristics.
Identify the combinations below and write a short description of sex determination
in humans.
XY: ______________________________ XX: ______________________________
______ ______
XXY: ______________________________ XO: ______________________________
______ ______
XXYY ______________________________ XXX ______________________________
: ______ : ______
Karyotypes
Karyotypes are a visual way to represent the complete set of chromosomes found in
a cell. Scientists can take microscope photographs of stained chromosomes during
cell replication and then arrange the images of the chromosomes with their
homologous pairs. You can see a microscope image in A below, which is digitally
enhanced in B, then arranged by chromosome number in C. This karyotype shows a
genetically normal human female.
Ghazizadeh, M et al. (2008). Microsc Microanal 14(4):357-61
Chromosomes are identified by three characteristics:

 Size: Size corresponds the number of nucleotides in a chromosome.
Chromosome 1 has 249 million bases, while chromosome 21 has only 48
million bases.
 Banding pattern: Giemsa stain (a dye that sticks to the phosphate groups of
DNA) causes unique banding patterns on each chromosome. Banding is not
very clear in the example karyotype above.
 Centromere position: The centromere is a structure on a chromosome that
holds two sister chromatids (identical copies of chromosomes) together
during the early stages of cell division. They appear in karyotypes as pinched
in regions toward the top or centre of the chromosome.
Have a go at matching chromosomes in this online karyotype
https://ilias.hhu.de/ilias.php?baseClass=ilSAHSPresentationGUI&ref_id=884328
Karyotypes from different organisms
Rat Wild sheep
Cow Guinea pig

Examine the karyotypes above and fill in the table.
What is similar between all Why do you think there are What is different
of the karyotypes shown? similarities between them? between the
karyotypes?
Loci, genes and alleles

This module is about genetics; the study of the heritable traits called genes. What
you think of as a gene probably isn’t what is meant by gene within Science. Look at
the descriptions below to understand the difference between a locus, a gene and
an allele.
Locus
A locus is a specific location on a chromosome. For example, if you look at the long
arm of chromosome 11, between sub-band 4 of band 1 and sub-band 1 of band 2
you will find a stretch of DNA that carries the information for making a protein
associated with the formation of pigments in your skin and eyes. This exact spot
could be described as 11q1.4-a2.1.
Gene
A gene is a sequence of DNA in a chromosome, found at a specific locus, that codes
for a protein or other genetic trait. The locus described above is quite complicated,
put more simply it is where you look to find the OCA1 gene which is involved in a
specific type of genetic albinism. You have this gene, just like you have copies of
the BRCA1 gene, an important sequence related to hereditary breast and ovarian
cancer. In fact, you have all the genes in the human genome!
Allele
When you have said “gene” in the past, you probably meant allele. An allele is a
specific version of a gene. Your parents each gave you a full set of human genes, but
with specific alleles. If you have albinism caused by the OCA1 gene, this means that
you received two copies of the allele that leads to problems in melanin production. If
you don’t have albinism caused by OCA1 this means that one or both of your copies
of this gene are versions that allow for normal melanin production. Your specific
combination of alleles is what makes you genetically unique, your genotype.
1. Label the following statements as true (T) or false (F).

a. DNA has the same general structure in all organisms
b. All the bases in DNA nucleotides are the same.
c. All the sugars in DNA nucleotides are the same.
d. Any two nucleotides of DNA can form a base pair.
e. Any two nucleotides of DNA can form a covalent (phosphodiester) bond.
f. The bases A and T always exist in equal proportions in a DNA molecule.
g. The bases A and C always exist in equal proportions in a DNA molecule.
2. a. Write the complimentary sequence for the DNA strand shown below.
Base strand: A G C T T G G A C T A C G T G
b. Label the start, end and direction of the complimentary sequence.

c. Analyse the double stranded DNA you have completed and identify:
Length of ________
sequence:
Total count: G___ C___ A___ T___

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DNA

guanine pairs with cytosine adenine pairs with thymine

nucleotide structure cartoon structure

DNA in chromosomes is normally found as a double strand with each nitrogenous

Organism System Female Male Determining factor

Complicated sex genetics in humans

Ghazizadeh, M et al. (2008). Microsc Microanal 14(4):357-61

Chromosomes are identified by three characteristics:

Have a go at matching chromosomes in this online karyotype

Cow Guinea pig

Loci, genes and alleles

1. Label the following statements as true (T) or false (F).

b. Label the start, end and direction of the complimentary sequence.

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