Nucleotides

Question 1

Define ‘nucleotide’ ?

Answer 1

Nucleotides : Monomers from which DNA and RNA polymers are built

Question 2

What are the components of a nucleotide ?

Answer 2

• Pentose sugar
• Nitrogen-containing organic base
• Phosphate group

Question 3

Draw a diagram of nucleotide structure ?

Answer 3

Question 4

What are the two types of nucleotides ?

Answer 4

• DNA nucleotide
• RNA nucleotide

Question 5

What are the components of a DNA nucleotide ?

Answer 5

• Deoxyribose sugar
• Phosphate group
• One of four nitrogenous bases: adenine (A), cytosine (C), guanine (G) and thymine (T)

Question 6

What are the components of a RNA nucleotide ?

Answer 6

• Ribose sugar
• Phosphate group
• One of four nitrogenous bases: adenine (A), cytosine (C), guanine (G) and uracil (U)

Question 7

What is a hexose and pentose sugar ?

Answer 7

• Hexose sugar : A sugar contain six carbon atoms
• Pentose sugar : A sugar contains five carbon atoms

Question 8

What is the difference between deoxyribose and ribose ?

Answer 8

Deoxyribose contains one fewer oxygen atom that ribose ( Carbon 2 in ribose contains a OH group while deoxyribose contains a H atom )

Question 9

What are the two types of nitrogenous bases ?

Answer 9

• Purines
• Pyrimidines

Question 10

Which nitrogenous bases are purines and pyrimidines ?

Answer 10

• Purines : Adenine and Guanine
• Pyrimidines : Ctyosine, Thymine and Uracil

Question 11

What are the differences between purine sand pyridines ?

Answer 11

• Purines have a double ring structure
• Pyrimidines have a single ring structure

Question 12

What is the difference between RNA and DNA nucleotide structure ?

Answer 12

Question 13

Define ‘polynucleotide’ ?

Answer 13

Polynucleotide : A long chain molecule made up of many nucleotides chemically joined together by phosphodiester bonds

Question 14

Explain how phosphodiester bonds are formed and broken ?

Answer 14

• A condensation reaction between the phosphate group of one nucleotide and a pentose sugar of another forms a phosphodiester bond
• A water molecule is released
• A water molecule is required to break the hydrolyse the phosphodiester bond to produce two nucleotides

Question 15

What does ATP stand for ?

Answer 15

Adenosine Triphosphate

Question 16

What is energy required for ?

Answer 16

• Anabolic reactions ( building larger molecules from smaller molecules )
• Movement of substances ( across the partially permeable membrane or substance within cells )
• Muscle contraction ( to coordinate movement at the whole-organism level )

Question 17

What is ATP composed of ?

Answer 17

• A nitrogenous base ( Adenine )
• RIBOSE SUGAR
• Three phosphate groups

Question 18

Explain how ATP is not a long-term energy store ?

Answer 18

• ATP is not stored long-term/ used immediately
• ATP is continually broken down into ADP + Pi
• ADP is constantly recycled to produce ATP

Question 19

What is the structure of DNA ?

Answer 19

• DNA molecules are made up of two polynucleotide strands that are parallel but run in opposite direction ; antiparallel
• This forms a DOUBLE HELIX
• Each DNA polynucleotide strand is made up of a large number of DNA nucleotides bonded together by phosphodiester bonds forming sugar-phosphate backbone
• There is HYDROGEN BONDING between complimentary base pairs ( two hydrogen bonds between adenine and thymine + three hydrogen bonds between cytosine and guanine )

Question 20

Explain the bonding that form the sugar-phosphate backbone ?

Answer 20

• The bonds between deoxyribose sugars an phosphate groups are phosphodiester bonds
• The phosphodiester bonds link the 5-carbon of one deoxyribose sugar molecule to the phosphate group from the same nucleotide
• The phosphate group is linked by another phosphodiester bond to the 3-carbon of the deoxyribose sugar molecule of the next nucleotide in the strand

Question 21

Explain complementary base pairings ?

Answer 21

• Two antiparallel strands are held together by hydrogen bonds between complementary bases
• Two hydrogen bonds form between the purine adenine and pyrimidine thymine
• Three hydrogen bonds form between purine guanine and pyridine cytosine

Question 22

What is DNA purification ?

Answer 22

The process by which DNA is purified via precipitation

Question 23

What are the steps involved in DNA purification ?

Answer 23

• Breaking the cell wall and disrupting the nuclear membranes to release the DNA
• Using enzymes to denature and remove the proteins (histones) associated with the DNA
• Precipitating the DNA using an organic solvent (e.g. ethanol)

Question 24

Describe the steps by which DNA is purified ?

Answer 24

• Place the ethanol in a freezer 24 hours before starting the investigation
• Cut up the onion into small pieces (5 mm × 5 mm)
• Add the washing-up liquid to 90 cm³ of tap water in a beaker
• Add some of the onion pieces to the beaker
• Place the beaker in a water bath at 60 °C for 15 minutes
• Cool the mixture in an ice-water bath for 5 minutes, stirring it continually
• Pour the mixture into a blender and blend for 5 seconds
• Using the filter paper, filter the mixture into another beaker
• Pour 10 cm³ of the filtrate into a test tube and add 2-3 drops of protease enzyme, mixing well
• Carefully add the ice-cold ethanol to the test tube and wait 2-3 minutes

Question 25

Why may certain cells be crushed when purifying DNA ?

Answer 25

Crushing breaks down/opens cell wall

Question 26

What happens when the beaker is placed in a water bath of 60oC for 15 minutes ?

Answer 26

- The detergent breaks down the cell/ nuclear membrane - The heat disrupts/ damages the phospholipid bilayer of the onion cell membranes and nuclear membranes, releasing DNA - The heat also denatures enzymes released from the cell that would otherwise begin to digest the DNA

Question 27

Explain why salt may be added to purify DNA ?

Answer 27

- Salt breaks hydrogen bonds between DNA and water molecules making DNA less soluble in water - This helps DNA shed water and precipitate

Question 28

Why is the mixture cooled in an ice water bath ?

Answer 28

- Lowering the temperature prevents the DNA itself from breaking down, which would occur if the high temperature from the previous step was maintained - Continual stirring ensures the whole mixture is cooled

Question 29

Why is the mixture placed in a blender ?

Answer 29

- Blending breaks down the cell walls and cell membranes of the onion cells even further, releasing more DNA - The mixture is only blended for a very short time to ensure the DNA strands themselves are not broken apart

Question 30

Why is the mixture filtered ?

Answer 30

- Filtering removes cell debris and membrane fragments - The filtrate now contains the DNA and its associated proteins

Question 31

Why are protease enemies added to the filtrate ?

Answer 31

The protease denatures and removes the proteins, leaving just the DNA

Question 32

Why is ice-cold ethanol added to the test tube ?

Answer 32

- Ice-cold to reduce enzyme activity to prevent DNA being broken down - Nucleic acids are insoluble in ice-cold ethanol so DNA forms a precipitate (white layer) at the top of the test tube mixture

Question 33

What is semi-conservative replication ?

Answer 33

- The process by which DNA replicates - Each new DNA molecule consists of one new strand and one old strand

Question 34

What enzymes are involved in semi-conservative replication ?

Answer 34

- DNA helicase - DNA polymerase

Question 35

What is the role of DNA helicase ?

Answer 35

- DNA helicase breaks the hydrogen bonds between complementary base pairs of two antiparallel DNA strands - This unzips the DNA double helix

Question 36

What is the role of DNA polymerase ?

Answer 36

- DNA polymerase catalyses the formation of phosphodiester bonds between DNA nucleotides - This results in formation of sugar-phosphate backbone

Question 37

What happens during semi-conservative replication ?

Answer 37

- DNA helicase breaks the hydrogen bonds between the base pairs on the two antiparallel strands - This allows the DNA double helix to unwind resulting in two DNA template strands - Free DNA nucleotides are attracted to the exposed bases on each of the template strands - DNA polymerase catalyses the formation of phosphodiester bonds between adjacent nucleotides - This forms a new sugar-phosphate backbone - Hydrogen bonds form between complementary bases forming two DNA double helix molecules

Question 38

Why is it important to conserve one DNA strand during semi-conservative replication ?

Answer 38

- This maximises accuracy during DNA replication since each new DNA strand is made from one original/template strand and one new strand - Each new cell will always contain the same genetic information as its parent, meaning that genetic continuity is ensured between generations of cells

Question 39

Define 'mutations' ?

Answer 39

Mutations : Changes to the DNA base sequence

Question 40

When do mutations occur during semi-conservative replication ?

Answer 40

- Mistakes/ mutations are random and occur spontaneously - They do not have a particular cause

Question 41

Why do errors/ mutations occur during semi-conservative replication ?

Answer 41

- Bases inserted into the complementary strand in the wrong order - An extra base being inserted - A base being left out

Question 42

Define 'gene' ?

Answer 42

Gene : A sequence of nucleotide bases in a DNA molecule that codes for the production of a specific sequence of amino acids, that in turn make up a specific polypeptide (protein)

Question 43

Define' triplet code/ codon' ?

Answer 43

A sequence of three nucleotide bases that codes for one amino acid

Question 44

What are stop and start codons ?

Answer 44

- Start and stop codons code for start and stop signals - These signals tell the cell where individual genes start and stop - This ensures the cell reads the DNA correctly and produces the correct sequences of amino acids

Question 45

What terms are used to describe the genetic code ?

Answer 45

- Universal - Degenerate - Non-overlapping

Question 46

Why is the genetic code described as non-overlapping ?

Answer 46

Each base in a codon, of which it is a part of, is only read once

Question 47

Why is the genetic code described as universal ?

Answer 47

- It is universal since almost every organism uses the same code - The same triplet codes code for the same amino acids in all living things

Question 48

Why is the genetic code described as degenerate ?

Answer 48

- Multiple codons can code for the same amino acids - The degenerate nature of the genetic code can limit the effect of mutations

Question 49

What are the two stages involved in protein synthesis ?

Answer 49

- Transcription - Translation

Question 50

Define 'Transcription' and 'Translation' ?

Answer 50

- Transcription – DNA is transcribed and an mRNA molecule is produced - Translation – mRNA is translated and an amino acid sequence is produced

Question 51

Where do transcription and translation occur ?

Answer 51

- Transcription occurs in the nucleus of the cell - translation occurs in the cytoplasm of the cell

Question 52

Describe the stages by which transcription occurs ( part 1 ) ?

Answer 52

- DNA helical breaks hydrogen bonds between complementary base pairs, causing DNA double helix to unzip and making the gene available - This results in two DNA polynucleotide strands : the template strand and the non-template/coding strand - The template strand is used to produce the mRNA molecule - Free RNA nucleotides pair up with their complementary bases of the template strand of the ‘unzipped’ DNA molecule by forming hydrogen bonds

Question 53

Describe the stages by which transcription occurs ( part 2 ) ?

Answer 53

- RNA polymerase catalyses the formation of phosphodiester bonds between adjacent RNA nucleotides - When the gene has been transcribed, the hydrogen bonds between the mRNA and DNA strands break and the double-stranded DNA molecule re-forms - mRNA molecule contains the exact same sequence of nucleotides as the DNA coding non-template strand - The mRNA molecule then leaves the nucleus via nuclear pore in the nuclear envelope

Question 54

What is tRNA ?

Answer 54

- Transfer RNA - These tRNA molecules have a triplet of unpaired bases at one end (known as the anticodon) and a region where a specific amino acid can attach at the other

Question 55

Describe the stages by which translation occurs ( part 1 ) ?

Answer 55

- In the cytoplasm, the mRNA attaches to a ribosome - Each tRNA has the complementary anticodon to the codon on the mRNA - The first tRNA forms hydrogen bonds with the first or 'start' codon of the mRNA - The second tRNA bonds with the next codon on the mRNA - A peptide bond form between the amino acids which is catalysed by the rRNA subunits of the ribosome

Question 56

Describe the stages by which translation occurs ( part 2 ) ?

Answer 56

- The ribosome moves along the mRNA 'reading' the next codon - The third tRNA bonds with the complementary codon - The first tRNA ( now without an amino acid ) is released - The ribosome continues to 'read' the mRNA molecule until it reaches a 'stop' codon, the amino acid chain then forms a final polypeptide