Biology: Chapter 2: Biological molecules: Proteins

Biology: Chapter 2: Biologica molecules: Proteins

Hydroxyl group

Carboxyl group

Amino group

Sulfhydryl

Methyl group

• Proteins are an extremely important class of macromolecules. 
• Proteins make up 50% of the dry mass of most cells.
• Some of the many functions of proteins are as hormones, enzymes, antibodies, oxygen carrying pigments

Amino acids

• Structure: Central carbon atom bonded to an amine group and a carboxylic acid group (-COOH-) and a Hydrogen.

• The R group is what makes every amino acid different.
• 20 amino acids with different R groups occur naturally in proteins of living organisms
• Many new ones have been synthesized in laboratories

Peptide bond

• Covalent bond between two amino acids
• One amino acid loses a hydroxyl group (-OH-) from its carboxylic acid group (-COOH-) 
• The other loses a hydrogen from its amine group (-NHH-)
• Carbon of 1st amino acid bonds with nitrogen from amine group of the 2nd.
• Condensation reaction - H20 is removed
• Dipeptide - Two amino acids bonded by a peptide bond
• Polypeptide - Many amino acids linked by a peptide bond

• Ribosomes - Site where amino acids join together to form polypeptides - controlled by enzymes
• Peptide bond can be broken by adding H20 - hydrolysis - digestion of protein in stomach and small intestine

Primary structure

• Sequence of amino acids in a polypeptide chain
• Polypeptide can consist of several hundred amino acids linked by a peptide bond
• A change in one amino acid can completely alter the polypeptide properties

Secondary structure

• Structure of a protein molecule due to regular coiling/folding of the polypeptide chain of amino acids eg. alpha helices or beta pleated sheets
• Amino acids in a polypeptide chain have an effect on each other even if they are not directly next to each other 
• Oxygen from -CO- group of one amino acid bonds to hydrogen of -NH- group of the amino acid four places ahead of it. 

• Easily broken by high temperatures and pH changes
• Some proteins/ parts of proteins have no regular arrangement - depends on R groups of amino acids present therefore what attractions occur

Tertiary structure

• Compact structure of 3D coiling of the already-folded chain(secondary structure) of the amino acids. 
• The secondary structure (folding) of the amino acid chain (alpha helix or beta pleated sheet) coiled into a 3-dimensional (3D) structure
• Although it may look random and disorganized, the shape is very precise for each protein and is held in shape by four different types of bonds between amino acids in the chain.

1. Disulfide bonds - Strong double covalent bond formed between the sulfurs of two cysteine molecules (S=S)
2. Ionic bonds - Bond between two oppositely charged R groups (NH3+ and COO- groups). Can be broken by pH changes.
3. Hydrogen bonds - Between strong polar groups eg. -NH-, -CO- and -OH- groups
4. Weak hydrophobic interactions - Between non polar R groups. Hydrophobic R groups are repelled by the watery environment around them and stick together, though these bonds are weak.

• The tertiary structure of a protein can be broken by heat - increasing the kinetic energy makes the molecules vibrate more, so bonds holding the structure in shape (which are mostly weak non-covalent bonds) are more likely to break, and therefore changing its shape. This is called denaturing.

Quaternary structure

• 3D arrangement of two or more polypeptide chains or a polypeptide chain and a non protein molecule
• Forms a protein
• Bonded by the same four bonds used in the tertiary structure

Globular proteins

• Proteins whose molecules curl up into a 'ball' shape.
• Usually curl up so that the non-polar, hydrophobic R groups point towards the centre of the molecule, away from the watery environment.
• Most globular proteins are soluble - hydrophilic R groups on the outside of the protein, therefore water molecules cluster around them.
• Enzymes are globular proteins

Haemoglobin

• Oxygen carrying pigment in red blood cells
• Globular protein
• Made of four polypeptide chains - quaternary structure
• Each chain is known as a globin
• Two of the haemoglobin chains are called alpha chains and made from alpha-globin, while the two other ones are made from beta chains and are called beta-globin.
• The hydrophobic R groups point inside while the hydrophilic R groups are on the outside.
• Hydrophilic R groups on the outside maintain the haemoglobin's solubility.
• Interactions between hydrophobic R group on the inside help maintain it's correct 3D shape.
• Sickle cell anemia: Glutamic (hydrophilic amino acid) on the surface beta-chain is replaced with Valine (hydrophobic amino acid) - non-polar R group on the outside makes it less soluble.
• Prosthetic group: Important part of a protein molecule not made of amino acids
• Each polypeptide chain has a prosthetic haem group
• Each haem group has an iron atom, which can bind with O2 (two oxygen atoms). 
• Therefore a complete haemoglobin molecule can bind with 4 oxygen molecules (8 oxygen atoms) at one time since there are four polypeptide chains. 
• Haem group is responsible for colour of haemoglobin, depending on whether iron atoms have combined with oxygen. 
• Oxyhaemoglobin - When the iron atoms are combined with oxygen.

Fibrous proteins

• Form long strands
• Insoluble in water
• Usually have structural roles
• Keratin is a fibrous protein

Collagen

• Fibrous protein
• Makes up 25% of total protein in mammals - most common
• Structural protein 
• Consists of 3 polypeptide chains wound around each other in the shape of a helix (triple helix)
• Almost every third amino acid is glycine, the smallest amino acid - found on the inside, allows 3 strands to lie closer together and form a tight coil, since any other amino acid would be too large.
• Fibrils: Each 3 stranded collagen molecule interacts with other collagen molecules parallel to it. Covalent bonds form between R groups of amino acids next to each others, forming cross-links which hold many collagen molecules side by side forming the fibrils.
• Fibres: Strong bundle of many fibrils lying alongside each other.
• Collagen fibres line up according to forces they must withstand.
• Flexible but can withstand large tensile strength - withstand large pulling forces without stretching or breaking.
• Achilles tendon can withstand a pulling force of 300N

Biology: Chapter 2: Biological molecules: Lipids

Biology: Chapter 2: Biological molecules: Lipids

Carboxyl group

Hydroxl group

• Organic molecules which are insoluble in water.
• Esters formed by fatty acids combining with an alcohol.

Fatty acids

• Series of acids
• Contain acidic group (-COOH-) and long hydrocarbon tail (-CH-)
• Hydrocarbon chain is usually 15-17 carbon atoms long
• Some of the hydrocarbon tails have double bonds between the neighbouring carbon atoms       (-C=C-).
• Unsaturated: With double bonds -  do not contain maximum possible amount of hydrogen. Form unsaturated lipids. Double bonds make fatty acids and lipids melt more easily. Fatty acids/ Lipids with only one double bond are called monounsaturated, one or more double bonds are called polyunsaturated. Examples: Plants lipids - Oils eg olive oil 
• Saturated: Only single bonds - maximum possible amount of hydrogen. Examples: Animal lipids eg fats

Alcohols and Esters

• Alcohol: Organic molecule that contains a hydroxyl group (-OH-) attached to a carbon atom.
• Ester: Chemical produced in reaction between an acid and alcohol.
• Ester bond: Chemical link between acid and alcohol. -COOH- acid reacts with -OH- alcohol to form the ester bond -COO-. Condensation reaction. 

Triglycerides

• Fats and oils
• Most common lipid
• Glyceride: Ester formed by fatty acid bonding with the alcohol glycerol
• Glycerol: Alcohol with 3 hydroxyl groups; each of Glycerol's hydroxyl groups bond with a fatty acid through condensation
• Hydrocarbon 'tail' vary in length depending on fatty acids used.
• Insoluble in water but soluble in a few organic solvents eg. ethanol and chloroform 
• Hydrocarbon tails are non-polar (no uneven distribution of electrons) which means they are hydrophobic
• Energy reserves: Lipids are better for storing energy than carbohydrates because they have more carbon-hydrogen bonds - Lipids of one mass will yield more energy on oxidation than the same mass of a carbohydrate.
• Insulator against loss of heat: Stored around organs and under the skin
• Buoyancy for aquatic animals: Blubber
• Metabolic source of water: When lipids are oxidised in respiration they are converted to carbon dioxide and water, which is useful for animals in dry climates eg. the desert kangaroo never drinks water but instead relies on this process.

Phospholipids

• Special type of lipid
• One of the three fatty acid 'tails' is replaced with a phosphate group
• Phosphates are polar - dissolve in water (hydrophilic)
• One end of the lipid is soluble in water - The phosphate group is hydrophilic and makes the head of the phospholipid hydrophilic, but the two remaining fatty acid tails are hydrophobic.
• Used to form membranes

Biology: Chapter 2: Biological molecules: Carbohydrates

Biology: Chapter 2: Biological molecules: Carbohydrates

 Sugar quiz

Polysaccharide quiz

• General formula for a carbohydrate is Cx(H2O)y
• Contain elements Hydrogen, Carbon and Oxygen
• Saccharide: Sugar

Common groups:

     Hydroxl Group

        Carbonyl Group

Monosaccharides

• Single sugar molecule
• General formula: (CH2O)n
• All monosaccharides end with -ose eg. glucose, fructose, galactose
• Trioses: 3 carbons, Pentoses: 5 carbons, Hexoses: 6 carbons.
• Source of energy, due to large amount of C-H bonds.
• Building blocks for larger molecules

Molecular and structural formula

• Molecular formula for hexose: C6H12O6
• Below is the structural and ring structure of glucose

• Pentoses and Hexoses have carbon chains long enough to close in on itself and form a more stable ring. Above is an example of a glucose ring structure. 
• Carbon 1 joins to Carbon 5, leaving Carbon 6 out of the ring.
• The hydroxl group in glucose, -OH, can be above or below Carbon 5.
• α Glucose (alpha): -OH is below the ring
• β Glucose (beta): -OH is above the ring
• These are called isomers (two forms of the same chemical).

Disaccharides and Glycosidic bond

• Disaccharides: Two monosaccharides joint together  by condensationeg. Maltose (glucose + glucose), Sucrose (glucose + fructose)
• Condensation: Two Hydroxyl (-OH) groups line up alongside each other. One combines with a H atom from the other to form a H20 molecule, which is the waste product of the reaction.
• The Oxygen becomes the bridge between both molecules, holding them together. This is called a glycosidic bond.
• The reverse of this is called hydrolysis.

Polysaccharides

• Polymers whose subunits (monomers) are monosaccharides, bonded by glycosidic bonds.
• Final unit can be several 1000 monosaccharides long, forming a macromolecule.
• Not sugars
• Energy storage unit for monosaccharides (glucose), since glucose itself cannot be stored therefore is converted into polysaccharides, which are convenient - compact and inert

Starch

•     Mixture of two substances – Amylose and amylopectin
•    Commonly found in chloroplasts – energy storage
•    Never  found in animal cells
•  Amylose: Long, unbroken chain of alpha α glucose molecules bonded by a glycosidic bond through condensation at 1,4 linkages.
• 1,4 linkages: The glycosidic bond is formed between the Carbon 1 of one glucose molecule and Carbon 4 of the next.
• Chains are curved and coil into helical structures – more compact.
•  Amylopectin: Also made of 1,4 linkages, but has shorter chains than amylose and has branches.
•  Branches: Formed by 1,6 linkages – Carbon 1 of one glucose molecule forming a bond with Carbon 6 of another.

Glycogen

•   Similar to Amylopectin – Chains of α glucose made of 1,4 linkages and 1,6 linkages, forming branches.
• More branched than amylopectin
• Clump together to form granules – visible in liver and muscle cells
• Energy storage for animal cells

Cellulose 

•  Structural role – Mechanically strong molecule
•  Polymer of beta β gluclose instead of alpha α glucose.
• In beta glucose, the –OH attached to Carbon 1 is above the ring, but on Carbon 4 it is below the ring
• This means every 2^nd beta glucose in the chain needs to rotate 180 degrees (upside down) to be able to form a glycosidic bond with the glucose in front.
• Strong molecule - Hydrogen bonding between different cellulose molecules 
• The hydrogen bonds are individually weak, but many can form due to large number of Hydroxl (-OH) groups
• Around 60-70 celluolose molecules tightly crosslink to form Microfibrils
• Microfibrils hydrogen bond together to form bundles called Fibres
• Celluloe fibres have high tensile strength but are still freely permeable 
• Found in cell wall - provide support for plant and helps it withstand the large pressures from osmosis

Biology: Chapter 2: Biological Molecules: Water

Biology: Chapter 2: Biological Molecules: Water

Dipoles and Hydrogen Bonds

• In covalent bonds, atoms share electrons. Each shared electron is one covalent bond.
• However electrons are not shared equally. Some particles have a higher electron affinity (electron attraction) than others.
• In water, oxygen has a higher electron affinity, so the electron spends more time with the oxygen atom, making it slightly negative, which is called delta minus (δ-)
• Hydrogen has a weaker electron affinity, so the electron spends less time with them, making them slightly positive - delta plus (δ+)
• This unequal distribution of charge is called a dipole.

• The negatively charged oxygen of one H20 is attracted to the positively charged hydrogen of another.
• This is called a hydrogen bond. 
• Weaker than a covalent bond, but still has a significant effect.
• Hydrogen bonds are not inclusive to water; dipoles can occur in many different molecules, particularly ones with -NH-, -CO-, or -OH- groups. 
• Important for the structure of proteins and carbohydrates.
• Molecules with dipoles are called polar molecules; they are attracted to water hydrophilic) because water is also polar. 
• Molecules without dipoles are called non-polar molecules; they are not attracted to water (hydrophobic) .

Properties of water 

Solvent

• Excellent solvent ( substance that dissolves a solution) for ions and polar molecules (unevenly charged molecules) because of water is also a polar molecule and is therefore attracted to ions and polar molecules.
• The H2O molecules collect around the molecule and separates them, which we can also called dissolving. This allows the separate ions or chemicals to move freely and react with other chemicals.
• Most chemical processes in living organisms take place this way.

• Water also pushes together non-polar molecules, such as lipids.
• This is because water molecules are attracted to each other(hydrogen bonds).
• Important in hydrophobic interactions in protein and membrane structure
• Transport medium

Raegent

• Water can take part in some chemical reactions 
• Photosynthesis: Sunlight is used to separate hydrogen from water. The hydrogen is then used as a fuel to produce energy needed for the plant - eg. making glucose (C6H12O6), which is rich in energy, 
• The plant produces oxygen as a waste product, which is then used by aerobic organisms for respiration.
• Water is also used for hydrolysis reactions, where water is needed for large molecules to be broken down eg. digestion.

High specific heat capacity and high latent heat of vapourisation

• To raise the temperature of water or change it to a gas, molecules need to gain energy to move more rapidly. Hydrogen bonds prevent water molecules from moving too much, so they need to be broken first which requires more energy.
• Allows water to store more energy for the given temperature. 

• Specific heat capacity: Amount of heat required to raise it's temperature by a given amount; in water, it is the amount of heat energy needed to raise the temperature of 1kg of water by 1C.
• Water has a high heat capacity because of it's hydrogen bonds.
• Water has a more constant temperature that is less likely to be affected by air temperature.
• Temperatures of the water inside living organisms is more constant so chemical reactions can happen at constant rates and are less likely to be affected by changes in outside temperature.
• Large bodies of water ( eg. lakes and oceans) less likely to be affected by air temperature, providing more stable environments for aquatic organisms.

• Latent heat of vapourisation: Measure of heat needed to change a liquid to gas.
• Water has a high latent heat of vapourisation because the hydrogen bonds need to be broken
• Water absorbs a lot of heat from it's surroundings before evaporating.
• Living organisms use this as a cooling mechanism, by producing water droplets we call sweat.
• A large amount of heat can be lost for a small amount of water, which reduces risk or dehydration or overheating. 
• Plants also use this to cool leaves during transpiration.
• Works the other way - Water is less likely to freeze, so aquatic animals' bodies are less likely to freeze 

Density and freezing properties

• Ice is less dense than water.
• Below 4C, density of water starts to decrease, 
• Ice floats on water, insulating the water underneath it.
• Reduces chances of large bodies of water (eg. lakes) to freeze completely, and makes it more likely for aquatic life surviving in cold conditions.
• Changes in water density move nutrients in the ocean.

High surface tension and cohesion

• Cohesion: Tendency of molecules to 'stick' to each other.
• Water has high cohesion because of hydrogen bonding.
• Helps water move in long, unbroken columns through and up vascular tubing in plants.
• This also results in high surface tension at the surface of water 
• Small organisms, such as pond skaters, can 'skate' over water without falling in, providing a good habitat for them.