Biological molecules - enzymes, DNA, water, ATP

what do enzymes do?

lower the activation energy required to drive a reaction, enabling conditions to be met

how do enzymes lower activation energy?

they form an enzyme-substrate complex

why are enzymes necessary?

molecules must combine with sufficient energy for the reaction to happen so the bonds are put under sufficient strain

intracellular enzymes

work inside cells eg DNA polymerase

extracellular enzymes

secreted by cells and work outisde cells eg amylase

anabolic reactions

enzymes bring the substrate molecules together to build up molecules, reducing repulsion between molecules

catabolic reactions

enzyme active site affects/strains the bonds in substrate so they’re easier to break

how do enzyme bonds work?

substrate forms temporary bonds with amino acids in active site

what is the active site determined by?

the enzymes tertiary structure

lock and key mechanism

substrate molecules bind with active site as a consequence of complementary shapes and the enzyme produces environment necessary but remains unchanged

lock and key limitation

when other molecules bind to the enzyme at other places than the active site, the activity of the enzyme is altered

induced fit hypothesis

• enzymes have 3d flexibility

• binding of substrate induces enzyme to change shape

• so no exact fit when substrate is bound

• as it changes shape, enzyme puts strain on substrate

• strain distorts particular bonds in substrate

as temperature increases what happens to rate of reaction?

it increases because there is more kinetic energy and so more collisions and more enzyme-substrate complexes

what happens when temperature is too high?

enzymes denature because bonds that stabilise the tertiary structure are broken and protein unravels and loses shape so the active site changes

what happens when pH is too high or too low?

H+ and OH founds in acids and alkalis can disrupt ionic and hydrogen bonds that hold tertiary shape so denatures

substrate concentration?

as it increases, rate of reaction increases until excess of substrate concentration where maximum reaction rate is maintained

what is the limiting factor for substrate concentration?

enzyme concentration

enzyme concentration?

rate of reaction is directly proportional

competitive inhibitors

molecule competes with normal substrate for active site

what happens if the substrate concentration increases with a competitive inhibitor?

the inhibitors are overcome due to competition and maximum rate is reached

non competitive inhibitors

attach away from the active site and the inhibitor changes the shape of active site preventing induced fit

what happens if the substrate concentration increases with a non competitive inhibitor?

effect of inhibitor is not overcome and there is no change

what does RNA do in all living cells?

transfers genetic information from DNA to the ribosomes

what are ribosomes formed from?

RNA and proteins

examples of polymers of nucleotides

RNA and DNA

what are the components of DNA?

deoxyribose, a phosphate group and an organic base

what are the 4 organic bases in DNA?

adenine, cytosine, guanine and thymine

what are the components of RNA?

ribose, a phosphate group and an organic base

what are the 4 organic bases in RNA?

adenine, cytosine, guanine and uracil

what does a condensation reaction between 2 nucleotides form?

a phosphodiester bond

whats a nucleotide made up of?

phosphate, pentose sugar and nitrogen containing base

how do nucleotides run?

antiparallel - look in notes about 3 prime stuff

4 ways RNA differs from DNA

• sugar is ribose sugar

• uracil replaces thymine as a base (pairing with adenine)

• nucleotides form a single polynucleotide strand

• RNA strands are much shorter

why did scientists doubt that DNA held the genetic code?

it has a relatively simple composition

why does DNA replicate?

before cell division so that each new cell has full amount of DNA

what is the method of DNA replication called?

semi-conservative replication

what does enzyme DNA helicase do in the first step?

break the hydrogen bonds between bases on the two polynucleotide DNA strands making the helix unwind to form 2 single strands

what do the original strands do in step 2?

act as template for new strand with complementary base pairings meaning that free floating DNA nucleotides are attracted to their complementary exposed bases on original template strand

what catalyses the condensation reactions which join the nucleotides of the new strand together and what forms?

DNA polymerase and hydrogen bonds are formed between the bases on the original and new strands

why is the new strand made in a 5’ to 3’ direction?

the active site of DNA polymerase is only complementary t the 3’ end of the new strand

who’s experiment validated the semi conservative theory?

Meselson and Stahl

what isotopes were used in the experiment?

nitrogen (as DNA contains it) , heavy ^15N and light ^14N

how was the experiment prepared?

• 2 samples of bacteria were grown for many generations, one in a nutrient broth containing light and one heavy nitrogen

• as the bacteria reproduced they took up nitrogen to help make nucleotides so it gradually became part of bacteria’s DNA

• then spun in centrifuge and heavy settled low

• then bacteria grown in heavy taken out and placed in light for one round of DNA replication

results of experiment (pic)

what would have happened if the conservative theory was correct?

the original heavy DNA would still be together and settle at the bottom and the new light DNA would settle at the top

what does ATP stand for?

adenosine triphosphate

what is the structure of this nucleotide derivative?

nucleotide base adenine, ribose sugar and 3 phosphate groups

where is ATP made and stored?

made from energy released from glucose and stored in high energy bonds between the phosphate groups

what is ATP broken down into?

ADP (adenosine diphosphate) and Pi (inorganic phosphate)

what reaction is the breakdown of ATP and what catalysed it?

hydrolysis reaction where phosphate bond is broken and energy is released catalysed by ATP hydrolase

what can ATP hydrolysis do?

couple to other energy required reactions meaning the energy released can be used directly to the coupled reaction rather than being lost as heat

what can the inorganic phosphate do?

phosphorylate other compounds often making them more reactive

how is ATP resynthesised?

by the condensation of ADP and Pi catalysed by ATP synthase during photosynthesis or respiration

what is the polarity of water?

water is a polar molecule with slight negative charge on one side and slight positive on the other

why are there hydrogen bonds between molecules of water?

sightly negative charged oxygen atoms of water attract the slightly positive hydrogen atoms

how does water help in metabolic reactions?

it is a metabolite which means its involved in many reactions like hydrolysis and condensation

how is being a solvent useful for water?

living organisms can take up useful substances dissolved in water and these can be transported around the organisms body

why is water having a high heat capacity good?

it can buffer changes to temperature meaning that water doesn’t experience rapid temperature change in habitats and in organisms helping to maintain a constant body temperature

why is having a high latent heat of vapourisation good?

there is a cooling effect with little loss of water through evaporation because it takes a lot of energy to break hydrogen bonds between water molecules so lots of energy is used up

what is cohesion and why is water cohesive?

the attraction between molecules of the same type which molecules have because they are polar

why is it god that water is very cohesive?

this supports columns of water in the tube-like transport cells of plants and produces surface tension where water meets air

where do inorganic ions occur?

in solution in the cytoplasm and body fluids of organisms, some in high concentrations and others in very low concentrations

what are inorganic ions?

ions that don’t contain carbon

where are iron ions found?

in haemoglobin and it is the molecule that binds to oxygen

what are hydrogen ions used in?

pH based on the concentrations of it and enzyme controlled reactions are all affected by this

what are sodium ions used in?

the co transport of glucose and amino acids

what are phosphate ions used in?

components of DNA and ATP