Nucleotides & Nucleic Acids

Question 1

How is the structure of DNA related to its function?

Answer 1

Long and coiled- lots of genetic information condensed into a small space.
Double helix- can unzip allowing DNA to copy itself for cell division and reproduction. Also strengthens and stabilised the molecule.
Complementary base pairing- only one strand is needed to produce the exact complementary strand, no mistakes occur.
Sequence of bases- decides order of amino acids/ the protein.
Hydrogen bonds- holds strands together and weak so can be broken for replication.

Question 2

What is a pentode sugar?

Answer 2

A monosaccharide with 5 carbon atoms

Question 3

How does RNA differ from DNA?

Answer 3

Ribose sugar in RNA nucleotides. 
Shorter, single polynucleotide strand. 
Stands for ribonucleic acid. 
Uracil replaces thymine as a base to pair with adenine. 
Used to make proteins.

Question 4

What is the difference between ribose and deoxyribose?

Answer 4

Ribose- carbon2 carries a hydroxyl group which causes RNA to be more reactive than DNA.
Deoxyribose- carbon2 carries a hydrogen atom, making DNA fairly stable.

Question 5

What are the three components of a nucleotide?

Answer 5

A phosphate group
(Joined by a phosphodiester bond to)
A sugar
(Joined by a covalent bond to)
A nitrogenous base

Question 6

What is a purine?

Answer 6

A type of base with 2 nitrogen-containing rings in its structure.
E.g. Adenine and Guanine

Question 7

What is a pyrimidine?

Answer 7

A type of base with 1 nitrogen-containing ring in its structure.
E.g. Cytosine, thymine and uracil.

Question 8

How do bases bond together when two polynucleotide strands join?

Answer 8

Adenine–thymine
Cytosine–guanine
Held together by weak hydrogen bonds.

Question 9

How many hydrogen bonds form in each base pairing?

Answer 9

A-T 2 Hbonds

C-G 3 Hbonds

Question 10

What type of reaction occurs when nucleotides are bonded together?

Answer 10

Condensation reaction (occurs between phosphate group and sugar).

Question 11

Why is DNA referred to as an anti parallel strand?

Answer 11

The two polynucleotides lie side by side and running in opposite directions: the 3’ end (carbon3 attached to phosphate) and 5’ end (carbon5 attached to phosphate) are in opposite orientations on either strand.

Question 12

What are phosphorylation nucleotides?

Answer 12

Those containing more than one phosphate group

Question 13

What is a nucleoside?

Answer 13

It has no phosphate group (e.g. Adenosine)

Question 14

What is adenosine triphosphate (ATP) needed for?

Answer 14

Metabolic processes and pathways:
Movement
Synthesis
Transport

Question 15

What is the difference between ATP and DNA?

Answer 15

ATP has three phosphate groups; DNA has one.
ATPs pentode sugar is ribose.
ATP always has adenosine as its nitrogenous group.

Question 16

What happens during the ADP to ATP stage of the ATP cycle?

Answer 16

Energy from a catabolic reaction that is exergonic (e.g. Breakdown of glucose in respiration) is used to bond an inorganic phosphate to ADP in a condensation reaction. Bonds break, energy is taken in, water is formed and chemical energy is stored in the phosphate bond. The reaction is catalysed by the enzyme ATP synthase.

Question 17

What happens to ATP when energy is need by a cell?

Answer 17

ATP is broken back down into ADP and an inorganic phosphate in a hydrolysis reaction that breaks the phosphate bond. The bonds from water reform in the phosphate, releasing energy. ATPase catalysed this reaction.

Question 18

Why does a cell always have an immediate supply of energy?

Answer 18

The ADP and phosphate are both recycled and ATP cannot pass out of the cell.

Question 19

What does DNA stand for?

Answer 19

Deoxyribonucleic acid

Question 20

What are the 4 stages of DNA purification?

Answer 20

Lysis
Precipitation
Washing
Resuspension

Question 21

Why is the ethanol chilled overnight and then kept on ice throughout the procedure?

Answer 21

It is very flammable (boils at 60C).

Prevent enzyme action in cell that could digest the DNA.

Question 22

Describe the lysis stage, explaining each step.

Answer 22

Burst open cell walls in material by blending, UHT, grinning or sonification.
Filter to collect a liquid filtrate in a beaker.
Add salt. This interrupts the hydrogen bonds between DNA and water, helping DNA to coagulate.
Add washing up liquid. This breaks down the cell membranes by emulsifying the phospholipid bilayer- hydrophilic regions in the detergent are attracted to water and surround the bilayer, allowing them to dissolve.

Question 23

Describe the precipitation stage, explaining each step.

Answer 23

Add the mixture to a water bath at 60C- increases yield by increasing breakdown of cell and nuclear membranes.
Add some protease enzymes (to digest proteins) or phenol/chloroform which dissolve denatured proteins.
Pour cold ethanol into a test tube of filtrate at 45 degrees- ethanol is less dense than water and floats on top. SALTED DNA is insoluble in ethanol and forms a precipitate that can be pulled out.

Question 24

What are the drawbacks of placing the filtrate in a water bath?

Answer 24

Now the DNA is free in the cytoplasm, the action of DNase enzymes may be stimulated to break it down and decrease the yield.

Question 25

What is semi-conservative DNA replication?

Answer 25

When each new molecule of DNA consists of one old strand and one new strand of DNA.

Question 26

Describe how DNA replicates itself.

Answer 26

1. Gyrase enzyme unravels the double helix to form a straight ladder. 2. The enzyme DNA helicase breaks the hydrogen bonds to form two separate polynucleotide DNA strands. Free-floating DNA nucleotides (NTPs) in the nucleus bond to the exposed bases using complementary base pairing. 3. DNA polymerase joins the nucleotides by forming phosphodiester bonds, since the only thing to strengthen them at this point are weak hydrogen bonds.

Question 27

What is a gene?

Answer 27

A sequence of DNA nucleotides that codes for a polypeptide.

Question 28

What is a sense and non-sense mutation?

Answer 28

Sense- effect on protein | Nonsense- no effect on protein

Question 29

What are the four features of the genetic code?

Answer 29

``` Triplet (one codon codes for a specific amino acid) Non-overlapping (no bases are shared in codons and a 'start' codon ensures the ribosomes read the mRNA in a specific way) Universal Nature (used by all organisms, except for small variations in mitochondria and microbes) Degenerate (prevents mutations as some amino acids are coded for by more than one codon) ```

Question 30

What happens during transcription of protein synthesis?

Answer 30

1. In the nucleus, gyrase unwinds double helix and DNA helicase breaks H bonds to separate strands. 2. Section of DNA is used to produce messenger RNA, whereby free nucleotides join up to exposed DNA bases (uracil, not thymine). 3. RNA polymerase catalyses the formation of phosphodiester bonds between ribose and phosphate groups of adjoining molecules. 4. Ligase allows DNA stands to reform.

Question 31

What happens during translation stage of protein synthesis?

Answer 31

1. mRNA leaves the nucleus via nuclear pore and binds to ribosomes on rough ER. 2. Transfer RNA (single strand that brings amino acids and is folded into a clover leaf shape due to H bonding, where one area is exposed to reveal an anticodon) brings amino acid that corresponds to mRNA codon. 3. mRNA moves along ribosome one codon at a time, H bonds from between codons and anti codons so tRNA molecules are released after peptide bonds have formed between subsequent amino acids. 4. Polypeptide is transported from rough ER to Golgi for modification.