unit 1B - biological molecules Flashcards
DNA, RNA, Water, ATP and inorganic ions
what is DNA?
this is a type of nucleic acid and are found in all living cells which carry information.
DNA (deoxyribonucleic acid) is used to store genetic information - thats all the instructions an organism needs to grow and develop from a fertilised egg to a fully grown adult.
what is RNA?
this is a type of nucleic acid and are found in all living cells which carry information.
RNA (ribonucleic acid) is similar in structure of DNA. one of its main functions is to transfer genetic information from the DNA to the ribosomes. ribosomes are the bodies ‘protein factories’ - they read the RNA to make polypeptides (proteins) in a process called translocation. ribosomes themselves are made from RNA and proteins.
what is a nucleotide?
this is a type of biological molecule. its made from
- pentose sugar (with 5 carbon atoms)
- a nitrogen - containing organic base (organic means that it contains carbon)
- a phosphate group
RNA and DNA are polynucleotides and are made up of nucleotides (the monomer)
what is a nucleotide made out of?
1) the pentose sugar in the DNA nucleotide is called deoxyribose
2) each DNA nucleotide has the same sugar and a phosphate group. the base on each nucleotide can vary though.
3) there are four possible bases - adenine (A) and thymine (T), cytosine (C) and guanine (G)
What is the sugar in RNA and what is it made out of?
1) RNA contains nucleotides with a ribose sugar (not deoxyribose)
2) like DNA, an RNA nucleotide also has a phosphate group and one of four different bases
3) in RNA though, uracil (U) replaces thymine as a base
how do nucleotides form to polynucleotides?
1)a polypeptide is a polymer of nucleotides. both DNA and RNA nucleotides form polynucleotides.
2) the nucleotides join up via a condensation reaction between the phosphate group of one nucleotide and the sugar of another.
3) this forms a phosphodiester bond (consisting of the phosphate group and two ester bonds)
4) the chain of sugars and phosphate is known as the sugar-phosphate backbone
what is the structure and function of DNA?
1) two DNA polynucleotides strands join together by hydrogen bonding between the bases
2) each base can only join with one particular partner - this is called complementary base pairing.
adenine always pairs with thymine (A - T) with 2 hydrogen bonds
cytosine always pairs with Guanine (C -G) with 3 hydrogen bonds
3)two antiparallel (running in the opposite direction) polynucleotide strands twist to form the DNA DOUBLE HELIX
what is the history of the DNA structure
DNA was first observed in the 1800s but argued it couldn’t carry genetic code because of the simple chemical composition and some argued genetic information was carried by proteins which are more chemically varied.
however by the 1953, they found DNA was the carrier of the gentic code this was laso the year in which the double helix structure which helps DNA to carry out its function was determined by Watson and Crick.
structure of RNA
RNA is made up from a single polynucleotide chain (not a double one). its much shorter than most DNA polynucleotides
what are features and functions of water in living organisms?
1) water is metabolite in loads of important metabolic reactions, including condensation reactions and hydrolysis reactions
2) water is a solvent which means some substances dissolve in it. most metabolic reactions take place in solution (e.g. cytoplasm of eukaryotic and prokaryotic cells) so its very essential
3) water helps with temperature control because it has a high latent heat of vaporisation and a high specific heat capacity
4) water molecules are very cohesive (sick together) which helps water transport in plants as well as transports in organisms.
what is the structure of water?
1) a molecule of water is one atom of oxygen joined to two atoms of hydrogen by shared electrons
2) because the shared negative hydrogen electrons are pulled towards the oxygen atom, the other side of each hydrogen atom is left with a slight positive charge
3) the unshared negative electrons on the oxygen atom give it a slight negative charge
4) this makes water a polar molecule - it has a partial negative charge on one side and a partial positive charge on the other.
5) the slightly negatively charged oxygen atoms attract the slightly positively charged hydrogen atoms of other water molecules.
6) this attraction is called hydrogen bonding and it gives water some of its useful properties.
why is water an important metabolite?
1) many metabolic reactions involve a condensation reaction or hydrolysis reaction
e.g amino acids are joined together to make polypeptides by condensation reactions.
energy fromATP is released through a hydrolysis reaction
why is it important for water to have a high latent heat of vaporisation?
1) it takes a lot of energy (heat) to break the hydrogen bonds between water molecules.
2) so water has a high latent heat of vaporisation - a lot of energy is used up when water evaporates
3) this is useful for living organisms because it means they can use water loss through evaporation to cool down (e.g human sweat to cool down) without loosing too much water.
why is it important for water to have a high specific heat capacity
HSHC is the heat needed to raise the temp of 1kg of water by 1 degree.
1) the hydrogen bonds between water molecules can absorb a lot of energy so the HSHC is very high and buffers change.
2) this is useful for living organisms because it means water doesn’t experience rapid temperature changes. tis makes water a good habitat because the temperature under water is likely to be more stable than on land. the water inside organisms also remain at a fairly stable temperature - helping them to maintain a constant internal body temperature.
why is it important for water to be an important solvent
1) a lot of important substances in metabolic reactions are ionic (like salt). this means they’re made from one positively charged atom or molecule and one negatively charged atom or molecule.
2) because water is polar, the positive end of a water molecule will be attracted to the negative ion, and the negative end of a water molecule will be attracted to the positive ion.
3) this means the ions will get totally surrounded by water molecules - in other words dissolve
4) so waters polarity makes it a useful solvent
why is there a strong cohesion between water molecules?
1) cohesion is the attraction between molecules of the same type (two water molecules). water molecules are very cohesive (they stick together) because they are polar
2) strong cohesion helps water to flow making it great for transporting substances. e.g water travels up the xylem in plants
3) strong cohesion also means that water has a high surface tension when it comes into contact with air. this is the reason why sweat forms droplets which evaporates from the skin to cool down the organism. it also the reason that pond skaters and some other insects can ‘walk’ on the surface of ponds.
where/how is ATP made
ATP synthesis
1)plant and animal cells release energy from glucose (respiration)
2) a cell cant get its energy dire4ctly from glucose so the energy released from glucose in respiration is used to make ATP (adenosine triphosphate)
what makes up ATP?
ATP is made from the nucleotide base adenine, combined with a ribose sugar and three phosphate groups.
its known as a nucleotide derivative because it is modified from a nucleotide.
adenine - ribose - 3 phosphate
what happens when ATP is made?
once made, ATP diffuses to the part of the cell that needs energy.
the energy in ATP is stored in high energy bonds between the phosphate groups. its released via hydrolysis reaction.
what’s the process of ATP releasing energy?
1) when energy is needed by a cell, ATP is Broken down into ADP (adenosine diphosphate) and Pi (inorganic phosphate)
2) this is a hydrolysis reaction. a phosphate bond is broken and energy is released. the reaction is catalysed by the enzyme ATP hydrolase.
3) ATP hydrolysis can be ‘coupled’ to another energy- requiring reactions in the cell - this means the energy released can be used directly to make the coupled reaction happen, rather then being lost as heat.
4) the released inorganic phosphate can also be put to use - it can be added to another compound (known as phosphorylation) which often makes the compound more reactive.
5) ATP can be re-synthesised in a condensation reaction between ADP and Pi. this happens during both respiration and photosynthesis, and is catalysed by the enzyme ATP synthase.
(adenosine diphosphate (2)
atp synthase
ATP + Pi —-> ATP (adenosine triphosphate (3)
<—–
hydrolysis (energy released)
what’s an ion??
an atom with an electric charge
what’s an ion with a positive charge?
cation
what’s an ion with a negative charge
anion
what’s an inorganic ion
one which doesn’t contain carbon (some exceptions)
some are found in solution in the cytoplasm of cells and in the body fluids of organisms. each ion has a specific role, depending on its properties. an ions roles determines whether it is found in high or low concentrations.
how do iron ions have an important part of haemoglobin?
haemoglobin is a larger protein that carries oxygen around the body in the red blood cells. its made up of 4 different polypeptide chains each with an iron ion (Fe^2+) that actually binds to the oxygen in haemoglobin - so its a pretty key component. when oxygen is bound the Fe^2+ ion temporarily becomes an Fe^3+ ion, until oxygen is released.
how do hydrogen ions determine pH?
pH is calculated based on the concentration of hydrogen ions (H^+) in the environment. the more hydrogen present, the lower the pH (and the more acidic the environment). Enzyme controlled reactions are all affected by pH.
how does sodium ions help transport glucose and amino acids across membranes?
- glucose and amino acids need a bit of help crossing cell membranes
- a molecule of glucose or an amino acid can be transported into a cell (across the cell-surface membrane) alongside sodium ions. this is known as co-transport.
how are phosphate ions essential components of ATP and ADP?
- when a phosphate ion is attached to another molecule, its known as phosphate group.
- DNA, RNA and ATP all contain phosphate groups.
- its the bonds between phosphate groups that store energy in ATP.
- the phosphate groups in DNA and RNA allow nucleotides to join up to form the polynucleotides.
explain how does DNA replicate by semi-conservative replication?
- the enzyme DNA helicase breaks the hydrogen bonds between bases on the two polynucleotide DNA strands. this makes the helix unwind to form two single strands.
- each original single strand acts as a template for a new strand. complementary base pairing means that free floating DNA nucleotides are attracted to their complementary exposed bases on each original template strand
A with T and C with G - condensation reactions join the nucleotides of the new strands together - catalysed by the enzyme DNA polymerase. hydrogen bonds form between the bases on the original and new strands.
- each new DNA molecule contains one strand from the original DNA molecule and one new strand
describe semi-conservative replication?
this is the process where DNA copies itself before cell division so that each cell has the full amount of DNA.
this method means that both daughter cells are genetic continuity between generations of cells because half of the strands in each new DNA molecule are from the original DNA molecule.
describe why DNA polymerase moves in the opposite ways along antiparallel DNA strands
each end of a DNA strand is slightly differnt in its structure. one end is called the 3’ (three prime) end and one end is called the 5’ (five prime) end. in DNA helix, the strands run in opposite directions - there antiparallel.
explain how DNA polymers move in opposite ways along antiparallel DNA strands
the active site of DNA polymerase is only complementary to the 3’ end of the newly forming DNA strand - so the enzyme can only add nucleotides to the new strand at the 3’ end.
this means that the new strand is made in a 5’ to 3’ direction and that DNA polymerase moves down the template strand in a 3’ to 5’ direction. because the strands in the double helix are antiparallel, the DNA polymerase working on one of the template strands moves in the opposite direction to the DNA polymerase working on the other template strand.
who discovered evidence for Watson and Crick theory of semi conservative DNA replication?
Watson and crick determined the structure of DNA and the theory of semi conservative DNA replication.
Meselson and Stahl experiment proved this theory.
this sorted the debate whether DNA replication was conservative or semi-conservative.
how did Meselson and stahl conduct the experiment proving DNA is replicated using the semi-conservative method
1) two samples of bacteria were grown - one in a nutrient broth containing light nitrogen, and one in a broth with heavy nitrogen. as the bacteria reproduced, they took up nitrogen from the broth to help make nucleotides for new DNA. so the nitrogen gradually became part of the bacteria’s DNA.
2) a sample of DNA was taken from each batch of bacteria and spun in a centrifuge tube than the DNA from the light nitrogen bacteria - because its heavier.
3) then the bacteria grown in the heavy nitrogen broth were taken out and put in a broth containing only light nitrogen. the bacteria were left for one round of DNA replication and then another DNA sample was taken out and spun in the centrifuge.
4) if replication was conservative, the original heavy DNA which would still be together would settle at the bottom and the new light DNA would settle at the top.
5) if replication was semi-conservative, the new bacterial DNA molecules would contain one strand of the old DNA containing heavy nitrogen and one strand of new DNA containing light nitrogen. so the DNA would settle out between light nitrogen DNA settled out and where the heavy nitrogen DNA settled out.
6) as it turned out, the DNA settled out in the middle, showing that the DNA molecules contained a mixture of heavy and light nitrogen. the bacterial DNA had replicated semi-conservatively in the light nitrogen
