1. Molecules

Water as a medium of life

Water is important because all life evolved from it and most processes of life occur in it.

cohesion

attraction of water molecules to other water molecules

Adhesion

water molecules with other molecules which are polar

Water moving up xylem

Cohesion moves the water up adhesion helps it stay in place.

surface tension

water molecules show strong attraction next to each other, thus they create strong surface tension which can provide a habitat for very light animals

Solvent properties of water linked to its role as a medium for metabolism

• hydrophillic molecules dissolve in water and most enzymes catalyse reactions in aqueous solutions.

buoyancy, viscosity, thermal conductivity, specific heat capacity

• V:waters resistance to something moving through it

• SHC: the energy required to increase the temperature of a substance.

water origin

A common theory is that earlier, earth only had hot magma on the surface but after many asteroids struck its surface it also brought hydrated minerals that released water and then became a part of the earths crust. It was able to retain water due to gravity and low enough temperatures.

Goldilocks zone

the habitable zone where:

• there is a suitable temperature for water to exist as a liquid

• sufficient gravity for retaining the water.

What is DNA

The molecules which provides the long term stored genetic information for all organisms on earth

Nitrogenous bases

Adenine

guanine

cytosine

thymine

RNA uracil

complementary base pairing

Hydrogen bonding is based off of ydrogen bonds formed between the bases.

A-T is two bonds

G-C is 3 bonds

directionality

nucleotides are added next to the growing chain in a 5’ end to 3’ end

Double helix

the purine and pyrimidine bonding results in the nucleotides being the same distance from each other so they double helix structure is the same no matter what base pair occurs.

Condensation reactions

form covalent bonds between molecules and produce water as a result

hydrolysis

break covalent bonds between monomers

Starch in plant

a polymer of glucose which contains amylose and amylopectin.

• it is very large therefor not readily soluble in water therefor does not disturb the osmotic balance in living tissue

glycogen in animals

• is a polysaccharide made of glucose monomers bonded similarly to amylopectin

• it has more branching and is a form of excess glucose

• the macromolecules in glycogen are not readily soluble in the cytoplasm meaning they do not effect the osmotic balance in living tissue.

cellulose

• primary component of the cell walls of plants

• uses beta glucose

Blood types glycoproteins

There are two different glycoproteins on blood cells, A and B.

White blood cells detect if these cells are self or not self

their presence can trigger the immune system.

glycoprotein

• cell to cell communication

• cell to cell adhesion

  • recognition of body cells

triglyceride

one glycerol molecule can link three fatty acid molecules

saturated fatty acids

no double bonds, high melting points

fat in animal meat or butter

monounsaturated

one double bond, some animals and many plants

polyunsaturated

many double bonds, relatively low melting points liquid at room temp. mainly plants

adipose tissue

composed of cells that store fat in the form of triglycerides.

triglycerides are useful for long term energy storage because they are insoluble in body fluids and will not move from their adipose storage sites.

blubber

a form of thick adipose tissue found on animals living in the arctic, it helps trap heat generated by the inner metabolic activity of the organism

amphipathic

molecules with both hydrophobic and hydrophilic regions.

essential amino acids

are not naturally synthesized and must be obtained from food. 9/20

variation in polypeptide chains

• chains can have any number of amino acids

• the amino acids can be in any order

Basic examples of polypeptides

insulin

histone

haemoglobin

R- groups

variable group or portion of molecules which differs between different amino acids.

the polarity and acidity of amino acids is based solely on the R-groups.

Primary structure of a protein

the number and sequence of the amino acids in a polypeptide chain. the precise position of each amino acid eventually determines the three dimensional shape it folds into.

tertiary structure of a protein

• ionized r groups align with each other and form an ionic bond

• pairs of cysteine amino acids form covalent bonds between themselves within the polypeptide, when two non-adjacent cysteine amino acids get close to each other the two hydrogens get removed and the sulfur atoms become covalent bonded to each other resulting in a disulphide bond.

quaternary structure

more than one chain is bonded together

collagen

I: makes up connective tissue, fibrous protein consisting of 3 PP chains

strong and elastic but does not need much variability.

globular

most globular proteins are made up of many amino acids and for that reason they can be specialised for a specific purpose.

catalysts

molecules which speed up chemical reactions which occur too slow to sustain life naturally

anabolism

build macromolecules from monomers and release water by condensation reactions

catabolism

break down macromolecules into their monomers by hydrolysis.

active site

area of the enzyme which matches the substrate

the active site is composed of only a few amino acids

its the interaction between the amino acids and the overall three dimensional enzyme shape which provides an active site.

induced fit model

many enzymes undergo chemical and physical changes when combining with their substrates.

the interaction changes the shape of both the enzyme and substrate which causes stress upon the chemical bonds in the substrate in turn the bonds become destabilised so the reaction occurs at a faster rate.

effect of enzymes on activation energy

enzymes lower the energy required for the destabilisation of bonds to occur which allows them to happen quicker.

important of molecular motion in enzyme substrate bonding

enzymes and substrates need to collide with the right geometry and enough energy to find the active sites.

often the substrate or enzyme is immobilised by being anchored to the membrane which is efficient.

mechanism of enzyme action

1. substrate makes contact with the active site on an enzyme

2. enzyme and substrate change shape to provide fit

3. enzyme substrate complex is formed

4. activation energy is lowered and substrate is altered

5. the transformed substrate and the product is released from the active site

6. the unchanged enzyme is then free to combine again with other substrate molecules.

reactions catalysed by intracellular enzymes

glycolysis and krebs

reactions catalysed by extracellular enzymes

chemical digestion within the gut

metabolic efficiency

roughly 35% of energy available to an organism is used for cellular activities, the rest is transferred as heat. without this release of heat, endotherms would not be able to maintain constant body temperature.

linear metabolic pathway

one intermediate becomes another until the final product is used

cyclic metabolic pathway

where an intermediate is used to create the initial reactant and can keep going.

statins

act as competitive inhibitors because they combine w the active site on an enzyme essential for the synthesis of cholesterol in liver.

feedback/ end-product inhibition

when the end product of a reaction is present in sufficient quantity the pathway shuts down.

this is usually because the end product inhibits the action of the enzyme in the first step.

when present in high enough content, the end product binds with the allosteric site of the first enzyme.

isoleucine, bnds with theorine deaminase.

penicillin, mechanism based inhibition

penicillin irreversible binds to the enzyme transpeptidase which builds the cell walls of bacteria by bonding to a particular group in the enzymes active site.

changes in transpeptidase

if mutations occur within the transpeptidase active site, penicillin will no longer work.

properties of ATP which make it suitable to use as energy currency within cells.

the last 2 phosphate groups of ATP are attached to the main molecule by high energy bonds. these bonds can be easily broken and they release energy which can then be used to perform cellular work.

cellular processes which require ATP

• active transport across cell membranes

• synthesis of macromolecules

• movement of cells or components like flagellum.

cell respiration

involves the release of energy from carbon compounds especially glucose and fatty acids.

anaerobic cell respiration general

• doesnt require oxygen but does require glucose

• in the cytoplasm

• net gain of 2 ATP

aerobic cell respiration general

• requires oxygen and glucose

• begins in cytoplasm

• net gain of 30-35 ATP

role of NAD

a coenzyme utilised by enzymes part-taking in cell respiration to reduce and oxidise.

is also said to be a hydrogen carrier, when hydrogen is added to NAD, it is said to be reduced.

Anaerobic cell respiration in yeast

generate a net of 2 ATP in glycolysis

yeast converts the two 3 carbon molecules of pyruvate to 2 carbon molecules of ethanol

the lost carbon molecule gives off CO2

both ethanol and CO2 are released into the environment.

word equation of photosynthesis

CO2+water———> glucose+ocygen

Rf value

distance moved by substance/distance moved by solvent

absorption spectrum vs action spectrum

AB:amount of light absorbed plotted against the wavelength of light produces the absorption spectrum

AS:the rate of photosynthesis at different wavelengths of light.

excitation

when a pigment absorbs light, that energy is used to raise the electron to a higher energy level.

what is photosynthetic rate dependent on

• intensity of light

• air tempereture

• amount of water

• CO2 concentration

What experiments have been done to measure photosynthesis

Controlled green house

CO2 enrichment experiments

photosystems

always located in a membrane, thylakoids of chloroplasts. Centre of a photosystem is. a reaction centre which contains various pigment molecules

Light dependent reaction general

• occur in the thylakoids

• use light energy to form ATP and reduced NADP

• include 2 electron transport chains

Light independent reaction general

• occur in stroma

• Use ATP and reduced NADP to form triose phosphate

why is DNA replication required

because DNA is essentially the code for life so it is required for the reproduction of organisms. and for growth and tissue replacement in multicellular organisms.

semi conservative

the two strands of DNA unwind from each other, and each acts as a template for synthesis of a new, complementary strand. This results in two DNA molecules with one original strand and one new strand.

PCR

technique used to take small quantity of DNA and copy all of the nucleotides to make millions of copies of the DNA.

Primers PCR

single stranded short polymers that are complementary to the nucleotides of the target DNA to be copied provide a starting point of DNA synthesis.

taq polymerase PCR

enzyme which can withstand high temperatures.

PCR Process

once, primer taq polymerase and free nucleotides are mixed in a tube, it is placed in a thermocycler.

denaturation:mixture is heated which breaks the hydrogen bonds between the the two DNA strands

annealing:the mixture is then cooled to allow primers to bind with the nucleotides on both strands at the ends of the target sequence.

elongation:the taq pilymerase catalyses the synthesis of the new strand by extending the primers.

phosphodiester bond

molecules in DNA are held by a covalent bond called…

importance of stability of DNA templates in somatic cells

• need to be stable for somatic cells which do not divide but do need RNA and protein throughout their life.

the genetic code is degenerate

for each amino acid, there may be more than one codon.

genetic code is universal

all organisms share essentially the same code.

point mutation effecting structure

cause of the disorder, sickle cell anemia.

the point mutation leads the shape of the haemoglobin to shape to a sickle of sorts.

initiation of transcription

transcription factor proteins bind to the promotor sequence which then attracts RNA polymerase to bind.

transcription factors

proteins which play a role in the regulation of transcription. important in determining which genes in are active in each cell of an organism.

introns

stretches of non-coding DNA

post transcriptional modification

when a region of DNA is transcribed, the first RNA created is primary RNA which contains both exons and introns.

• the introns are removed by spliceosomes and sometimes the mature RNA is rearranged.

• he spliceosomes then help join the remaining exons together.

• 5’ modified guanine nucleotide w/3 phosphates.

• 3’ poly a tail

protects from degradation.

modification of insulin

1. signal peptide is removed as the pre pro insulin enters the ER to produce pro insulin. signal peptide is a short chain on teh end of the polypeptide for secretion. it directs the pre pro insulin to the ER.

2. pro insulin is then exposed to enzymes which break the peptide bonds, removing c peptides.

frameshifts

when an insertion or deletion occurs in non-multiples of three. the genetic code is read in triplets so the code is shifted.

mutagens

chemicals that cause genetic mutations

when radiation hits the DNA molecule, it can sometimes knock one or more base pairs out of place modifying teh genetic code.

randomness of mutations

uncoiled DNA HAS A HIGHER RISK OF MUTATION BECAUSE IT IS MORE EXPOSED.

gene knockout

Rendering a gene unusable in order to see what affects it has on the organism.

important role of knockout organisms

• testing pharmaceutical drugs

Cas 9

enzyme hwich can cut DNA

guide RNA

can recognise the sequence of DNA to be edited

how does Crispr work

• scientist first identify the sequence of the genome which causes an issue

• then they create a specific guide RNA to recognise that particular stretch of DNA.

• the guide RNA is attached to Cas 9 enzyme

• the complex is introduced to the target cells, it locates the target sequence and cuts the DNA, then the existing genome can be edited.

possible advantages of CRISPR

• capable of deleting a while chromosome, like the 21st chromosome in down syndrome.

conserved sequences

genetic sequences in DNA which are found to have minimal changes over time.

highly conserved sequences

sequences which show no changes over time.