2.3 biological molecules

why is water important?

• reactant, in lots of chemical reactions including hydrolysis

• ice floats, water is less dense when it is a solid and forms and insulating layer

• habitat, organisms survive and reproduce in it

• solvent, some substances dissolve in it. Most biological reactions take place in solution

• transports substances, like glucose and oxygen around plants and animals

• temperature control, high specific heat capacity and high latent heat of vaporisation

why is water polar?

In each molecule the hydrogen is positive and oxygen is negative. So water has both a slightly negative and positive side meaning its ‘polar’. But is neutral overall.

Where do hydrogen bonds exist?

formed between a highly electro-negative atom of a polar molecule and a hydrogen

Is hydrogen bonds weak?

• one hydrogen bond is weak

• many hydrogen bonds are strong

what are properties of water?

• cohesion

• adhesion

• high specific heat

• high latent heat of vaporisation

• density

• solvent

What is the meaning of Cohesion?

Attraction between molecules of the same type due to polarity of the molecule. This results in surface tension.

What is meaning of Adhesion?

Attraction between two different substances. Water will make hydrogen bonds with other surfaces.

What is meaning of specific heat capacity?

The energy needed to raise 1kg of water by 1 degree. Due to H bonds, water can absorb or release large amounts of heat energy with little change in actual temperature.

How is High specific heat lead to an excellent habitat?

• prevention of temperature fluctuations that are outside the range suitable for life

• a stable marine environment

What is meaning of high latent heat of vaporisation?

The energy needed to convert 1kg of a substances from a liquid to a gas. In order for water to evaporate hydrogen bonds must be broken. As water evaporates it removes a lot of heat with it.

What is High Latent Heat of Vaporisation responsible for?

• moderating earth’s climate

• preventing organisms from overheating

why is the density of water important?

• prevents water from freezing from the bottom up

• ice forms on surface first- freezing water releases heat to the water below creating insulation

• makes transition between seasons less abrupt

most dense at 4 degrees

contracts until 4 degrees

expands from 4 degrees to 0 degrees

Is water less dense as a Solid or as a liquid?

Less dense as a solid because liquid water has H bonds that are constantly being broken and reformed. Frozen water forms a crystal-like lattice whereby molecules are set at fixed distances

How does a solvent work?

Negative and positive parts of water is attracted to negative and positive parts of a solute. Water molecules cluster around solute, keeping them apart. At this point they dissolve and solution is formed

Give 3 important functions of water in mammals

• solvent as can transport substances in the blood

• reactions are carried out in the cytoplasm which is mostly water

• water is used in metabolic reactions to make and break bonds (hydrolysis and condensation)

what is the role of calcium ions?

• muscle contraction

• bone formation

what is the role of sodium ions?

• nerve impulses

• affects absorption of carbohydrate in the intestine

what is the role of potassium ions?

• nerve impulses

• stomatal opening

what is the role of hydrogen ions?

• production of ATP

• ph determination (more H+ ions than OH- ions in solutions creates and acid)

what is the role of ammonium ions?

• production of nitrate ions by bacteria

what is the role of nitrate ion?

• component of nucleic acids

• a component of nitrogen cycle

what is the role of hydrogen carbonate ions?

• involved in the transport of co2

what is the role of chloride ions?

• involved in transport of co2

• regulates affinity of haemoglobin

what is the role of phosphate ions?

• component of phospholipid, ATP and nucleic acids

• helps root growth

what is the role of hydroxide ions?

• involved in regulation of blood pH (more OH- ions that H+ ions in solutions creates and alkali)

what are condensation reactions?

joining of compounds to form a chemical bond, with an elimination of water

what are hydrolysis reactions?

breaking down of compounds by breaking down chemical bonds with the usage of water

what do condensation reactions form?

polymers

what do hydrolysis reactions form?

monomers

what is a hydroxyl group?

alcohol group

what is a glycosidic bond?

covalent bond which links carbohydrate group to another group

what is a peptide bond?

covalent bond which links amino acids together in proteins

what type of molecules is carbohydrates made up of?

• carbon

• hydrogen

• oxygen

what type of molecules is proteins made up of?

• nitrogen

• carbon

• hydrogen

• oxygen

what type of molecule is nucleic acid made up of?

• carbon

• oxygen

• phosphorus

• nitrogen

• hydrogen

what type of molecule if lipids made up of?

• carbon

• hydrogen

• oxygen

what is the monomer of carbohydrates?

monosaccharides

what is polymer of carbohydrates?

polysaccharides

what is the monomer of proteins?

amino acids

what is the polymer of proteins?

polypeptides

what is the monomer of nucleic acids?

nucleotides

what is the polymer of nucleic acids?

RNA
DNA

what is the difference between a-glucose ring and B- glucose ring?

for a glucose the H is at the top and OH is bottom but opposite for B

what are some uses of carbohydrates?

• substrate for respiration (glucose)

• energy store (starch and glycogen)

• structural  (cellulose, chitin in arthropod exoskeletons)

• hereditary information (pentose sugar deoxyribose)

• recognition of molecules outside of cells (attaches to proteins or lipids on cell membranes)

what is structure of a monosaccharide?

• carbon backbone can be made of 3,4,6 carbon atoms

• one C forms a double bond with an oxygen atom

• other carbons in chain are bonded to one hydrogen atom and one hydroxyl group

• the sugars taste sweet and are soluble in water

what do glucose and glucose make?

maltose. (malt sugar)

what do galactose and glucose make?

lactose (milk sugar)

what does glucose and fructose make?

sucrose (table sugar)

what is the formula for the maltose, sucrose, lactose from condensation?

C12 H22 O11 +H2O

what is the name of the reaction to create a glycoside linkage between two sugars?

condensation

what is the scientific term for a pair of carbohydrate

monomers linked together?

disaccharide

what are examples of polysaccharides?

• starch

• glycogen

• cellulose

4 Features of Starch

• ONLY plants store excess glucose as starch

• insoluble in water so doesn't affect osmosis

• mixture of amylose and amylopectin

• alpha glucose

What is structure of amylose?

• unbranched helix- shaped chain

• 1,4 glycosidic bonds between a-glucose molecules

• helix shaped allows more compact and thus more resistant to digestion

• 10-30% starch

• compact so good for storage

• alpha glucose

what is structure of amylopectin?

• branched molecule

• 1,4 and 1,6 glycosidic bonds

• 70-90% starch

• glucose can be released quickly as is easier for enzymes to get to branches

• alpha glucose

Where is starch found?

plants

where is glycogen found?

animals

where is cellulose found?

plants

what glucose is starch?

alpha glucose

what glucose is glycogen?

alpha glucose

what glucose is cellulose?

beta glucose

what is structure of glycogen?

• alpha glucose

• 1,4 and 1,6 glycosidic bonds 

• branched molecule

• more branches than amylopectin

what is structure of cellulose?

• Beta glucose

• 1,4 glycoside bond rotated 180 degrees allowing bond of hydroxyl groups

• any chains run parallel to each other forming microfibrils, which is strengthened with cross-linkages (hydrogen bonds), giving cellulose its stability, valuable structural material and difficult to digest

• space between microfibrils to allow water and minerals to pass but some cases gaps blocked to make it waterproof

what are three types of lipids?

• triglycerides

• phospholipids

• steroids

what is triglyceride made up of?

one molecule of glycerol and 3 fatty acids

what are triglycerides functions?

• energy source (broken down in respiration)

• insulation (around nerve cells across the as electrical insulation)

• energy store (insoluble in water so don’t affect water potential)

• buoyancy (fat is less dense than water so allows animals to float)

• protection (fat around organs acts as a shock absorber)

what does it mean to be saturated?

single bonds

what does it mean to be unsaturated?

has at least one double bond

what does it mean to be polyunsaturated?

many double bonds

what type of reaction happens between glycerol and fatty acid?

esterification (condensation)

what type of bond is between glycerol and fatty acid?

ester bond

what is a phospholipid made up of?

• diglyceride

• phosphate group

• simple organic molecule such as chlorine

what is the difference between phospholipid and triglyceride?

in phospholipid there are only two fatty acid groups unlike the three fatty acids in triglyceride because one of them is replaced by phosphate group

in a phospholipid what part is hydrophilic and hydrophobic?

phosphate is hydrophilic

fatty acids tail is hydrophobic

how would phospholipids form a layer on surface of water?

heads in the water and tails sticking up and out of the water

phospholipids in water could also form micelles what are they?

tiny balls with tails tucked inside and heads pointing in the water

what is a phospholipid bilayer?

two rows of phospholipids with tails pointing inwards and heads pointing outwards

what is structure of cholesterol?

4 carbon based rings and a hydrocarbon tail

the ring with a hydroxyl group

what does cholesterol do  relating to phospholipids?

fits in-between phospholipids and regulates the fluidity of the cell surface membrane

are animal fats saturated or unsaturated?

saturated and that’s why they’re solid at room temp

are plant fats saturated or unsaturated?

unsaturated and that’s why oils are liquid at room temperature

what are sterols?

complex alcohol molecules based on a four carbon ring structure with a hydroxyl group at one end

what is peptides?

polymers made up of amino acids

what are proteins?

consists of one or more polypeptides arranged as a complex macromolecule and have specific biological functions

what are essential amino acids?

amino acids that our bodies cannot make and can only be obtained through diet

what are the different parts that make up an amino acid?

• amino group

• the R group

• carboxyl acid group

How Is a peptide bond formed?

• the hydroxyl group of the carboxylic group reacts with the hydrogen group of amino group of an another amino acid

• condensation reaction

• resultes in a dipeptide

what is it called when lots of amino acids form peptide bonds?

polypeptide

How do R groups do to make a protein from a polypeptide?

• R groups interact with each other (R group interactions) forming different types of bonds

• leading to long chains of amino acids (polypeptides) folding into complex structures (proteins)

explain the primary structure of protein structure?

• sequence of which amino acids are joined

• directed by information carried in the DNA

• particular amino acids in sequence will determine how polypeptide folds to create protein’s final shape, and in turn its function

• peptide bonds only

explain the secondary structure of protein structure?

• weak negatively charged nitrogen and oxygen atoms interact with weak positively charged hydrogen atoms

• can form a-helix (coil shape), or B-pleated sheets (sheet like structure)

• hydrogen bonds

explain the tertiary structure of protein structure?

shapes formed by bending and twisting

addition bonds form between R groups

• hydrogen bonds (numerous but easily broken)

• disulphide bonds (covalent, strong but only between sulphur in R groups)

• ionic bonds (form between oppositely charged R groups)

• hydrophobic and hydrophilic interactions ( weak interactions between polar groups or non-polar groups R groups)

explain the quaternary structure of protein structure?

• more than one polypeptide chain working together as a functional macromolecule eg haemoglobin

• each polypeptide chain is referred to a subunit of a protein

• there may be a non-protein 

what are the two main categories that tertiary and quaternary structures fall under?

• globular proteins

• fibrous proteins

what are the features of globular proteins?

• almost spherical in shape

• soluble in water because the hydrophilic groups are on outside and the hydrophobic R groups are on inside

• 3D shape

• e.g enzymes

what are the features of fibrous proteins?

• repetitive sequence of amino acids

• insoluble in water because of high proportion of amino acids with hydrophobic

• organised structures

• not folded into complex three dimensional shapes like globular proteins

• e.g collagen

is haemoglobin globular or fibrous protein?

globular

what is haemoglobin made up of?

• two a-globin

• two B-globin

• haem area called prosthetic group as a molecule of oxygen can bind to each haem group (contains iron)

what is a conjugated protein? With An Example

• a protein with a non-protein group attached

• haemoglobin

What are the features of Insulin?

• globular protein

• involved in the regulation of glucose concentration

• made of two polypeptide chains

• chain A starts with section of a-helix and B chain ends with section of B-pleat 

• both chains joined by disulphide links

• hydrophilic are on outside making it soluble