Biology Learning Goals - Biological molecules

Describe the structure of a water molecule

An oxygen atom covalently bonded to 2 hydrogen atoms. It is a non-linear shape.

Name the bond that can link two water molecules together

Hydrogen bond

Explain what a hydrogen bond is, which types of atoms it can join together and where they occur in biology

A hydrogen bond is a weak interaction that can occur whenever molecules contain a slightly negatively charged atom bonded to a slightly positively charged hydrogen

Draw two water molecules and draw and label the bond that links them together

Define the term 'Polar'

Has 2 poles, one slightly positive the other slightly negative

Explain why water is a polar molecule

Water is a polar molecule because the oxygen atom is more attractive to electrons than hydrogen so pulls the shared electrons towards it. This causes the O to be slightly negative and the Hs to be positive.

Define the term "electronegativity" and "dipole"

Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons.

A dipole is a molecule in which a concentration of positive electric charge is separated from a concentration of negative charge

List the roles water plays in life (at least 5)

Solvent transport medium, habitat, reactant, thermal stability, solvent

Explain why the polar nature of water allows it to be a useful solvent, transport medium, coolant and habitat

Solvent: Dissolves polar and charged molecules as charges interact with polar water molecules which cluster around them keeping them apart

Transport medium: Liquid over large temp. range as H bonds require lots of energy to break. It dissolves many molecules

Coolant: High specific heat capacity as H bonds require lots of energy to break

Habitat: Maintains a constant temp. due to energy required to break H bonds

Define the terms "hydrophilic" and "hydrophobic"

Hydrophilic: The physical property of a molecule that is attracted to water

Hydrophobic: The physical property of a molecule that is repelled by water

Define the terms "cohesion" and "adhesion".

Cohesion: Water molecules attracted to one another

Adhesion: Water molecules attracted to other substances

Describe any other properties (not related to its polar nature) water has that makes it useful for life

Transparent to light - plants growing under water can get light for photosynthesis and aquatic animals can see underwater

List examples of how water is used from across the whole diversity of life (prokaryotes and eukaryotes; plants, animals and fungi; unicellular and multicellular organisms).

Supports - keeping plant cells turgid, the hydrostatic skeletons of earthworms

Lubrication - Joints such as elbow called synovial joints have sac of synovial fluid stopping bones rubbing against each other

Bouyancy - Whales couldn't be so big etc.

Swimming - When something pushes against water there is an equal reactive force propelling forward

Reactions - Photosynthesis, hydrolysis

High surface tension allows organisms to suspend themselves at/on the surface e.g. pond skaters

Ice floats as less dense so insulates water underneath where organisms can survive

Regulating temperature and reaction conditions etc. - sweating as well as high heat capacity

Using the "polar nature of water" explain the how water can dome above the level of the glass container it is in, the shape of the meniscus in a glass measuring cylinder and capillary action in a narrow glass tube.

Dome: Cohesion between water molecules causing surface tension due to hydrogen bonds

Meniscus: Adhesion to sides of container draws molecules up.

Capillarity: Cohesion between water molecules and adhesion to other molecules explains why water moves up narrow spaces. Important for water in xylem vessels.

Define the terms "monomer", "polymer", and "macromolecule".

Monomer: Individual molecules that make up a polymer

Polymer: Long-chain molecules composed of linked (bonded) multiple individual molecules (monomers) in a repeating pattern

Macromolecule: Large complex molecules with large molecular masses

Define the terms "dimer" and "oligomer"

Dimer: a molecule consisting of two identical molecules linked together

Oligomer: a polymer whose molecules consist of relatively few repeating units

Define the terms "condensation reaction" and "hydrolysis reaction"

Condensation reaction: a reaction between two molecules to form a larger molecule and the release of a water molecule. (opposite to hydrolysis)

Hydrolysis reaction: the breakdown of a molecule into two smaller molecules requiring the addition of a water molecule (opposite to condensation)

Define the terms "metabolism", "catabolic reaction", "anabolic reaction"

Metabolism: the chemical processes that occur within a living organism in order to maintain life

Catabolic reaction: reactions of metabolism that break molecules down into smaller units. These reactions release energy.

Anabolic reaction: reactions of metabolism that construct molecules from smaller units. These reactions require energy from the hydrolysis of ATP.

List the 4 main categories of biological molecule.

Carbohydrates, Lipids, Proteins, Nucleic acids

Summarise the name of the building blocks, the name of the dimer, the name of the macromolecule, whether or not the macromolecule is a polymer, the name of the bond that links the building blocks together, the name of the reaction that joins the building blocks together, the name of the reaction that breaks the macromolecule apart, examples of the functions of the molecules and the elements that make up the molecules for carbohydrates, lipids, proteins and nucleic acids. Include examples of names of specific molecules where appropriate

Carbohydrates: monosaccharides, disaccharides, polysaccharides, they are polymers, glycosidic bond, condensation reaction, hydrolysis, respiration-cell wall-cell signalling etc.

Lipids: fatty acids and glycerol, (monoglyceride, diglyceride) and triglyceride, not a polymer, ester bond, condensation, hydrolysis, source of energy-membrane structure-hormones etc.

Proteins: amino acids, dipeptide, polypeptide, they are polymers, peptide bond, condensation, hydrolysis, transport molecules-enzymes-antibodies etc.

Nucleic acids: nucleotides, dinucleotide, polynucleotide, they are polymers, phosphodiester bond, condensation, hydrolysis, genetic material-protein synthesis etc.

Define the terms "single bond" and "double bond"

single bond: a chemical bond in which one pair of electrons is shared between two atoms

double bond: a chemical bond in which two pairs of electrons are shared between two atoms

State the elements present in carbohydrates

Carbon, Hydrogen and Oxygen

State the general formula of carbohydrates

(CH2O)n

Define the term "monosaccharide", "disaccharide" and "polysaccharide"

Monosaccharide: A single sugar molecule

Disaccharide: A molecule comprised of two monosaccharides joined by a glycosidic bond

Polysaccharide: A polymer made of many sugar (monosaccharides) monomers

Define the term "pentose sugar" and "hexose sugar"

Pentose - a monosaccharide composed of 5 carbons

Hexose - a monosaccharide composed of 6 carbons

Define the term "triose sugar" and name an example

Triose - monosaccharide composed of 3 carbons

E.g. glyceraldehyde

Describe what is meant by a "furanose ring" and a "pyranose ring"

Furanose ring - 5 membered ring e.g. fructose

Pyranose ring - 6 membered ring e.g. glucose

Draw a molecule of alpha-glucose

Draw a molecule of beta-glucose

Draw a molecule of ribose

Define the term "isomer"

Molecules with the same molecular formulae but different structural formulae (same atoms but arranged differently)

Describe the difference between alpha- and beta-glucose

The hydrogen and hydroxyl groups on carbon 1 are reversed.

Describe the differences between alpha glucose and ribose

Glucose is pyranose but ribose is furanose

Glucose used in starch and glycogen

Ribose used in RNA

List 3 examples of disaccharides and for each state which monosaccharides they are composed of

Sucrose - alpha-glucose and fructose

Maltose - two alpha-glucose

Lactose - alpha-glucose and galactose

State the properties and functions of glucose, fructose, galactose, maltose, sucrose and lactose. For each also state where they occur.

Glucose - monosaccharide used in respiration and to make polymers such as starch

Fructose - hexose sugar commonly found in fruit

Galactose - another hexose sugar

Maltose - found in barley

Sucrose - found in sugar cane and beet

Lactose - found in milk

Draw a labelled diagram demonstrating how two molecules of glucose form a disaccharide in a condensation reaction, showing the location of a 1,4-glycosidic bond and from where a water molecule is generated

Condensation reaction involves hydroxyl groups on carbons 1 and 4. Water is lost and the bond is formed by the remaining oxygen atom.

Describe, using a diagram, how hydrolysis of maltose occurs and why water is needed

Glycosidic bond is broken by the addition of water. Catalysed by enzymes at 35-40°C or by being boiled with an acid for acid hydrolysis

Explain why alpha-glucose links together to form starch whereas beta-glucose links together to form cellulose

Due to the arrangement of the hydrogen and hydroxyl groups on carbon-1...

The 1-4 glycosidic bonds using alpha mean all the monomers are the same way up, but with beta each is rotated 180° from the last.

List the two different polysaccharides that make up starch.

Amylose (1-4 bonds only) and Amylopectin (mainly 1-4 but some 1-6)

Explain with the use of diagrams why glycosidic bonds are called 1,4 or 1,6

Whether they are between the OH groups on carbons 1 and 4 or 1 and 6.

Describe the structure of a cellulose fibre

Several cellulose molecules produce a microfibil

Several microfibrils hydrogen bonded together produce a macrofibril

Macrofibrils are laid down in layers to form cell wall etc.

Describe and explain the properties and functions of starch, glycogen and cellulose

Starch: Coils into helix, amylase unbranched and amylopectin branched. Compact and insoluble so ideal for storage - food store in plants

Glycogen: More branched than amylopectin, coils into helix. Compact and insoluble so ideal for storage - animals and fungi

Cellulose - Unbranched, does not form helix - forms layers of fibres to give great strength to cell wall

State the elements present in lipids (and the additional element needed to make phospholipids)

Carbon, Hydrogen and Oxygen

Phophorus

State the 3 categories of lipids (or lipid derived molecules)

Triglycerides, Steroids and Phosopholipids

Draw a labelled diagram showing the basic structure of a triglyceride.

3 fatty acids joined to a glycerol

Draw diagrams to show the difference between saturated, monounsaturated and polyunsaturated fatty acids/triglycerides.

Unsaturated fatty acids have kinks in the chain due to the double bonds (1 for mono, several for poly)

Explain why saturated triglycerides tend to be solid (fats) at room temperature whereas unsaturated triglycerides tend to be liquid (oils).

Saturated fatty acids can pack more tightly as do not have kinks and therefore have higher melting points than unsaturated which are more spread out so melt at lower temperatures.

State the difference between the triglycerides found in non-fish animals and those in plants and fish.

Plant and fish triglycerides tend to be unsaturated whereas other animal fats tend to be saturated

Draw a labelled diagram showing the basic structure of a phospholipid.

Phosphate head with fatty acid tails

State the property that each end of the phospholipid has.

Head is hydrophilic and fatty acid tails are hydrophobic

Describe the difference between a triglyceride and a phospholipid.

Phospholipids have a phosphate group in place of one of the fatty acids

Draw a diagram to show how a triglyceride is formed and broken down.

Name the bond that holds the building blocks of a triglyceride together

Ester bond

State the names of the reaction that forms triglycerides and the reaction that breaks them apart

Form by condensation

Broken down by hydrolysis

Explain how an ester bond is formed between glycerol and a fatty acid

Called esterification

Reaction between hydroxyl of glycerol and carboxyl of fatty acid, expelling water

State the number of water molecules produced in the production of one triglyceride

3

State the products of digestion of a triglyceride (include partial digestion) and state what would happen to the pH of the solution (and why)

Produces fatty acids and glycerol or partially only removes some of the fatty acids to produce a monoglyceride etc.

Due to fatty acids, pH would decrease (more acidic)

Describe the structure of sterols/cholesterol

Base nucleus of 4 connected organic rings

They differ from each other due to different side groups

List the functions of triglycerides (5 functions), phospholipids (2 functions) and cholesterol (2 functions) and relate these functions to the properties of the molecules

Triglycerides - Energy store, thermal insulation, cushioning for internal organs, buoyancy, waterproofing

Phospholipids - Membranes, myelin sheaths

Cholesterol - Membranes, hormones (made by adding different side groups)

Due to hydrophobic qualities useful for waterproofing

Explain why triglycerides store more energy per gram than carbohydrates

They require more oxidation to be broken down into CO2 and O2 so release more energy although it takes longer.

Explain how phospholipids form a membrane

Phopholipid bilayer

Two layers with the hydrophobic fatty acid tails sandwiched on the inside and the hydrophilic heads on the outside

Describe how the presence of cholesterol affects the properties of cell membranes

Regulates membrane fluidity

Draw and label a diagram of an amino acid

State how many amino acids occur in life

20

Describe the different types of amino acid in life

Nonpolar hydrophobic

Polar hydrophilic

Polar hydrophilic basic (positively charged)

Polar hydrophilic acidic (negatively charged)

Draw a labelled diagram demonstrating the condensation and hydrolysis of peptide bonds. Draw a dipeptide and label the peptide bond.

Explain how the variety of amino acids leads to a wide range of dipeptides and very quickly to an incredible variety of polypeptide chains

20 amino acids therefore 400 dipeptides as the order does change the molecule

There are 20^3 tripeptides and so on giving rise to incredible variation in polypeptides

Define the terms "polypeptide chain" and "protein"

polypeptide chain - chains of three or more amino acids

protein - one or more polypeptides arranged as a macromolecule

Describe how one end of a polypeptide chain differs from the other end

One end is the C terminal which is the carboxyl end and the other is the N terminal, the amine group.

Define the term "primary structure" of a protein and describe how it is held together

The number and sequence of amino acids in a polypeptide is its primary structure. Each amino acid is bonded to the next by peptide bonds.

Define the term "secondary structure" of a protein, describe the two different types and describe how the secondary structure is held in place

All or part may fold into a secondary structure most commonly and alpha-helix or a beta-pleated sheet. To produce one of these there needs to be a regular repeating pattern of amino acids. The structures are held together by hydrogen bonds between N-H groups and C=Os.

Define the term "tertiary structure" of a protein, and describe how it is held in place (include all the different possible bonds)

The compact 3-D shape adopted by most polypeptides. These molecules are called globular. The R groups form the bonds that hold the structure in place.

Hydrogen bonds form between slightly charged R groups

Ionic bonds form between R groups carrying opposite charges

Disulphide bonds or bridges form between the sulfur containing R groups of two cysteine amino acids - strong covalent bond

Hydrophobic interactions - protein folds so that hydrophobic R groups lie in centre of the molecule away from the aqueous environment.

Explain how the primary structure of a protein determines its tertiary structure

As tertiary structure depends on the R groups and therefore which amino acids are present and in which order it is highly dependent on primary structure.

Define the term "quaternary structure" of a protein, and describe how it is held in place (include all the different possible bonds)

A protein with quaternary structure contains two or more polypeptide chains bonded together which have no function on there own and only form a functional molecule when bonded. Bonds that hold tertiary structure also hold quaternary; hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions

Define the terms "globular protein" and "fibrous protein"

globular protein - spherical, water soluble proteins

fibrous protein - long, insoluble, structural proteins

Define the terms "prosthetic group" and "conjugated protein"

prosthetic group - non-protein component of a conjugated protein

conjugated protein - A protein that is joined to a non-protein group (prosthetic group). Both parts are needed to function.

Describe an example of a conjugated protein, an enzyme and a peptide hormone and for each identify key structural components, properties and functions.

Haemoglobin - each of the four polypeptide chains is bonded to a haem group. It carries oxygen.

Catalase - quaternary protein with four heam groups. The presence of iron II ions allows it to calayse break down of hydrogen peroxide which is a harmful waste product of metabolism

Antidiuretic hormone - Regulates the body's retention of water by increasing water absorption of kidney's collection duct

Give 3 examples of fibrous proteins

Keratin, Elastin, Collagen

Compare the structure, properties, location and functions of collagen, keratin and elastin

Collagen - Connective tissue found in skin, tendons, ligaments and the nervous system. £ polypeptides wound round each other to form a rope like structure

Keratin - Hair, skin and nails. Many sulphur containing amino acids means many disulphide bridges which make it very strong. Nails more disulphide bridges - less flexible

Elastin - Found in elastic fibres in blood vessels and alveoli allowing them to expand and return to normal as needed. Made by linking many soluble tropoelastin protein molecules which act as little springs together to form an isoluble macromolecule.

Compare the structure, properties and functions of globular and fibrous proteins

Globular - Spherical and water soluble due to folding so that hydrophobic regions are inside ut hydrophilic regions are on the outside.

Fibrous - Long, strong, insoluble molecules. Tend to contain a limited range of amino acids with small R groups and arranged in a pretty regular pattern containing many hydrophobic amino acids.

Define the term "inorganic", "cation" and "anion"

Inorganic - relating to or denoting compounds which are not organic (broadly, compounds not containing carbon)

cation - positive ion

anion - negative ion

Draw a table showing the chemical symbol and at least one example of a biological process they are involved in for: calcium ions, sodium ions, potassium ions, hydrogen ions, ammonium ions, nitrate ions, hydrogen carbonate ions, chloride ions, phosphate ions and hydroxide ions.