Biological molecules

Water composition

\-2 hydrogen atoms

\-1 oxygen atom

\-Joined by covalent bonds

\-Triangular shape with unusual distribution of charges

Charge of water

\-Overall neutral but uneven

\-Oxygen has negative charge

\-Hydrogen has positive charge

Oxygen draws

Negative electrons

Polar molecule

Molecule with negative and positive charge eg. water

Dipole

Separation of charge due to electrons in covalent bonds being unevenly shared

Hydrogen bonding

\-Form between water molecules

\-Due to polarity of water, they form between the positively and negatively charged regions of adjacent molecules

\-Negative oxygen attracts positive hydrogen, so they flow together

\-Bonds are strong when in large numbers

\-Contribute to water molecules properties

Water properties

\-Solvent

\-High specific heat capacity

\-High latent heat of vaporisation

\-Less dense as a solid

\-High cohesion and adhesion

Water properties: solvent

\-Many ions and polar molecules will dissolve in water because its polar (eg. glucose and sodium chloride)

\-Allows chemical reactions to occur within cells, dissolved solutes are free to move and more chemically reactive

\-Metabolites can be transported efficiently

\-Ideal transport medium

Water properties: high specific heat capacity

\-4200 J/kg°C

\-Large amount of energy needed to raise waters temperature

\-Due to many hydrogen bonds present in water it takes a lot of thermal energy to break them and build them, so temp does not fluctuate greatly

\-This provides suitable habitats for marine life and means optimal temps are maintained within cells and bodies (eg. enzyme activity and water in blood plasma)

Water properties: high latent heat of vaporisation

\-Large amount of thermal energy is needed to be absorbed to break hydrogen bonds and evaporate (change state from liquid to gas)

\-Means only a little water is needed to evaporate for organism to lose great amount of heat, its a coolant

\-Eg. evaporation of water as sweat

Water properties: less dense as a solid

\-Ice is less dense than liquid water due to hard to break hydrogen bonds, so it floats

\-Creates insulating layers in bodies of water, keeping water underneath a constant temp, helping organisms survive

Water properties: high cohesion and adhesion

\-Water molecules stick together due to polarity, so water can flow to transport substances

\-Water molecules bond to each other, allowing water to move up xylem in transpiration

\-Important in plants water movement

The essential roles of water due to what properties

Water molecules polarity and hydrogen bonds

Key molecules needed for organisms to function

\-Carbs

\-Proteins

\-Lipids

\-Nucleic acids

\-Water

Monomer

Single small molecule

Can bond together to form polymers

Dimer

2 monomers joined by a condensation reaction

Polymer

Molecules made from many monomers joined by covalent bonds in a condensation reaction

Polymerisation

Process of joining monomers together to make a polymer

Covalent bonding

\-Sharing of 2+ electrons between 2 atoms

\-Very stable as high energy is needed to break the bonds

\-Electrons shared equally = non polar

\-Electrons shared unequally = polar

Condensation reaction

2 molecules joined with a covalent bond to form a polymer

\-Release 1 molecule of water

Hydrolysis reaction

The breaking of a covalent bond between 2 molecules using 1 molecule of water (water is added)

Macromolecules

Very large molecules with high molecular mass

Covalent bond in carbohydrates

Glycosidic bond

Monomer of carbohydrates

Monosaccharides (glucose and ribose)

Covalent bond in proteins

Peptide bond

Monomer of proteins

Amino acids

Covalent bond in lipids

Ester bond

Monomer of lipids

Fatty acids and glycerol

Covalent bond in nucleic acids

Phosphodiester bond

Monomer of nucleic acids

Nucleotides

What makes biological molecules organic compounds

Them containing the chemical elements carbon and hydrogen

Why are carbon atoms key to organic compounds

\-Each can form 4 covalent bonds (making compounds very stable)

\-Can form the bonds with oxygen, nitrogen and sulfur

\-Can form straight chains, branched chains and rings

Chemical elements of carbohydrates and lipids

C, H, O

(Proportion of O in lipids is lower)

Chemical elements of proteins

C, H, O, N, S

Chemical elements of nucleic acids

C, H, O, N, P

Carbohydrates

\-1C:2H:1O

\-C*x* (H2O)*y*

\-3 types are monosaccharides, disaccharides and polysaccharides

\-Source and store of energy

\-Structurally important

Monosaccharides

\-Simplest carbohydrate

\-Made of 1 simple sugar monomer

\-Reducing sugars

\-Includes glucose and ribose (and galactose and fructose)

Isomer

\-Organic molecules that have the same molecular formula but different structures

\-Results in different properties

\-Eg. glucose

Glucose

\-Has 6 carbon atoms (hexose)

\-C6 H12 O6

\-Most common monosaccharide

\-Main energy source in animals and plants

\-Main substrate used in respiration, releases energy for ATP production

\-Its soluble and so easy to transport in water

\-Exists as alpha and beta glucose (an isomer)

Alpha glucose (α)

\-OH group below the ring

\-In starch and glycogen (polysaccharides)

\-In maltose and sucrose (disaccharides)

Beta glucose (β)

\-OH group above the ring

\-In cellulose (polysaccharide)

Hexose

Monosaccharide with 6 carbon atoms

eg. glucose

Pentose

Monosaccharide with 5 carbon atoms

eg. ribose and deoxyribose

Ribose

\-Has 5 carbon atoms (pentose)

\-Ribose and deoxyribose found in nucleotides that make up RNA and DNA

\-The oxygen atom at C2 is lost in deoxyribose

\-A monosaccharide

OIL RIG

\-Oxidation Is Loss (of electrons)

\-Reduction Is Gain (of electrons)

Disaccharides

\-Complex sugars

\-2 monosaccharides joined by a glycosidic bond in a condensation reaction

\-Includes maltose, lactose and sucrose

Maltose

\-Alpha glucose and alpha glucose

\-Sugar formed in production and breakdown of starch

\-A disaccharide

\-1,4 glycosidic bond

Sucrose

\-Alpha glucose and fructose

\-Main sugar produced in plants

\-A disaccharide

\-1,2 glycosidic bond

Lactose

\-Alpha glucose and galactose

\-Sugar found only in milk

\-A disaccharide

Glycosidic bond

\-An oxygen bridge

\-Formed by condensation reactions (water molecule removed)

\-Since each bond is catalysed by enzymes specific to which OH groups are interacting, there are different types of glycosidic bonds (1,4 / 1,2)

Breakage of the glycosidic bond

Bond is broken when water is added (hydrolysis reaction)

Synthesis of disaccharides and polysaccharides

Hydrogen atom bonds to a hydroxyl group (OH) on another monosaccharide, releasing a water molecule (condensation)

Strong covalent bond formed (glycosidic bond)

Breakdown of disaccharides and polysaccharides

A water molecule reacts with the glycosidic bond, breaking it apart (hydrolysis)

Polysaccharides

2+ monosaccharides joined by glycosidic bonds through condensation reactions

\-Starch, glycogen and cellulose molecules

\-Macromolecules

\-Chains formed (branched/unbranched, folded/straight)

Starch

\-A polysaccharide

\-Main energy storage for plants

\-Excess glucose stored (when plants need energy, the starch is broken down to release glucose)

\-Formed from 2 polysaccharides of alpha glucose (amylose and amylopectin)

\-Coiling and folding makes its structure compact and stable

\-Insoluble in water (water can’t enter the cell) = more storage and no effect to osmotic properties of cell

Amylose

\-20% of starch

\-Long, unbranched chain of alpha glucose

\-Linked with 1,4 glycosidic bonds that give a coiled structure

\-Compact and good for storage

Amylopectin

\-80% of starch

\-Long, branched chain of alpha glucose

\-Linked with 1,4 glycosidic bonds

\-Side branches linked with 1,6 glycosidic bonds (allow enzymes to get at the bonds easier, releasing glucose quickly)

Glycogen

\-A polysaccharide

\-Main energy storage for animals

\-Excess glucose stored as glycogen granules

\-Short chains of alpha glucose linked with 1,4 glycosidic bonds

\-Highly branched with 1,6 glycosidic bonds (similar to amylopectin)

\-Lots of branches mean stored glucose can be released quickly

\-Smaller chains mean it hydrolyses quicker

\-Very compact molecule = good for storage

Cellulose

\-A polysaccharide

\-Major component of cell wall in plants

\-Long, unbranched chains of beta glucose linked with 1,4 glycosidic bonds

\-Each chain linked to each other by hydrogen bonds, forming microfibrils (strong fibers that are tightly crossed)

\-Every alternate beta glucose molecule is inverted, so even more hydrogen bonds can form, making it very strong for structural support

Carbohydrate summary

Monosaccharides: single molecule, soluble, function of energy source eg. glucose and ribose

Disaccharides: 2 molecules, soluble, function of energy release and storage eg. maltose, lactose, sucrose

Polysaccharides: 2+ molecules, insoluble, function of energy storage and structural support eg. starch, glycogen, cellulose

Macromolecules

Proteins, carbs, lipids, nucleic acids

Lipids

\-Act as an energy source, store and insulating layer

\-All contain C, H and O

\-Triglycerides and phospholipids

Triglycerides

\-Fats and oils formed from a condensation reaction between fatty acids and glycerol with an ester bond

\-3 fatty acid molecules combine with 1 glycerol molecule

Fatty acid molecules

\-Form triglycerides

\-Have long tails of hydrocarbon chains

\-Carboxyl group (COOH) at one end (this reacts with the hydroxyl (OH) group on the glycerol molecule)

\-Methyl group (CH3) at the other end makes the chain hydrophobic (repels water molecules)

Glycerol molecules

\-Form triglycerides

\-Have 3 hydroxyl (OH) groups (3 carboxyl groups on the fatty acid molecules can bond to the glycerol by 3 condensation reactions)

Synthesis of a triglyceride

3 condensation reactions occur between the 3 hydroxyl groups (on 1 glycerol molecule) and 3 carboxyl groups (on 3 fatty acids molecules)

3 water molecules are lost and 3 ester bonds are formed (esterification)

Methyl group on the end opposite the carboxyl groups make the fatty acid hydrophobic

Breakdown of triglycerides

Hydrolysis reaction occurs using 3 water molecules to break down the 3 ester bonds

Saturated fatty acids

\-No double bond between their carbon atoms

\-Fats

\-Higher melting point

Unsaturated fatty acids

\-Have at least 1 double bond between their carbon atoms

\-Oils

\-Lower melting point

\-Chain kinks

Features of triglycerides

\-Efficient energy stores (long hydrocarbon tails contain lots of chemical energy which is released when broken down)

\-Insoluble (hydrophobic fatty acid tails prevent cell’s water potential to change)

\-Poor conductor of heat, so good for insulation (eg. aquatic animals like whales)

\-Provides protection around vital organs like kidneys

Phospholipids

\-Similar to triglycerides, but 1 fatty acid is replaced by a phosphate group

\-1 glycerol molecule, 2 fatty acid molecules (hydrophobic), 1 phosphate group (hydrophilic)

\-Found in all cell membranes (make up the phospholipid bilayer)

Cholesterol

\-Hydrocarbon ring structure attached to a hydrocarbon tail in a phospholipid

\-Small size and flattened shape, so can fit in between phospholipids in the cell membrane

\-They regulate the fluidity and strength of a cell membrane

\-At high temps, they bind to tails to pack more closely = rigid membrane

\-At low temps, they prevent tails from packing too tight = increased fluidity

Structure of amino acids

\-Central carbon atom (C)

\-Carboxyl group (COOH) to the right of C

\-Amine group (NH2) to the left of C

\-R group attached to C

\-Hydrogen atom attached to C

Proteins

\-Basic materials for cell growth, repair and replacement

\-Polymer, made up of amino acid monomers

\-Made up of polypeptides

\-All contain C, H, O, N, S

Dipeptide

2 amino acids join together

Polypeptide

2+ amino acids join together

Synthesis of dipeptides and polypeptides

2 amino acids joined by condensation reaction (between carboxyl group (OH) on one and amino group (H) on another) so a water molecule is lost

Covalent bond formed is a peptide bond

Breakdown of dipeptides and polypeptides

A water molecule is added during a hydrolysis reaction to break the peptide bond

Levels of protein structure

Primary

Secondary

Tertiary

Quaternary

Protein primary structure

\-Sequence of amino acids in the polypeptide chain

\-Different proteins have different sequences of amino acids so a change in one may change the whole protein structure

Primary structure bonds

Peptide bonds

Protein secondary structure

\-Hydrogen bonds form between nearby amino acids in the polypeptide chain

\-They coil into an alpha helix or fold into a beta pleated sheet

Secondary structure bonds

Hydrogen bonds

Protein tertiary structure

\-The 3D shape of the polypeptide, when the secondary structure becomes even further coiled/folded

\-More bonds form between the R groups to stabilise it and hold it in place

Tertiary structure bonds

\-Ionic bonds

\-Disulfide bonds

\-Hydrogen bonds

\-Hydrophobic and hydrophilic interactions

Ionic bonds - tertiary structure

Attraction between positively charged R groups and negatively charged R groups on different amino acids

Disulfide bonds - tertiary structure

Covalent bonds between sulfur atoms of R groups of 2 cysteine amino acids

Hydrogen bonds - tertiary structure

Weak bonds between positively charged groups on one amino acid and negatively charged groups on another

Hydrophobic and hydrophilic interactions - tertiary structure

Hydrophobic R groups close together tend to clump and cluster on the inside of a protein

This means hydrophilic R groups are pushed to the outside to interact with surrounding water molecules

Effects how the protein folds up into its final structure

Protein quaternary structure

1+ polypeptide chains assembled together

Final 3D structure for proteins

Influenced by all bonds in previous structures

Determined by tertiary structures being bonded together

Quaternary structure bonds

Peptide, hydrogen, ionic, disulfide bonds

Heating a protein up to a high temperature does what

Breaks up ionic and hydrogen bonds

Disrupts hydrophobic and hydrophilic interactions

Causes a change in proteins 3D shape

Globular proteins

\-Circular shaped

\-Structural function

\-Soluble (easily transported in fluids)

\-Some are fairly reactive

\-Tertiary structure

\-Non polar hydrophobic R groups placed towards centre of protein

\-Polar hydrophilic R groups placed on outside of protein

\-eg. haemoglobin, amylase and insulin

Haemoglobin as an example of a globular protein with a prosthetic group

\-Carries oxygen around the body in red blood cells

\-The prosthetic group haem is attached, making haemoglobin a conjugated protein

\-Has a quaternary structure of 4 polypeptide chains (2 alpha, 2 beta)

Amylase as an example of a globular protein

\-An enzyme that catalyses the breakdown of starch

\-Made of a single chain of amino acids

Insulin as an example of a globular protein

\-A hormone secreted by the pancreas

\-Regulates blood glucose level

\-Has 2 polypeptide chains held by disulfide bonds

Fibrous proteins

\-Long stranded shape with cross linkages from hydrogen bonds

\-Physiological function

\-Insoluble

\-Fairly unreactive

\-Strong and flexible

\-Little tertiary structure

\-Large number of hydrophobic R groups

\-eg. collagen, keratin and elastin

Collagen as an example of a fibrous protein

\-Very strong molecule in connective tissue (bone and cartilage)

\-Has Quaternary structure of 3 polypeptide chains

Keratin as an example of a fibrous protein

\-Found in external structures

\-Flexible (skin)

\-Hard (nails)

Elastin as an example of a fibrous protein

\-Stretches and returns to original shape

\-Found in elastic connective tissues (skin and tendons)