Biological molecules

How are molecules bound to haemoglobin

• The presence of the haem group (and Fe2+) enables small molecules like oxygen to be bound more easily

• This is because as each oxygen molecule binds it alters the quaternary structure (due to alterations in the tertiary structure) of the protein which causes haemoglobin to have a higher affinity for the subsequent oxygen molecules and they bind more easily

• (Fe2+) in the prosthetic haem group also allows oxygen to reversibly bind as none of the amino acids that make up the polypeptide chains in haemoglobin are well suited to binding with oxygen

What is the function of haemoglobin

• Responsible for binding oxygen in the lungs and transporting the oxygen to tissue to be used in aerobic metabolic pathways

• as oxygen isn't very soluble so it can be carried around the body more efficiently when bound to haemoglobin

How does haemoglobin appear bright red

The prosthetic haem group contains an iron II ion (Fe2+) which is able to reversibly combine with an oxygen molecule forming oxyhaemoglobin and results in the haemoglobin appearing bright red

Why is the arrangement of R-groups in haemoglobin important to the functioning of haemoglobin

• how is this relevant to sickle cell disease

• If changes occur to the sequence of amino acids in the subunits this can result in the properties of haemoglobin changing

• This causes SCA

  • where base substitution results in the amino acid valine (non-polar) replacing glutamic acid (polar) making haemoglobin less soluble

Outline the structure of haemoglobin

• their polar hydrophilic R groups orientate themselves on the outside of the protein which are globin proteins

  • 2x alpha global 2x beta globin (each subunit has a prosthetic harm group)

• The four globin subunits are held together by disulphide bonds and arranged so that their hydrophobic R groups are facing inwards and the hydrophilic R groups are facing outwards

  • this preserves the 3D spherical shape

  • and also helps maintain its solubility

• Each haemoglobin with the four haem groups can therefore carry four oxygen molecules (eight oxygen atoms)

Why do globular proteins form a spherical shape when folding into their tertiary structure

• their non-polar hydrophobic R groups are orientated towards the centre of the protein away from the aqueous surroundings

• their polar hydrophilic R groups orientate themselves on the outside of the protein

What is a conjugated protein

• outline any other features about them and prothetic groups

A protein that contains a non-protein chemical group such as a prosthetic group or cofactor

• some globular proteins are conjugated

A prothetic group is a permanent non-protein part of a protein molecule

• haemoglobin contains the prosthetic group haem

Outline the properties and functions of globular proteins

• Compact and soluble in water

• The solubility of globular proteins in water means they play important physiological roles as they can be easily transported around organisms and be involved in metabolic reactions

• The folding of the protein due to the interactions between the R groups results in globular proteins having specific shapes

• Thus, enabling globular proteins to have physiological roles, e.g enzymes can catalyse specific reactions and immunoglobulins (antibodies) can respond to specific antigens

What are the properties of haemoglobin

NOMAPS

No. of polypeptides

• 4 - 2x alpha global and 2x beta globin

Outline (shape)

• Spherical, round

Main function

• Functional (transport of oxygen)

Amino acid variation

• Variable

Prosthetic group?

• Yes, haem group

Solubility

• Soluble in water

What are the properties of collagen

NOMAPS

No. of polypeptide chains

• 3 - triple helix

Outline (shape)

• Long and thin

Main function

• structural

Amino acid variation

• Repetitive - every third amino acid is glycine

Prosthetic group?

• none

Solubility

• insoluble in water

What are the functions and properties of collagen

• flexible structural protein forming connective tissues

• the presence of many hydrogen bonds within the triple helix structure of collagen results in great tensile strength

  • this enables collagen to be able to withstand large pulling forces without stretching or breaking

• the staggered ends of the collagen molecules within the fibrils provide strength

• stable protein due to the high proportion of proline and hydroxyproline amino acids

  • these amino acids increase stability as their R groups repel each other

• The length of collagen molecules means they take too long to dissolve in water (insoluble)

What are the properties of globular proteins

SPANDS

Shape

• Round and spherical

Purpose

• Functional

Acid sequence

• Irregular amino acid sequence

Durability

• more sensitive to change in pH and temp

Solubility

• Generally soluble in water

Outline the properties of fibrous proteins

SPANDS

Shape

• Long and narrow strands

Purpose

• Structural

Acid sequence

• Repetitive amino acid sequence

Durability

• less sensitive to change in pH and temp

Solubility

• Generally insoluble in water

What are three common fibrous proteins and their functions

• Keratin

  • compose fingernails, horns and hair

• Collagen

  • connective tissue found in skin, hair and tendons

• Elastin

  • found in connective tissue, tendons, skin, bone and artery walls

Why are fibrous proteins good for structural roles

Their insolubility as well as its very organised structure make these proteins suitable for structural roles

Outline the features of fibrous proteins

• Long strands of polypeptide chains that have cross-linkages due to H bonds

• These proteins have little or no tertiary structure

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

• Fibrous proteins have a limited number of amino acids with the sequence usually being highly repetitive

What are some examples of quaternary proteins

• Haemoglobin - made of 4 subunits (2 alpha, 2 beta and held together by disulphide bridges)

• Collagen

• Insulin - Weak interactions between the subunits in the insulin polypeptide help to stabilise the overall quaternary structure

Outline the Quaternary structure of proteins

• Multiple 3D polypeptides can come together to form a complex, quaternary structure (same a tertiary)

  • also involves the interaction/bonding between R-variable side groups of amino acids in separate polypeptide chains

Describe the hydrogen bonds between amino acids

• Hydrogen bonds also form between amino acids

• Hydrogen bonds are relatively weak but when there are many, the overall stability of the tertiary structure increases

Describe the disulphide bridges in amino acids

• what type of bonds are they and what proteins do they contain

• These are covalent bonds set up within proteins containing cysteine (CYS) amino acids

• often help proteins resist denaturing

Describe ionic bonds in amino acids

• Charged amino acids have a positively or negatively charged ion in their side chain

• Charged amino acids can form relatively strong ionic bonds with other charged amino acids

• Ionic bonds between amino acids are quite rare

Outline the tertiary structure of proteins

• Interactions between R groups creates the complex 3D tertiary structure of a protein

• The 3D structure is usually coiled or folded

• Bonds are either hydrophilic, ionic or disulphide

Outline the secondary structure of proteins

• how is the structure determined

• what else can it form

• Amino acids in a polypeptide chain can form hydrogen bonds between other amino acids within the chain

• The hydrogen bonds cause the protein to fold into specific structures

• Folding of the polypeptide determines its secondary structure

• Can form beta-plated sheets or an Alpha Helix

Outline the primary structure of proteins

• what determines the primary structure of polypeptides

• what determines the sequence of amino acids

• the sequence of amino acids in a polypeptide chain determines the structure of the polypeptide

• amino acids are polymerised by condensation reactions to form peptide bonds

• determined by the gene encoding the protein

What are peptide bonds formed between

• two amino acids

• an amino group and a carboxyl group

How are peptide bonds digested

Hydrolisis

What is a Peptide formed by

Condensation reaction

What are ester bonds formed between

• Glycerol and fatty acids

• A carboxyl group and a hydroxyl group

How are ester bonds digested

Hydrolisis

How are ester bonds formed

Condensation reactions

What are glycosidic bonds formed between

• two monosaccharides

• hydrogen and a hydroxyl group

How are glycosidic bonds digested

Hydrolisis

The two functional groups in amino acids are

• The carboxyl group (COOH)

• The amino group (NH₂)

Describe how peptide bonds are formed

• When two amino acids react together, a bond forms between the carboxyl group of one amino acid and the amino group of a second amino acid

• One water molecule is released as a by-product

• The bond formed between two amino acids is a covalent bond called a peptide bond

What is a peptide bond

A peptide bond is a chemical bond that links two amino acids together in a protein. It forms when the carboxyl group of one amino acid reacts with the amino group of another, releasing a molecule of water (H₂O).

Outline the structure of polypeptides

• Polypeptides are made from chains of amino acids

• There are amino acids at each end of the polypeptide chain

• These amino acids form the two end terminals:

  • The N-terminal (amine terminal)

  • The C-terminal (carboxyl terminal)

What is an R group

• The R group is different in each amino acid.

• The R group determines how the amino acid interacts and bonds with other amino acids in the polypeptide.

What are glycosidic bonds formed by

Condensation reactions

Outline the structure of amino acids

• how do you distinguish an amino acid

• Contain Carbon, Hydrogen, oxygen and nitrogen

• They are polar and soluble

An amino acid should contain

• NH2 (an amino group)

• COOH (a carboxyl group)

• H (a hydrogen atom)

• R (a side group)

How are dipeptides and polypeptides formed

• what are bonds between amino acids called

• 2 amino acids polymerise in a condensation reaction to form water and a dipeptide

• Many amino acids can polymerise to form a polypeptide

• bonds between amino acids are called a peptide bond

What is the display formula of a generic amino acid

Amino group

Side chain

Carboxyl group

What is the display formula of cellulose

What happens to cholesterol at low temperatures

• Cholesterol prevents phospholipid from packing too close together to increase membrane fluidity

What happens to cholesterol at high temperatures

• they bind to the hydrophilic tails of phospholipids, causing them to pack together more closely

• Makes the membrane more rigid and contain less fluid

Outline the features of Cholesterol

• what is its structure

• what does it stabilise

• Cholesterol is a type of lipid

• Cholesterol has a ring steroid structure so it can be converted into steroid hormones (oestrogen and testosterone)

• Used to stabilise cell membranes

• It's a flat molecule so it can fit between phospholipids

What is Saponification

• traditional soaps made using lipids

• the lipids (animal or vegetable) are broken down into glycerol and fatty acids

• the fatty acids are reacted with the salts of carboxylic acids in a saponification reaction

Outline the features of phospholipids

• describe the structure

• Special type of lipid that contain phosphate groups and found in biological membranes

• Phospholipids aren't considered lipid for triglycerides

• have a polar phosphate head (hydrophilic) and a non-polar fatty acid tail (hydrophobic)

• Form into phospholipid bilayers to make biological membranes with hydrophilic/polar phosphate heads pointing outwards towards water

• Centre of the bilayer is hydrophobic so soluble substances can't pass through

Do unsaturated fatty acids contain a double CC bond

• what are they called if they have one CC double bond

• what are they called if they have multiple CC double bonds

Yes

• 1 CC - monounsaturated

• multiple CC - polyunsaturated

Do saturated fatty acids contain a double CC bond

No

What is the display formula of triglyceride

• what type of bond is in it

Ester bond

What is the simple structure of a triglyceride

How do biological organisms make use of lipids

• strong energy

• insulation

• waterproofing

• protection of foetuses in mammals

Outline the features of Chitin

Chitin is a polysaccharide found in the shells of arthropods (spiders and insects)

Forms the cell walls in fungi and yeast (Murein and Peptidoglycan)

What is a microfibril?

When several cellulose polymers align and hydrogen bonds form between the chains

They are held together by proteins called pectin and carbohydrates called hemicellulose

How do beta glucose molecules orientate in cellulose

The beta-glucose molecules alternate between up and down orientation. This allows several cellulose polymers to align and hydrogen bonds form between the polymer chains to make a structure called a myofibril

Outline the features of cellulose

• how many glycosidic bonds does it have

• Polymer of the monomer beta glucose

• has 1,4 glycosidic bonds only

• It forms into straight chains

• Large insoluble molecule

Why do we need to store glucose

• When glucose dissolves in water (as it's soluble), it causes a low water potential to form (low concentration of water)

  Osmosis occurs

• Cells/tissue with higher glucose concentration will have water move into them, causing them to become turgid (swell) and then cause tissue damage or kill the cell by lysis (cell bursting)

Outline the features of Glycogen

• how many glycosidic bonds does it contain

• how rapidly does it hydrolyse

• does it have more branches than amylopectin?

• Polymer of alpha glucose

• Contains 1,4 glycosidic bonds and 1,g glycosidic bonds which make side chains

• Large insoluble chains

• Rapid to hydrolyse back to glucose as it has many ends that can be acted on by enzymes

• Glycogen has more branches and free ends than amylopectin - more compact energy store

• stored in liver and muscle cells

What is the display formula of Amylopectin

What is the display formula of Amylose

Outline the features of Amylopectin

• how many glycosidic bonds does it contain

• how fast does it hydrolyse back to glucos

• Polymer of Alpha glucose

• Contains 1,4 glycosidic bonds and 1,6 glycosidic bonds which make side chains

• Large insoluble molecule

• compact branched structure with many side chains

• Rapid to hydrolyse back to glucose as it has many ends that can be acted on by enzymes

Outline the features of Amylose

• how many glycosidic bonds does it contain

• what is it a polymer of

• how fast does it hydrolyse back to glucose

• Polymer of Alpha Glucose

• contains 1,4 glycosidic bonds

• Large insoluble molecule

• forms into a single/unbranched compact coil/helix

• slow to hydrolyse back to glucose as it has only 2 ends which can be acted on by enzymes

What are the two types of starch

Amylose and amylopectin

Outline the features of starch

• Long chain of glucose

• excess glucose during photosynthesis is converted to starch

• plants convert starch back into simple sugars at night, as no photosynthesis will occur

How is Water a polar molecule

• oxygen atoms in water are slightly negatively charged

• hydrogen atoms in water are slightly positively charged

List all of the special properties of water

• Metabolic importance

• High SHC

• High SLH

• Cohesive properties

• Useful as a solvent

What are the biological properties of water in terms of AQUATIC LIFE

• allows organisms to push against it to swim

• water creates upthrust on the organisms called buoyancy

• water is transparent so animals can see through it to find food or hunt

• light can pass through water so it can be absorbed for photosynthesis

• water dissolves in oxygen - can be absorbed by marine life via diffusion

• water dissolves carbon dioxide - can be absorbed plant and algae for photosynthesis

What are the physical properties of water in terms of surface tension

• Water molecules on the surface of water form hydrogen bonds which can support objects on the surface such as water skaters or paperclips

• If a detergent is added, this breaks down surface tension

What are the physical properties of water in terms of COHESION AND ADHESION

• how is this this important in transport systems

• cohesion is where water molecules stick together

• Adhesion is when water molecules form hydrogen bonds with other molecules

• In the Xylem, water molecules stick to each other and to the walls of the Xylem, allowing the water to be drawn up the Xylem, which also transports nitrate ions and other molecules

• This is called Capillary action

How does the density of ice insulate the water bellow, and how does this help living organisms

• Ice at 0°C has a lower density than at 4°C meaning it will float on water

• This means the surface of the water will freeze but the highest density at 4° will sink to the bottom

• This insulates the water bellow

What are the physical properties of water on terms of DENSITY

• Density of 998.23 kg/m³ at room temp and pressure

• As temp decrease the density increase (like most liquids) until it reaches 1000 kg/m³ at 4°C

• When the temp goes bellow 4°C the density starts to decrease

What are the thermal properties of water in terms of SLH

• how are these properties useful in a biological context

• High SLH of vaporisation (2,269,000 J/kg)

• Takes 2,269,000 J/kg of energy to change 1kg of water from liquid to gas with no change in temperature

• Utilises evaporation to remove energy such as by sweating

• Harder for water to vaporise from living organisms or bodies of water in which they might live or drink from

What are the thermal properties of water in terms of SHC

• why are these properties good for biological organisms

• has an SHC of 4200 J/kg °C

• It takes 4200 J of energy to raise 1kg of water by 1°C

• This is because it requires a lot of energy to break the hydrogen bonds between water molecules

  • this means that water requires a lot of energy to increase in temperature

• This is good for biological organisms made mainly of water as they will not change temperature quickly if the environmental temperature increases

What are the chemical properties of water in terms of it as a SOLVENT

• Because water is a dipolar molecule, it can form bonds with ions and other polar molecules such as glucose

• makes water a universal solvent

• both oxygen and carbon dioxide gas can dissolve in water

How would you describe the charge of Hydrogen

• what does this look like

• Hydrogen has a slightly positive charge

How would you describe the charge of oxygen

• what does this look like

• Oxygen has a slightly negative charge

What are the chemical properties of water in terms of DIPOLE

• what types of molecules are they

• what charges do the ions have

• Water molecules are polar

• An oxygen atom has more protons in its nucleus than hydrogen, it draws the shared electrons in the covalent bond more towards oxygen

• The oxygen has a slight negative charge

• The hydrogen has a slight positive charge

• The charge isn't fully ionic, but called a dipolar molecule

What are the chemical properties of water in terms of SHAPE

• electron configuration

• covalent bonding

• Oxygen has 6 electrons on its outer shell

• Hydrogen atoms have 1 electron on their outer shell

• Two O-H covalent bonds form between the hydrogen and oxygen atoms as they share electrons

• Two pairs of electrons that aren't involved in covalent bonds repel the other electrons

What does Water look like

• display formula

d

What is a pentose carbohydrate

• deoxyribose and ribose are both pentose carbohydrates

• they have 5 carbons

• used in DNA and RNA respectively

What are the features of Lactose

• disaccharide

• made of glucose - galactose

• sugar found in water

• produced by lactating mammals (some reptiles as well)

What are the features of sucrose

• disaccharide

• made of glucose - fructose

• table sugar

• plants convert glucose to sucrose for transport in the phloem

What are the features of Maltose

• Disaccharide

• made of Glucose - glucose

• product of hydrolysis

• involved in the process of malting in brewing and baking

What is a use of galactose

• Polymerise to form lactose

• monosaccharide

What is a use of fructose

• Produced in fruits and nectar

• Sweetest sugar

• monosaccharide

What is a use of beta-glucose

• Polymerised to form cellulose

• monosaccharide

What is a use of alpha-glucose

• Substrate in respiration

• monosaccharides

• Polymerised to form Maltose and Starch

• Combined with nitrates to form amino acids

Outline the hydrolysis of Maltose

• can be split into two glucose molecules

• Maltose + water ---> Glucose + Glucose

• It can be done either way using 1M Hal at 60°C or an enzyme (maltose)

What are isomers

• examples

Isomers have the same molecular formula but a different arrangement of atoms in space

• Alpha glucose

• Beta glucose

Is glucose a hexose or pentose sugar

• what does this mean

Glucose is a hexose sugar

• Each molecule of glucose has 6 carbon atoms

What are Oligosaccharides

Oligosaccharides are made of 3-25 monosaccharides and are used as cell surface antigens

What are polysaccharides

Polysaccharides are made from 100+ monosaccharides polymerised into a lay chain

What are Disaccharides

• how are they made

Disaccharides are made two monosaccharides via a condensation reaction

What are monosaccharides

Monosaccharides are a monomer from which larger carbohydrates can be made

What are the elements found in nucleic acid

• Carbon

• Hydrogen

• Oxygen

• Nitrogen

• Phosphorus

What are the elements found in Proteins

• carbon

• hydrogen

• oxygen

• nitrogen

• sulfur

What are the elements found in carbohydrates

• oxygen

• carbon

• hydrogen

How do you differentiate between Alpha and Beta glucose

(molecule diagram)

• The configuration of an alpha molecule will have OH below the Carbon atom

• The configuration of a beta molecule will have OH above the Carbon atom

What molecule is this?

Alpha glucose

What molecule is this?

Beta glucose