Chemistry of life: Terms(Questions) & Definitions

	Terms	Definitions
	What are the 4 most commonly occurring elements in living things?	Carbon, hydrogen, oxygen, nitrogen.
	What are 5 other elements living things require?	Sulfur, calcium, phosphorus, iron, sodium.
	What is the function of sulfur?	Used in proteins in prokaryote, animal and plant cells.
	What is the function of calcium?	Flagella movement in prokaryotes forms cell plate during cytokinesis in plants, used in shells, bones, teeth and vesicle fusion in animals.
	What is the function of phosphorus?	Nucleic acids and ATP in animals, plants and prokaryotes.
	What is the function of iron?	Cytochrome (used in respiration) in palnts, and in cytochrome for mitochondrial respiration in plants and animals, hemoglobin.
	What is the function of sodium?	Main cation in cytoplasm of plant cells, nerve impulse transmission in animals.
	Why is water polar?	Because it has positive and negative ends/poles.
	Why is water cohesive?	Because the negative end of one molecule's oxygen can form a hydrogen bond with the positive hydrogen of another molecule.
	What can be said about water's specific heat capacity?	It is high i.e. it can store a lot of heat.
	What solvent property is water given by its polarity?	It can dissolve other polar molecules and ions such as sugars, amino acids and sodium ions.
	Give the three main functions of water in organisms.	Coolant, medium for metabolic reactions and a transport medium.
	Why can water be used as a coolant?	It requires a high input of energy to break the hydrogen bonds and turn it into a vapour; so, evaporation of water off of the surface of an organism allows it to lose heat.
	Give an example of water being used as a coolant.	Plants in deserts increase transpiration when in danger of overheating.
	Why can water be used as a medium for metabolic reactions?	It is a good solvent, and is a liquid between 0-100 degrees centigrade, the temperature in most regions of the Earth.
	What function does a watery habitat serve for organisms?	It dissolves substances which can then be absorbed by organisms.
	What function does a watery cytoplasm serve for organisms?	It dissolves substances, and metabolic reactions can take place easily between substances dissolved in a liquid medium.
	Why can water be a transport medium?	Its high specific heat capacity means it can store heat energy, and so organisms use if for heat transport (e.g. in blood). It is a good solvent and a dense medium, so it can dissolve substances and support heavy particles, and the cohesive property of water creates the transpiration stream in plants.
	What are organic compounds?	Those that contain carbon and are found in living organisms.
	What do organic compounds not contain?	Carbonates, hydrogencarbonates and oxides of carbon.
	What do amino acids contain?	Nitrogen and a variable R side group.
	How many amino acids are there which are used in proteins?	20.
	What is the formula of glucose?	C6H12O6
	What is the formula of ribose?	C5H10O5
	What functional groups do fatty acids have?	A CH3 on one side and a COOH on the other.
	How many CH2 groups are there in fatty acids?	Variable, but usually between 12 and 22.
	What other groups can fatty acids have?	CH groups with double bonds between adjacent carbons.
	What is an unsaturated fatty acid?	One with double bonds.
	What is a saturated fatty acid?	One without double bonds.
	What is a polyunsaturated fatty acid?	One with a large number of double bonds.
	What are the three main types of carbohydrate?	Monosaccharides, disaccharides, polysaccharides.
	Name 3 monosaccharides.	Glucose, galactose, fructose.
	Name 3 disaccharides.	Maltose (2xglucose), lactose (glucose+galactose), sucrose (glucose+fructose).
	Name 3 polysaccharides.	Starch, glycogen, cellulose (all poly-glucose).
	Give a function of glucose.	It is broken down in animal respiration to release energy.
	Give a function of lactose.	It is a sugar in milk produced by mammals.
	Give a function of glycogen.	It is an energy store in liver and skeletal muscles.
	Give a function of fructose.	It is an energy source for plants and a component of sucrose.
	Give a function of sucrose.	It is un reactive and so is transported around the plant.
	Give a function of cellulose.	It is the main component of cell walls.
	What happens during condensation?	2 units are joined together with the release of water.
	What happens during hydrolysis?	2 units are separated using water.
	What are 6 functions of lipids?	Cuticle on leaf to prevent water loss, thermal insulation in animals as sub-cutaneous fat, energy store in plants and animals, oil on feathers and fur for water-proofing, main component of myelin sheath of neurons, buoyancy in aquatic animals.
	Give 4 features of using carbohydrates as energy stores.	17kJ/g energy released, easily built up and broken down, present as glycogen in animals and starch in plants, converted to glucose when energy is needed.
	Give 4 features of using lipids as energy stores.	38kJ/g energy released, hence more efficient than carbohydrate, hydrophobic, so less mass taken up storing water, metabolic pathways for build up and breakdown more complex and slower, converted to fatty acids and glycerol when energy is needed, then to coenzyme A.
	What are the three parts of a nucleotide?	A phosphate group, a deoxyribose sugar and a base.
	What links the sugar to the base and phosphate?	Strong covalent bonds.
	What are the four bases in DNA?	Adenine, thymine, cytosine, guanine.
	How does the double helix form?	Complementary base pairing (A-T, C-G), where the 2 sugar phosphate chains are anti-parallel. Weak hydrogen bonds form between the bases to hold the chains together.
	What are cytosine and thymine?	Pyramidines.
	What are adenine and guanine?	purines.
	How many hydrogen bonds does the A-T connection have?	2.
	How many hydrogen bonds does the C-G connection have?	3.
	What directions do the DNA strands have?	One is 5'-3', the other is 3'-5'.
	What does 5' mean?	Carbon 5 of the sugar has a phosphate attached and nothing else - it is a 'free end'.
	What does 3' mean?	Carbon 3 contains a hydroxyl group and is the other 'free end'.
	What is linked to the 5 and 3 carbons?	The sugars.
	What do nucleosomes consist of?	A group of histone proteins with the DNA wrapped around; the DNA is locked in place by a second type of histone.
	What are the 2 functions of nucelosomes?	They help supercoil the chromosomes and help to regulate transcription.
	What are the 2 types of nuclear DNA?	Unique or single-copy genes and highly repetitive sequences.
	What does 55-95% of the DNA consist of?	Sequences, called genes that only have a single copy.
	What do the single-copy genes code for?	The functional polypeptides used by the cell or body, such as structural proteins, transport proteins, enzymes, hormones.
	What does 5-45% of the DNA consist of?	Highly repetitive sequences.
	What are highly repetitive sequences?	They can be 5-300 base pairs long, and can be repeated a moderate number of times, or up to 10^5 times in a genome. The location of these sequences shows no apparent patter, and their function is generally unclear.
	What can we use the highly repetitive sequences for?	DNA profiling.
	What else do eukaryotic genes contain?	Introns and exons.
	Is DNA replication conservative or semi-conservative, and what does this mean?	Semi-conservative; the DNA double helixes produced will both contain one strand of the old DNA and one new strand.
	What is the first step of DNA replication?	DNA helicase unwinds the DNA double helix by breaking the bonds between the bases; this forms the replication fork.
	what does DNA polymerase III do?	It adds on new nucleotides to create the complementary strand of DNA, with hydrogen bonds between the bases, i.e. adds deoxynucleoside triphosphates to the 3' end.
	What is the genetic code?	The linear sequence of bases.
	How is the genetic code preserved?	By complementary base pairing.
	What direction does DNA replication occur in?	5'-3'.
	What does RNA primase do?	Adds nucleoside triphosphates on the lagging strand to form an RNA primer.
	What does DNA polymerase I do?	Removes the RNA primer, replaces it using deoxynucleoside triphosphates.
	What does DNA ligase do?	Joins the Okazaki fragments together.
	What are Okazaki fragments?	Short lengths of single-stranded DNA made on the lagging strand.
	What are deoxynucleoside triphosphates?	The building blocks of DNA; consist of the deoxyribose sugar, with a base and three phosphates.
	What happens when the deoxynucleoside triphosphates are attached to others in DNA synthesis?	The two phosphates are removed, leaving only one for the sugar-phosphate backbone.
	What are nucleoside triphosphates?	The molecules used to synthesise RNA, which is the same thing with ribose sugar instead.
	Does DNA replication occur at one point only?	No - it is initiated at many points within eukaryotic chromosomes.
	What are the 3 structural differences between RNA and DNA?	RNA is single stranded (but can fold back on itself to form double-stranded regions), has the base uracil instead of thymine, and has the sugar ribose instead of deoxyribose.
	What are the 3 main differences of transcription compared to DNA replication?	Only one strand of the DNA is copied, RNA nucleotides are used (there is a pool of these in the nucleoplasm), the enzyme RNA polymerase is used.
	What are the 3 key steps of transcription?	DNA is unzipped by RNA polymerase, RNA polymerase builds mRNA by pairing mRNA nucleotides onto the strand of DNA opposite the desired gene, mRNA is released and leaves the nucleus.
	How many RNA bases code for one amino acid?	3.
	How many codes are there for stop codons?	3.
	What are stop codons?	Markers of the end of the 'message' on mRNA.
	How many codes are there in total?	64.
	What is degeneracy?	When two codes code for the same amino acid.
	Why is the code universal?	Because all organisms use this same code.
	What is translation?	The process used to manufacture a polypeptide chain from the mRNA code.
	What direction does transcription occur in?	5'-3'.
	What is the sense strand?	The side of the DNA double helix that is a gene.
	What is the antisense strand?	The complementary sequence of bases, which is transcribed into RNA.
	Which strand has the same sequence of bases as the RNA strand?	The sense strand, replacing T with U.
	What is the promoter region?	A specific sequence of DNA bases at the start of a gene on the sense strand where RNA polymerase binds.
	What is the purpose of RNA polymerase?	Adds nucleoside triphosphates using base pairing to the DNA template. It can only bind to DNA in the presence of other special proteins made by genes elsewhere in the genome.
	What does the RNA polymerase do as it moves forwards?	It unwinds and separates the DNA at the front, and rewinds it at the back.
	When does the RNA separate from the DNA?	As it is synthesised.
	What is the terminator region?	A specific sequence of DNA bases marking the end of the transcription process on the sense strand.
	What happens to the RNA polymerase when it reaches the terminator region?	It breaks free and the mRNA is released.
	What does primary RNA contain?	Introns.
	What are introns?	Sequences that are not translated into part of the protein, and must be removed.
	What do the exons do?	They make up the mature RNA.
	Where does the post-transcriptional modification of mRNA take place?	In the nucleus.
	How many types of tRNA are there?	61, as there are 61 codons (excluding stop codons).
	Where does the amino acid join on the tRNA?	At the 3' end.
	What does adding the amino acid require?	Energy from ATP and a specific enzyme.
	What are ribosomes composed of?	Ribosomal RNA and protein, in two subunits.
	What does the small subunit of the ribosome do?	Binds to the mRNA.
	What does the large subunit of the ribosome do?	Has three binding sites to bind to tRNA.
	Where are ribosomes manufactured?	In the nucleolus within the nucleus.
	What are the 4 stages of transcription?	Initiation, elongation, translocation and termination.
	What happens during initiation?	The small ribosome subunit binds to mRNA and the first charged tRNA binds to the start codon (charged means it has an amino acid attached).
	What is the start codon in prokaryotes?	AUG.
	What does initiation form?	The initiation complex.
	Where does initiation take place?	In the cytoplasm, where the ribosomal subunits are.
	What happens during elongation?	The large ribosome subunit attaches so that the 1st charged tRNA is in binding site 1 (in the middle). The second charged tRNA binds in the second binding site (on the right). A peptide bond is formed between the two amino acids.
	What is a peptide bond?	A bond between the C of a C=O and the N of an N-H.
	Where is the polypeptide synthesised if it is designed for expot?	on the rER.
	How is it known that a polypeptide is for export?	The first part of the polypeptide is a signal that causes the ribosome to bind to the rER.
	What happens to the polypeptide as it is released if it has been synthesised on the rER?	It is passed through a protein channel in the rER.
	What happens during translocation?	The mRNA is moved along one codon, and so the ribosome has moved along one codon in the 5'-3' direction. The uncharged tRNA is now in the 3rd site and is separated from the mRNA. It breaks free and picks up another amino acid from the cytoplasm. The 3rd charged tRNA moves into the 2nd binding site, and this process repeats.
	What happens during termination?	The ribosome reaches the stop codon. There are no tRNAs with an anticodon for a stop codon. Release factors bind to site 2, and the ribosome subunits break free and the polypeptide is released.
	What kind of polypeptides do free ribosomes synthesise?	Those primarily for use within the cell and cytoplasm.
	What kind of polypeptides do ribosomes bound to the rER synthesise?	Those primarily for secretion or lysosomes.
	How does the cell overcome the need to produce many polypeptides in large quantities?	As it would be energetically inefficient for each mRNA to synthesis only one polypeptide before being destroyed, ribosomes join behind the first ribosome so that multiple copies of the polypeptide can be synthesised rapidly.
	What are enzymes?	Large molecules folded to form a 3-dimensional globular structure that act as catalysts.
	What is an enzyme's active site?	A specifically shaped "pocket" for that enzyme's substrate to fit into. The shape of the active site matches the shape of the substrate, so that substrates are brought together in the correct orientation.
	What happens to the bonds in substrates when bound to an enzyme?	They are weakened, making a reaction easier.
	Which 3 factors affect enzyme action?	Substrate concentration, pH, temperature.
	How does substrate concentration affect enzyme action?	Amount of enzymes, and therefore active sites, is fixed. As substrate concentration increases, more collisions occur with the enzymes and so more reactions occur. At a point, all the active sites are occupied by substrate at any one time, and so there can be no further increases in reaction rate.
	How does pH affect enzyme action?	The 3D shape of the enzyme is held in place by bonds, which are strongest at the optimum pH. Changing the pH affects these bonds and the shape of the active site; if the substrate can no longer bind to the active site, reaction rate drops.
	How does temperature affect enzyme action?	Temperature increases the molecular movement, and so the molecules in the solution collide with more energy, so more reactions occur. However, beyond the optimum temperature, the amino acids in the protein are moving so much that weak bonds are broken and the molecule begins to fall apart. The shape of the active site no longer fits the substrate and the reaction cannot take place.
	Define "denaturation"	The irreversible, structural change in an enzyme that makes it unable to catalyse due to the substrate no longer fitting its active site.
	Give a practical use of enzymes.	Production of lactose-free milk.
	Why is lactose-free milk needed?	Some adults are intolerant to lactose, as the gene producing lactase gets switched off with age, and as lactose is a disaccharide it cannot be absorbed in the gut. The lactose is then fermented by bacteria in the large intestine resulting in nausea, abdominal pain and diarrhea.
	How can milk be made lactose-free?	It is treated with lactase; this breaks down lactose to the monosaccharides glucose and galactose, which are easily absorbed by the gut.
	Where is the lactase obtained from?	The fungus Kluyveromyces lactis.
	Practically, how is the milk treated with lactase?	The lactase is immobilized and the milk is passed over it; this prevents the lactase from being in the product and is more economical, as it can then be reused.
	What are 3 commercial applications of lactose-free milk?	Making ice cream (lactose crystallises and makes the ice cream grainy, whereas glucose and galactose stag dissolved). Yoghurt production, as bacteria can ferment glucose and galactose quicker than lactose, making production quicker. Lactose is also less sweet-tasting than glucose and galactose, so using lactose-free milk means less added sugar has to be added to products.
	What do metabolic pathways consist of?	Chains and cycles of enzyme-catalysed reactions.
	What does the "induced-fit model" mean?	The shape of the active site only corresponds to the shape of the substrate once it binds, which prevents possible but undesirable substrates from binding. The active site is flexible, so it allows a group of related molecules with similar shapes to be able to bind (e.g. peptidases). The reduces the number of different types of enzymes needed.
	What is needed for a reaction to occur?	The necessary activation energy.
	What do enzymes do to the activation energy?	They lower it, so that the reaction can take place at lower physiological temperature (usually between 0 and 40 degrees celsius).
	What are the two types of enzyme inhibition?	Competitive and non-competitive.
	What happens in competitive inhibition?	The substrate and inhibitor have similar shapes and compete for the active site.
	What is an example of competitive inhibition?	In the liver, the metabolic pathway is: ethanol -> acetaldehyde -> acetate. Aldehyde dehydrogenase is the enzyme to convert acetaldehyde to acetate. Disulfiram is a drug used to help recovering alcoholics; it blocks the active side of aldehyde dehydrogenase, so acetaldehyde is not broken down in the liver and its accumulation in the blood causes severe headaches and nausea.
	What happens in non-competitive inhibition?	The inhibitor has its own binding site, and binding of the inhibitor causes a conformational change in the shape of the active site, preventing the binding of the substrate.
	Give an example of non-competitive inhibition.	Enzyme: acetylcholinesterase, substrate: acetylcholine, inhibitor: nerve gas Sarin.
	What is the difference in effect of non-competitive and competitive inhibition at high concentrations?	Non-competitive inhibition will always reduce the rate of reaction at any concentration as the inhibitor binds to a separate site, whereas at higher substrate concentrations, the concentration of a competitive inhibitor becomes so low that it has no effect.
	Where is non-competitive inhibition often used in the body?	To regulate metabolic pathways.
	What are enzymes that are inhibited non-competitively in metabolic pathways called?	Allosteric enzymes.
	What is the inhibitor for allosteric enzymes called?	The effector.
	How do allosteric enzymes work?	The enzyme has two subunits, one with the substrate active site and the other with the allosteric site, where the effector binds (there may be more than one of these). The enzyme can alternate between an active form, which reacts with the substrate, and an inactive form, which does not. The effector can be an activator or inhibitor of the enzyme: the activator stabalises the active form, and the inhibitor stabalises the inactive form.
	Give an example of an allosteric enzyme.	Phosphorylase is an enzyme in muscle which removes a glucose phosphate from the end of glycogen at the start of glycolysis. If the muscle is resting, its relative concentration of ATP will be high. If it is active, it will use up ATP and its relative concentration of AMP (adenosine monophosphate) will be high. AMP is the activator and ATP is the inhibitor; the enzyme is thus regulated so that glycogen is not broken down unnecessarily.