Nucleic acids and Enzymes

Question 1

What are nucleotides

Answer 1

-form monomers of nucleic acids DNA and RNA
-in RNA the nucleotide pentose sugar is ribose
-in DNA the nucleotide sugar is deoxyribose
-one phosphate group e.g ADP and ATP is an energy rich end product of most energy releasing biochemical pathways and used to drive energy requiring metabolic processes
-may be components of coenzymes

Question 2

Describe DNA as a nucleic acid

Answer 2

-DNA is found in the nuclei of all eukaryotic cells within cytoplasm of prokaryotic cells and inside some viruses
-it is hereditary material and carries coded instructions used in development and functioning of all known organisms
-DNA is an important macromolecule that makes up the structure of all living organisms, others being proteins, carbohydrates and lipids

Question 3

Describe structure of DNA

Answer 3

-DNA is a polymer as its made up of many nucleotides
-a molecule DNA consists of 2 polynucleotide strands run in opposite directions ‘antiparallel’
-covalent bond between sugar residue and phosphate group is called phosphodiester - these are broken when polynucleotides breakdown and formed when polynucleotides are synthesised
-DNA molecules long and carry encoded genetic information

Question 4

Purines and pyrimidines

Answer 4

PURINES= adenine, guanine
PYRIMIDINES= thymine, cytosine

Question 5

What is the importance of hydrogen bonds

Answer 5

-adenine always pairs with thymine by 2 hydrogen bonds
-guanine always pairs with cytosine by 3 hydrogen bonds
-a purine always pairs with a pyrimidine giving equal sized rungs of DNA ladder
-it can twist around an imaginary axis to form a double helix - gives the molecule stability
-hydrogen bonds allow molecules to unzip for transcription and replication

Question 6

How is DNA organised in eukaryotic cells

Answer 6

-majority of DNA content of genome is in nucleus
-each large molecule of DNA is tightly wound around special histone proteins - each chromosome therefore is a molecule of DNA
-there is also a loop of DNA without histone proteins inside mitochondria and chloroplasts

Question 7

How is DNA organised in prokaryotic cells

Answer 7

-DNA is in a loop and is in within cytoplasm not enclosed in a nucleus
-it is not wound around histone proteins - is described as naked
-viruses that contain DNA also have it in the form of a loop of naked DNA

Question 8

How is DNA a self replicating molecule

Answer 8

-all DNA within a cell (the genome) and within every cell of an organism carries the coded instructions to make and maintain that organism
-every time a cell divides the DNA has to be copied so that each new daughter cell receives full set of instructions
-each molecule of DNA replicates
-this replication takes place during interphase
-in eukaryotes this results in each chromosome having an identical copy of itself
-as first they are joined together by centromere forming two sister chromatids
-the DNA within mitochondria and chloroplasts also replicates each time these organelles divides

Question 9

Describe semi-conservative replication

Answer 9

-to make a new copy, each DNA molecules
-unwinds so the double helix is untwisted a bit at a time, catalysed by gyrase enzyme
-unzips - hydrogen bonds between the nucleotide bases are broken - this is catalysed by DNA helicase and results in two single strands of DNA with exposed nucleotide bases
-free phosphorylated nucleotide present in nucleoplasm within nucleus are bonded to exposed bases following complementary base pairing rules
-the enzyme DNA polymerase catalyses the addiction of new nucleotide base sin the 5’ to 3’ directions to the single strand of DNA; it uses each unzipped DNA stand as a template
-the leading strand is synthesised continuously whereas the lagging strand is in fragments (discontinuous) that are later joined catalysed by ligase enzymes
-hydrolysis of the activated nucleotides to release the extra phosphate groups supplies the energy to make phosphodiester bonds between the sugar residue of one nucleotide and phosphate group of next nucleotide
-the product of replication is 2 DNA molecules identical to each other and parent molecule

Question 10

Why is it called semi conservative replication

Answer 10

-each of the new DNA molecules contains one old strand and one new strand

Question 11

How do mutations occur

Answer 11

-during DNA replication errors may occur and wrong nucleotide may be inserted
-this is estimated to occur 1 in 10^8 base pairs
-this could change genetic code and example of point mutation
-during replication process there are enzymes that can proof read and edit out such incorrect nucleotides reducing rate of mutations produced
-not all mutations are harmful - some appear to give neither advantage or disadvantage - e.g. rolling tongue
-some can be advantageous - white coat in winter for camouflage

Question 12

RNA structure in comparison to DNA

Answer 12

-the sugar molecule in each nucleotide is ribose
-the nitrogenous base is uracil which is pyrimidine, places pyrimidine base thymine
-polynucleotide chain usually single stranded
-polynucleotide chain shorter
-3 forms of RNA - messenger RNA, transfer RNA and ribosomal RNA

Question 13

What is transcription and translation

Answer 13

TRANSCRIPTION
-process of making messenger RNA from DNA template
TRANSLATION
-formation of a protein at ribosomes by assembling amino acids into a particular sequence according to coded instructions from DNA to ribosome by mRNA

Question 14

What are genes

Answer 14

-on each chromosome there are specific lengths of DNA called genes
-each gene contains code that determines sequence of amino acids in particular protein
-some proteins as structural e.g. cytoskeleton where as others are metabolic such as enzymes
-within each gene there is sequence of DNA base triplets that determine amino acid sequence or primary structure of polypeptide
-as long as primary structure correct, it will fold correctly and carry out unction

Question 15

Why must transcription occur

Answer 15

-as instructions inside genes, on chromosomes, cannot pass out of nucleus, a copy of each gene has to be transcribed into length of mRNA
-in this form sequence of base triplets now called codons can pass out of nucleus to ribosome ensuring coded instructions translated and protein assembled correctly

Question 16

Describe the nature of the genetic code

Answer 16

-the genetic code is near universal because in almost all living organisms the same triplets of DNA bases codes for same amino acid
-genetic code described as degenerate because for all amino acids, except two, there is more than one base triplet - this may reduce effect of point mutations as a change in one base of triplet could produce another base triplet that still codes for same amino acid
-genetic code is non overlapping and it’s read from fixed point in groups of 3 bases
-if base added or deleted causes frame shift as every base triplet is changed

Question 17

Describe transcription

Answer 17

-a gene unwinds and unzips
-hydrogen bonds between complementary nucleotide bases break
-enzyme RNA polymerase catalyses formation of temporary hydrogen bonds between RNA nucleotides and complementary unpaired DNA bases
-A to T, C to G, U to A on one strand of unwound DNA
-this stand called template strand
-length of RNA that is complementary to template strand of gene produced
-it is therefore copy of other DNA strand - coding strand
-mRNA now passes out of nucleus through nuclear envelope and attaches to ribosome

Question 18

How are ribosomes made

Answer 18

-ribosomes made in nucleolus in two smaller subunits
-these pass separately out of nucleus through pores in nuclear envelope then come together to form ribosome
-magnesium ions help bind two subunits together
-ribosomes made of ribosomal RNA and protein

Question 19

Describe translation

Answer 19

-transfer RNA molecules are made in nucleolus and pass out of nucleus into cytoplasm
-they are single stranded in polynucleotide
-at one end of trionucleotide base that recognises and attaches to specific amino acid
-at loop of hairpin is another triplet of bases called anticodon that is complementary to specific codon

Question 20

Describe translation at ribosome

Answer 20

-transfer RNA bring amino acids and find place when anticodon binds by temporary hydrogen bonds to complementary codon on mRNA
-as ribosome moves along length of mRNA it reads code and when two amino acids adjacent to each other a peptide bond forms
-energy from ATP needed for polypeptide synthesis
-amino acid sequence for polypeptide determined by sequence of triplet nucleotide bases on length of DNA - gene
-after polypeptide assembled mRNA breaks down- its component molecules can be recycled into new lengths of mRNA with different codon sequences
-newly synthesised polypeptide helped by chaperone proteins to fold correctly into 3D shape or tertiary structure to carry out functions

Question 21

What are enzymes

Answer 21

-enzymes are biological catalysts as they speed up metabolic reactions
-at end they remain unchanged and reusable
-small amount catalyst can catalyse conversion of large number of substrate molecules to product molecules
-number of reactions that enzyme can catalyse per second is turnover number

Question 22

Compare biological and chemical catalysts

Answer 22

-chemical enzymes usually need very high temperatures, increased pressures and extreme pH where as biological enzymes speed up metabolic reactions by up to 10^12 times at lower temperatures, neutral pH and normal pressure - hence can function in conditions that sustain life
-enzymes more specific than chemical catalysts
-do not produce unwanted by products and rarely make mistakes
-cells in which they are made and/or act can regulate their activity and production

Question 23

How does enzyme structure determines function

Answer 23

-for enzymes to catalyse some reactions they may need help from cofactors
-the instructions for making enzymes are encoded in genes
-if gene has mutation that alters the sequence of amino acids in the protein then this may alter enzymes tertiary structure and prevent it from functioning
-if enzyme catalyses formation of organisms structural components such as collagen in bone, cartilage, blood vessel walls, joints and connective tissue
-genetic disorders cause malformation of connective tissue and can be very harmful such as stone man syndrome

Question 24

Describe the active site of enzymes

Answer 24

-enzymes are large molecules with specific area, an indentation or cleft on surface of molecule called active site
-this consists of just few amino acids
-tertiary structure of active site is crucial as its shape is complementary to shape of substrate molecule
-each type enzyme is highly specific in its function as it can only catalyse reaction involving particular type of substrate molecules
-shape of enzymes active site can be altered by changes in temperature and pH as these affect tertiary structure

Question 25

Describe intracellular enzymes

Answer 25

-each metabolic pathway in living cell is series of consecutive reactions, catalysed by specific enzyme that produces specific product
-various reactants and intermediates act as substrates for specific enzymes
-the reactants, intermediates and products are known as metabolites
-in some metabolic pathways described as anabolic, energy used to synthesis larger molecules from smaller molecules
-in others, described as catabolic, metabolites broken down to smaller molecules and release energy

Question 26

What is catalase

Answer 26

-found in nearly all living organisms that are exposed to oxygen
-it is a very important enzyme as it protects cells from damage by reactive oxygen by quickly breaking down hydrogen peroxide, a potentially harmful by product of many metabolic reactions to water and ocygen
-catalase consists of four polypeptide chains and contains a haem group with an iron
-in eukaryotic cells, catalase is found inside small vesicles called peroxisomes
-then white blood cells ingest pathogens they use catalase to help kill invading microbe
-the optimum pH for human catalase is around pH 7

Question 27

Describe extracellular enzymes

Answer 27

-some enzymes are secreted from the cells where they are made and act on their substrates extracellularly
-fungi such as bread mould release the hydrolytic enzymes from their thread-like hyphae enzymes digest carbohydrates, proteins, and lipids in bread
-glucose, amino acids, glycerol and fatty acids are absorbed into the fungal hyphae for use in respiration and growth

Question 28

Describe digest enzymes

Answer 28

-in our digestive system many enzymes are secreted from cells lining the alimentary canal into the gut lumen
-they extracellularly digest the large molecules such as proteins, lipids, carbohydrates and nucleic acids found in food
-the products of digestion are then absorbed via epithelial cells of gut wall into bloodstream in order to be used for respiration, growth and tissue repair
-amylase is produced in the salivary glands and acts in the mouth to digest the polysaccharide starch to disaccharide maltose
-it is also made in the pancreas and acts to catalyse the same reaction in the lumen of the small intestine
-trypsin is made in the pancreas and acts in the lumen of the small intestine to digest proteins into smaller peptides by hydrolysing peptide bonds
-its optimum pH is between 7.5-8.5

Question 29

Steps of translation

Answer 29

-transfer RNA (tRNA)
-made in the nucleus and passes into the cytoplasm through nuclear pore
-tRNA brings amino acids to form polypeptide chain
-peptide bonds form between amino acids
1) anticodon binds with temporary H bonds to the codon
2) peptide bond forms between 2 amino acids
3)ATP required
4) DNA triplet - mRNA codon- tRNA codon - amino acid sequence
5) secondary/tertiary structure depends on correct sequence

Question 30

What is the lock and key hypothesis

Answer 30

-the substrate molecules fit to the active site due to the tertiary structure of the active site; gives it a shape that is complementary to that of substrate molecule
-this idea about how enzymes work is called lock and key hypothesis

Question 31

Steps of lock and key hypothesis

Answer 31

1) substrate molecule fits into enzyme active site. Temporary hydrogen bonds hold 2 together and form enzyme substrate complex
2) substrate molecule is broken into smaller product molecules that leave active site
3)substrate molecules fit into the active site forming an enzyme-substrate complex
4) bonds form between substrate molecules and form enzyme product complex
5)larger product molecule leaves active site

Question 32

Describe the induced fit hypothesis

Answer 32

-the active site still has a shape complementary to shape of substrate molecule; on binding the subtle changes of shape of side chains of amino acids that make up active site give a more precise conformation that exactly fits substrate molecule
-this moulding enables substrate to bind more effectively to active site
-an enzyme substrate complex is formed and non covalent forces such as hydrogen bonds, ionic attractions, hydrophobic interactions bind the substrate molecule to active site
-when substrate molecule have been converted to product molecules and these are still in the active site, they form an enzyme product complex
-as product molecules have a slightly different shape from substrate molecule, they detach from active site
-the enzyme molecule is now free to catalyse another reaction with another substrate molecule of same type

Question 33

Who developed the induced fit theory

Answer 33

-1958, Daniel Koshland modified lock and key hypothesis by suggesting active site of enzymes is not rigid, fixed structure but that presence of substrate molecule induces a shape change, giving it good fit
-suggested that: when substrate molecules fit into the enzymes active site, the active site changes shape slightly to mould itself around substrate molecule

Question 34

How do enzymes lower activation energy of a reaction

Answer 34

-chemical reactions need energy to activate/ begin
-many chemicals can use heat- this increase kinetic energy of molecules so move more and therefore more likely to successfully collide and react together
-in living cells the temperature cannot be raised too much or proteins within it denature and lipids melt
-because enzymes have active specific to only substrate molecules they bring substrate molecules close enough together to react without need of excessive heat
-therefore lower activation energy and hence speed up metabolic reactions

Question 35

How does heat effect kinetic energy

Answer 35

-it substance is heated-
-extra energy in form of heat cause molecules to move faster
-increase rate of collisions between molecules
-also increases force with which collide due to moving faster

Question 36

How does temperature effect the collisions between enzymes and substrate molecules

Answer 36

-if reactant mixture containing enzyme and substrate heated
-both types molecule gain kinetic energy and move faster - increase rate of successful collisions
-rate of formation of ES complexes increase and rate of reaction increases - increase number of enzyme-product complexes per second up to a point
-at particular temperate (enzymes optimum temperature) rate of reaction is at its maximum

Question 37

How is vibration effected by heat

Answer 37

-this may make some of weak bonds break such as hydrogen and ionic that hold tertiary structure of enzymes active site
-as active site changes, substrate molecules that will not fit in so well and rate of reaction begins to decrease
-as more heat applied, enzymes active site changed completely and irreversible so its no longer complementary reaction cannot proceed at all
-enzyme is denatured - heat doesn’t break peptide bonds between amino acids so primary structure is not altered

Question 38

Describe the optimum temperature

Answer 38

-temperature at which enzyme works best - maximum rate of reaction
-some enzymes work best at cool temperatures - for example psychrophilic bacteria
-some organisms, like thermophilic bacteria in hot springs live at very high temperatures
-their enzymes are heat stable due to more disulfide bonds that do not break with heat and keep shape of protein molecules stable

Question 39

What is the temperature coefficient Q10

Answer 39

-refers to increase in rate of process when temperature increased by 10 degrees
Q10= rate of reaction at T+10/ rate of reaction at T

Question 40

What is pH

Answer 40

-pH indicates whether substance acidic, alkaline or neutral
0-6= acidic
7=neutral
8-14=alkaline
-acids such as hydrochloric acids and sulfuric acids dissociated into protons and negatively charged ion
-organic acids are also proton donors -
-lactic acids dissociates into H+ and lactate
-pyruvic acid dissociates into H+ and pyruvate

Question 41

Describe buffers

Answer 41

-a buffer is something that resists changes in pH
-there are certain chemicals in blood that help resist changes in pH so it stays close to 7.4
-they donate or accept hydrogen ions

Question 42

How do changes in pH affect molecule bonds

Answer 42

-a hydrogen ion has a positive charge so it is attracted towards negatively charge ions. molecules or parts of molecules
-hydrogen bonds and ionic forces between amino acids hold tertiary structure of an enzyme, particularly active site, in correct shape
-excess hydrogen ions will interfere with hydrogen bonds and ionic forces so active site changes shape
-if substrate molecule doesn’t fit well to active site, rate of reaction that enzyme catalyses will be lowered
-increasing concentration of hydrogen ions will also alter changes on active site of enzyme molecules as more protons will cluster around negatively charged groups in active site- this interferes with binding of substrate to active site
-hydrogen bonds hold structures like an alpha helix in place in protein molecules