Biological molecules Flashcards
What is a monomer?
Small, basic molecular units that can form a polymer
Examples of monomers?
Monosaccharides, amino acids and nucleotides
What are polymers?
Large, complex molecules composed of long chains of monomers joined together
Examples of polymers?
Carbohydrates, proteins and nucleic acids
What reaction forms polymers?
Condensation reaction from monomers
Forms a chemical bond between monomers, releasing a molecule of water
What reaction breaks down polymers?
Hydrolysis reaction
Breaks chemical bond between monomers using a water molecule
What elements do carbohydrates contain?
C, H, O
What monomers are carbohydrates made from?
Monosaccharides
Examples of monosaccharides?
Glucose, fructose and galactose
What type of sugar is glucose?
Hexose sugar - monosaccharide with six carbon atoms in each molecule
What are the two types of glucose?
Alpha and beta - isomers (molecules with the same molecular formula as each other, but with the atoms connected in a different way)
What is a disaccharide?
Formed when two monosaccharides join together.
How do monosaccharides join together?
Condensation reaction with glycosidic bond between the two monosaccharides as a molecule of water is released
What are the monosaccharides of sucrose?
Glucose and fructose
What are the monosaccharides of maltose?
Glucose and glucose
What are the monosaccharides of lactose?
Glucose and galactose
Benedict’s test for reducing sugars
Add benedict’s reagent to a sample and heat it in a water bath that’s been brought to boil.
What does a positive result for reducing sugars show?
Blue to brick-red precipitate
What happens with a higher concentration of reducing sugar?
Higher concentration means further colour change - you can use this to compare the amount of reducing sugar in different solutions.
How can you compare concentrations of reducing sugar solutions?
Filter solution and weigh the precipitate, or to remove the precipitate and use a colorimeter to measure the absorbance of the remaining Benedict’s reagent
Benedict’s test for non-reducing sugars
Get new sample of test solution, add dilute HCl and carefully heat in water bath brought to boil. Then you can neutralise it by adding sodium hydrogencarbonate. Carry out Benedict’s test again
What is a polysaccharide?
Formed when more than two monosaccharides are joined together by condensation reactions
How can polysaccharides be broken down?
Hydrolysis
Give three polysaccharides
Starch, glycogen and cellulose
What is starch?
Plants store excess glucose as starch. Mixture of two polysaccharides of alpha-glucose: amylose and amylopectin
Describe amylose
Long, unbranched chain of alpha-glucose. The angles of the glycosidic bonds give it a coiled structure, like a cylinder. This makes it compact, so it is really good for storage because you can fit more into small space
Describe amylopectin
Long, branched chain of alpha glucose. It’s side branches allow the enzymes that break down the molecule to get at the glycosidic bonds easily. This means that the glucose can be released quickly
Properties of starch
Insoluble in water
Doesn’t affect water potential so it doesn’t cause water to enter cell by osmosis, which would make them swell
This makes it good for storage
Describe glycogen
-Animal cells get energy from glucose too.
-But animals store excess glucose as glycogen - another polysaccharide of alpha-glucose.
-Its structure is very similar to amylopectin, except that it has loads more side branches coming off it.
-Loads of branches means that stored glucose can be released quickly, which is important for energy release in animals.
-Very compact molecule so good for storage
Describe cellulose
-Cellulose is made of long, unbranched chains of beta-glucose.
-When beta-glucose molecules bond, they form straight cellulose chains.
-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
Describe the iodine test for starch?
-Add iodine dissolved in potassium iodide solution to the test sample.
-If there is starch present, the sample changes from browny-orange to a dark, blue-black colour
What are lipids made from?
A variety of different components, but they all contain hydrocarbons. The components they’re made from relates to the lipid’s function.
What are the two types of lipid (needed to know)?
Triglycerides
Phospholipids
Describe triglycerides
One molecule of glycerol with three fatty acids attached to it. Fatty acid molecule have long tails made of hydrocarbons. The tails are hydrophobic so insoluble in water
Describe fatty acids
All consist of the same basic structure, but the hydrocarbon tail varies. They have a variable R group - hydrocarbon tail. Carbon atom links fatty acid to glycerol
What are the two types of fatty acids?
Saturated and unsaturated
What’s the difference between a saturated and unsaturated fatty acid?
Saturated have no double bonds between their carbon atoms - unsaturated do
How are triglycerides formed?
Condensation reactions. Fatty acid joins to glycerol molecule.
What bond forms between glycerol and fatty acids and what reaction is it?
Ester bond, releasing molecule of water
Condensation
How many times does the condensation reaction need to happen for a triglyceride to form?
Two more
What are phospholipids?
Two fatty acids, one glycerol and one phosphate group
Hydrophilic head and hydrophobic tails
Properties of triglycerides
Mainly used as energy storage molecules due to long hydrocarbon tails of the fatty acids contain lots of chemical energy - a load of energy is released when they’re broken down.
Because of these tails, lipids contain about twice as much energy per gram as carbohydrates
Insoluble in water –> wont affect water potential (making them swell)
Triglycerides bundle together as insoluble droplets in cells because the fatty acid tails are hydrophobic - the tails face inwards, shielding themselves from water with their glycerol heads
Properties of phospholipids
Make up a bilayer of cell membranes.
Hydrophilic phospholipid heads and hydrophobic tails.
Heads face outwards towards the water
The centre of the bilayer is hydrophobic so water-soluble substances can’t pass through it easily - membrane acts as a barrier to those substances
What is the function of cell membranes?
Cell membranes control what enters and leaves a cell
Describe the emulsion test for lipids
Shake test substance with ethanol for a minute then pour solution into water.
Any lipid will show up as a milky emulsion
The more lipid there is, the more noticeable the milky colour will be
What are the monomers of proteins
Amino acids
What is a dipeptide?
Two amino acids joined together
What is a polypeptide?
Formed when more than two amino acids join together
What are proteins?
Made up of one or more polypeptides
What is the structure of amino acids?
Carboxyl group, an amine or amino group, carbon-containing R group attached to C atom
How many amino acids are there?
20
What bond and reaction forms dipeptides and polypeptides?
Peptide bonds and condensation reactions
Reverse reaction is hydrolysis
Describe the primary structure
Sequence of amino acids in the polypeptide chain
Describe the secondary structure
The polypeptide chain doesn’t remain flat and straight. Hydrogen bonds form between amino acids in the chain. This makes it automatically coil into an alpha helix or beta pleated sheet
What is the tertiary structure?
-The coiled or folded chain of amino acids is coiled and folded further
-More bonds form between different parts of the polypeptide chain, including hydrogen and ionic bonds (attraction between negative and positive charges on different parts of the molecule)
-Disulfide bridges form when two molecules of amino acid cysteine come close together
-For proteins made from a single polypeptide chain, the tertiary structure forms final 3D structure
Describe the quaternary structure?
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. For proteins made from more than one polypeptide chain
Describe the biuret test for proteins
Add few drops of sodium hydroxide solution
Add copper(II) sulphate solution
What does a positive test look like?
Blue to purple
What is an enzyme?
Speed up chemical reactions by acting as biological catalysts
Proteins
Have an active site - specific shape
How are enzymes highly specific?
Tertiary structure
How do enzymes speed up reactions?
Lower the amount of activation energy needed, making reactions happen at a lower temperature than they could without an enzyme. This speeds up rate of reaction
What is the name for when a substrate fits into an enzyme’s active site?
Enzyme-substrate complex
Why does an enzyme-substrate complex lower the activation energy? Give two reasons why
-If two substrate molecules need to be joined, being attached to the enzyme holds them close together, reducing any repulsion between the molecules so that they can bond easily
-If the enzyme is catalysing a breakdown reaction, fitting into the active site puts a strain on bonds in the substrate, so the substrate molecule breaks up more readily
How do you calculate hydrogen ion concentration?
pH=-log10[H+]
What is the lock and key model of enzyme action?
Every lock can only be opened by a particular key which matches the lock. In order for the lock to open, the key has to fit into the lock perfectly.
The enzyme is the lock, and substrate the key. In order for a substrate to bind to the active site of an enzyme, it must have the correct shape which allows it to “fit” into the active site.
What are the limitations to the lock and key model?
Enzymes are very selective in substrate binding, but many substrates can have similar shapes. With the lock and key theory, this should lead to inappropriate binding. However, enzymes still manage to have a surprisingly high level of specificity, and this is due to the induced fit model.
How does the induced fit model explain why enzymes are so specific?
The induced fit model suggest that when a substrate binds to an enzyme’s active site, it causes the active site to change shape as well. For the reaction to happen, the substrate has to change the active site’s shape in the right way.
Describe the induced-fit model of enzyme action and how an enzyme acts
as a catalyst
Substrate binds to active site/enzyme making an enzyme-substrate complex
Active site changes shape slightly so it is complementary to substrate so distorting bonds in substrate
Reduces activation energy
What do the properties of enzymes depend on?
Tertiary structure
Why are enzymes specific?
Only one complementary substrate will fit into the active site
The active site’s shape is determined by the tertiary structure
What happens if a substrate shape doesn’t match the active site?
No enzyme substrate complex
Reaction won’t be catalysed
What happens if the tertiary structure of a protein is altered?
Shape of active site will change
Substrate won’t fit into active site
No enzyme-substrate complex formed
How can the tertiary structure of an enzyme be altered?
Changes in pH
Changes in temperature
Mutation in gene
Give two ways of measuring enzyme activity
How fast the product is made
How fast the substrate is broken down
State four factors affecting enzymes activity
Temperature
pH
Substrate concentration
Enzyme concentration
How does temperature affect enzyme activity?
-Rate of reaction increases as temperature does
–More heat means more kinetic energy so molecules move faster
—Makes substrate molecules more likely to collide with enzymes’ active sites
—-The energy of these collisions also increases, meaning collision is more likely to result in a reaction
-If temp gets too high, reaction stops
–Rise in temp means enzyme molecules vibrate more
—-If temp goes above certain level, this vibration breaks some of the bonds that hold the enzyme in shape
—–Active site changes shape and enzyme and substrate no longer fit together
——Enzyme is denatured-no longer functions as a catalyst
Describe a graph showing temperature (x) against rate of reaction (y)
Begins at zero and steadily increases until optimum is reached (peak)
Decrease rapidly after optimum back to 0
How does pH affect enzyme activity?
All enzymes have an optimum pH value
Above and below the optimum pH, the H+ and OH- ions found in acids and alkalis can disrupt the ionic bonds that hold the enzyme’s tertiary structure in place
The enzyme becomes denatured, and the active site changes shape
Describe a graph showing pH (x) against rate of reaction (y)
Bell-shaped curve
Highest around optimum
How does substrate concentration affect enzyme activity?
Higher substrate conc. = faster reaction
More substrate molecules = more likely collisions between substrate and enzyme so more active sites occupied
This is only true until saturation point. After that, there are so many substrate molecules that the enzyme active sites are full so adding more substrate makes no difference
Describe a graph showing substrate concentration (x) against rate of reaction (y)
-Steady increase as more substrate molecules are available
-All active sites full - increase in substrate concentration has no further effect
How does enzyme concentration affect enzyme activity?
More enzyme molecules in solution = more likely substrate molecule is to collide with one and form an enzyme-substrate complex
Increasing enzyme conc. = increases in ROR
IF sub is limited, eventually there’s more than enough enzyme molecules to deal with all the available substrate, so adding more enzyme has no further effect
Describe a graph showing enzyme concentration (x) against rate of reaction (y)
Steady increase as more active sites are available
If substrate amount is limited, an increase in enzyme conc. eventually has no further effect
How do you compare the difference between curves on a graph given>
Compare the rates of reaction at the start of the graph
Look at the rest of the graph and compare the differences e.g. plateaued
What catalyses the breakdown of hydrogen peroxide?
Catalase
What are competitive inhibitors?
Molecules that have a similar shape to that of substrate molecules. They compete with the substrate molecules to bind to the active site, so no substrate molecules can fit in
What does the extent to which an enzyme can be inhibited depend on?
Relative concentrations of inhibitor and substrate
If there’s a high concentration of the inhibitor, it’ll take up nearly all the active sites and hardly any of the substrate will get to the enzyme
But if there’s a higher concentration of substrate, then the substrate’s chances of getting to an active site before and inhibitor increase. So increasing the conc. of substrate will increase ROR
What is a non-competitive inhibitor?
Bind to enzyme away form active site
This causes active site to change shape so substrate molecules can no longer bind to it
How will increasing the concentration of substrates affect the rate of reaction when a non-competitive inhibitor is present?
Non-competitive inhibitor molecules don’t bind to the active site as they are different shapes
Increasing conc. of substrate will have no effect
Enzyme activity will still be inhibited
How can you measure the rate of an enzyme-controlled reaction
- Measure how fast the product of the reaction appears and use this to compare the rate of reaction under different conditions.
You can do this using an upside down boiling tube in water connected to a delivery tube - Measure how fast substrate is broken down and use this to compare the rate of reaction under different conditions
You can do this by dropping iodine in potassium iodine solution in spotting tile then add starch solution and record seconds for colour change
How do you estimate the initial rate of reaction?
Draw a tangent at curve at t=0
Calculate gradient of tangent - initial rate of reaction
Equation: gradient = change in y axis / change in x axis
Work out units by dividing units on y axis by units on x axis
What is DNA?
Deoxyribonucleic acid
Holds genetic information
What is RNA?
Ribonucleic acid
Transfers genetic information from DNA to ribosomes
What are ribosomes formed from?
RNA
Proteins
What do ribosomes do?
Read RNA to make polypeptides in translation
What is the structure of a nucleotide?
Pentose sugar
Nitrogen-containing organic base
Phosphate group
What molecules are polymers of nucleotides?
DNA
RNA
What is the structure of a polynucleotide?
Many nucleotides join together to form polynucleotide strands
The nucleotides join up via a condensation reaction between the phosphate group of one nucleotide and the sugar of another
This forms a phosphodiester bond
What is the chain of phosphates and sugars known as?
Sugar-phosphate backbone
What is the structure of DNA?
-Double helix
DNA is formed from two separate strands that wind around each other to form a spiral
The strands are polynucleotides
-DNA molecules are really long and coiled up very tightly: lots of genetic information can fit into a small space in the cell nucleus
Describe the DNA nucleotide structure
Made from a phosphate group, pentose sugar deoxyribose and a nitrogen-containing base
Each DNA nucleotide has the same sugar and phosphate
The base on each nucleotide can vary - Adenine, thymine, cytosine and guanine
What is complementary base pairing?
Two DNA polynucleotide strands join together by hydrogen bonds between the bases. Each base can only join with one particular partner
A-T
C-G
Two hydrogen bonds form between A and T, three between C and G
Describe the structure of RNA
Ribose pentose sugar
Phosphate group
One of four bases: C, G, A, U
Nucleotides form a single polypeptide strand
RNA strands are much shorter than most DNA polynucleotides
Compare the structure of DNA and RNA
DNA:
Double-stranded - twisted into double helix and held together by hydrogen bonds
Deoxyribose sugar
A, T, C, G
Long
RNA:
Single-stranded
Ribose sugar
A, U, C, G
Relatively short
How is DNA replicated?
Semi-conservative replication
Describe the process of semi-conservative replication
1)The enzyme DNA helicase breaks the hydrogen bonds between bases on the two polynucleotide DNA strands. Helix unwinds to form two strands
2)Each og single strand acts as a template for a new strand. Complementary base pairing means that free-floating DNA nucleotides are attracted to their complementary exposed bases on each original template strand
3)Condensation reactions join the nucleotides of the new strand together - catalysed by the enzyme DNA polymerase. H bonds form between the bases on the og and new strands
EAch new DNA molecule contains one strand from the og DNA molecule and one new strand
What is the evidence for semi-conservative replication?
Meselson and Stahl
Experiment with two isotopes of nitrogen (DNA contains nitrogen) - heavy 15N and light 14N
Two samples of bacteria were grown for many generations - one in nutrient broth containing light and one with heavy. As bacteria reproduced, they took up nitrogen from the broth to help make nucleotides for new DNA. So the nitrogen gradually became part of the bacteria’s DNA
A sample of DNA was taken from each batch of bacteria and spun in centrifuge. DNA from heavy settled lower than DNA from light
Then bacteria grown in heavy was put in light and left for round of DNA replication and another DNA sample was taken out and spun
Why is energy important?
Plant and animal cells need energy for biological processes to occur
e.g. active transport
What is ATP made from?
Nucleotide base adenine, combined with a ribose sugar and three phosphate groups
It’s a nucleotide derivative
What is a nucleotide derivative?
Molecule that comes from a nucleotide
What happens to the ATP after it has been made?
Diffuses to the part of the cell that needs energy
The energy in ATP is stored in high energy bonds between the phosphate groups
What is ATP broken down into?
ADP and Pi
What reaction occurs to break ATP down?
Hydrolysis
What bond is broken when breaking down ATP?
Phosphate bond
What enzyme catalyses the breakdown of ATP?
ATP hydrolase
How can the released Pi be used?
Phosphorylation
What reaction resynthesises ATP?
Condensation reaction
What enzyme catalyses the resynthesis of ATP?
ATP synthase
What are the five important things about what?
-Good metabolite
-Solvent
-High latent heat of vaporisation
-High specific heat capacity
-Very cohesive molecules
How is water polar?
The shared negative hydrogen electrons are pulled towards the oxygen atom, the other side of each hydrogen atom is left with a slight positive charge
The unshared negative electrons on the oxygen atom give it a slight negative charge
This makes water a polar molecule - it has a slight partial negative charge on one side and a slight partial positive charge on the other
Describe how water is a good metabolite?
Many metabolic reactions involve hydrolysis or condensation reactions
-Hydrolysis used a molecule of water to break a bond
-Condensation releases a molecule of water to make a bond
Describe how water is a good solvent
A lot of important substances are ionic - one positively charged atom and one negative
Slightly positively charged end of water molecule will be attracted to the negative ion and the negative charged end to positive ion
Means ions will get surrounded by water molecules - dissolve
Water’s polarity is useful as a solvent
This means living organisms can take up useful substances dissolved in water and these dissolved substances can be transported around the organism’s body
Describe how water has a high latent heat of vaporisation and how it is useful
Water vaporises when the H bonds holding water molecules together are broken
This allows the water molecules on the surface of the water to escape into the air as a gas.
It takes lots of energy to break the H bonds between water molecules, so a lot of energy used up when water evaporates.
This means water has high latent heat of vaporisation - lot of heat used from liquid to gas
This is useful for living organisms as it means they can use water loss through evaporation to cool down without losing too much water
When water evaporates it carries away heat energy from a surface, which cools the surface and helps lower the temp
Why does water have a high specific heat capacity and why is it useful?
H bonds give water a high SHC
When water is heated, a lot of the heat energy is used to break the H bonds between water molecules
This means less heat energy available to actually increase the temp of water
So water has a high SHC - takes lots of energy to heat up
Useful for living organisms as it means water doesn’t experience rapid temp changes
Makes a good habitat as temp under water more stable than on land
Water inside organisms remains fairly stable temp - maintain constant internal body temp
Why is water very cohesive and how is that useful?
Cohesion - attraction between molecules of the same type
Water molecules very cohesive as they’re polar
Strong cohesion helps water to flow, making it great for transporting substances
What are ions?
Atom or group of atoms with an electric charge
What is a positive ion called?
Cation
What is a negative ion called?
Anion
What is an inorganic ion?
One that doesn’t contain carbon
