Lecture 7- Introduction to Nucleic acids, nucleotide biosynthesis and catabolism

Question 1

The building blocks of DNA

Answer 1

DNA nucleotides

Question 2

Name the four types of DNA nucleotides

Answer 2

• deoxyadenosine phosphate
  -deoxyguanosine phosphate
• deoxythymidine phosphate
• deoxycytidine phosphate

Question 3

Draw the structure of deoxyadenosine phosphate

Answer 3

Question 4

Draw the structure of deoxyguanosine phosphate

Answer 4

Question 5

Draw the structure of deoxythymidine phosphate

Answer 5

Question 6

Draw the structure of deoxycytidine phosphate

Answer 6

Question 7

Three components of a nucleotide

Answer 7

• phosphate, sugar, base- a ring of nitrogen and carbon atoms

Question 8

The deoxyribose sugar and phosphate are always the same in DNA nucleotides. What is the variable group?

Answer 8

base.

Question 9

Nucleoside

Answer 9

sugar and base

Question 10

Nucleotide

Answer 10

sugar, phosphate and base

Question 11

Do the deoxyribose sugars in DNA nucleotides exist as beta or alpha anomers?

Answer 11

beta

Question 12

Give the two categories of bases in DNA nucleotides. Which bases fall into these categories?

Answer 12

• adenine and guanine are purines
• cytosine and thymine are pyrimidines

purines= two rings
pyrimidines= one ring

Question 13

What is the primary structure of DNA?

Answer 13

• Contains all the genetic information that we need.
• The information is contained in the sequence of bases in the DNA
• Primary structure- the sequence of bases held together by the sugar phosphate backbone. The phosphate and ribose sugar bond- this is called a phosphodiester bond.

Question 14

DNA sequence is read from ‘5 to ‘3. What does this refer to?

Answer 14

The carbon atom in the deoxyribose sugar to which the phosphate group bonds.

Question 15

What is the secondary structure of DNA?

Answer 15

• The secondary structure= Two antiparallel polynucleotide strands coiled around each other to form a double helix.

Question 16

What causes the two polynucleotide strands to come together to form the secondary structure of DNA? How many hydrogen bonds form between A and T and how many form between C and G?

Answer 16

• complementary base pairing
• 2 hydrogen bonds form between A and T
• 3 hydrogen bonds form between C and G- due to three hydrogen bonds the C and G pair bind much more strongly than A and T

Question 17

The 2 hydrogen bonds between A and T and the three between C and G is important because….

Answer 17

the base pairing maintains a constant distance between the sugar-phosphate backbones of the two chains as they coil around each other.

Question 18

The two strands are antiparallel in DNA double helix. What does this mean?

Answer 18

One strand goes from 5’-3- and the other from 3’-5’.

Question 19

Describe the tertiary structure of DNA.

Answer 19

• The way in which the double helix is packed into the cell.
• DNA strands wind around chromatin proteins. chromatin is made up of histones with DNA and RNA. This looks like beads on a string.
• The chromatin fibre is arranged into a type of solenoidal scaffolding which condenses and makes up the chromosomes.

Question 20

The primary structure of RNA is ……….. to the primary structure of the DNA it was formed from during transcription

Answer 20

complementary

Question 21

RNA contains ribose sugars. What is the difference between ribose and deoxyribose sugar? Draw a ribose sugar

Answer 21

the ribose sugar contains an OH group rather than an H group

Question 22

In RNA nucleotides which base replaces thymine?

Answer 22

uracil

Question 23

DNA is used for long term storage. How is this different to RNA?

Answer 23

• RNA is used only briefly.
• RNA is typically very unstable because it doesn’t need to hang around for very long.

Question 24

Draw adenosine 5’ phosphate

Answer 24

Question 25

Draw Guanosine 5 phosphate

Answer 25

Question 26

Draw cytosine 5 phosphate

Answer 26

Question 27

Draw uridine 5 phosphate

Answer 27

Question 28

Secondary structure of RNA

Answer 28

- Some regions within the single polynucleotide strand interact with themselves through base pairing. The shape of RNA is determined by how the bases interact within the polynucleotide strand - Adenine pairs to uracil - Guanine pairs to cytosine

Question 29

mRNA

Answer 29

- mRNA= relays the code for a protein from DNA to the protein production site

Question 30

tRNA

Answer 30

the adapted unit linking the triplet code on mRNA to specific amino acids

Question 31

rRNA

Answer 31

present in ribosomes- the site of protein synthesis. It is important both structurally and catalytically.

Question 32

Describe the central dogma. In what situations would RNA be used to form DNA?

Answer 32

DNA stores genetic info. DNA is used to produce RNA which is used to form proteins. - Some organisms store info as RNA and to infect cells the RNA is reverse transcribed back to DNA (retroviruses)

Question 33

Biosynthesis of nucleic acids...There are two pathways to form nucleic acids. Explain.

Answer 33

- Salvage= used to recreate DNA/RNA by recycling molecules. - De Novo= ‘from the beginning’. This pathway makes the nucleotides that form DNA and RNA, from scratch. Small precursors undergo reactions to form ribonucleotides, which can later be converted into deoxyribonucleotides.

Question 34

Outline the key points of purine de novo synthesis. Draw ribose 5 phosphate.

Answer 34

- In purine nucleotides, the base- made up of two nitrogen-containing rings are built on top of the ribose sugar. This is done through a series of multistep reactions. - A ribose-5-phosphate is phosphorylated into a PRPP molecule. Two phosphates are added to ribose-5-phosphate from ATP, which is then dephosphorylated into AMP. PRPP synthetase catalyses this reaction. - A nucleophilic substitution reaction then converts PRPP into -5-phosphoribosyl-1-amine. The phosphates in PRPP are substituted for an NH2 group. Now that amine has been substituted, the rings can be built in a series of multistep reactions. - At the end, we produce inosine 5’ phosphate which is a common precursor which can form both adenosine and guanosine- the two purine ribonucleotides. Formation from a common precursor saves energy and enzymes .

Question 35

Where does energy for the reactions in de novo synthesis of purines come from?

Answer 35

- Energy for the reaction comes from the dephosphorylation of ATP to ADP

Question 36

In de novo synthesis of purine how do we get a single carbon in a multistep reaction when one is needed?

Answer 36

Where a single carbon addition is required, the C is often provided from a tetrahydrofolate compound and this provides a useful approach to inhibition of synthesis.

Question 37

How does de novo synthesis of pyrimidine nucleotides differ from that of purines?

Answer 37

The nucleic acid ring (the base) is built first rather than last and then attached to the ribose ring.

Question 38

There are many stages in the de novo synthesis of pyrimidine nucleotides. One of which is the conversion of monophosphates from triphosphates. State the two step reaction

Answer 38

1. Nucleotide monophosphate (NMP) + ATP -> Nucleotide diphosphate (NDP) + ADP The enzyme which catalyses this reaction is a monophosphate kinase- specific for each base but not for the sugar. 2. NDP + ATP -> NTP + ADP The enzyme which catalyses this step is a diphosphate kinase- non-specific.

Question 39

give the example of conversion of nucleotide monophosphate to triphosphate that occurs at the end of de novo synthesis of pyrimidine nucleotides. Hint: it forms the purine nucleotide cytidine triphosphate.

Answer 39

UMP/ uridylate is phosphorylated and changed from monophosphate UMP to triphosphate UTP Uridine triphosphate/UTP is then converted into the purine nucleotide cytidine triphosphate/ CTP

Question 40

How are ribonucleotides converted to deoxyribonucleotides?

Answer 40

- Ribonucleotides have an OH group in their sugar, deoxyribonucleotides do not. - The ribonucleotides are reduced to get rid of the OH group and form deoxyribonucleotides. - An enzyme- reductase does this reaction. A thiol- SH reducing agent. Ribonucleotide + Reductant (SH)2 --> deoxyribonucleotide + Reductant (s-s)

Question 41

What is the difference between uracil and thymine? How do we get from uracil to thymine?

Answer 41

thymine has a methyl group added in the nucleotide monophosphate stage. The enzyme which catalyses the reaction is thymidylate synthase.

Question 42

How can pyrimidine nucleotides be broken down?

Answer 42

reduction or oxidation

Question 43

Describe reduction of Pyrimidine nucleotides. What is formed

Answer 43

- The ring is reduced to break the bonds within the ring- NADPH is used as a reducing agent and it regenerates as NADP. The ring will open as a result of this reduction. - Reductive metabolism of pyrimidines gives small water-soluble metabolites

Question 44

Describe oxidation of pyrimidine nucleotides. What is formed?

Answer 44

- In the oxidative catabolism, oxygen opens up the ring. Products of this catabolism are also small, water-soluble compounds. Any degradation products are readily excreted, as with reduction.

Question 45

In purine nucleotides, how does the catabolism of adenosine differ from guanosine?

Answer 45

- Adenosine- amine is removed and then ribose. - Guanosine- the ribose is removed and then the amine.

Question 46

The catabolism of the purine nucleotides leads to the production of....

Answer 46

uric acid. Uric acid is large- two rings- and solubility is low. It is secreted into the urine as sodium urate crystals.

Question 47

Effects of abnormal catabolism of purine nucleotides...

Answer 47

disease. This is caused from the insolubility of the degradation of the by-product, uric acid. excess accumulation of uric acid causes gout.

Question 48

What is the treatment for gout and how does it work/

Answer 48

The treatment for gout is Allopurinol. Allopurinol inhibits xanthine oxidase which oxidises xanthine into uric acid. Therefore, uric acid cannot be formed. Xanthine can then be converted into the soluble hypoxanthine instead.