module 2 - DNA and enzymes

Question 1

NUCLEOTIDES & POLYNUCLEOTIDES - what is the structure of a nucleotide as the monomer from which nucleic acids are made?

Answer 1

• each nucleotide consists of :
• a pentose sugar (a sugar with 5 carbon atoms)
• an organic nitrogen-containing base
• a phosphate group —> nucleotides are monomers and many repeating units of them make up nucleic acids : DNA is a nucleic acid, RNA is a nucleic acid

Question 2

describe the synthesis and breakdown of polynucleotides by the formation and breakage of phosphodiester bonds

Answer 2

• DNA and RNA are polynucleotides, which means they are composed of numerous nucleotides linked in long chains
• through condensation processes, individual nucleotides are joined together
• these condensation processes involve the phosphate group of one nucleotide and the pentose sugar of the next nucleotide

Question 3

when is a phosphodiester bond formed?

Answer 3

• a phosphodiester bond is formed when two nucleotides undergo a condensation reaction
• because it consists of a phosphate group and two ester bonds, it is known as a phosphodiester bond

Question 4

what is the ‘sugar-phosphate backbone’ referring to?

Answer 4

• refers to the chain of alternating phosphate groups and pentose sugars formed by many phosphodiester linkages (of the DNA/RNA molecule)

Question 5

what does the breakdown of polynucleotides require?

Answer 5

• requires the breakdown of phosphodiester bonds

Question 6

describe the structure of DNA

Answer 6

• a nucleic acid made up of DNA nucleotides
• these are the constituents of a DNA nucleotide :
• a deoxyribose sugar that contains hydrogen at the 2’ position
• a phosphate group
• adenine (A), cytosine (C), guanine (G) or thymine (T) are the four possible nitrogenous bases
• DNA molecule is a double helix composed of two polynucleotides joined together by hydrogen bonds between complementary bases

Question 7

describe the structure of RNA

Answer 7

• a nucleic acid made up of RNA nucleotides
• these are the constituents of an RNA nucleotide :
• a ribose sugar with a 2’- hydroxyl (OH) group
• a phosphate group
• any one of the nitrogenous bases adenine (A), cytosine (C), guanine (G) or uracil (U)
• is a relatively short single polynucleotide chain

Question 8

what are the structures of ATP and ADP as phosphorylated nucleotides?

Answer 8

• ATP stands for adenosine triphosphate, it is a phosphorylated nucleotide
• has the same structure as an RNA nucleotide except :
• the base is always adenine (A)
• it has three phosphate groups rather than one
• is formed through a condensation reaction during respiration
• hydrolysis of ATP gives ADP+ one of the phosphates —> this reaction also provides energy for metabolic processes to occur

Question 9

how does the structure of ADP make it suitable for energy transfer?

Answer 9

• soluble
• releases small quantities of energy
• prevents energy wastage as a result
• has an easily broken phosphate bond which is unstable
• this makes breakdown into ADP and a phosphate easy

Question 10

NUCLEOTIDES AND NUCLEIC ACIDS - what is semi-conservative DNA replication?

Answer 10

• ensures genetic continuity between generations of cells meaning that genetic information is passed on from one generation to the next

Question 11

why is semi-conservative an important process?

Answer 11

• before a parent cell can divide, its DNA must be copied
• doubling the DNA guarantees that each of the two new (daughter) cells formed receives a complete copy of the parental DNA

Question 12

why is the process called ‘semi-conservative replication’?

Answer 12

• it is called semi-conservative replication because one of the polynucleotide DNA strands (half of the new DNA molecule) in each new DNA molecule is created from the original DNA molecule being duplicated
• keeping one original DNA strand guarantees genetic continuity between cell generations

Question 13

when does DNA replication occur?

Answer 13

• the S phase of the cell cycle
• occurs during interphase, when a cell is not dividing

Question 14

describe the process of semi-conservative replication (1)

Answer 14

• FIRST : histone proteins are removed
• THEN, helicase unwinds the DNA double helix by breaking the hydrogen bonds between the base pairs on the two antiparallel polynucleotide DNA strands, resulting in the formation of two single polynucleotide DNA strands

Question 15

describe the process of semi-conservative replication (2)

Answer 15

• each of these single polynucleotide DNA strands serves as a template for the development of a new strand composed of free nucleotides attracted to the exposed DNA bases via base pairing
• DNA polymerase then catalyses condensation reactions between the newly synthesised nucleotides to generate a new strand

Question 16

describe the process of semi-conservative replication (3)

Answer 16

• the new DNA molecule is formed when the original strand and the new strand combine through hydrogen bonding between base pairs

Question 17

what is the nature of genetic code? (1)

Answer 17

• a triplet (three-letter) codon determines the sequence of DNA nucleotide bases contained inside a gene
• each triple sequence of bases in a gene codes for a certain amino acid
• there are 20 amino acids that cells use to generate different proteins

Question 18

what is the nature of genetic code? (2)

Answer 18

• there are 4 bases, hence 64 distinct codons are conceivable (4^3 = 64), yet only 20 amino acids are often found in biological proteins

Question 19

why is genetic code ‘degenerate’?

Answer 19

• genetic code is ‘degenerate’ because several codons can code for the same amino acids
• degeneration of the genetic code can reduce the impact of mutations

Question 20

what is meant by the genetic code being ‘universal’?

Answer 20

• means that virtually all organisms employ the same code
• there are a few rare and minor exceptions

Question 21

how does the transcription of genes result in the synthesis of polynucleotides? (1)

Answer 21

following steps produce messenger RNA (mRNA) strand from a DNA sequence during transcription:
- typically, helicase unwinds DNA along the base sequence of a single gene
- RNA nucleotides attach to corresponding DNA bases on the antisense strand (template)

Question 22

describe the steps of the transcription of genes, resulting in the synthesis of polypeptides (2)

Answer 22

• RNA polymerase links RNA nucleotides together via phosphodiester bonds
• a stop codon causes RNA polymerase to detach
• the mRNA molecule dissociates from DNA, exits the nucleus

Question 23

how does the translation of genes result in the synthesis of polypeptides? (1)

Answer 23

translation takes place at ribosomes and involves the following sequence of events :
- the mRNA binds to the groove between the two subunits of a ribosome
- the initial mRNA codon binds to a transfer RNA (tRNA) molecule with a complementary anticodon
(continued)

Question 24

describe the steps involved in the translation of genes (2)

Answer 24

• the tRNA is linked to an amino acid that is unique to its anticodon
• a second tRNA transporting an additional amino acid attached to the adjacent mRNA codon
• between the two amino acids, a peptide bond forms
• the ribosome moves from codon to codon along the mRNA molecule
• amino acids form a polypeptide chain until they reach a stop codon
• the release of the polypeptide takes place

Question 25

ENZYMES - what is the mechanism of enzyme action?

Answer 25

• a substrate collides with the active site of an enzyme
• the shape of the active site is complementary to the substrate
• the substrate binds to the active site to form an enzyme-substrate complex (ESC)
• bonds within the substrates become strained and break, and the enzyme provides an alternative reaction pathway which reduces the activation energy
• the enzyme-product complex is formed and the product is released

Question 26

what is the role of enzymes in catalysing intracellular reactions?

Answer 26

• intracellular refers to when the enzyme is working inside cells
• this can be anabolic, which means their function is in the formation of molecules from smaller subunits
• EXAMPLE : DNA replication which involves the enzyme DNA polymerase

Question 27

what is the role of enzymes in catalysing extracellular reactions? (1)

Answer 27

• extracellular refers to when the enzyme is working outside cells
• these are mostly catabolic enzyme, which means their function is to break down molecules
• EXAMPLE : digestion —> like when the enzyme maltase breaks down maltose into glucose (two molecules result)

Question 28

what is the role of enzymes in catalysing extracellular reactions? (2)

Answer 28

• in many-celled organisms, they secrete digestive enzymes from their cells into their digestive system to break down food - in single-celled organisms such as yeast, they secrete their digestive enzymes straight into their immediate environment

Question 29

what is the role of enzymes in catalysing reactions that affect metabolism at a cellular and whole organism level?

Answer 29

• metabolism is the sum of all chemical reactions which take place in an organism
• metabolic reactions are controlled by enzymes
• they can either be anabolic or catabolic reactions

Question 30

FACTORS AFFECTING ENZYME ACTIVITY - what is the effect of pH on enzyme activity? (1)

Answer 30

• every enzyme has an optimal pH where it functions most effectively
• there is no general rule about which pH increases the rate of reaction as this is highly specific to the enzyme
  (continued)

Question 31

what is the effect of pH on enzyme activity? (2)

Answer 31

• the tertiary structure of a protein, or an enzyme, is held together by hydrogen bonds and ionic bonds
• solutions containing an excess of H+ ions (acidic solutions) and OH- ions (alkaline solutions) can cause these bonds to break below and above the optimal pH of an enzyme
• bond breaking changes the structure of the active site, making it more difficult for enzyme-substrate complexes to form

Question 32

what is the effect of pH on enzyme activity? (3)

Answer 32

• enzyme-substrate complexes eventually cannot form at all and the enzyme has completely denatured at this point
• denaturation is therefore caused by extreme deviations from an enzyme’s optimal pH

Question 33

what is the effect of temperature on enzyme activity?

Answer 33

• there is a certain optimal temperature for enzymes to function at
• generally, with greater temperatures there is a greater rate of reaction
• however past a specific temperature, this is no longer the case because the enzyme starts to denature and the active site is permanently damaged

Question 34

describe the effect of a lower temperature on enzyme activity

Answer 34

• either stop reactions from occurring or cause them to continue more slowly because :
• with reduced kinetic energy, there are fewer successful collisions between substrate molecules and the active sites of the enzymes, which results in fewer occurrences of the formation of enzyme-substrate complexes
• substrates and enzymes collide with less energy, linkages are less likely to form or break

Question 35

describe the effect of a higher temperature on enzyme activity

Answer 35

• cause reactions to speed up because :
• molecules travel more swiftly at higher temperatures and have greater kinetic energy
• a higher frequency of successful collisions between substrate molecules and the active sites of the enzymes is brought on by increased kinetic energy, which facilitates the formation of enzyme-substrate complexes more often
• substrates and enzymes clash more forcefully, linkages are more likely to form or break

Question 36

what is the effect of enzyme concentration on enzyme activity? (1)

Answer 36

• generally, with increased enzyme concentration, there is a greater rate of reaction
• the number of active sites that are accessible and the probability of the formation of an enzyme-substrate complex increases when enzyme concentration increases in a reaction mixture

Question 37

what is the effect of enzyme concentration on enzyme activity? (2)

Answer 37

• the initial rate of reaction increases linearly with enzyme concentration so long as there is enough substrate available
• when the amount of substrate becomes a limiting factor, any additional increase in enzyme concentration will eventually have no effect on the rate of reaction
• overall, the reaction rate increases linearly as enzyme concentration increases, but reaches a plateau when there is no longer available substrate

Question 38

what is the effect of substrate concentration on enzyme activity? (1)

Answer 38

• generally, with increased substrate concentration, there is a greater rate of reaction
• the number of substrate molecules that are accessible and the probability of the formation of an enzyme-substrate complex increases when substrate concentration increases in a reaction mixture

Question 39

what is the effect of substrate concentration on enzyme activity? (2)

Answer 39

• the initial rate of reaction increases linearly with substrate concentration so long as there are enough active sites available to bind to
• when the amount of available active sites becomes a limiting factor, any additional increase in enzyme concentration will eventually have no effect on the rate of reaction
• overall, the reaction rate increases linearly as substrate concentration increases, but reaches a plateau when all the possible active sites are saturated

Question 40

COFACTORS & ENZYME INHIBITION - define the word ‘coenzyme’

Answer 40

• coenzymes are small organic molecules that are required by certain enzymes to carry out their catalytic functions
• larger organic cofactors are known as coenzymes
• some coenzymes are permanently bound to the enzyme, while others bind temporarily during the reaction

Question 41

describe the need for coenzymes in some enzyme-controlled reactions

Answer 41

• coenzymes link enzyme-catalysed reactions in metabolic processes like photosynthesis and respiration
• vitamins are important sources of coenzymes
• they often participate in enzyme-substrate reactions by accepting or donating specific chemical groups
• EXAMPLES OF COENZYMES : NAD+ and FAD, which play crucial roles in redox reactions

Question 42

what are cofactors?

Answer 42

• inorganic ions or non-protein molecules that are essential for enzyme activity
• they can bind to the enzyme or the substrate, facilitating proper enzyme-substrate interactions
• some enzymes require inorganic ions for proper function
• inorganic ions required by enzymes are called inorganic cofactors

Question 43

list some examples of cofactors used in enzyme-controlled reactions

Answer 43

• chloride ions act as a cofactor for amylase, which digests starch into maltose
• metal ions such as magnesium (Mg2+) and zinc (Zn2+) are common cofactors involved in enzymatic reactions

Question 44

what are prosthetic groups?

Answer 44

• non-protein components that are tightly bound to the enzyme and are necessary for its function
• they can be organic or inorganic molecules, such as haem in haemoglobin and iron-sulphur clusters in electron transport chain enzymes

Question 45

why is there a need for prosthetic groups in some enzyme-controlled reactions?

Answer 45

• they are essential for proper enzyme function and contribute to the enzyme’s 3D shape
• EXAMPLE : a zinc ion acts as the prosthetic group for carbonic anhydrase, an enzyme converting CO2 and H2O to carbonic acid in red blood cells

Question 46

what is competitive inhibition?

Answer 46

• competitive inhibitors resemble the substrate and bind to the active site of the enzyme, preventing the substrate from binding
• the presence of a competitive inhibitor increases the concentration of substrate required for enzyme activity, slowing down the reaction rate

Question 47

what is non-competitive inhibition?

Answer 47

• non-competitive inhibitors bind to a site on the enzyme other than the active site, altering the enzyme’s shape and decreasing its activity
• the inhibitor and substrate can bind simultaneously to the enzyme, but the presence of the inhibitor reduces the rate of catalysis

Question 48

what is reverse inhibition?

Answer 48

• both competitive and non-competitive inhibition can be reversible, meaning the inhibitor can dissociate from the enzyme, allowing it to regain its activity
• reversible inhibitors can compete with the substrate for binding or interact with the enzyme through non-covalent interactions

Question 49

what is irreversible inhibition?

Answer 49

• irreversible inhibitors form covalent bonds or irreversible modifications with the enzyme, permanently inactivating it
• these inhibitors typically react with functional groups on the enzyme, rendering it unable to catalyse reactions