Biology ~ Biological Molecules + Nucleic Acids

Biological Molecules

particular groups of chemicals that are found in living organisms. The study is known as molecular biology

What are all molecules made up of?

atoms

3 ways atoms can combine

Covalent Bonding, Ionic Bonding, Hydrogen Bonding

Covalent Bonding

when atoms share a pair of electrons in their outer shells. The outer shells of both atoms fill and a more stable compound called a molecule is formed

Ionic Bonding

ions with opposite charges attract one another, they are weaker than covalent bonds

Hydrogen Bonding

negatively charged regions (polar molecules) of one molecule attract to positively charged regions of another, a weak electrostatic bond is formed between the two. This is especially true for water

Monomers

smaller molecules in which large molecules are made from e.g. glucose, fructose, galactose

Polymers

made up of repeating long-chains of monomer sub-units

Polymerisation

the process of polymers being formed

condensation reaction

two monomers join together with the formation of covalent bonds which involve the elimination of water molecules, produce water, in polymerisation each time a new sub-unit is attached a molecule of water is formed. Also formation of polypeptides and polysaccharide

Hydrolysis Reactions

reaction breaking the covalent bonds between monomers and involves the addition of a water molecule

metabolism

all chemical processes that take place in living organisms

Mole

in SI unit for measuring the amount of a substance

Molar Solution

a solution which contains one mole of solute in each litre of solution

Atoms

smallest units of a chemical element that can exist independently, no overall charge

neutrons

in the nucleus of an atom, same mass as protons but no electrical charge

protons

in nucleus of an atom, same mass as neutrons but have a positive charge

electrons

orbits shell around nucleus negatively charged

atomic number

number of protons in an atom

mass number

total number of protons and neutrons in an atom

ion

an atom that has lost or received an electron

carbohydrates

carbon molecules combined with water

monosaccharides

individual sugar molecules (monomers) that make up disaccharides and polysaccharides

properties of monosaccharides

crystalline, sweet and soluble

examples of monosaccharides

glucose, fructose, galactose

what’s OILRIG

oxidation is loss reduction is gain

reduction

chemical reaction involving the gain of electrons or hydrogen

reducing sugar

a sugar that can donate electrons to another chemical e.g. all monosaccharides and some disaccharides

How do you test for reducing sugar?

Benedict’s Test

How do you carry out Benedict’s Test

put food sample in test tube, add benedict’s solution, put in water bath for 5 mins at 80 degrees Celsius

What colour does the solution turn if a reducing sugar is present?

orange-brown

Disaccharides

two monosaccharides joined together

properties of disaccharides

crystalline, sweet, soluble

examples of disaccharides

lactose, sucrose, maltose

how is lactose formed?

glucose + galactose

how is sucrose formed?

glucose + fructose

how is maltose formed?

glucose + glucose

what bond is formed when monosaccharides join?

glycosidic bond is formed from the condensation reaction

what happens when you break down disaccharides?

a hydrolysis reaction breaks the glycosidic bond releasing the constituent monosaccharide

how do you test for non-reducing sugars

do a benedict’s test, if colour doesn’t change it must by hydrolysed then treat acid with HCI, heat for 2 mins, allow to cool, if present it will turn orange-brown

Polysaccharides

formed when more than two monosaccharides are joined together by glycosidic bonds made by condensation reactions, can be broken down by hydrolysis, they are insoluble

how do you test for starch?

put food sample in test tube, add iodine solution, if starch is present it will turn a blue-black colour

Starch

storage carbohydrate found in plant cells, made from the polymers, amylose and amylopectin both made from alpha glucose. Its insoluble, can be hydrolysed to release glucose for respiration, stores access glucose that’s too large to leave the cell. its a polysaccharide

amylose

long unbranched forms coiled/ spring shape

amylopectin

long branched chain due to 1-6 or 1-4 glycosidic bonds

amylose chains form?

a helix held together by hydrogen bonds, the coiling makes it more compact and stores more in a smaller space

glycogen

found in animals and bacteria similar to amylopectin, but more branched, its insoluble, made from alpha glucose molecules bonded together by an alpha 1-4 glycosidic bonds, side chains bond to each other via an alpha 1-6 glycosidic bond

cellulose

main component in cell walls of plants, provides support and allows cell to become turgid, its long unbranched straight chains of beta glucose, linked by hydrogen bonds, between the glucose molecules in each chain to form thicker fibres called microfibrils

Lipids

varied group of substances that contain carbon,hydrogen and oxygen, insoluble in water, soluble in organic solvents such as alcohols and acetone, have a proportion of oxygen to carbon and hydrogen smaller than in carbohydrates

what are the main group of lipids

triglycerides (fats and oils) and phospholipids

Roles of lipids

~ cell membranes, the flexibility and the transfer of lipid-soluble substances across them

~ source of energy

~ waterproofing, insoluble in water

~insulation, fats are slow conductors of heat

~ protection, fat stored round delicate organs e.g. kidneys

~ used as a respiratory substrate, form a bilayer in cell membranes and make some hormones

role of carbohydrates

respiratory substrates which provide energy for the cells, cell membranes structure and walls in plants

molecules of life

contain carbon, hydrogen, oxygen and are all organic

biochemistry

study of biochemistry across all organisms, indirect evidence of evolution

whats cell membrane made of?

2 layers ~ inner is made from phospholipids

outer is made from fatty acids

triglycerides

three fatty acids combined with glycerol, each fatty acid forms an ester bond with glycerol in a condensation reaction, hydrolysis is opposite

how many fatty acids are there?

over 70 all with a carboxyl (-COOH) group with a hydrocarbon chain attached

mono-unsaturated

saturated except for one multiple bond

polyunsaturated

containing several double or triple bonds between carbon atoms

structure of triglycerides

~ high ratio of energy-storing carbon-hydrogen bonds to carbon atoms, excellent source of energy

~ low mass to energy ratio, good storage molecules, energy stored in small volumes

~ large, non-polar molecules, insoluble to water, storage doesn’t affect osmosis or water potential

~ high ratio of hydrogen to oxygen atoms, release water when oxidised

phospholipids

a glycerol molecule, a phosphate group and two fatty acid chains, two parts, a hydrophilic ‘head’ and a hydrophobic ‘tail’

hydrophilic

water loving, its attracted to it

hydrophobic

water hating, orientates away

polar molecules

molecules that have two ends (poles) that behave differently

what part of a phospholipid is hydrophobic?

the tail of 2 fatty acids

what part of a phospholipid is hydrophilic?

phosphate head

what happens to a phospholipid in an aqueous environment?

the phospholipids form a bilayer with-in cell-surface membranes, as a result, a hydrophobic barrier is formed between the inside and outside of a cell

what is the test for lipids called?

the emulsion test

how do you test for lipids?

1. take a completely dry and grease free test tube

2. to 2cm of the sample being tested add 5cm of ethanol

3. shake tube thoroughly to dissolve any lipids in sample

4. add 5cm of water and shake gently

5. a milky white emulsion indicates the presence of a lipid

6. as a control, repeat using water instead of sample and it should be clear

why does the test for lipids result in a cloudy solution?

its due to any lipid being finely dispersed in the water to form an emulsion, light passing through it is refracted as it passes from oil droplets to water droplets making it appear cloudy

how many amino acids are there?

about 100, 20 of which occur naturally in proteins

what are amino acids?

the basic monomer units which combine to make up a polymer called a polypeptide, which can be combined to form proteins

what does every amino acid have?

a central carbon atom

what are the 4 different chemical groups that attach to an amino acid?

~amino group (-NH2) amino name is derived from

~ carboxyl group (-COOH) acid part of the name

~ hydrogen atom (-H)

~ R (side) group- a variety of different chemical groups, each amino acid has a different R group

how are dipeptides formed?

amino acid monomers combine using a condensation reaction, the two amino acids become linked by a peptide bond

how can a peptide bond by broken down?

hydrolysis

polymerisation

joining many monomers together through a series of condensation reactions, resulting in polypeptides

polypeptide

a chain of hundreds of amino acids

primary structure of proteins

the sequence of amino acids in a polypeptide chain forms the primary structure of any protein

how many primary structures of protein are there?

limitless as there is so many different combinations of amino acids

what does the primary structure determine?

its ultimate shape and function

what can changing one part of a primary structure lead to?

change in the shape and may stop it carrying out its function - a proteins shape is specific to its function

how many chains are proteins made up of?

a simple protein may consist of a single polypeptide chain, but more commonly they are made up of a number of them

what is the secondary structure?

the shape which the polypeptide chain forms as a result of hydrogen bonding, often a spiral known as an alpha helix

what 3 types of bonds contribute to the maintenance of the tertiary structure?

disulfide bridges - fairly strong, not easily broken

ionic bonds - formed between any carboxyl and amino group that aren’t involved in peptide bonds, weaker and easily broken by change in the pH

hydrogen bonds - numerous but easily broken

what is the tertiary structure?

when the polypeptide helix bends and twists into a compact structure

what is the quaternary structure?

a combination of a number of different polypeptide chains and associated non-protein (prosthetic) groups into a large, complex protein molecule e.g. haemoglobin

what is the test for proteins called?

the biuret test

how do you test for proteins?

1. place a sample of the solution in a test tube and add an equal volume of sodium hydroxide solution at room temperature

2. add a few drops of dilute copper 2 sulfate solution and mix gently

3. a purple colouration indicates the presence of peptide bonds and hence a protein, if not it remains blue

activation energy

minimum amount of energy needed to activate a reaction

active site

a specific region of the enzyme that is functional made up of relatively small numbers of amino acids

substrate

the molecule on which the enzyme acts

enzyme-substrate complex

when the substrate binds with the active site

induced fit model (lock and key)

when the substrate collides, the active sight changes shape slightly to fit around the substrate to form an enzyme substrate complex, its not always complimentary

catalyst

speed up reactions without undergoing permanent changes themselves, can be reused repeatedly and aren’t used up

enzymes

biological catalysts, globular proteins

how do you measure the rate of change on a graph?

measuring the gradient of the tangent

how does an increase in temperature effect enzyme action?

it increases the kinetic energy of molecules, they move round more rapidly and collide more, which results in more enzyme-substrate complexes being formed and rate of reaction increases

how does pH effect how the enzymes work?

it alters the charges of amino acids that make up the active site, so the substrate can no longer bind

it may also cause bonds to break and changes the active sites shape

what is a humans optimum temperature?

37 degrees celsius