Nucleic Acids

Question 1

What bond joins the pentose sugar to the nitrogenous base?

Answer 1

A glycosidic bond

Question 2

Which carbon of the sugar is the phosphate group joined to?

Answer 2

5 or 3

Question 3

What is a phosphodiester bond?

Answer 3

The linkage between the 5’ carbon of one pentose sugar and the 3’ carbon of another pentose sugar. The hydroxyl group on the phosphate group on 5’ carbon of one nucleotide lines up the hydroxyl group on the 3’ carbon on the adjacent deoxyribose sugar, a water molecule is produced as a condensation reaction occurs

Question 4

On the non-rotated chain of the DNA molecule in which direction does the chain run?

Answer 4

5’ to 3’

Question 5

On the rotated strand of the DNA molecule, which way does the chain run?

Answer 5

3’ to 5’

Question 6

What are the monomers for nucleic acids?

Answer 6

Nucleotides

Question 7

When does a nucleotide become phosphorylated?

Answer 7

When it contains more than one phosphate group

Question 8

What are the functions of nucleotides?

Answer 8

• Act as monomers for nucleic acids
• Help regulate many metabolic pathways (cAMP)
• Component of many coenzymes, adenine nucleotides are the components of NADP and NAD and FAD, coenzymes used in photosynthesis and respiration respectively

Question 9

Describe the structure of DNA?

Answer 9

• DNA is comprised of two strands each running parallel to each other but in opposite directions, hence the structure f DNA is referred to as anti-parallel
• Each DNA nucleotide is composed of a nitrogenous base, phosphate group and a deoxyribose sugar
• Phosphodiester bonds link adjacent deoxyribose sugars together, the phosphate group is attached to the 5’ carbon on one sugar and the 3’ carbon on another sugar
• DNA molecules are long and therefore can carry a lot of encoded genetic information
• Hydrogen bonds are formed between complementary nitrogenous bases opposite each other on the strands of DNA

Question 10

How is DNA organised in eukaryotic cells?

Answer 10

• The majority of DNA, or the genome, is in the nucleus
• Each large molecule of DNA is wound tightly around histone proteins into chromosomes, each chromosome is therefore one molecule of DNA
• There is a loop of DNA in the mitochondria and the chloroplasts without the histone proteins, therefore DNA doesn’t exist as chromosomes in the mitochondria and the chloroplasts

Question 11

How is DNA organised in prokaryotes?

Answer 11

• DNA is in a loop and is within the cytoplasm, it is not enclosed in a nucleus, prokaryotes don’t have a nucleus
• It is not wound around histone proteins and therefore doesn’t exist as chromosomes in prokaryotes
• Viruses that contain DNA have it in a loop of naked DNA

Question 12

What is the function of DNA?

Answer 12

The genome within every cell of an organism contains the coded instructions to make and maintain that organism

Question 13

Why does DNA need to be replicated?

Answer 13

So that each new daughter cell receives the full set of instructions for making and maintaining the organism

Question 14

Describe the process of DNA replication

Answer 14

• DNA molecule unwinds, the double helix untwists, this is catalysed by a gyrase enzyme
• The DNA unzips, the hydrogen bonds are broken between the nucleotide bases, this is catalysed by DNA helicase and results in two single strands of DNA with unpaired nucleotide bases
• Free phosphorylated nucleotides present in the nucleoplasm are complementarily bonded with the exposed bases
• DNA polymerase catalyses the addition of the new nucleotides in the 5’ to 3’ direction
• The leading strand which is the 3’ to 5’ strand is synthesised continuously whereas the lagging strand which is the 5’ to 3’ strand is synthesised in fragments which have to be joined together in reactions catalysed by ligase enzymes
• The free nucleotides are triphosphate nucleotides, these need to be hydrolysed into monophosphate nucleotides so they can be added to the strand. This releases energy that is used to from phosphodiester bonds that link the 5’ carbon on one nucleotide and the 3’ carbon on the next carbon
• 2 new DNA molecules are produced that are identical to each other and the parent molecule
• Each DNA molecule produced contains one new strand and one original strand, this is semi-conservative replication

Question 15

What is the product of DNA replication?

Answer 15

2 DNA molecules each identical to each other and the parent molecule that they were replicated from

Question 16

Why is DNA replication described as semi-conservative?

Answer 16

Each new DNA molecule contains one new strand and one original strand

Question 17

What were the three theories for DNA replication in the 1950s?

Answer 17

Conservative- original molecule acts as a template and a new molecule is formed
Semi-conservative- new molecule consists of one newly formed strand and one original strand
Dispersive- Each molecule breaks up into nucleotides and each one joins to a complementary nucleotide and a new strand is formed

Question 18

How does DNA replication occur in prokaryotes?

Answer 18

A bubble sprouts out from the loop and unwinds and unzips, then complementary nucleotides join to the exposed nucleotides and the loop is eventually copied

Question 19

Why is the 3’ to 5’ the leading strand and the 5’ to 3’ the lagging strand

Answer 19

• The 3’ to 5’ strand can unwind and have free nucleotides added continuously as nucleotides are added in the 5’ to 3’ direction to make the strands anti-parallel which is essential to allow the bases to be in the right orientation to form hydrogen bonds. DNA polymerase adds bases in the 5’ to 3’ direction which means that new nucleotides can be added as the strand unwinds
• The 5’ to 3’ strand has to have its complementary strand running in the 3’ to 5’ direction to make the strands anti-parallel, this means that DNA polymerase has to add the new nucleotides from bottom to top as the complementary strand runs from 3’ to 5’. This means that as the strand unwinds, DNA polymerase adds the nucleotides in fragments as part of the DNA strand unwinds, the nucleotides are added from the bottom of the unwound section of the strand to the top. Once these have been added the next part of the strand unwinds and nucleotides are added from the bottom of the unwound section to the top again. This leaves unjoined fragments that have to be joined together, catalysed by ligase enzymes

Question 20

Which enzymes are involved in DNA replication?

Answer 20

Gyrase enzyme- catalyses the unwinding of the DNA strands
DNA helicase- catalyses the breaking of the hydrogen bonds between nucleotide bases
DNA polymerase- catalyses the addition of new nucleotide bases in the 5’ to 3’ direction to the single strands of DNA, using each of these single strands as a template
Ligase enzymes that catalyse the joining of fragments in the DNA molecule containing the lagging strand

Question 21

How is an RNA molecule structurally different to DNA?

Answer 21

• It has a ribose sugar instead of a deoxyribose sugar, this has an OH on carbon 2 instead of an H
• It has the nitrogenous base uracil instead of thymine
• RNA is single stranded
• There are three forms of RNA: mRNA, tRNA, rRNA

Question 22

What is a gene?

Answer 22

A specific length of DNA on a chromosome, each gene codes for a protein

Question 23

What percentage of an organism’s dry mass is protein?

Answer 23

75%

Question 24

How should amino acids be arranged in a channel protein?

Answer 24

Hydrophilic amino acids should be on the inside of the channel protein so that the ion that is transporting can pass through as the ion will be aqueous. It needs to have lipophilic (hydrophobic) amino acids on the outside of the channel protein, this enables the channel protein to embed itself into the membrane

Question 25

Why is the genetic code described as universal?

Answer 25

As the same triplet of DNA bases (codon) codes for the same amino acid in almost all organisms

Question 26

Why is the genetic code described as degenerate?

Answer 26

Because the same amino acid is coded for by multiple different codons

Question 27

If a base or added or removed from the sequence of bases, what happens to the amino acid sequence?

Answer 27

A frameshift mutation occurs because every base triplet after the point of addition or removal is altered meaning every amino acid coded for after the point is altered, this affects the tertiary structure of the protein and means the protein won’t be able to carry out its function

Question 28

Describe the process of transcription

Answer 28

• The gene unwinds and unzips
• Hydrogen bonds between complementary nucleotide bases break
• RNA polymerase catalyses the formation of temporary hydrogen bonds between free RNA nucleotides and exposed DNA bases on one strand of the DNA
• RNA polymerase also catalyses the formation of the sugar phosphate backbone of the mRNA, by catalysing the formation of the phosphodiester linkages between the phosphate group on 5’ carbon of one nucleotide and carbon 3’ of the adjacent nucleotide
• A length of RNA that is complementary to the template strand is produced, this is therefore a copy of the coding strand but with uracil bases in place of thymine bases
• The mRNA then passes out of the nucleus through the nuclear envelope and attaches to a ribosome (ribosome could be on rough ER)

Question 29

Describe the process of translation

Answer 29

• tRNA molecules bring amino acids to the ribosome, tRNA has an anticodon at one end of the molecule and an amino acid at the other end of the molecule
• The anticodon on the tRNA molecule forms weak hydrogen bonds with the complementary codon on the mRNA strand
• The ribosome moves along the length of mRNA and it reads the code, when two amino acids are adjacent to each other, they form a peptide bond, energy from ATP is required for the formation of peptide bonds
• The sequence of DNA bases on the template strand therefore determines the amino acid sequence in the polypeptide chain
• After the polypeptide chain has been assembled the mRNA breaks down and the its component molecules can be recycled into new lengths of mRNA with different codon sequences
• The newly synthesised polypeptide chain is helped by chaperon proteins to fold into its tertiary structure, so it can carry out its function

Question 30

How are ribosomes formed?

Answer 30

Ribosomes are formed in the nucleolus, two sub units of a ribosome are formed that pass out of the nucleus separately (through the nuclear pores). Once they have left the nucleus they come together to form ribosomes, this is catalysed by Mg2+ ions

Question 31

What are ribosomes made of?

Answer 31

rRNA and proteins

Question 32

Which bases are purine?

Answer 32

Adenine and guanine, 2 rings

Question 33

Which bases are pyrimidine?

Answer 33

Thymine/uracil and cytosine, one ring

Question 34

Is the tRNA strand different to the template strand?

Answer 34

No, it is identical

Question 35

Is the mRNA strand different to the coding strand?

Answer 35

No, it is identical apart from it has uracil in place of thymine

Question 36

How is a peptide bond formed?

Answer 36

The OH from the carboxyl group of one amino acid lines up with the H from the amine group of another amino acid, a water molecule is removed as a condensation reaction occurs, a peptide bond between C and N is formed

Question 37

What is the complementary base pairing?

Answer 37

A,T/U and G,C

Question 38

Does a purine base pair with a pyrimidine base or a purine base?

Answer 38

Pyrimidine

Question 39

How many hydrogen bonds form between A and T?

Answer 39

2, 2 also form between adenine and uracil

Question 40

How many hydrogen bonds form between G and C?

Answer 40

3

Question 41

Which strand is the coding strand?

Answer 41

The 3’ to 5’ strand, this is so RNA nucleotides can be added continuously in the 5’ to 3’ direction by RNA polymerase as the strands have to be anti-parallel for the bases to be orientated correctly to form hydrogen bonds with each other