Module 2 Section 2: Biological Molecules Flashcards
What is water useful for in organisms
Reactant for important chemical reactions, including hydrolysis
Acts as a solvent for substances to dissolve in as most biological reactions take place in a solution ( e.g. in the cytoplasm )
Water transports substances e.g. dissolved substances like glucose and oxygen
Helps with temperature control due to it’s high specific heat capacity and high latent heat of evaporation
Water is a habitat, the fact that it helps with temperature control, is a solvent and becomes less dense when frozen means many organisms can survive and reproduce in it
Explain the structure of water
Water molecules have a simple structure
A molecule of water is one atom of oxygen and two atoms of hydrogen joined through shared electrons
Because the shared negative electrons are pulled towards the oxygen atom, the other side of each hydrogen atom is left with a slight positive charge
The unshared electrons on the oxygen give it a slight negative charge
This makes water a polar molecule - it has a partial negative charge ( δ- ) on one side and a partial positive charge ( δ+ ) on the other
These slightly opposite charges attract water molecules to each other
This attraction is called hydrogen bonding and gives water it’s useful properties
How do hydrogen bonds give water a high specific heat capacity
Hydrogen bonds can absorb a lot of energy so water has a high specific heat capacity
This means water doesn’t experience rapid change in temperature, which makes it a good habitat - the temperature under water is likely to be more stable than on land
How do hydrogen bonds give water a high specific latent heat of evaporation
Takes a lot of energy to break the hydrogen bonds between water molecules
So a lot of energy is used up when water evaporates
This is useful for organisms because it means water is great for cooling things
This is why some mammals sweat when they’re too hot as when water evaporates it cools the surface of the skin
Why does water’s polarity make it cohesive and why is this important
Cohesion is the attraction between molecules of the same type (e.g. two water molecules)
Water molecules are very cohesive and tend to stick together
This helps water to flow, making it great for transporting substances
It also helps water to be transported up plant stems in the transpiration stream
How does water’s polarity make it a good solvent and why is this important
A lot of important substances in biological reactions are ionic which means they’re made from one positively charged atom or molecules and a negatively charged atom or molecule
Because water is polar, the slightly positive end of a water molecule will be attracted to the negative ion, and the slightly negative end of there molecule will be attracted to the positive ion
This means the ions will get totally surrounded by water molecules and dissolve
Water polarity makes it useful as a solvent in living organisms
How does water become less dense when it is solid and why is this important
At low temperatures water freezes
Water molecules are held further apart in ice than they are in liquid water because each water molecules forms 4 hydrogen bonds to other water molecules, making a lattice shape
This makes ice less dense than liquid water
This is useful for living organisms because, in cold temperatures, ice forms an insulating layer on top of water - the water below doesn’t freeze which means that organisms that live in water will not freeze
Structure of carbohydrates
Most carbohydrate are polymers (a molecule made up of many similar, smaller molecules called monomers bonded together)
These monomers are called monosaccharides
Structure of glucose
Glucose is a monosaccharide with six carbon atoms - its a hexose monosaccharide
There are two of glucose - alpha (α) and beta (β). they both have a ring structure (alpha has OH on the bottom, beta has it on top)
Glucose’s structure is related to its function as the main energy source in animals and plants
Its structure makes it soluble so it can be easily transported
Its chemicals bonds contains lots of energy
Structure of ribose ( in words )
ribose is a monosaccharide with five carbon atoms
This means its a pentose monosaccharide
( must know how to draw structure)
What do all carbohydrates have in common
All made up of the same three elements - carbon (C), hydrogen (H) and oxygen (O)
For every carbon atom in the carbohydrate there are usually two hydrogen atoms and one oxygen atom
How are monosaccharides bonded together
Monosaccharides are joined together by glyosidic bonds
What happens during a synthesis reaction and what is the reverse
During a synthesis, a hydrogen atom on one of the monosaccharides bonds to a hydroxyl (OH) group on the other, releasing a molecule of water (a condensation reaction)
The reverse of this synthesis reaction is called a hydrolysis: a molecules of water reacts with the glycosidic bond, breaking it apart
How do monosaccharides join to form disaccharides and polysaccharide
A disaccharide is formed when two monosaccharides join together
Sucrose is formed when α-glucose and fructose join together
Lactose is formed by α-glucose or β-glucose and galactose
Two α-glucose molecules join to form maltose
A polysaccharide is formed when more than one monosaccharides join together
lots of α-glucose molecules are joined together by glyosidic bonds to form amylose
Structure of ribose
Structure and function of starch
Main energy storage material in plants
Cells get energy from glucose, but plant store excess glucose as starch
Starch is a mixture of two polysaccharides of alpha glucose – amylose and amylopectin
– Amylose – along, unbranched chains of alpha glucose
The 1,4 glycosidic bonds give it a code structure like a cylinder
This makes it compact, which means it can be stored in high quantities as more can fit into a small place
– Amylopectin – a long, branched chains of alpha glucose
Its 1,4 and 1,6 glycosidic bonds provide side branches allow the enzymes that break down the molecule to hydrolyse the glycosidic bonds easily
This means that the glucose can be released quickly
Starch is insoluble in water, so it doesn’t cause water to enter cells by osmosis which would make them swell
This makes it good for storage
Structure and function of glycogen
Main energy storage in animals
Cells get energy from glucose, but animals store excess glucose as glycogen
Structure is similar to amylopectin, except it has more side branches extending off
Many branches means that stored glucose can be released quickly which is important for energy release in animals
Also a very compact molecule so it can be stored in high quantities
Made up of 1-4 and 1-6 glycosidic bonds
Structure and function of cellulose
Major component of cell walls in plants
Made of long, unbranched chains of beta glucose joined with 1,4 glycosidic bonds
When beta glucose molecules bond, they form straight cellulose chains with every other beta glucose molecule inverting 180° so the monosaccharides can bond
The cellulose chains are linked together by hydrogen bonds to form strong fibres called microfibrils
The strong fibres mean cellulose provides structural support for cells
What are triglycerides
They are a kind of lipid
They are macromolecules - complex molecules with a relatively large molecular mass
Like all lipids, they contain the chemical elements carbon, hydrogen and oxygen
Triglycerides have one molecule of glycerol with 3 fatty acids attached to it
Structure of a triglyceride
Fatty acid molecules have long tails made of hydrocarbons
The tails are hydrophobic ( repel water )
These tails make lipid molecules insoluble in water
All fatty acids have the same basic structure, but the hydrocarbon tail varies
Basic structure of a fatty acid
R: variable ‘R’ group hydrocarbon tail
How do triglycerides contain ester bonds
Triglycerides are synthesised by the formation of an ester bond between each fatty acid and the glycerol molecule
Each ester bond is formed by a condensation reaction ( where a water molecule is released )
The process in which triglycerides are synthesised is called esterification
Triglycerides break down when ester bonds are broken
Each ester bond is broken in a hydrolysis reaction ( where a water molecule is used up )
Types of fatty acids
Fatty acids can be saturated or unsaturated
Structure of saturated fatty acids
Saturated fatty acids don’t have any double bonds between their carbon atoms
The fatty acid is ‘ saturated ‘ with hydrogen
Solid at room temperature
Structure of unsaturated fatty acids
Unsaturated fatty acids have at least one double between carbon atoms, which cause the chain to kink
Liquid at room temperature
General formula for a saturated fatty acid
Cn H(2n+1) COOH
Structure of phospholipids
Phospholipids are also macromolecules
They are similar to triglycerides except one of the fatty acid molecules is replaced by a phosphate group
The phosphate group is hydrophilic ( it attracts water molecules ) whereas the fatty acid tails are hydrophobic
Properties of triglycerides
In animals and plants, triglycerides are mainly used as energy storage molecules
Some bacteria use triglycerides to store bond energy and carbon
They are good for storage because:
1). The long hydrocarbon tails of the fatty acids contains lots of chemical energy - lots of energy is
released when they are broken down
Because of these tails, lipids contain about twice as much energy per gram as carbohydrates
2). They are insoluble, so they don’t cause water to enter the cells by osmosis which would make them swell
The triglycerides bundle together as insoluble droplets in cells because the fatty acids tails are hydrophobic - the tails face inwards, shielding themselves from water with their glycerol heads
Properties of phospholipids
Found in the cell membranes of all eukaryotes and prokaryotes
They make up the phospholipid bilayer
Cell membranes control what enters and leaves a cell
1) Phospholipid heads are hydrophilic and their tails are hydrophobic, so they form a double layer with their heads facing out towards the water on either side
2) The centre of the bilayer is hydrophobic, so water soluble substances can’t easily pass through it - the membrane acts as a barrier to those substances
Properties of cholesterol
Cholesterol is another type of lipid - it has a hydrocarbon ring structure attached to a hydrocarbon tail
The ring structure has a polar hydroxyl ( OH ) group attached to it
In eukaryotic cells, cholesterol molecules help to regulate the fluidity of the cell membrane by interacting with the phospholipid bilayer
1) Cholesterol has a small size and flattened shape - this allows cholesterol to fit in between the phospholipid molecules in the membrane
2) At higher temperature, they bind to the hydrophobic tails of the phospholipids, causing them to pack more closely together
This helps to make the membrane less fluid and more rigid
3) At lower temperatures, cholesterol prevents phospholipids from packing too close together, and so increases membrane fluidity
(Orange hydrophilic, rest hydrophobic)
Basic structure of proteins
They are polymers like carbohydrates
Amino acids are the monomers in proteins
How is a dipeptides and polypeptides made
A dipeptide is formed when two amino acids join together
A polypeptide is formed when more than two amino acids join together
Proteins are made up of one of more polypeptides
General structure of amino acids
All amino acids have the same general structure:
A carboxyl group: COOH
Amino group: NH2
The difference between different amino acids is the variable group ( R group ) they contain
All amino acids contain the chemical elements carbon, oxygen, hydrogen and nitrogen
Some contain sulfur
How are amino acids joined together and how are they broken
Amino acids are linked together by peptide bonds to form dipeptides and polypeptides
A molecule of water is released during the reaction - its a condensation reaction
The reverse of this reaction adds a molecule of water to break the peptide bond - its a hydrolysis reaction
What are the four structural levels of proteins
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Primary structure of proteins
Sequence of amino acids in the polypeptide chain
Different proteins have different sequences of amino acids in their primary structure
A change in just one amino acid may change the structure of the whole protein
Secondary structure of proteins
The polypeptide chain doesn’t remain flat and straight
Hydrogen bonds form between nearby amino acids in the chain
This makes it automatically coil into an alpha (α) helix or fold into a beta (β) pleated sheet
Tertiary structure of proteins
The coiled or folded chain of amino acids is often coiled and folded further
More bonds form between different parts of the polypeptide chain
For proteins made from a single polypeptide chain, the tertiary structure forms their final 3D structure
Quaternary structure of proteins
Some proteins are made of several different polypeptide chains held together by bonds
The quaternary structure is the way these polypeptide chains are assembled together
E.g. haemoglobin is made of four polypeptide chains, bonded together
For proteins made from more than one polypeptide chain, the quaternary structure is the protein’s final 3D structure
What can computer modelling do
Computer modelling can create 3D interactive images of proteins
This is useful for investigating the different levels of structure in a protein molecule
How are primary structure proteins held together
Primary structure proteins are held together by the peptide bonds between amino acids
How are secondary structure proteins held together
Secondary structure proteins are held together by hydrogen bonds
How are tertiary structure proteins held together
Tertiary structure proteins’ are affected by different kinds of bonds:
Ionic bonds: attractions between negatively charged R groups and positively charged R groups on different parts of the molecule
Disulfide bonds: whenever two molecules of the amino acid cysteine come close together, the sulfur atom in one of the cysteine bonds to sulfur in the other cysteine, forming a disulfide bond
Hydrophobic and hydrophilic interactions: when hydrophobic R groups are close together in the protein, they tend to clump together.
This means that hydrophilic R groups are more likely to be pushed to the outside, which affects how the protein folds up into its final structure
Hydrogen bonds: these weak bonds form between slightly positively charged hydrogen atoms in some R groups and slightly negatively charged atoms in other R groups on the polypeptide chain
How are quaternary structure proteins held together
Tends to be determined by the tertiary structure of the individual polypeptide chains being bonded together
Because of this, it can be influenced by all the bonds mentioned in tertiary structure proteins
What does heating a protein do
Heating a protein to a high temperature will break up its ionic and hydrophobic/ hydrophilic interactions and hydrogen bonds
In turn this will cause a change in the protein’s 3D shape
Properties of globular proteins
Round and compact
The hydrophilic groups on the amino acids tend to be pushed to the outside of the molecule
This is caused by the hydrophobic and hydrophilic interactions in the protein’s tertiary structure
This makes the globular proteins soluble, so they’re easily transported in fluids
What are the functions of globular proteins
Globular proteins have a range of functions in living organisms:
Haemoglobin
Insulin
Amylase
What is haemoglobin
Haemoglobin is a globular protein that carries oxygen around the body in red blood cells
It’s known as a conjugated protein - this means it’s a protein with a non-protein group attached
The non-protein section is called a prosthetic group
Each of the 4 polypeptide chains in haemoglobin has a prosthetic group called haem
A haem group contains iron, which oxygen binds to
What is insulin
A hormone secreted by the pancreas
It helps to regulate the blood glucose level
It’s solubility is important - it means it can be transported in the blood to the tissues where it acts
An insulin molecules consists of two polypeptide chains, which are held together by disulfide bonds
What is amylase
Amylase is an enzyme that catalyses the breakdown of starch in the digestive system
It is made up of a single chain of amino acids
It’s secondary structure contains both alpha-helix and beta-pleated sheet sections
Most enzymes are globular proteins
Properties of fibrous proteins
Fibrous proteins are strong and insoluble
They’re structural proteins and are fairly unreactive ( unlike many globular proteins )
What are three fibrous proteins
Collagen
Keratin
Elastin
Collagen
Found in animal connective tissues, such as bone, skin and muscle
It is a very strong molecule due to triple helix polypeptide arrangement
Minerals can bind to the protein to increase its rigidity e.g. in bone
Keratin
Keratin is found in many of the external structures of animals, such as skin, hair and nails, feathers and horns
It can either be flexible ( as in skin ) or hard and tough ( as it is in nails )
Elastin
Elastin is found in elastic connective tissue, such as skin, large blood vessels and some ligaments
It is elastic, so it allows tissues to return to their original shape after they have been stretched
What is an ion
An ion is an atom ( or group of atoms ) that has an electric charge
A positive ion is called a cation
A negative ion is an anion
What is an inorganic ions
An inorganic ion is one which doesn’t contain carbon ( although there are a few exceptions to this rule )
Inorganic ions are really important in biological processes
List of cations
Calcium: Ca2+
Sodium: Na+
Potassium: K+
Hydrogen: H+
Ammonium: NH4 +
List of anions
Nitrate: NO3 -
Hydrogencarbonate: HCO3 -
Chloride: Cl-
Phosphate: PO4 3-
Hydroxide: OH-
Role of calcium in biological processes
Involved in transmission of nerve impulses and release of insulin from the pancreas
Acts as a cofactor for many enzymes e.g. those involved in blood clotting.
Is important for bone formation
Role of sodium in biological processes
Important for generating nerve impulses, for muscle contraction and for regulating fluid balance in the body
Role of potassium in biological processes
Important for generating nerve impulses, for muscle contraction and for regulating fluid balance in the body
Activates essential enzymes needed for photosynthesis in plant cells
Role of hydrogen in biological processes
Affects pH substances ( more H+ ions that OH- ions in a solution creates an acid )
Also important for photosynthesis reactions that occur in the thylakoid membranes inside chloroplasts
Role of ammonium in biological processes
Absorbed from the soil by plants and is important source of nitrogen
( which is then used to make, e.g. amino acids, nucleic acids )
Role of nitrate in biological processes
Absorbed from the soil by plants and is an important source of nitrogen
( which is then used to make, amino acids, nucleic acids )
Role of hydrogencarbonate in biological processes
Acts as a buffer, which helps to maintain the pH of blood
Role of chloride in biological processes
Involved in the ‘chloride shift’ which helps to maintain the pH of the blood during gas exchange
Acts as a cofactor for the enzyme amylase
Also involved in some nerve impulses
Role of phosphate in biological processes
Involved in photosynthesis and respiration reactions
Needed for the synthesis for many biological molecules, such as nucleotides ( including ATP ), phospholipids and calcium phosphate ( which strengthen bones )
Role of hydroxide in biological processes
Affects the pH of substances ( more OH- ions than H+ ions in a solution creates an alkali )
How to test for reducing sugars
Add Benedict’s reagent (blue) and heat it in a water bath until it starts to boil
A positive test will form a coloured precipitate
The higher the concentration of reducing sugar, the further the colour change goes to (blue->green->yellow->orange->brick red)
You can use this to compare the amount of reducing sugar in different solutions
How to test for non-reducing sugars
If the result For reducing sugars is negative, they could still be a non-reducing sugar present
To test for non-reducing sugars, like sucrose, first you have to break them down into monosaccharides
You do this by getting a new sample the test solution, adding dilute hydrochloric acid and carefully heating them in a water bath until they start to boil
The neutralise it with sodium hydrogencarbonate, Then just carry out the Benedix test as you would for a reducing sugar
If they test positive it will form coloured precipitate, if the test negative the solution will stay blue, which means it doesn’t contain any sugar at all
How to test for glucose
Can be tested for using test strips coated in a reagent
Strips are dipped in a test solution and change colour if glucose is present
The colour change can be compared to a chart to give an indication of the concentration of glucose present
The strips are useful for testing a person’s urine for glucose, which may indicate they have diabetes
How to test for starch
Add iodine dissolved in potassium iodide solution to the test sample
If starch is present, the sample changes from browny-orange to blue-black
If there’s no starch it stays browny orange
How to test for proteins
The buiret test has two stages
The solution needs to be alkaline, so first you add a few drops of sodium hydroxide solution
Then add some copper (II) sulfate solution
- if protein is present the solution turns purple
- if there is no protein the solution stays blue
How to test for lipids
Use the emulsion test
Shake test tube with ethanol for a minute, then pour the solution into water
If the lipid is present, the solution will turn milky
The more lipid there is, the more noticeable the milky colour will be
If there’s no lipid, the solution stays clear
How does colorimetry determine a concentration of a glucose solution
Use Benedict’s reagent and a colorimeter to get a quantitative estimate of how much glucose ( or another reducing sugar ) there is in a solution
A colorimeter measures the strength of a coloured solution by seeing how much light passes through it
A colorimeter measures absorbance ( the amount of light absorbed by the solution ).
The more concentrated the colour of the solution, the higher the absorbance is
It’s easiest to measure the concentration of the blue Benedict’s solution that’s left after the test ( the paler the solution, the more glucose there was )
So, the higher the glucose concentration, the lower the absorbance of the solution
How to carry out a serial dilution
Make 5 serial dilutions with a dilution factor of 2, starting with an initial glucose concentration of 40mM
1. Line up 5 test tubes in a rack
2. Add 10cm3 of the initial 40mM glucose solution to the first test tube and 5cm3 of distilled water to the other 4 test tubes
3. Use a pipette to transfer 5cm3 of the solution from the first test tube, add it to the distilled water in the second test tube and mix the solution. This gives 10cm3 of solution that’s half as concentrated as the solution in the first test tube (it’s 20mM)
4. Repeat this process three more times to create solution of 10mM, 5mM and 2.5mM
How make a calibration curve
After you have the glucose solutions from serial dilution:
1. Do a Benedict’s test on each solution (plus a negative control of pure water), use the same amount of Benedict’s solution in each case
2. Remove any precipitate - either leave for 24hrs ( so ppt settles ) or centrifuge them
3. Use a colorimeter ( with red filter ) to measure the absorbance of the Benedict’s solution remaining in each tube
4. Use the results to make the calibration curve, showing absorbance against glucose concentration
You can then test the unknown solution in the same way as the known concentrations and use the calibration curve to find its concentration
What is chromatography used for
Used to separate solutions in a mixture
Once it’s separated out, you can often identify the components
E.g. can be used separate out and identify biological molecules such as amino acids, carbohydrates, vitamins and nucleic acids
Types of chromatography
Paper chromatography and thin layer chromatography
Difference between the mobile phase and stationary phase
Mobile phase: where the molecules can move
In both paper and thin layer chromatography the mobile phase is a liquid solvent such as ethanol or water
Stationary phase: where the molecules can’t move
In paper chromatography the stationary phase is a piece of chromatography paper
In thin layer chromatography the stationary phase is a thin layer of solid, e.g. silica gel, on a glass or plastic plate
How does chromatography work
The mobile phase moves through or over the stationary phase
The components in the mixture spend different amounts of time in the mobile phase and the stationary phase
The components that spend longer in the mobile phase travel faster or further
The time spent in the different phases is what separates out the components of the mixture
Examples of polysaccharides
Glycogen
Starch
Cellulose
What does a glycosidic bond look like on a diagram
Structure of glycerol
Diagram for formation of peptide bond
What are reducing sugars
Reducing sugars include all monosaccharides (e.g. glucose) and some disaccharides (e.g. maltose and lactose)
More accurate way of comparing results for reducing sugar test
A more accurate way is to filter the solution and weigh the ppt
