Nucleic acids and inorganic molecules

what does DNA stand for

deoxyribose nucleic acid

what does RNA stand for

ribonucleic acid

what are nucleotides made up of

• They are the monomers of nucleic acids (DNA and RNA)

they are made up of a phosphate, sugar, and a base

• phosphate gives the nucleic acid acidic properties

• sugar is a pentose sugar and is a deoxyribose sugar in DNA or a ribose sugar in RNA

• base is nitrogenous (contains nitrogen) and is either a purine or a pyrimidine

what is the difference in bases between RNA and DNA

RNA contains uracil (U) instead of thymine (T) in DNA

what are purines and pyrimidines (bases)

purines- are double ringed structures and include bases adenine (A) and guanine (G)

pyrimidines- are single ringed structures and include bases thymine (T) and cytosine (C) and uracil (U) in RNA

what is the difference between a codon and a triplet

codon- three bases in mRNA

triplet- three bases in DNA

how is a double helix formed from nucleotides

polymerisation

first strand:

• nucleotides join together via phosphodiester bonds which are between carbon 3 to carbon 5 on the next adjacent pentose sugar

• phosphodiester bonds form via condensation reactions, as a water molecule is released

• two nucleotides make a dinucleotide

• DNA is a polynucleotide

• the joining of nucleotides creates the back bone (sugar-phosphate backbone)

• this makes up one strand

second strand:

• hydrogen bonds form between nucleotides with a complimentary base to make up the double helix

• there are 2 hydrogen bonds between A and T

• there are 3 hydrogen bonds between G and C

how is the structure of DNA related to its function

sugar phosphate backbone- protects the more chemically reactive organic bases inside the double helix from being corrupted by chemical and physical forces

stable structure- allows for DNA to be passed through generation, without it’s structure changing, it only rarely changes via mutations

separate strands joined by hydrogen bonds- allows DNA to separate for processes such as DNA replication and protein synthesis

large molecule- can carry a large amount of genetic information

base pairing- replicate and transfer information as mRNA

differences between RNA and DNA

• DNA is double stranded, whereas RNA is single stranded

• DNA contains deoxyribose sugars, whereas RNA contains ribose sugars

  • DNA contains thymine (T), whereas RNA contains uracil (U)

what is the role of messenger RNA (mRNA)

carries instructions for polypeptide synthesis from the nucleus to the ribosomes in the cytoplasm

what is the role of transfer RNA (tRNA)

carries the amino acids to the ribosome during translation

what is the role of ribosomal RNA (rRNA)

form an important part of both subunits of a ribosome

what are the requirements for semi conservative replication

• 4 types of nucleotide

• both strands of the DNA molecule act as s template strand for nucleotides to attach to

• DNA polymerase enzyme and helicase enzyme

• a source of chemical energy is required to drive this process

what is the role of DNA helicase enzyme

unzips the DNA molecule by breaking hydrogen bonds between the nitrogenous bases of the strands. This allows the DNA strands to act as template strands, so nucleotides can attach to the template strands

what is the role of DNA polymerase enzyme

forms phosphodiester bonds between adjacent nucleotides

describe the process of semi conservative replication

• DNA helicase enzyme breaks hydrogen bonds between the nitrogenous bases in the DNA molecule which unzips the DNA molecule into two strands

• these two strands can act as template strands

• free nucleotides in the nucleus can attach to the exposed nitrogenous bases on the template strand according to complimentary base pairing

• adenine pairs with thymine and guanine pairs with cytosine

• DNA polymerase enzyme helps to form phosphodiester bonds between adjacent nucleotides which forms a newly synthesised strand of DNA

• hydrogen bonds form between the complimentary bases on the template strand and the newly synthesised strand.

• there are two hydrogen bonds between bases A and T

• there are three hydrogen bonds between bases C and G

why can nucleotides only be added in a 5’ to 3 direction

• the shape of the 5’ and 3’ end are different

  • DNA polymerase is an enzyme which active site is specific and complimentary to the 5’ end

what does a stop codon do

signals for the ribosomes to release from the polypeptide chain, which stops translation

what is semi conservative replication

two strands of DNA unzip, each of these strands act as a template strand for the synthesis of a new complimentary strand. This results in two DNA strands, both consisting of one original and and one newly synthesised strand

describe the meselson and stahl experiment

Evidence for semi conservative replication

All DNA bases are nitrogenous, meaning that they contain nitrogen

nitrogen has two forms, 15N and 14N

used a centrifuge at each stage to sort out DNA into different densities

15N is the most dense, so it’s located at the bottom

14N is the least dense, so it’s located at the top

Method

• G0- grew bacteria (E.coli) in medium contain 15N for many generations, so that all the nitrogenous bases were 15N

  100% of DNA is 15N 15N

• G1- grew bacteria in 14N medium, so that the nitrogenous bases in the newly synthesised strand would be made up of 14N

  100% of DNA is 15N 14N

• G2- 14N growth medium

  50% of DNA is 15N 14N

  50% of DNA is 14N 14N

• G3- 14N growth medium

  25% of DNA is 15N 14N

  75% of DNA is 14N 14N

What processes require energy from ATP

metabolic processes- ATP provides energy to build macromolecules from their basic units e.g. starch from glucose monomers

movement- ATP provides energy for muscular contraction

active transport- ATP is required to change the configuration of carrier proteins in the membrane, to allow water soluble ions to pass through the membrane

secretion- ATP provides the energy for lysosomes to be formed

describe the structure of ATP

adenosine triphosphate

• adenine (base)

• ribose sugar

• 3 phosphate molecules

How does ATP release energy

• ATP is hydrolysed via ATP hydrolase which breaks the bonds between the phosphate groups in the ATP molecule

• ATP has a low activation energy because the bonds between the phosphate groups are unstable

• when these bonds are broken they release energy

  • ATP + H2O —> Pi + ADP + energy

How is ATP resynthesised

energy Pi + ADP —> ATP (condensation reaction via ATP synthase)

why is ATP more reactive than ADP

during the resynthesis of ATP, ADP becomes phosphorlysed by the inorganic phosphate

why do we need to synthesise more than our body mass of ATP every day

• we can’t store ATP in cells

• ATP only releases a small amount of energy at a time

Properties of ATP

small- easily transported in and out of cells

water soluble- energy requiring processes happen in aqueous environments and it means that ATP is easily transported around the cell

releases energy in small quantities- appropriate quantity of energy for cellular reactions, so energy isn’t wasted as heat

easily resynthesised- can be recharged with energy quickly and easily e.g. short recovery times during sports which can provide the muscles with energy quickly, so that they have the energy to contract again

why is water classified as a dipolar molecule

oxygen is delta negative, due to the free electrons on the outer shell of the oxygen molecule

hydrogen is delta positive

what makes water a sticky molecule

due to the hydrogen bonds formed between the delta negative oxygen and the delta positive hydrogen in different water molecules, because of the dipolar nature of the water molecule

what are the properties of water

sticky molecules

• cohesion- tendency of water molecules to stick together (due to hydrogen bonds between water molecules)

• adhesion- where water meets air, the tendency for water to be pulled back into the body of the water (hydrogen bonds between water molecules and walls)

high specific heat capacity- takes a lot of energy to increase the temperature of 1cm3 of water by 1.C

high latent heat of vaporisation- takes a lot of energy to evaporate 1 gram of water due to the hydrogen bonds between water molecules

can freeze- water expands upon freezing —> water molecules are held further apart —> less dense —> floats

solvent- due to the dipolar nature of water the delta positive hydrogen in the water molecule can bind to the negative ends of other molecules and the delta negative of the oxygen atom is attracted to positively charged ions and molecules surrounding the water molecule

why is having a high specific heat capacity and a high latent heat of vaporisation helpful for organisms

helps to avoid rapid changes in body temperature

helps us to maintain a constant body temperature in aquatic environments and in organisms themselves

requires a lot of energy to evaporate during sweating which helps us to cool down

how is the freezing of water useful to the survival of aquatic organisms

water expands when freezing, which means water molecules are held further apart

this means that ice is less dense than water, so it floats

this insulates the aquatic environment and maintains the temperature of it, preventing the whole lake or ocean from freezing completely

what is role of water in metabolism

a water molecule is needed for hydrolysis, to break down complex molecules

water is produced from condensation reactions

cellular reactions take place in aqueous environments

water is required for photosynthesis

why is water a good transport medium for plants and animals

water is a solvent

it allows substances to dissolve in it such as gasses, ions, waste products, enzymes, and ATP and be transported around the plant or animal

it does this as the hydrogen is delta positive, so it can bind to the negatively charged ends of molecules. The oxygen is delta negative, meaning it is attracted to positively charged ions/molecules surrounding it

what is the function of a nitrate ion

a component in:

• amino acids

• proteins

• hormones

• nucleotides

what is the function of phosphate ions

a component in:

• phospholipids that make up the cell membrane

• nucleotides

• ATP

what is the function of potassium ions

• involved in active transport

• involved in protein synthesis

• helps to maintain electrical, osmotic and cation/anion balance across the cell membrane

• a constituent of vacuoles, so helps to maintain turgidity in plant cells

what is the role of calcium ions

• the main component in teeth, bones and shells

• required for muscle contraction

• required for clotting of the blood

role of sodium ions

• involved in active transport

• helps to maintain the osmotic, electrical, cation/anion balance across the cell membrane

• a constituent of vacuoles, so helps maintain turgidity of plant cells

what is the function of chloride ions

• helps to maintain the osmotic, electrical, cation/anion balance across a cell membrane

• needed for the formation of HCL in the gastric juices

what is the role of magnesium ions

• component in bones and teeth

• constituent of chlorophyll

• an activator for some enzymes

what is the role of iron ions

• required for the formation of chlorophyll

• found in electron carriers used in respiration and photosynthesis

• forms part of haemoglobin, found in red blood cells