Biological Molecules

Metabolism – some of the total metabolic reactions in the body.
Organic molecule – a compound containing carbon and hydrogen
Macromolecules, giant molecule: polysaccharides, proteins (polypeptide) and nucleic acids (polynucleotides)
Molecules are polymers, made up of many repeating subunits monomers
Monosaccharides =) polysaccharides
Amino acids =) proteins
nucleotides + organic bases =) nucleic acids
Fatty acids + glycerol =) lipids

Carbohydrates
Contains carbon, hydrogen: oxygen 2:1
Cx(H2O)
Monosaccharides, disaccharides, and polysaccharides

Monosaccharides
Sugars, (CH2O)n molecule consisting of a single sugar unit
Classified by the number of carbon present
Triode (3C), pentose (5C), hexose (6C)
Common hexoses – glucose, fructose and galactose
Common pentoses – ribose, deoxyribose
Ring structures – pentoses and hexoses are long enough to close itself up to form a stable ring structure
When OH is below the ring – alpha molecule  (alpha glucose)
When OH is above the ring – beta molecule  (beta molecule)
Forms of same chemicals are isomers
Have two major functions:
-used as source of energy for respiration because has a lot of carbon-hydrogen bonds which can break to release energy which is transferred to form ATP (adenosine triphosphate)
-used as building blocks for larger molecules, glucose used to make polysaccharides starch, glycogen and cellulose, ribose (pentose) is one of the molecules used to make RN and ATP , deoxyribose (pentose) used too make DNA

Disaccharides
Polymer whose subunits are monosaccharides joined together by glycosidic bonds
Common polysaccharides – maltose (glucose+glucose), sucrose (glucose+fructose), lactose (glucose+galactose)
Sucrose is the transport sugar in plants, lactose found in milk for young mammals
Joining of two monosaccharides takes place by condensation, two hydroxyl groups line up along each other, one hydroxyl group combines with a hydrogen from the other to form a water molecule, this allows an oxygen bridge between the two molecules holding the together to form disaccharides, bridge is called glycosidic bond
Shape of enzyme controlling the reaction determines which -OH groups come alongside each other
Addition of water is the reverse of condensation – hydrolysis, takes place during digestion of disaccharides and polysaccharides  when they are broken down to monosaccharides
OH + OH =) O + H2O

Polysaccharides
Polymers whose subunits (monomers) are monosaccharides, not sugars
Made by joining many monosaccharides by condensation, each added by a glycosidic bond
Most important are starch, glycogen and cellulose
If glucose accumulates in cells it will dissolve and make contents of cell too concentrated and interfere with the osmotic properties, it is also very reactive and would interfere with normal cell chemistry. This is avoided by converting glucose to a storage polysaccharide by condensation reaction which is convenient, compact, inert (unreactive). Storage polysaccharides is starch in plants and glycogen in animals.  Glucose can be made available again by an enzyme controlled reaction.

Reducing sugars test – add benedict reagent and heat in a water bath, will turn from green yellow or orange to red brown
Non reducing sugars test – heat sugar with hydrochloric acid to release free monosaccharides, add sodium hydroxide to make it alkaline, add Benedict reagent and heat. Should turn red for positive, if it doesn’t change color at all , no sugar of any kind is present.

Starch and glycogen
Starch is a mixture of two substances – amylose and amylopectin.
Amylose is made by condensation between alpha glucose molecules 1-4 links (carbon atom 1 and 4 successive glucose units)
Amylopectin also made of 1-4  linked alpha glucose molecules, chains are shorter, branches formed at the sides by 1-6 linkages
Amylose and amylopectin form large starch grains commonly found in chloroplasts and potato tubers; can be seen with a light microscope especially if stained by rubbing it on  glass slide and staining with iodine potassium iodide solution
Starch never found in animal cells, instead, very similar storage carbohydrate are found – glycogen.
Glycogen also made of 1-4 linked alpha glucose molecules with 1-6 linkages forming branches, but the it is even more branched than amylopectin molecules. They clump together to form granules, visible in liver cells and muscle cells where they form an energy reserve.

Test for starch – add a drop of iodine solution, turns from orange brown to blue black

Cellulose
Present in cell walls of plants, has a structural role, mechanically strong molecule.
Polymer of beta glucose, the -OH group on carbon atom 1 projects above the ring. To form a glycosidic bond with atom 4, the -OH must be rotated 180 degrees upside down, successive go like a zig zag.
The arrangement of beta glucose molecules result in strong molecules because the hydrogen atoms of -OH are weakly attracted to the oxygen atoms in the same cellulose molecule and to the neighboring.
Hydrogen bonds are individually weak but collectively provide enormous strength.
60 to 70 cellulose molecules become tightly cross linked to form bundles called microfibrils, they are held together in bundles called fibers by hydrogen bonding.
Cell wall has several layers of fibers going in different directions to increase strength. Other molecules form a glue like matrix which further increases strength.
Cellulose fibers have high tensile strength, can withstand high pressure that develops as a result of osmosis. WIthout cell wall, cell would burst when in a dilute solution. Makes tissues rigid, responsible for cell expansion during growth.  Despite their strength, cellulose fibers are freely permeable allowing water and solutes to reach or leave the cell surface membrane.

Dipoles and hydrogen bonds
When atoms in molecules are held together by covalent bonds they share electrons.
Electrons are not shared equally. In water, oxygen atoms get more and has a negative charge – delta minus, hydrogen atoms get less and are written delta plus.
The unequal distribution of charge is called dipole.
In water, negatively charged oxygen is attracted to positively charged hydrogen, this attraction is called a hydrogen bond. Weaker than covalent bond but significantly higher effect.
Dipoles occur in molecules that have -OH, -CO or -NH groups. Hydrogen bonds form between these groups because negatively charged particles are attracted to the positively charged ones.
Molecules that have dipoles groups are polar, they are attracted to water – hydrophilic, soluble in water. Molecules that don’t have dipoles are non-polar, they are hydrophobic. Make formation of cell membranes possible.

Lipids
Organic molecules insoluble in water. Fats solid at room temperature, oils liquid, chemically similar.

Fatty acids
Acids found in fat. Contain the acidic group -COOH, carboxyl group,  long hydrocarbon tails attached to acid heads of molecules. Hydrocarbon tails made of chain of carbon atoms combines with hydrogen.
Tails of fatty acids have double bonds between neighbouring carbon atoms -C=C-. Such fatty acids are described as unsaturated, do not contain the max amount of hydrogen. The form unsaturated lipids.  Double bonds make fatty acids and lipids melt easier, most oils are unsaturated.
If there is more than one double bond, fatty acids or lipids are polyunsaturated, if only one bond – monounsaturated. Animal lipids are often saturated – no double binds and occurs as fats, plant lipids are often unsaturated occur as oils.

Alcohol and esters
Organic molecules contain hydroxyl group, -OH attached to a carbon atom. Glycerol is a  alcohol with three hydroxyl groups. Reaction between an acid and an alcohol produces an ester chemical. Chemical link between acid and alcohol – ester bond or ester linkage.
The -COOH group reacts with -OH to form the ester bond -COO- condensation reaction because water is formed as a product. Ester can be converted back to water and alcohol by the reverse reaction of adding water, hydrolysis.

Triglycerides
Common lipids. Fats and oils. A glyceride is an ester formed  by a fatty acid combining with alcohol glycerol. Glycerol has three hydroxyl groups, each one reacts with a fatty acid by condensation. When triglyceride is made, final molecule contains three fatty acids tails and three ester bonds.
Triglycerides are insoluble in water but soluble in organic solvents such as ether, chloroform and ethanol because the non-polar nature of the hydrocarbon tails have an uneven distribution of electrical charge. They don’t mix freely with water molecules and are hydrophobic.

Test for presence of lipids – Lipids are insoluble in water but soluble in ethanol (alcohol). Emulsion test is used. Substance is shaken vigorously with absolute ethanol then poured in a tube containing water, if lipid is present, cloudy white suspension will be formed.

Proteins
Important macromolecules in living organisms, more than half of dry mass of cells is protein.
Proteins have important functions such as

• All enzymes are proteins
• Essential compounds of cell membranes such a receptor proteins and signalling proteins
• Some hormones are proteins – insulin, glucagon
• Oxygen-carrying pigments haemoglobin and myoglobin are proteins
• Collagen is a protein, adds strength to animal tissues
• Hair, nails and surface layer of skin contains the protein keratin
• Actin and myosin are proteins responsible for muscle contractions
• Proteins may storage products – casein in milk and ovalbumin in egg whites

All proteins are made of the same basic monomers – amino acids

Amino acids
Glycine – simplest amino acid, a central carbon atom which is bonded to an amine group -NH and a carboxyl group -COOH. Hydrogen atom is always bonded to the carbon atom.
Amino acids differ from each other by the R group. There are 20 amino acids which occur in the proteins of living organisms, all with different R group.

Peptide bond
When proteins join together, they lose a hydroxyl -OH group from its hydroxylic acid group while the other loses a hydrogen atom from the amine group, this leaves the first amino acid free to bind with the nitrogen atom of the second –  peptide bond. The oxygen and two hydrogen atoms removed from the amino acid form a water molecule – condensation reaction. The new molecule made up of two linked amino acids is a dipeptide. A molecule made up of many amino acids is a polypeptide. In living cells, ribosomes are the site where amino acids are joined together to form polypeptides, the reaction is controlled by enzymes.  Polypeptides can be broken down to amino acids by breaking the peptide bond. This is a hydrolysis reaction involving addition of water, happens in stomach and small intestine during digestion. Protein molecules in food are hydrolysed into amino acids before being absorbed into blood.
Primary structure
Amino acid contained in the chain and the sequence in which they are joined is called the primary structure. Sequence of amino acids in a polypeptide.

Secondary structure
A polypeptide chain or part of it coiled in a corkscrew shape is an alpha helix. Coiled or folded. This secondary structure is due to  hydrogen bonding between oxygen of the -CO- group of one amino acid and the hydrogen of -NH- group of amino acid four places ahead. Hydrogen bonding is a result of polar characteristics. Sometimes hydrogen bonding results in a looser, straighter shape than alpha helix – a beta pleated sheet. Hydrogen bonds easily broken by high temperature or pH changes.  Structure of a protein molecule resulting from the regular coiling or folding of the chain of amino acids, alpha helix or beta pleated sheet.

Tertiary structure
The way in which a protein coils up to form a precise rd shape. Molecules are held into exact shape by bonds between amino acids in different parts of chain. Compact structure of a protein molecule resulting from the three-dimensional coiling of the already folded chains of amino acids.
Hydrogen bonds – between variety of R groups, broken by reducing sugars
Disulfide bonds – between two cysteine molecules containing sulfur atoms, broken by reducing sugars
Ionic bonds – between R groups containing amine and carboxyl groups, broken by pH
Hydrophobic interactions – between R groups which are non polar or hydrophobic
Quaternary structure – 3d arrangement of two or more polypeptides or of a polypeptide and a non protein such as haem. Haemoglobin has four polypeptide chains in each molecule.

Globular and fibrous proteins
A protein whose  molecules curl up into a ball shape such as haemoglobin and myoglobin – globular.
They curl up so their non polar, hydrophobic R groups point into the center of the molecule, away from surrounding watery surroundings. The polar, hydrophilic R groups remain outside, globular proteins are soluble because water molecules cluster around their outward pointing hydrophilic R groups.
Proteins that form long strands – fibrous proteins. Not soluble in water and mostly have structural roles, ex keratin forms nail, hair, outer skin layer making these structures waterproof; collagen.

Haemoglobin
Oxygen carrying pigment found in red blood cells, a globular protein, made of four polypeptide chains so has a quaternary structure, each chain is a globin. Globin is related to myoglobin (found in muscle)  and so has a similar tertiary structure.
Two types of globin used to make hemoglobin – alpha globin and beta globin.
Haemoglobin is nearly spherical. Four polypeptide chains pack closely together, their R groups pointing towards the centre of the molecule, their hydrophilic R groups point outwards.
In sickle cell anemia, the beta chain glutamic acid which is polar is replaced by a different amino acid valine which is non-poalr. Having a non-polar R group at the on the outside of the molecule makes haemoglobin less soluble, causing dangerous symptoms of sickle cell anemia.
Each polypeptide chain has a haem group, permanent part of the protein which is not made of amino acids – prosthetic group. Each haem group contains an iron atom, one oxygen molecule can bind to each iron atom. Haem group is responsible for color of haemoglobin, color changes depending on whether or not the iron atoms are combined with oxygen, if they are – oxyhaemoglobin is bright red, if not then color is purplish.

Collagen
25% of total mammal protein. Found in skin, tendons, cartilages, bones, teeth and walls of blood vessels, structural protein. Consists of three polypeptide chains in shape of helix wound around each other in a rope – triple helix, held together by hydrogen bonds and some covalent bonds. Every third amino acid is a glycine, smallest amino acid, can lie close together to form a tight coil. Any other amino acid would be too large.
Each complete three stranded molecule of collagen interacts with other collagen molecules running parallel to it. Covalent bonds form between the R groups of amino acids lying next to each other. Three cross-links hold many collagen molecules side by side forming fibrils; the ends of each parallel molecule are staggered to not form a weak spot across the collagen fibril. Many fibrils alongside each other form strong bundles called fibres.
Collagen is flexible but has a lot of tensile strength, it can withstand large pulling forces without stretching or breaking, ex Achilles tendon. Collagen fibres line up according to the forces they must withstand, line up parallel bundles along the length of tendon, the direction of tension.

Testing presence of proteins
Biuret reagent added to the solution, no heat required, if positive – turns purple color.  

Water properties
Hydrogen bonding of water molecules makes the molecules more difficult to separate.
– Solvent – for polar molecules (uneven charge distribution) because they attracted to the ions and polar molecules, collect around and separate them. Chemical dissolves in water forming a solution and is free to move and react with other chemicals. Lipids are insoluble in water and tend to be pushed together since the water molecules are attracted to each other, important in hydrophobic interactions in protein structure and in membrane structure, increases stability.
– Transport medium – in the blood, the lymphatic, excretory and digestive system of animals and in the vascular tissues of plants.  Solvent properties are essential.
– High specific capacity – the amount of heat required to raise its temperature of 1 kg of water by 1 degree celsius. Water has relatively high heat capacity, molecules must gain a lot of energy for temp to increase. Hydrogen bonds make water molecules stick to each other and make it difficult for them to move freely, bonds must be broken to allow free movement.  Heat capacity of water makes water more resistant to changes in temperature, temperature in cells and within the body tend to be more constant than of the air around it – biochemical reactions operate at constant rates, less likely to be affected by temperature. Large water bodies such as lakes and oceans are slow to change temperature providing stable habitats for aquatic organisms.
– high latent heat vapourisation – heat energy needed to vaporise a liquid to change from liquid to gas. Water has high latent heat capacity, hydrogen bonds need to be broken in order to evaporate. Living organisms can use evaporation as a cooling mechanism such as sweating or panting. A lot of heat can be lost with relatively little loss of water to prevent dehydration. Also important in cooling leaves during transpiration. When changing from liquid to ice, water molecules must lose a large amount of energy making it less likely to freeze, advantage for aquatic organisms as it makes their bodies not freeze.
– density and freezing point – ice floats on liquid water and insulates the water under it, increases the chance of life surviving in cold conditions, decreasing the tendency of large bodies to freeze. Changes in density of water with temperature causes currents, help maintain circulation of nutrients in oceans.
– reagent – water takes part in chemical reactions such as photosynthesis; energy from sun used to separate hydrogen from oxygen and use hydrogen for making glucose.Essential for all hydrolysis reactions in order to break down large molecules to small as in digestion.
– high cohesion that affects how it moves through narrow tubes such as xylem