AQA A Level Biology Biological Molecules

what are monomers?

Monomers are the smaller units from which larger molecules are made

what are polymers?

Polymers are molecules made from a large number of monomers joined together in a chain

what are carbohydrates made from?

Carbohydrates, proteins, lipids and nucleic acids contain the elements carbon (C) and hydrogen (H) making them organic compounds

why are carbon atoms key to organic compunds?

Carbon atoms are key to the organic compounds because:Each carbon atom can form four covalent bonds - this makes the compounds very stable (as covalent bonds are so strong they require a large input of energy to break them)

Carbon atoms can form covalent bonds with oxygen, nitrogen and sulphur

Carbon atoms can bond to form straight chains, branched chains or rings

How many bonds can nitrogen form?

3

Neccesity of water and use in the body?

cooling effect from evaporation can help with heat loss

makes up 70% in the body and used as solvent

Polar and non polar?

2 types of covalent bonds, where in a polar substance there is an imbalance of charge for example in H2O. O is more electronegative so there is an imbalance of charge,

is water polar or non polar?

water is polar forming weak intermolecular forces of hydrogen bonds.

what is the process of polymerisation?

Carbon compounds can form small single subunits (monomers) that bond with many repeating subunits to form large molecules (polymers) by a process called polymerisation

what is a macromolecule?

Macromolecules are very large molecules. That contain 1000 or more atoms therefore having a high molecular mass

Polymers can be macromolecules

However not all macromolecules are polymers as the subunits of polymers have to be the same repeating units

What are the three types of carbohydrates?

The three types of carbohydrates are monosaccharides, disaccharides and polysaccharides

what is one main function of a carbohydrate?

store energy in plants and animals

What is the formula for carbohydrates?

Cx (H2O)y

what is a monosaccharide?

small organic building blocks used to build more complex carbohydrates

what are monosaccharides used for?

- Energy

- Building blocks

formula for monosaccharides?

(CH2O)n

What is an isomer?

An isomer is a compound with the same chemical formula but different chemical structure, such as alpha and beta glucose. Each have a different of hydroxyl group

definition of disaccharide

two monosaccharides joined together, with the release of a water (H2O) molecule by dehydration

when two monosaccharides bond, what do they form?

A glycosidic bond

when forming a disacharide, what kind of reaction takes place?

Condensation reaction

What is a polysaccharide?

When three or more monosacchraides are joined together, large complex molecules known as polymers

define polymerisation

Bonding many monomers via condensation reactions to form one large molecule

What are Monomers

Individual monosacharides which join to form the polysacharide

What are some examples of polysacharides

Starch

cellulose

glycogen

function of a disacharide

maltose which is sugar found in germinating seeds

some examples of disacharides?

maltose (alpha glucose + glucose)

sucrose (alpha glucose + fructose)

lactose (alpha glucose + galactose)

examples of polysacharides?

cellulose (beta glucose)

amylose and amylopectin (alpha glucose)

glycogen (alpha glucose)

amylose structure and bond

1,4 glycosidic bonds

spiral structure

amylopectin structure and bond

1,4 and 1,6 glycosidic bond

branched structure

why do animals use glycogen and not starch?

Glucose can be liberated at the ends of the branches more easily

1,4 reactions are harder because their hydroxyl groups are on opposite ends

What is a hydrolisis reaction?

addition of water

why are lipids not considered polymers

lipid molecules are not made from monomers or polymers as each fatty acid joins to a glycerol molecule, rather than to each other. Separate lipid molecules, such as triglycerides, are not held together by covalent bonds and therefore lipids cannot be classed as polymers.

how do glycogen and starch differ from cellulose in bonding?

- Glycogen and starch are formed by the condensation of α-glucose.

- Cellulose is formed by the condensation of β-glucose.

glycogen structure and bonding

1,4 and 1,6 glycosidic bond

branched structure

What are lipids?

Macromolecules which contain carbon, hydrogen and oxygen atoms. However, unlike carbohydrates lipids contain a lower proportion of oxygen

are lipids polar or non polar?

Non-polar and hydrophobic (insoluble in water)

what are the two types of lipids?

There are two groups of lipid that you need to know:

Triglycerides (the main component of fats and oils)

Phospholipids

what is a triglyceride composed of?

composed of a glycerol molecule and 3 fatty acids (which are carboxylic acids)

what is the fatty acid structure

R - C - OH

=

O

'r' group is a hydrocarbon chain

in which ways can a fatty acid vary?

Length of r group

saturated or unsaturated

when a triglyceride is formed what kind of reaction takes place?

condensation reaction

what bond is formed when a triglyceride is formed?

ester bond

how is an ester bond formed

An ester bond forms when the hydroxyl (-OH) group of the glycerol bonds with the carboxyl group (-COOH) of the fatty acid

The formation of an ester bond is a condensation reaction

For each ester bond formed a water molecule is released

Three fatty acids join to one glycerol molecule to form a triglyceride

Therefore for one triglyceride to form, three water molecules are released

what are the functions of triglycerides?

Energy storage (highly oxidised so when broken down high energy released)

Insulation

Buoyancy

Protection

what is the difference in terms of bonding between an unsaturated and saturated fat?

unsaturated fats have a double carbon bond, if there is only one double bond it is monounsaturated, if there is more it is polyunsaturated

what does polysaturation cause in terms of bonding?

a kink is formed in the chain so it can not pack close together, therefore it is a liquid at room temperature.

unsaturated fatty acids and there risk?

If H atoms are on the same side of the double bond they are cis-fatty acids and are metabolised by enzymes.

If H atoms are on opposite sides of the double bond they are trans-fatty acids and cannot form enzyme-substrate complexes, therefore, are not metabolised. They are linked with coronary heart disease

what are phospholipids?

Phospholipids are a type of lipid, therefore they are formed from the monomer glycerol and fatty acids

what is the role of a phospholipid

The main component (building block) of cell membranes

what are the roles of the hydrophilic and hydrophobic ends?

Due to the presence of hydrophobic fatty acid tails, a hydrophobic core is created when a phospholipid bilayer formsThis acts as a barrier to water-soluble molecules

The hydrophilic phosphate heads form H-bonds with water allowing the cell membrane to be used to compartmentaliseThis enables the cells to organise specific roles into organelles helping with efficiency

what are proteins made up of?

proteins are made up of polypeptide chains which are made up of peptides (monomers/amino acids). They contain carbon, hydrogen, oxygen and nitrogen

what are the main functions of proteins?

structural

hormonal

antibodies

enzymes

how many amino acids are found in all organisms?

20

how can you tell an amino acid apart?

different R group

how is a peptide bond formed?

In order to form a peptide bond a hydroxyl (-OH) is lost from the carboxylic group of one amino acid and a hydrogen atom is lost from the amine group of another amino acid

The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid

This is a condensation reaction so water is released

what is the difference between a dipeptide and a polypeptide

Dipeptides are formed by the condensation of two amino acids

Polypeptides are formed by the condensation of many (3 or more) amino acids

what are polypeptide bonds broken down into

During hydrolysis reactions, the addition of water breaks the peptide bonds resulting in polypeptides being broken down to amino acids

what are the 4 types of protein

primary

secondary

tertiary

quaternary

what are the two types of secondary structures?

alpha helix --> this is where the peptide chain coils up forming hydrogen bonds.

beta pleated sheet --> this is where the polypeptide chains lie on top of each other forming hydrogen bonds

when a tertiary fold is made what happens?

the polypeptide becomes a protein

explain the structure of a tertiary protein

secondary structure of polypeptide chains coil/fold allowing the r groups to be close enough for them to react

what 4 bonds are found in a tertiary structure and take into account their strength

hydrogen bonds (very weak)

di-sulfide bonds (strongest)

ionic bonds (stronger)

hydrophobic interactions

haemoglobin has what structure and what type of protein is it?

haemoglobin is an example of a globular protein and a quaternary structure.

it has 4 polypeptide chains with 2 alpha sub units and 2 beta subunits

What are globular proteins?

proteins that are water soluble, they have hydrophobic r groups facing outwards and hydrophilic ones facing outwards

e.g insulin

What does the solubility of globular proteins allow the proteins to do?

they can be used in chemical reactions and muscle contractions

what are conjugated proteins?

these contain a prosthetic group, these can be lipids, metal ions, vitamins or carbohydrates

e,g haemoglobin

what is needed to break down a protein

protease and water

4 bonds

Disulphide

Disulphide bonds are strong covalent bonds that form between two cysteine R groups (as this is the only amino acid with a sulphur atom)

These bonds are the strongest within a protein, but occur less frequently, and help stabilise the proteins

These are also known as disulphide bridges

Can be broken by oxidation

Disulphide bonds are common in proteins secreted from cells eg. insulin

Ionic

Ionic bonds form between positively charged (amine group -NH3+) and negatively charged (carboxylic acid -COO-) R groups

Ionic bonds are stronger than hydrogen bonds but they are not common

These bonds are broken by pH changes

Hydrogen

Hydrogen bonds form between strongly polar R groups. These are the weakest bonds that form but the most common as they form between a wide variety of R groups

Hydrophobic interactions

Hydrophobic interactions form between the non-polar (hydrophobic) R groups within the interior of proteins

what is a catalase

catalase is an enzyme which speeds up the rate of a reaction, however each enzyme is specific to a certain reaction.

catalase has an iron prosthetic group which can interact with hydrogen peroxide, a dangerous chemical produced by metabolism

Why are fibrous proteins insoluble?

contain lots of amino acids in the primary group with hydrophobic R groups

what are fibrous proteins?

Fibrous proteins are long strands of polypeptide chains that have cross-linkages due to hydrogen bonds

They have little or no tertiary structure

why is it good that fibrous proteins only have limited numbers of amino acids?

The highly repetitive sequence creates very organised structures that are strong and this along with their insolubility property, makes fibrous proteins very suitable for structural roles, for example, keratin that makes up hair, nails, horns and feathers and collagen which is a connective tissue found in skin, tendons and ligaments

what bonds make up keratin and what kind of protein is it?

fibrous

mad up of dsiulphide bonds, the more bonds the less flexible

where is elastin found?

lungs, walls of large arteries, elastic ligaments

why is elastin beneficial

very flexible and allows for organs to stretch

where is collagen found and why is it beneficial?

nervous system, ligaments, tissue of skin and is beneficial because its very flexible.

what is an enzyme

they are a biological catalyst

they are globular proteins

they interact with substrates

what are anabolic reactions

reactions to build up a human and use enzymes

What are catabolic reactions?

Chemical reactions that break down large molecules

what is the v max?

The point of saturation of enzyme active sites

No further increase in substrate concentration will help as all active sites are occupied. (can only increase ror to a certain point)

What is the lock and key hypothesis?

The idea that the enzyme has a fixed shape and only the right substrate will fit into the active site.

Exact fit.

The R groups in the active sites will react producing bonds, speeding up the ROR

why is the induced fit model favored

explains how enzyme stresses bonds of substrate

explains why enzyme releases products

What is the induced fit model?

This theory proposes that:

- The complementary substrate binds to the active site of the enzyme

- This forms an enzyme substrate complex

- As the substrate binds, the active site changes shape slightly, which provides a better fit

- This puts strain on the substrate molecule, causing bonds to be distorted with the substrate molecule.

- This therefore lowers the activation energy to bread bonds, and the bonds can then break

- The product is formed

Factors that affect enzyme activity

Temperature

pH

Enzyme concentration

Substrate concentration

Why do we use initial rate of reaction as a basis to start rate of reaction rather than 0

Because initial rate of reaction is a point where there is plenty of substrate available as it has not yet been broken down yet allowing the reaction to proceed

What is V max

V max = maximum rate of reaction

Why do enzyme become denatured and what is the affect of this denaturing

Enzymes become denatured due to vibrations breaking hydrogen and ionic bonds. This disturbs tertiary structure and 3D shape, therefore altering shape of the active site

Why are many enzymes in our bodies optimum temperature 40c when out body temperature is 37c

As if our enzymes were to have a optimum temperature of our body temp 37c if our body temperature was to get higher for instance we get a fever then the enzymes would denature, however because their optimum temperature is close to 40c they won't as a matter of fact they would probably get more productive as the temperature would be closer to their optimum temperature. Also so other proteins in our body don't denature.

what is an intracellular enzyme?

an intracellular enzyme is found within a cell, it catalyses processes such as the formation of polymers from monomers

what is an extracellular enzyme?

they break down polymers to be used within the cell for different processes

e.g digestion

describe the induced fit model theory?

The enzyme and its active site (and sometimes the substrate) can change shape slightly as the substrate molecule enters the enzyme

These changes in shape are known as conformational changes

This ensures an ideal binding arrangement between the enzyme and substrate is achieved

This maximises the ability of the enzyme to catalyse the reaction

how is starch digested?

starch polymers are broken down into maltose

this is done by amalyse produced in the pancreas and salivary glands

maltose = broken down into glucose (a monosacharide) by maltase found in the small intestine

glucose can then be absorbed by the small intestine into the bloodstream

What are cofactors?

they transfer atoms from one reaction or another

or they form part of the active site

where do inorganic cofactors come from

diet. Chloride, zinc so on...

name a coenzyme and what it does

vitamin B3 for synthesising NAD for repiration

What are prosthetic groups?

similar to cofactors, but they are bound to the enzyme, rather than being separate molecules or atoms. they are also tightly bound and are more vital in enzyme activity

why is precursor activation beneficial?

Protein precursors are often used by an organism when the subsequent protein is potentially harmful, but needs to be available on short notice and/or in large quantities.

This reduces the concentration of the initial substrate.

what is precursor activation?

where an enzyme must be activated to begin its function

how do you activate a precursor enzyme?

adding a co factor into the active site, changing the shape of its tertiary structure

Before the cofactor is added, what is the precursor protein called? and after?

apoenzyme and then a haloenzyme