Nucleic acids and chromosomes

Question 1

Nucleic acid structure: explain the structures of DNA and RNA, list the bases found in DNA and RNA and indicate which ones are purines and which ones are pyrimidines

Answer 1

DNA and RNA: molecules of heredity

DNA carries genetic information. The genes of all cells are made of DNA.

Chromosomes (DNA + proteins) segregate as cells divide.

Structure of Nucleic Acids

• Nucleotide = Phosphate Group + Pentose Sugar + Nitrogenous Base
• Nucleoside = Pentose Sugar + Nitrogenous Base

BLUE: Phosphate Group (any number)

GREEN: Pentose Sugar

• Deoxyribose (DNA): deoxyribose, lacks an oxygen atom that is present in ribose, the parent compound.
• Ribose (RNA)

RED: Nitrogenous Base

Pyrimidine: (small)

• Cytosine
• Thymine (DNA)/ Uracil (RNA)

Purine (big)

• Guanine
• Adenosine

Primes (’) are used in numbering the carbon atoms in the ribose: 1’ to 5’. The 1’ C is linked to the base; the 5’ C is linked to the phosphate.

NUCLEOTIDES polymerise to give NUCLEIC ACIDS

• Deoxyribose as sugar = Deoxyribonucleic Acid (DNA)
• Ribose as sugar = Ribonucleic Acid (RNA)
• Polymers add at points 3’ and 5’ via PHOSPHODIESTER BONDS

DNA primary sequence:

the sugar-phosphate backbone with the bases, defined by the linear sequence of the bases. The bases carry genetic information, the sugar and phosphates perform a structural role

DNA secondary structure: The double helix

1. Two strands of DNA run alongside each other forming a right-handed double helix.
2. The chains are antiparallel - they run in opposite directions.
3. The deoxyribose and phosphate groups run along the outside with the negative charges outside.
4. The bases point inwards and the flat planes are perpendicular to the helix.
5. The two chains are held together by hydrogen bonds between the bases.

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Question 2

Base-pairing: explain melting and re-annealing of complementary strands of nucleic acids and what is meant by Watson-Crick base-pairing

Answer 2

Watson-Crick base pairing:

• A nucleic acid will attract another nucleic acid that has COMPLIMENTARY bases
• Adenine always pairs with Thymine. Guanine always pairs with Cytosine
• This complimentary strand is ANTIPARALLEL (it runs 5’ to 3’)
• Will form hydrogen bonds between the two nucleic acids and become DOUBLE-STRANDED
• Bases will point inwards, with a phosphodiester backbone
• Gives some protection against radiation

Hydrogen bonds can be broken to separate the strands (called MELTING):

• Requires high temperature or low salt environments

Hydrogen bonds can be encouraged to form (called RE-ANNEALING)

• Requires cool temperature or high salt environments

Question 3

Explain DNA’s double helical structure

Answer 3

Nitrogenous Bases have polarity:

• Allows them to form hydrogen bonds with other bases
• Must be opposite type of base i.e. A pyrimidine must pair with a purine, and vice versa
• Purine ~ Pyrimidine
• 3 hydrogen bonds (stronger/more stable): Guanine ~ Cytosine
• 2 hydrogen bonds (weaker/less stable): Adenosine ~ Thymine (DNA) / Uracil (RNA)
• Double-Stranded DNA’s 3D structure is ALWAYS a double helix
• 10 base pairs per helical turn (includes 1 major and 1 minor groove)
• Double-Stranded RNA’s 3D structure is variable
• So it is termed dsRNA​

Question 4

Nucleic acid analysis: explain the methods used to analyse nucleic acids, including hybridisation, the polymerase chain reaction (PCR) and the use of restriction enzymes

Question 5

Chromosomes: explain the packaging of DNA into nucleosomes and relate this to chromosome structure; summarise the human karyotype

Answer 5

Packaging of eukaryotic DNA

• Eukaryotic DNA is tightly packaged, forming a complex with proteins. This complex is called chromatin.
• During interphase, when cells are not dividing, chromatin is more extended. Further condensation during mitosis produces chromosomes.

Lowest level of packaging:

1. Nucleosome
In each nucleosome:

• There is a histone octamer (8 core proteins, called histones: 4 types, 2 each)
• Histones are positively charged, to attract negatively charged phosphodiester backbone
• Each set of 8 core histones can have 150 bp wrap around
• The nucleosome causes an approximately 7-fold condensation of DNA

2. The chain of nucleosomes is further packed to generate a more compact structure: the 30 nm fiber, giving ~40-fold condensation.

3. Chromatin fiber folded into loops

4. Entire mitotic chromosome

Net result (image): each DNA molecule has been packaged into a mitotic chromosome that is 10 000 fold shorter than its fully extended length.

The karyotype

• A karyotype is an organised profile of someone’s chromosomes.
• A diploid human cell has 46 chromosomes
  
  • 22 pairs of ‘normal’ chromosomes (autosomes) and
  • 2 sex chromosomes (X and Y)
• Sex chromosomes: XX for female; XY for male
• Abnormalities in breast tumour: 48 chromosomes instead of 46, multiple translocations, eg two pieces of chromosome 8 plus piece of chromosome 17