2.1.2 Biological Molecules

What is the structure of water/ How is it bonded

• 2 hydrogen atoms covalently bonded to 1 oxygen atom

• Hydrogen shares a pair of electrons with oxygen. The oxygen has a greater affinity for the electrons (because it’s larger) so it pulls the electrons (and consequently the hydrogen) closer

• Oxygen is slightly delta negative and hydrogen is slightly delta positively charged

  • This creates different charged regions which makes water a polar molecule. Because it has 2 it’s dipolar.

• Water has a very stable structure due to its many hydrogen bonds, despite them being weak and despite water being a small molecule

Draw a water molecule

What gives water its high SHC and how is it used

• This is due to water having many hydrogen bonds which require lots of energy to overcome

• This means water is good at retaining heat and resists changes in temperature

• Which allows organisms to live in them despite the climate

• This also allows it to work as a coolant/moderator of temperature changes

What is cohesion in water

Cohesion allows water to move in one mass by allowing water molecules to stick together in chains

What is adhesion in water

• Adhesion allows water to stick to other materials

• Plants use this during transpiration when water moves up xylem vessels

• Animals use this when transporting dissolved compounds around the body via capillary action

What gives water its surface tension and how is it used

• Water molecules are more strongly cohesive to each other that to air, this results in water having a skin of surface tension

• This therefore allows a habitat to exist on the surface of water for organisms like pond skaters

How does waters role as a solvent work

• Many solutes of an organisms can be dissolved in water

• It can dissolve most organic and inorganic substances

• It is needed for all bio-chemical reactions

• In animals: used to remove excretory products such as urea and excess salts

• In plants: Root hairs absorb mineral salts present in soil in solution form

How does waters role as a insulator work

• When water freezes into ice it forms an open lattice structure, which leads to more space between molecules causing them to expand

• The expansion causes the density to decrease

• The decrease in density causes it to float

• In which it will form an insulating layer above the pond of water allowing organisms to survive under it

How does water work as a transport medium

• It’s solvent properties and cohesion forces allows water to be a transport medium

• In humans: Human blood plasma consists of 90% water

• In plants: Sugar and mineral salts are transported in solution in vascular bundles

How does water work as a reagent

It is used in hydrolysis and condensation

What is a condensation reaction

A reaction where molecules are joined together by forming a covalent bond and removing water

What is a hydrolysis reaction

A reaction that breaks a bond via the addition of a molecule of water

What are carbohydrates made up of

ONLY: Carbon, hydrogen, oxygen

What is Carbohydrates general formula

How do saccharides/sugars build up

• Monosaccharides: 1 sugar, simple sugar

• Disaccharides: Double sugars, formed from 2 monosaccharides

• Polysaccharides: Large molecules formed from many monosaccharides

Examples of Monosaccharides (4)

• Glucose

• Fructose

• Galactose

• Ribose

Examples of Disaccharides (3)

• Sucrose

• Maltose

• Lactose

Examples of polysaccharides (3)

• Glycogen

• Cellulose

• Starch

What is a monosaccharide

• Simplest ‘single sugars’

• Same number of ‘C’ as ‘O’ atoms e.g. glucose is C6H12O6

• If N=3 - triose e.g. glyceraldehyde

• If N = 5 - pentose e.g. deoxyribose, ribose

• If N = 6 - hexose e.g. glucose, galactose, fructose

• White crystalline solids

• They dissolve in water to form sweet tasting solutions

What is a hexose-glucose

• Abundant and very important monosaccharide

• It is a hexose sugar due to its 6 carbon atoms with a general formula of C6-H12-06

• Major energy source for most cells

• Highly soluble in water

• Is the main form in which carbohydrates are transported around the body

What are the different structural isomers of glucose called

• Alpha (OH group below)

• Beta (OH group above)

Draw the structure of (alpha) glucose

Draw the structure of beta glucose

How do monosaccharides bond to form disaccharides

The hydroxyl groups of the 2 glucose interact

• The bond via a condensation reaction

• One glucose bonds with its Carbon 1 and the other with its Carbon 4 to form a 1-4 glycosidic bond

Draw the structure of galactose

Draw the structure of fructose

What are the features of fructose

• Very soluble

• Main sugar in fruits and nectar

• Sweeter than glucose

What are the feature of galactose

• Not as soluble as glucose

• Has an important role in the production of glycolipids and glycoproteins

What is a pentose monosaccharide

• They contain 5 carbon atoms

• Examples include the structural isomers ribose and deoxyribose

Draw the structure of ribose

Draw the structure of deoxyribose

How is maltose formed

• Formed from 2 glucose molecules

• Joined by alpha 1-4 glycosidic bond

What is sucrose and how is it formed

• Table sugar

• Formed from 1 glucose and one fructose

• Joined by an alpha 1-2 glycosidic bond

• Fructose flips to allow this to happen

What is lactose and how is it formed

• Milk sugars

• Formed from 1 galactose and 1 glucose

• Joined by a beta 1-4 glycosidic bond

How do you test for reducing sugars (All the monosaccharides)

• The Benedict’s test

  • Benedict’s reagent is a turquoise liquid containing copper (II) sulfate ions in an alkaline solution

Why don’t reducing sugars don’t react with Benedict’s

The part of the molecules that needs to react is already in a glycosidic bond

How do you test for non-reducing sugars

• Therefore they need to be hydrolysed before being tested

• This is done by boiling with acid, neutralising and then boiling with Benedict’s

What is the structure of starch

• 20% of it is amylose in an alpha helix

• Remaining 80% is amylopectin which is branched in a 1-6 glycosidic bond

Why do plants store glucose as starch

• To get around the fact that glucose is soluble in water due to the hydroxyl groups

  • They can form hydrogen bonds with water molecules

What is the structure of amylose

• Amylose is a polysaccharide of alpha glucose molecules In a 1-4 glycosidic bond

• This then twists into an alpha helix - witch hydrogen bonds forming along the chain

What is the structure of Amylopectin

• Highly branched

• Can be hydrolysed quicker than amylose

  • due to being branched

    • gives it many ends

      • Many sites to break down starch to glucose

• A-glucose molecules joined by 1-4 glycosidic bonds with a 1-6 bond every 20-30 monomers

• Plants store it then hydrolyse it when they need a supply of energy

What are the properties and uses of starch

• Major carbohydrate storage molecule in plants

• Usually stored as intracellular grains in organelles called plastids

  • Includes green chloroplasts and colourless amylose

• Produced from glucose made during photosynthesis

• Broken during respiration to provide energy and is also a source of carbon

• Compact due to double helix - can store lots of it

• Insoluble - doesn’t cause osmosis for the cell its in

What is the structure of cellulose

• Polysaccharide

• Consists of long chains of beta glucose molecules joined by beta 1-4 glycosidic bonds

• It is a straight chain molecule because it is unable to coil or form branches

  • This is due to the fact that each alternate molecule flips in order to have the hydroxyl group of the glucoses close enough to react

What are the features and roles of cellulose

• Main component in cell walls

• Most abundant organic polymer

• Very strong - prevents cells from bursting when they take in water

• Permeable

• Humans cant digest cellulose as we dont produce cellulase (but cows do)

What is the structure of glycogen

• Contains many alpha 1-6 glycosidic bonds that produce a very branched structure (similar to amylopectin)

What are the features and roles of glycogen

• Animals store glucose as glycogen

• Stored as small granules, particularly in the liver

• Less dense ad more soluble than starch and is broken down quicker

• Indicates the higher metabolic requirements of animals compared to plants

Draw the general structure of a protein

What are the different types of proteins

• Structural: Proteins are the main components of body tissue - e.g. muscle, skin, ligaments and hair

• Catalytic: All enzymes are proteins, catalysing many biochemical reactions

• Signalling: Many hormones and all cell membrane receptors are receptors

• Immunological: All antibodies are made up f proteins

What elements do all proteins contain

• Carbon

• Hydrogen

• Oxygen

• Nitrogen

What is the R group in a protein

• It represents a side chain from the central ‘alpha’ carbon atom

• It defines the amino acid - they all have the same general structure, the only different being the nature of the functional/R group

How many different types of amino acids that are used to make proteins are there

• 20

• 5 non-essential (Can be made from other amino acids)

• 6 conditionally essential (only needed for infants and growing children)

• 9 Essential (Can only be obtained by our diet)

How are polypeptides formed

• Amino acids are joined together via condensation reactions to form a peptide bond making a dipeptide molecule

  • (dipeptide molecules are a transition between poly and peptides)

• Dipeptides then have more amino acids added to them to create a polypeptide chain

• The reaction is catalysed by the enzyme peptidyl transferase

• A protein consists of one or more polypeptide chain folded into a highly specific 3D chain

What does the primary structure of a protein consist of

• This is the sequence of amino acids within a polypeptide chain

• The particular amino acids will influence how the polypeptide folds - this in turn determines its function

• The only bonds involved in the primary structure are peptide bonds

What does the secondary structure of a protein consist of

• Often the sequence of amino acids causes the polypeptide chain peptide to fold into a simple repeating pattern

• Constitutes secondary structures such as alpha helixes and beta pleated sheets

• The are held together by hydrogen bonds (non-covalent and weak) between the CO and NH groups of the chains

• The O in the CO groups have a small negative charge

• The H in the NH groups have a small positive charge

• These charges can attract each other which can abuse hydrogen bonds to form which causes the chain to twist and fold

How is an Alpha helix formed

• The shape is formed of 36 amino acids per 10 turns of the helix

• Hydrogen bonds are formed between the CO of the carboxyl group and the NH of amine group of the amino acid 4 places ahead of it

How is a beta pleated sheet formed

Polypeptide chains can also lie parallel to one another joined by hydrogen bonds, forming sheet like structures

What does the tertiary structure of a protein consist of

• Often Includes sections of the secondary structure

• The coiling and folding brings R-groups closer together so that they will interact and cause further folding

• Interactions include:

• Hydrophobic & Hydrophilic interactions: Weak interactions between polar and non-polar R groups (hydrophobic)

• Hydrogen bonds: The weakest of the bonds formed, involved in all levels of structure, between polar R groups

• Disulphide bonds/bridges: Covalent, one of the strongest, most important type of bond, occurs between R groups that contain sulphur atoms e.g. cysteine amino acids

• Ionic bonds: Stronger than hydrogen bonds, forming between oppositely charged R groups

• Van der Waals forces: between non-polar molecules

What does the quaternary structure of a protein consist of

• Exists in proteins that have more than one polypeptide chain working together

• Each polypeptide chain in the quaternary structure is referred to as a subunit of the protein

• Interactions between the subunits are the same as in the tertiary structure but they are between different protein molecules rather then within one

• Haemoglobin has 4 subunits, made up of 2 sets of 2 identical subunits

What is a globular protein

• Compact

• Spherical

• Easily soluble (in water) - so they can be easily transported in fluids

How are globular proteins structured

• Spherical shape caused by tightly folded polypeptide chains

  • Chains usually folded so that hydrophobic groups are on the inside, while hydrophilic ones are on the outside

    • this is what makes them soluble

What are conjugated proteins

• A protein with a prosthetic group, that is non-protein

  • Part of the protein which enables it to do its job

• Can be lipoproteins, glycoproteins, metal ions or minerals from vitamins

• Attached to the main group via covalent bonds, ionic interactions and hydrogen bonds

• E.g haemoglobin has a prosthetic haem group

What are the key inorganic cations that could be part of the prosthetic group

• Calcium ions

• Sodium ions

• Potassium ions

• Hydrogen ions

• Ammonium ions

What are the key inorganic anions that could be part of the prosthetic group

• Nitrate

• Hydrogen

• Carbonate

• Chloride

• Phosphate

• Hydroxide

What is haemoglobin’s structure

• Globular protein

• Quaternary structure - four polypeptide chains (2 a-globin + 2 b-globin proteins) - each with a prosthetic haem group

• Chains held together by disulphide bonds

  • Hydrophobic groups face inwards while hydrophilic ones face outwards

• The haem group contains an Iron II ion which can reversible combine with oxygen to form oxyhaemoglobin

What are enzymes

• Biological catalysts - they speed up the rate of reaction

• Globular protein

• E.g. Catalase

  • Converts excess hydrogen peroxide from metabolic reactions into water and oxygen, preventing any damage to cells or tissues

What is the structure of insulin

• Globular protein

• Has two polypeptide chains

  • A has 21 amino acid residues

  • B has 30 amino acids residues

• 2 chains held together by three disulphide bridges

What are fibrous proteins

• High tensile strength (tough)

• Long strands of polypeptide chais

• Tend to be found in connective tissues e.g. tendons

• Have little or no tertiary structure

• Insoluble in water - due to large number of hydrophobic R groups

• limited number of amino acids + R groups

• The highly repetitive sequence creates very organised structures

Give and describe 3 examples of fibrous proteins

• Keratin

  • Makes up hair, nails, horns and feathers-very tough

  • Rich in cytosine

• Elastin

  • Found of in connective tissue, tendons, skin and bone

  • Can stretch and then return to its original form

• Collagen

  • Connective tissue found in skin, tendions and ligaments

What is a lipid

• Insoluble in water

• Soluble in organic substances

• Contain carbon, hydrogen + oxygen

  • But a higher proportion of hydrogen + a lower proportion of oxygen

• Twice the energy per gram than carbohydrates

• Used for long term storage in animals

• Triglycerides most common type

What is the structure of triglyceride

• Made up of 1 glycerol with 3 fatty acids

  • Glycerol = alcohol

  • Fatty acids = carboxylic acids

• Both of them contain hydroxyl groups

  • They interact causing the formation of 3 water molecules and ester bonds

  • The reaction is caused esterfication - another example of a condensation

What are saturated fats

• When a FA chain has the maximum number of hydrogen atoms (no more hydrogen can be added)

• Long and straight chains

• No carbon to carbon double bonds

• Considered less healthy - implicated n elevated cholesterol synthesis

• Generally solid

• More abundant in fats of animal origin

What are unsaturated fats

• Have at least one carbon to carbon double bond

• Healthier (except trans fat)

• Generally liquid at room temp

• Found in oils that originate from plants

• Fewer hydrogens due to carbon atoms in their chains

• Monounsaturated - One carbon to carbon double bonds in each fatty acid chain while polyunsaturated have many

• Double bond causes a kink in the hydrocarbon chain

• Prevent unsaturated hydrocarbon chains packing closely together

  • Triglycerides containing a high proportion of unsaturated fatty acids have low melting temperatures

What are the different lipid functions (7)

• Energy source

• Energy store

• Waterproof coverings - outer surface of insects and plants

• Insulation against heat loss - under the skin of mammals

• Electrical insulation - Fatty sheath around nerve cells - allows electrical impulses to travel faster

• Protection of organs - Protects them from damage by absorbing shocks

• Buoyancy - body fat of animals helps the, to float easily due to low density of fats

How do lipids work as an energy store

• Oils are used as a fat store in plants

  • Seeds, e.g. sunflower

  • Fruits, e.g. palm, olive

• Spare food often converted to fats or oils for use later

• Animals short fat in adipose tissue (this surrounds many organs ad works as in insulator)

How do lipids work as a energy source

• Provide twice the amount of energy of carbohydrates or proteins, 37KJ per gram of food

• Advantage is large amounts of energy need to be consumed in small masses of food

What is the structure of phospholipids

• Made up of glycerol, a phosphate group and fatty acids

• The fatty acid tails are bonded to the glycerol by ester bonds

• Phosphate head is hydrophilic, polar and soluble in water

• Fatty acid tails are hydrophobic, non-polar and insoluble in water

• They are amphipathic - have both hydrophobic and hydrophilic pats

What is the function of cholesterol

• Important for the structure of many cells membranes

• Also the starting point for the synthesis of steroid hormones such as

  • Oestrogen

  • Progesterone

  • Testosterone

• Bile salts: involved in lipid digestion and assimilations are also formed from cholesterol

What are nucleotides

Nitrogen-containing organic substances that form the basis of (they are the monomers) the nucleic acids DNA + RNA

Draw, label and explain the nucleotide structure

2 condensation reactions:

• Base and sugar form a glycosidic bond

• Phosphate and sugar form an ester bond

How are the 5 nitrogenous bases organised

Purine bases (double ring structure):

• Adenine (A)

• Guanine (G)

Pyramidine bases (single ring structure):

• Thymine (T)

• Cytosine (C)

• Uracil (U)

How is a polynucleotide formed

• Nucleotides (N) are linked together by condensation reactions

• The phosphate group at the 5th carbon of the pentose sugar at one N forms a covalent bond with the hydroxyl group (OH) at the 3rd carbon on the adjacent N

• The bonds formed are called phosphodiester bonds

• These form long chains called a sugar phosphate backbone

How do polynucleotides form the double helix in DNA

• Two parallel strands are arranged so that they run in opposite directions - antiparallel

• The bases hold the two strands together via hydrogen bonds

• The strand on the left is the 5’3 strand and the strand on the right is the 3’5 strand

• A & T are able to form 2 hydrogen bonds

• C & G are able to form 3 hydrogen bonds

• They can only bind to each other - complementary base pairing

What are the base pairing rules

• A small pyrimidine will always bond to a larger purine base

• This arrangement causes a constant distance between the DNA ‘backbones’, resulting in parallel chains

• Complementary base pairings mean that DNA always has equal amount of adenine and thymine and equal amounts of cytosine and guanine

Differences between DNA and RNA (4)

• DNA is Deoxyribose pentose sugar while RNA is ribose pentose sugar

• DNA uses thymine while RNA uses uracil

• DNA is double stranded while RNA is single stranded

• RNA is also used in mRNA and eRNA while DNA isn’t

Similarities between DNA and RNA (3)

• Both contain phosphate group, pentose sugar and nitrogenous base

• Both form via 2 condensation rections

• Both contain phosphodiester bonds

How is DNA packaged into cells

• DNA is large so when it is stored in a cell it is wound around histone proteins - giving chromosomes.

  • Therefore each DNA molecule gives one chromosome.

• DNA without histones can also be found in

  mitochondria and chloroplasts

Prokaryotes

• DNA is naked: not in a nucleus and it

  is not wound round histones

• Some viruses also contain naked DNA

Explain semi conservative replication

• DNA helicase uncoils and breaks the hydrogen bonds

• Double helix unwinds

• Free activated DNA nucleotides join the unpaired bases. DNA polymerase rejoins the sugar phosphate backbone

• Hydrogen bonds form

• Phosphodiester bonds form between nucleotides

• Half the molecules is old DNA, half is made of new molecules - hence semi conservative

• The leading strand (3-5) is replicated continuously while the lagging strand (5-3) is replicated in short fragments which are later joined by DNA ligase

• A winding enzyme winds the new strands up to form

  double helices

• The two new molecules are identical to the old molecule