Module 2: Section 3 - Nucleotides and Nucleic Acids

Question 1

What is a nucleotide made from and what elements do all nucleotides contain?

Answer 1

It’s made from:

• a pentose sugar (that’s a sugar with five carbon atoms)
• a nitrogenous (nitrogen-containing) base
• a phosphate group

All nucleotides contain the elements C, H, O, N and P

Question 2

What are nucleotides the monomers of?

Answer 2

Nucleotides are the monomers that make up DNA and RNA. DNA and DNA are both types of nucleic acid. DNA is used to store genetic information - the instructions an organism needs to grow and develop. RNA is used to make proteins from the instructions in DNA

Question 3

What is the pentose sugar in a DNA molecule called?

Answer 3

Deoxyribose

Question 4

What are the four possible bases of DNA?

Answer 4

Each DNA molecule has the same sugar and phosphate group. The bases on each nucleotide can vary though.

There are four possible bases - adenine (A), thymine (T), cytosine (C) and guanine (G)

Question 5

What DNA bases are purines and what DNA bases are pyrimidines?

Define a purine base and define a pyrimidine base

Answer 5

A and G are a type of base called a purine
C and T are a type of bases called a pyrimidine

A purine base contains two carbon-nitrogen rings joined together
A pyrimidine base only has one carbon-nitrogen ring. SO a pyrimidine base is smaller than a purine base

Question 6

What is the sugar in RNA called and how do the bases in RNA differ to the bases in DNA?

Answer 6

1) RNA contains nucleotides with a ribose sugar (not deoxyribose)
2) Like DNA, an RNA nucleotide also has a phosphate group and one of four different bases
3) In RNA though, uracil (a pyrimidine) replaces thymine as a base
4) An RNA molecule is made up of a single polynucleotide chain

Question 7

ADP and ATP are phosphorylated nucleotides. How do you phosphorylate a nucleotide and what does ADP and ATP contain?

Answer 7

1) to phosphorylate a nucleotide, you add one or more phosphate groups to it
2) ADP (adenosine diphosphate) contains the base adenine, the sugar ribose and two phosphate groups
3) ATP (adenosine triphosphate) contains the base adenine, the sugar ribose and three phosphate groups

Question 8

What does ATP provide and how is it synthesised?

Oi, mate, draw a diagram ATP being synthesised. The answer is on page 35.

Answer 8

• ATP provides energy for chemical reactions in the cell
• ATP is synthesised from ADP and inorganic phosphate using the energy from an energy-releasing action, e.g. the breakdown of glucose in respiration. The ADP is phosphorylated to form ATP and a phosphate bond is formed
• energy is stored in the phosphate bond. When this energy is needed by a cell, ATP is broken back down into ADP and inorganic phosphate. Energy is released from the phosphate bond and used by the cell.

Question 9

Nucleotides join together to form polynucleotides. How do they join together, what is this known as and how do they separate again?

Answer 9

1) the nucleotides join up between the phosphate group of one nucleotide and the sugar of another. This forms a phosphodiester bond (consisting of the phosphate group and two ester bonds)
2) the chain of sugars and phosphates is known as the sugar-phosphate backbone
3) polynucleotides can be broken down into nucleotides again by breaking the phosphodiester bonds

Question 10

Two polynucleotide strands join together to form a double helix. Talk me through the structure of this and how it is formed.

Answer 10

1) Two DNA polynucleotide strands join together by hydrogen bonding between the bases.
2) each base can only join with one particular partner - this is called complimentary base pairing
3) adenine always pairs with thymine (A-T) and cytosine always pairs with guanine (C-G). A purine (A or G) always pairs with a pyrimidine (T or C)
4) two hydrogen bonds form between A and T, and three hydrogen bonds form between C and G
5) two antiparallel polynucleotide strands twist to form the DNA double helix

Question 11

You can purify DNA using a ppt reaction. How is this reaction carried out (in 7 steps)?

Answer 11

1) break up the cells in your sample. You can do this by using a blender
2) make up a solution of detergent, salt and distilled water
3) add the broken up cells to a beaker containing the detergent solution. Incubate the beaker in a water baths at 60 degrees C for 15 minutes
4) once incubated, put your beaker in an ice bath to cool the mixture down. When its cooled, filter the mixture. Transfer a sample of your mixture to a clean boiling tube
5) add protease enzymes to the filtered mixture. These will break down some proteins in the mixture, e.g. proteins bound to the DNA. Adding RNase enzymes will break down any RNA in the mixture
6) slowly dribble some cold ethanol down the side of the tube, so it forms a layer on top of the DNA detergent mixture
7) if you leave the tube for a few minutes, the DNA will form a white ppt, which you can remove from the tube using a glass rod

Question 12

This is a nasty one - sorry J-dawg. How does DNA copy itself before cell division?

Answer 12

1) DNA helicase breaks the hydrogen bonds between the two polynucleotide DNA strands. The helix unzips to form two single strands
2) Each original single strand acts as a template for a new strand. Free-floating DNA nucleotides join to the exposed bases on each original template strand by complementary base pairing - A with T and C with G
3) The nucleotides of the new strand are joined together by the enzyme DNA polymerase. This forms the sugar-phosphate backbone. Hydrogen bonds form between the bases on the original and new strand. The stands twist to form a double helix.
4) Each new DNA molecule contains one strand from the original DNA molecule and one new strand

Question 13

Why is DNA replication known as semi-conservative?

Answer 13

This type of replication is called semi-conservative because half of the strands in each new DNA molecule are from the original piece of DNA (i.e. the new molecule contains one old strand and one new strand).

Question 14

DNA replication is really accurate - but what happens when it’s not?

Answer 14

DNA replication is really accurate - it has to be, to make sure genetic info is conserved each time the DNA is replicated

Every so often though, a random, spontaneous mutation occurs. A mutation is any change to the DNA base sequence. Mutations don’t always have an effect, but they can alter the sequence of amino acids in a protein. This can cause an abnormal protein to be produced which might function better than the normal protein or might not work at all.

Question 15

What is a gene?

What does the order of nucleotide bases in a gene determine?

Answer 15

1) a gene is a sequence of DNA nucleotides that codes for a polypeptide - the sequence of amino acids in a polypeptide forms the primary structure of a protein
2) different proteins have a different number and order of amino acids
3) it’s the order of nucleotide bases in a gene that determines the order of amino acids in a particular protein
4) each amino acid is coded for by a sequence of three bases (called a triplet) in a gene
5) different sequences of bases code for different amino acids. So the sequence of bases in a section of DNA is a template that’s used to make proteins during protein synthesis

Question 16

DNA molecules are found in the nucleus of the cell, but the organelles the make proteins (ribosomes) are found in the cytoplasm. How does DNA get past this problem?

Answer 16

DNA is too large to move out of the nucleus, so a section is copied into mRNA. This process is called transcription

the mRNA leaves the nucleus and joins with a ribosome in the cytoplasm, where it can be used to synthesise a protein. This process is called translation

Question 17

What are the three different types of RNA?

Answer 17

Messenger RNA
Transfer RNA
Ribosomal RNA

Question 18

Tell me three facts about messenger RNA

Answer 18

messenger RNA:

• made in the nucleus
• three adjacent bases are called a codon
• it carries the genetic code from the DNA in the nucleus to the cytoplasm, where it’s used to make a protein during translation

Question 19

Tell me three facts about transfer RNA

Answer 19

transfer RNA:

• found in the cytoplasm
• it has an amino acid binding site at one end and a sequence of three bases at the other end called an anticodon
• it carries the amino acids that are used to make proteins to the ribosomes during translation

Question 20

Tell me three facts about ribosomal RNA

Answer 20

ribosomal RNA:

• forms the two subunits in a ribosome (along with proteins)
• the ribosome moves along the mRNA strand during protein synthesis. The rRNA in the ribosome helps to catalyse the formation of peptide bonds between the amino acids

Question 21

What is the genetic code?

Answer 21

The genetic code is the sequence of base triplets (codons) in DNA or mRNA, which codes for specific amino acids

Question 22

How does the genetic code not overlap?

Answer 22

In the genetic code, each base triplet is read in sequence, separate from the triplet before it and after it. Base triplets don’t share their bases - the code is non-overlapping

Question 23

The genetic code is degenerate - what does this mean?

Answer 23

The genetic code is degenerate - there are more possible combinations of triplets than there are amino acids (20 amino acids but 64 possible triplets). This means that some amino acids are coded for by more than one base triplet, e.g. tyrosine can be coded for by UAU or UAC

Question 24

How does the genetic code stop or start?

Answer 24

Some triplets are used to tell the cell when to start and stop production of the protein - these are called start and stop signals (or start and stop codons). They’re found at the beginning and end of the gene. e.g. UAG is a stop signal

Question 25

The genetic code is universal - what does this mean?

Answer 25

The genetic code is universal - the same specific base triplets code for the same amino acids in all living things. e.g. UAU codes for tyrosine in all organisms

Question 26

Give me the seven steps of translation

Answer 26

1) the mRNA attaches itself to a ribosome and tRNA molecules carry amino acids to the ribosome.
2) a tRNA molecule, with an anticodon that’s complementary to the start codon on the mRNA, attaches itself to the mRNA by complementary base pairing
3) a second tRNA molecule attaches itself to the next codon on the mRNA
4) ribosomal RNA in the ribosome catalyses the formation of a peptide bond between the two amino acids attached to the tRNA molecules. This joins the amino acids together. The first tRNA molecule moves away, leaving its amino acid behind
5) a third tRNA molecule binds to the next codon on the mRNA. Its amino acid binds to the first two and the second tRNA molecule moves away
6) this process continues, producing a chain of linked amino acids (a polypeptide chain), until there’s a stop codon on the mRNA molecule
7) the polypeptide chain moves away from the ribosome and translation is complete