2.2 - E - Biological Molecules Flashcards
What is a condensation reaction?
A reaction that occurs where 2 molecules are joined together and water is removed
CONdensation - CONnect
What is a hydrogen bond?
A weak interaction that can occur wherever molecules contain a slightly negatively charged atom bonded to a slightly positively charged hydrogen atom.
What is a hydrolysis reaction?
A reaction that occurs where a molecule is split into 2 smaller molecules with the addition of water
Hydro - water
Lysis - split
What is a monomer?
A small molecule which binds to many other identical molecules to form a polymer
What is a polymer?
A large molecule made from many monomers
How many covalent bonds can the following form: Carbon Oxygen Nitrogen Hydrogen
4
2
3
1
What is a covalent bond?
Where 2 atoms share an electron(s)
This allows the outer shell to be full
What is formed when 2 monomers join together?
A dimer
What are the monomers and polymers of carbohydrates called?
Monomer - monosaccharide
Polymer - polysaccharide
What are the monomers and polymers of proteins called?
Monomer - amino acid
Polymer - polypeptides and proteins
What are the monomers and polymers of nucleic acids called?
Monomer - nucleotide
Polymer - DNA and RNA
What 3 things happen when a condensation reaction occurs?
A water molecule is released
A covalent bond is formed
A larger molecule is formed
What 3 things happen when a hydrolysis reaction occurs?
A water molecule is used
A covalent bond is broken
Smaller molecules are formed
Define polar
When an atom is slightly positively or negatively charged
In water, is the oxygen slightly positive or negative?
Is the hydrogen slightly positive or negative?
Why is this?
Oxygen is slightly negative.
Hydrogen atoms become slightly positive.
This is because the oxygen atom has a greater number of positive protons in its nucleus, this exerts a stronger attraction for the shared electrons.
What is weaker - a hydrogen bond or a covalent bond?
A hydrogen bond
What do polymer functions often rely on?
What helps this?
Their shape
Hydrogen bonds help them keep their shape
What can water do because it’s a liquid at room temperature?
Provide habitats for living things in rivers, lakes and seas
Form a major component if the tissues in living organisms
Provide a reaction medium for chemical reactions
Provide an effective transport medium, eg: in blood and vascular tissue
How is water a liquid at room temperature?
Hydrogen bonds between water molecules make it more difficult for them to escape to become a gas
Regarding organisms, what would happen if water was less dense?
They would struggle to float
Explain the density of water and ice
Why is this important?
It becomes more dense as it gets colder until 4°C. Between 4°C and 0°C, the water molecules align themselves in a structure which is less dense than liquid water, due to its polar nature.
Because ice is less dense than water, aquatic organisms have a stable environment in which to live through winters. Pond and rivers are insulated against extreme cold - the layer of ice reduces the rate of heat lost from the rest of the pond.
How is water soluble?
Because it’s polar, the + and - of water molecules are attracted to the - and + parts of the solute (the electrostatic charges). The water molecules cluster around the charged parts and help to separate and keep them separate.
H2O is a good solvent. What does this allow?
Molecules and ions can move and react together in water. Many such reactions happen in cytoplasm of cells (over 70%). Molecules and ions can be transported around living things whilst being dissolved in water.
Water molecules demonstrate cohesion.
Explain how.
Water molecules are hydrogen-bonded to the molecules beneath them in the surface of the water.
This means they are more attracted to the water than the air. This means the surface of the water contracts (molecules are being pulled inwards).
The surface is able to resist forces applied to it (aka: surface tension)
Water molecules demonstrate cohesion.
What does this allow?
Transpiration in xylem vessels take place
Insects like pond-skaters can walk on water
What is the specific heat capacity of water?
Is this high or low?
What does this mean?
Why is this important?
4.2kJ for 1kg of water by 1°C
High
This means that a lot of energy is needed to increase the temp of water - it doesn’t heat/cool easily.
This is important because:
Living things need a stable temperature for enzyme-controlled reactions.
Aquatic organisms need a stable environment in which to live.
Explain why water has a high latent heat of vapourisation
What does this allow?
When water evaporates, heat energy, known as the latent heat of vaporisation, helps the molecules to break away from each other to becomes a gas. Due to strong hydrogen bonds, large amounts of energy are needed to evaporate water.
This means water can help cool living things and keep temperatures stable eg: sweat.
Give examples of when water is a reactant
Photosynthesis
Hydrolysis reactions such as digestion’s of starch, proteins and lipids
What is water’s role as a reactant extremely important for?
Digestion and synthesis of large biological molecules
What is a carbohydrate?
A group of molecules containing carbon, hydrogen and oxygen atoms
What is a glycosidic bond?
A bond formed between 2 monosaccharides by a condensation reaction
What are the 3 functions of carbohydrates?
Give examples for each
Source of energy - glucose
Store of energy - starch, glycogen
Structural units - cellulose in plants, chitin in insects
What are the 3 main groups of carbohydrates?
Monosaccharides
Disaccharides
Polysaccharides
How can monosaccharides exist?
How do triose, hexose and pentose exist in solution?
Either as straight chains or in ring/cyclic forms
Triose - straight chains
Pentose, hexose - ring/cyclic form
What is the backbone of monosaccharides?
Single-bonded carbon atoms, one double-bonded to an oxygen atom to form a carboxyl group.
How many carbon atoms do each of the following sugars have:
Hexose
Pentose
Triose
6
5
3
What are monosaccharides important for?
How are they well suited for this role?
They are a source of energy in living things
There is a large number of carbon-hydrogen bonds
Explain the solubility of monosaccharides
Soluble in water
Insoluble in non-polar solvents
What is an isomer?
Molecules with the same formula, but whose atoms are arranged differently in space.
What is the difference between alpha and beta glucose?
Alpha has H coming up out of C1 and OH coming down out of it.
Beta has OH coming up out of C1 and H coming down out of it.
List the 3 most common disaccharides.
Are they reducing or non-reducing sugars?
Maltose - reducing
Lactose - reducing
Sucrose - non-reducing
What 2 monosaccharides form the following disaccharides: Maltose Sucrose Lactose Cellobiose
Alpha glucose + alpha glucose
Alpha glucose + fructose
Beta glucose + alpha glucose
Beta glucose + beta glucose
What type of reaction occurs to form a glycosidic bond?
Condensation reaction
What is the most common type of monosaccharide?
Hexose sugar
What are homopolysaccharides?
What are heteropolysaccharides?
Give an example of each
Homopolysaccharides - polysaccharides made solely of one kind of monosaccharide - starch
Heteropolysaccharides - polysaccharides made of more than one monosaccharides - hyaluronic acid (in connective tissue)
Why do polysaccharides form good stores of monosaccharides?
Glycogen and starch are compact - they don’t take up much space in cells. They both occur in dense granules within the cell.
Polysaccharides hold glucose molecules in chains, so they can be easily “snipped off” from the end by hydrolysis for respiration.
So,w chains are branched and unbranched. Branched chains tend to be more compact but also offer the chance for lots of glucose molecules to be snipped off at once, when lots of energy is required quickly.
Polysaccharides are less soluble in water that monosaccharides - due to their size. Sometimes the amylose molecule forms a double helix, which presents a hydrophobic external surface in contact with the surrounding solution. This presents a hydrophobic external surface.
Which enzymes hydrolyse which glycosidic bonds?
1,4 - amylase
1,6 - glucosidase
Describe amylose
Found in plants. It’s insoluble. It’s a long chain of alpha glucose molecules (homopolysaccharide). It has 1,4 glycosidic bonds.
It coils into a spiral shape, with hydrogen bonds holding the spiral in place. Hydroxyl groups on carbon 2 are situated on the inside of the coil, making the molecule less soluble and allowing hydrogen bonds to form to maintain the coils structure.
Describe amylopectin
Found in plants. It’s like amylose, but with extra branches formed by 1,6 glycosidic bonds. It coils into a spiral shape, held together with hydrogen bonds, but with branches emerging from the spiral.
Explain glycogen
Found in animals. Similar to amylopectin - 1,4 and 1,6 glycosidic bonds. The 1,4 bonded chains tend to be smaller than in amylopectin, so glycogen has less tendency to coil. However, it does have more branches, which makes it more compact. And it is easier to remove monomer units as there are more ends.
What is starch comprised of?
Amylose and amylopectin molecules
Where is glycogen found?
Found in glycogen granules in animal cells e.g. in liver and muscles.
List the similarities between starch and glycogen
Insoluble in water and so do not reduce the water potential of cells.
Store glucose molecules in chains so that they can easily be ‘broken off’ and the glucose be used in respiration.
What is cellulose?
Where is it found?
What are its features?
Homopolysaccharide of beta glucose bonded together through condensation reactions to form glycosidic bonds.
It is found in plants, forming the cell walls.
It is a tough, insoluble and fibrous substance.
What is special about the structure of cellulose?
Every other beta glucose molecule has to be flipped 180° in order to form the 1,4 glycosidic bonds.
Describe the structure of cellulose
Every other beta glucose molecule has to be flipped 180° in order to form 1,4 glycosidic bonds. This prevents the chain spiralling.
Hydrogen binding between the rotated molecules in each chain also gives the chain additional strength and stops it spiralling. It also gives the whole structure additional strength. The hydroxyl group on carbon 2 sticks out, enabling hydrogen bonds to be formed within chains.
What happens when 60-70 cellulose chains are bound together?
They form microfibrils
What is the diameter of a microfibril?
10-30nm
What are macrofibrils?
Bundles of up to 400 microfibrils, which are embedded in pectins (like glue) to form plant cell walls.
Why is cellulose such a good material for cell walls?
Microfibrils and macrofibrils have very high tensile strength, both because of the strength of the glycosidic bonds but also because of the hydrogen bonds between chains. Macrofibrils are stronger than steel wire of the same diameter.
Macrofibrils run in all directions, criss-crossing the wall for extra strength.
It is difficult to digest cellulose because the glycosidic bonds between the glucose molecules are less easy to break.
What key features help the plant cell wall do its job?
Because plants do not have a rigid skeleton, each cell needs to have strength to support the whole plant.
There is space between macrofibrils for water and mineral ions to pass on their way into and out of the cell. This makes the cell wall fully permeable.
The wall has high tensile strength, which prevents plant cells from bursting when they are turgid. When cells are like this, they press together and support the structure of the whole plants. The wall also protects the delicate cell wall.
The macrofibril structure can be reinforced with other substances for extra support or to make walls waterproof. Eg: lignin in xylem vessels.
How have humans exploited the structural strength of cellulose?
Cotton is 90% cellulose.
One of the main components in paper is cellulose.
Cellophane and celluloid (photographic film) are derived from cellulose.
List and explain 2 other structural polysaccharides
Bacterial cell walls - peptidoglycan (the whole thing surrounding the cell), made from long polysaccharide chains that lie in parallel, cross-linked by short peptide chains (made of amino acids).
Exoskeletons (insect and crustacean) - made of chitin. It differs from cellulose because it has an acetylamino group (NH. OCCH3) rather than a hydroxyl group on carbon 2. It forms cross-links between long parallel chains of acetylglucosamine, in a similar way to cellulose.
What are amino acids?
Monomers of all proteins, and all amino acids have the same basic structure.
What is a peptide bond?
A bond formed when 2 amino acids are joined by a condensation reaction
State the properties of proteins and how this allows them to function
They form structural components. Eg: muscle.
Their tendency to adopt specific shapes makes proteins important as enzymes, antibodies and some hormones.
Membrane have protein constituents that act as carriers and pores for active transport across the membrane and facilitated diffusion.
How many amino acids are there?
Over 500, but only 20 are proteinogenic (found in proteins).
Describe the structure of amino acids
Molecular backbone of N-C-C
Contains an amino feoup (-NH2) at the nitrogen end and a carboxyl group at the other end.
The R group is in the middle - this varies with every amino acid - and opposite it is a hydrogen atom.
What enzyme breaks down peptide bonds?
Where?
What else does it do?
Protease
Intestines during digestion
They also break down protein hormones so that their effects are not permenant
What is a dipeptide?
2 amino acids joined together
What is a polypeptide?
A protein - the polymer of amino acids
What is the primary structure of proteins?
The sequence of amino acids found in a molecule formed by covalent peptide bonds.
What is the secondary structure of proteins?
The initial coiling or folding of an amino acid chain, which arises often as a result of hydrogen bond formation between different parts of the chain. The main forms of secondary structure are the alpha helix and the pleated sheet.
What is the tertiary structure of proteins?
The overall 3D shape of a protein molecule.
There are 4 types of bonds:
Hydrogen bonding,
Disulphide bridges,
Ionic bonds,
Hydrophobic and hydrophobic interactions.
An example of this is enzymes
What is the quaternary structure of proteins?
Protein structure where a protein consists of more than one polypeptide chain. Eg: insulin.
Explain how hydrogen bonds work in proteins
Like in water, they form between hydrogen atoms with slightly positive charge and one with a slightly negative charge. In amino acids, these form in hydroxyl, carboxyl and amino groups.
Eg: one may form between the amine group of one A.A. and the carboxyl group of another.
Multiple hydrogen bonds can give protein molecules a lot of strength.
Explain how ionic bonds work in proteins
They can form between those carboxyl and amine groups that are part of R groups. These ionise into NH3+ and COO- groups. Positive and negative groups like this are strongly attracted to each other to form an ionic bond.
Explain how disulfide bridges work in proteins
The R group of the amino acid cysteine contains sulfur. Disulfide bridges are formed between the R groups of 2 cysteines. These are strong covalent bonds.
Explain how hydrophobic and hydrophilic interactions work in proteins
Hydrophobic parts of the R groups tend to associate together in the centre of the polypeptide to avoid water. In the same way, hydrophilic parts are found at the edge of the polypeptide to be close to water. Interactions between the 2 cause twisting of the amino acid chain, which changed the shape of the protein. These interactions can be a very important influence, given that most proteins are to be found surrounded by water inside a living organism.
What is a fibrous protein?
What does its features enable?
State some examples
A protein that has a relatively long and thin structure, is insoluble in water and is metabolically inactive, often having a structural role within an organism.
This enables them to form fibres, which tend to have a structural function.
Eg: collagen, elastin (in connective tissue), keratin (in hair).
What is a globular protein?
It is a molecule of a relatively spherical shape and often has metabolic roles within the organism.
Any hydrophilic R groups are turned inwards and any hydrophilic groups are on the outside. This makes it soluble in water.
They often have very specific shapes, which helps them to take up roles as enzymes, hormones (eg: insulin) and haemoglobin.
What is a prosthetic group?
A non-protein component that forms a permanent part of a functioning protein molecule.
What is the function of collagen?
How does it achieve this?
To provide mechanical strength.
In artery walls, a loader of collagen prevents the artery bursting when withstanding high blood pressures.
Tendons are made out of collagen and connect muscles to bones, allowing them to pull on bones.
Bones are made from collagen, and then reinforced with calcium phosphate which makes them hard.
Cartilage and connective tissue are made from collagen.
Where is keratin found?
What does it do?
Wherever a body part needs to be hard and strong.
Nails, hair, claws, horns, hooves, scales, fur and feathers.
It provides mechanical protection, but also provides an impermeable barrier to infection and, being waterproof, also prevents entry to water-borne pollutants.
Explain the structure of keratin
It’s rich in cysteine, so there are lots of disulfide bridges that form between polypeptide chains. Alongside, hydrogen binding, this makes the molecule very strong.
Explain the structure of haemoglobin
The quarter Mary structure is made up of 4 polypeptides: 2 alpha-globin chains and 2 beta-globin chains. Each of these has its own tertiary structure, but when fitted together they form one haemoglobon molecule.
At one position on the outside of each chain, there is a space in which a haem group is held. Groups like this are called prosthetic groups. The haem contains an iron ion.
What is a conjugated protein?
A protein associated with a haem group
What is the function of haemoglobin?
To carry oxygen from the lungs to the tissues.
Explain the structure of insulin
It’s made of 2 polypeptide chains. The A chain begins with a section of alpha-helix, and the B chain ends with a section of beta-pleated sheet. Both chains fold into a tertiary structure, and are joined together by disulfide links.
What is the function of pepsin?
It digests proteins in the stomach
What is a lipid?
A substance that is soluble in alcohol rather than water.
List 4 types of lipid
Triglycerides
Phospholipids
Glycolipids
Steroids
What is a macromolecule?
A very large, organic molecule
Describe what a lipid is?
It contains large amounts of carbon and hydrogen and smaller amounts of oxygen.
It is insoluble in water because they are not polar.
What are lipids an example of?
Macromolecules
What does a triglyceride consist of?
1 glycerol molecule and 3 fatty acids.
What are essential fatty acids?
Fatty acids that must be ingested complete as opposed to being made in our bodies.
Describe the molecular structure of glycerol
It has 3 carbon atoms with 3 OH groups.
Describe the molecular structure of fatty acids
They have a carboxyl group (-COOH) in one end, attached to a hydrocarbon tail, made of only carbon and hydrogen atoms.
This can range from 2-20 carbons long. The carboxyl group ionises into H+mane a -COO- group. This structure is therefore an acid because it can produce free H+ ions.
What does it mean if a fatty acid is saturated?
What does it mean if a fatty acid is unsaturated?
There are no C=C bonds in the molecule.
There is a double bind between 2 of the carbon atoms instead, which means that fewer hydrogen atoms can be bonded to the molecule.
Define monosaturation and polysaturation.
Give examples.
When a fatty acid has a single C=C bond. Eg: oleic acid.
When a fatty acid has more than one C=C bond. Eg: linoleic acid.
Describe what an ester bond is
A condensation reaction that happens between the -COOH group of the fatty acid and the -OH group of the glycerol. A water molecule is produced.
List and explain the functions of triglycerides
Energy source - they can be broken down in respiration to release energy and generate ATP. The first step is to hydrolyse the Ester bonds, and then both glycerol and fatty acids can be broken down completely into CO2 and water. Respiration of a lipid produces more water than respiration of a sugar.
Energy store - because they are insoluble in water, they can be stored without affecting the water potential of the cell.
Insulation - adipose tissue is a storage location for lipids in whales (blubber), acting as a heat insulator. Lipids in nerve cells act as an electrical insulator.
Buoyancy - because fat is less dense than water, it is used by aquatic mammals, to help them stay afloat.
Protection - humans have fat around delicate organs, such as their kidneys, to act as a shock absorber. The peptidoglycan cell wall of some bacteria is covered in a lipid-rich outer coat.
Describe the structure of a phospholipid
Glycerol attached to 2 fatty acid tails and 1 hydrophilic phosphate head. A condensation reaction between an OH group on the phosphoric acid molecule (H3PO4) and one of the 3 -OH groups on the glycerol forms an ester bond.
Describe the saturation of fatty acids in phospholipids
Most of them have an even number of carbon atoms (usually 16 or 18). Commonly, one of these chains is saturated and the other is unsaturated.
Discuss the behaviour of phospholipids in water
The head is hydrophobic, the tail is hydrophilic. This means the phospholipid is amphipathic. Membrane lipids tend to be this, whereas those involved in storage are not.
They may do 1 of 2 things:
Pop their tails out of the water,
Form micelles.
Define amphipathic
A molecule having both hydrophobic and hydrophilic parts.
What are micelles?
Tiny balls of phospholipids with the tails tucked away inside and the head splinting outwards towards the water.
What is cholesterol?
Explain its structure
What does it do?
Where is it found?
A lipid and a steroid alcohol that is not made from glycerol or fatty acids. It consists of 4 carbon-based rings or isoprene units.
It’s a small and hydrophobic molecule, which means it can sit in the middle of the bilayer. It regulates the fluidity of the membranes.
Where is cholesterol made?
Mainly in the liver of animals. Plants also have a cholesterol derivative in their membranes called the stigmasterol.
What steroid hormones are made from cholesterol?
Testosterone
Oestrogen
Vitamin D
List 5 cations
State their symbols
Calcium - Ca2+ Sodium - Na+ Potassium - K+ Hydrogen - H+ Ammonium - NH4+
List 2 anions
State their symbols
Nitrate - NO3-
Hydrogencarbonate - HCO3-
What does calcium do in biology?
Increases rigidity or bone, teeth and cartilage and is a component of the exoskeleton of crustaceans.
Important in blood clotting and muscle contraction.
Activated several enzymes eg: lipase ATPase and cholinesterase.
Stimulates muscle contraction and regulates transmission of nerves impulses.
Regulates permeability of cell membranes.
It’s important for cell wall development in plants, and formation of middle lamella between cells.
What does sodium do in biology?
Involved in regulation of osmotic pressure, control of water levels in body fluid and maintenance of pH.
Affects absorption of carbohydrates in the intestine, and water in the kidney.
Contributes to nervous transmission and muscle contraction.
Constituent of vacuole in plants which helps maintain turgidity.
What does potassium do in biology?
Involved in control of water levels in body fluid and maintaining of pH.
Assists active transport of materials across cell membranes.
Involved in synthesis of glycogen and proteins, and the breakdown of glucose.
Generates healthy leaves and flowers in flowering plants.
Contributes to nervous transmission and muscle contraction.
Component of vacuole in plants, helping to maintain turgidity.
What does hydrogen do in biology?
Involved in photosynthesis and respiration, the transport of oxygen and carbon dioxide in the blood, and the regulation of blood pH.
What does ammonium do in biology?
It’s a component of amino acids, proteins, vitamins and chlorophyll.
And essential component of nucleic acids eg: insulin.
Involved in maintenance of pH in the human body.
A component of the nitrogen cycle.
What does nitrate do in biology?
It’s a component of amino acids, proteins, vitamins and chlorophyll.
An essential component of nucleic acids.
Some hormones are made of proteins, which contain nitrogen eg: insulin.
It’s a component of the nitrogen cycle.
What does hydrogencarbonate do in biology?
It’s involved in the regulation if blood pH and the transport of carbon dioxide in and out of the blood.
How do you test for starch?
Add iodine to a sample. If starch is present, it will turn from yellow/brown to blue/black.
What are examples of reducing sugars?
Why are they called this?
All monosaccharides and some disaccharides.
Because they can reduce (give electrons to) other molecules.
How do you test for a reducing sugar?
Heat it with Benedicts solution. It will change from blue to green to yellow to orange/red.
How do you test for non-reducing sugars?
Test a sample for reducing sugars to check there are none first.
Take a separate sample and boil with hydrochloric acid to hydrolyse the sucrose into glucose and fructose.
Cool the solution and use sodium hydrogencarbonate solution to neutralise it.
Test for reducing sugars again.
How do you test for lipids?
The emulsion test.
Take a sample and mix it thoroughly with ethanol (coz they’re not soluble in water).
Filter.
Pour the solution into water in a clean test tube.
If a lipid is present, the solution will have a cloudy white emulsion. This is made up of tiny lipid droplets that come out of the solution when mixed with water.
How do you test for proteins?
Biuret test. If proteins are present, the colour changes from light blue to lilac.
What will happen if there is more sugar present when using quantitative testing for reducing sugar when using Benedict’s reagent?
The amount of precipitate will increase.
The amount of copper (II) ions remaining in the solution will decrease.
What is the aim of chromatography?
To separate a mixture into its constituents.
What are the 2 key components in chromatography?
The stationary phase.
The mobile phase.
What is the Rf value?
Distance travelled by the solution
——————————————
Distance travelled by the solvent
What are the 3 things we can use when molecules are colourless during chromatography?
UV light.
Ninhydrin - used to see amino acids.
Iodine.
