1. Biological Molecules Flashcards
What defines a condensation reaction
Water is produced
What is hydrolysis ?
A way polymers can be broken down through the addition of water
What is metabolism
A name for all the chemical reactions that take place in living organisms
What is a molar solution (M)
A solution that contains one mole of solute in each litre of solution
What are carbohydrates made of ?
Carbon molecules combined with water
What is a monomer
The individual molecules that make up the chain in a polymer
What is the basic monomer in a carbohydrate called ?
A sugar otherwise known as a saccharide
What are monosaccharides
Simplest sugars
Have the general formula (CH2O)n where n can be any number from 3 to 7
Name three examples of monosaccharides
Glucose, galactose and fructose
What are the 2 types of glucose
Alpha glucose
Beta Glucose
(Draw structures)
What is a disaccharide
Formed when 2 monomers join together in a condensation reaction
When two monosaccharides join together what is the bond called?
A glycosidic bond
Name three examples of disaccharides
Maltose
Sucrose
Lactose
(Draw structures)
What is maltose made up of
Glucose+ glucose
What is sucrose made of
Glucose + fructose
What is lactose made of
Glucose + galactose
What happens when water is added to a disaccharide?
Breaks the glycosidic bond releasing the constituent monosaccharides- process is called hydrolysis
What is the main component of a cell membrane
Phospholipid bilayer
Describe the components that make up a phospholipid
2 fatty acid chains, glycerol, phosphate group.
Hydrophilic (head) and hydrophobic (tail) regions
Glycogen function
Energy storage in animals
Starch function
Energy storage in plant cells
Amylose (in starch) : properties and structure
Polysaccharide
Unbranched chain of glucose molecules joined by 1,4 glycosidic bonds
This makes it coiled and compact so stores a lot of energy
Amylopectin (in starch) structure and properties
Polysaccharide
Branched - the side branches can be acted upon simultaneously by enzymes to be broken down to release energy
Made up of glucose joined by 1,4 AND 1,6 glycosidic bonds
Cellulose structure
Made from monomers of beta glucose
Straight unbranched chains running parallel to one another allowing hydrogen bonds to from cross- linkages between adjacent chains.
Test for reducing sugars
Benedict’s test
Benedict’s reagent - copper sulfate solution (alkaline)
1) add (liquified) food sample to test tube
2) add same amount of Benedict’s reagent
3) heat (in a thermostatically controlled) water bath for 5 mins
If positive: solution turns brick-red (precipitate)
Which carbohydrates are reducing
All monosaccharide and some disaccharides
These donate an electron to the Benedict’s reagent in the Benedict’s test
Test for non-reducing sugars
Acidified (hydrochloric acid) Benedicts test
HCl hydrolyses the disaccharides and polysaccharides into monosaccharides
Do test for reducing sugars first:
If colour doesn’t change from blue to brick-red:
1) add dilute hydrochloric acid to food sample and heat in water bath for 5 mins again
2) add sodium hydrogencarbodate to neutralise
3) add Benedict’s solution and heat in water bath
If positive: blue -> brick-red
Chemical test for starch
Iodine test
If positive: Orange-brown to blue/black
Which solvents are lipids only soluble in
Organic solvents
Therefore if you wanted to test a solid piece of food for lipids you would dissolve in alcohol instead of water and then do the test as normal
Main 2 types of lipids
Triglycerides and phospholipids
What are triglycerides made of
1 glycerol and 3 fatty acids
What bonds are in lipids
Ester bonds formed in a condensation reaction
Difference between saturated and unsaturated triglycerides
Saturated lipids:
Found in animal fats
Don’t contain any carbon-carbon double bonds
Unsaturated:
Found in plants
Contain carbon-carbon double bonds (C=C) which allows molecule to bend but aren’t as compact so they’re liquids at room temp
Triglycerides structure relating to their properties
- Being large and non-polar molecules = insoluble in water = doesn’t affect osmosis or water potential
- high ratio of hydrogen-oxygen = release important source of water when oxidised (important for dry/desert organisms)
- high ratio of energy storing C-H bonds to carbon atoms = energy source
- low mass to energy ratio = a lot of energy can be stored in small volume - beneficial to animals as it reduces mass they have to carry around
How are phospholipids polar molecules?
heads are hydrophilic - interact with water but not with fat
tails are hydrophobic - orientates itself away from water but mixes readily with fat
Phospholipids structure related to their properties
Polar - In aqueous environment, bilayer can be formed within cell-surface membranes resulting in hydrophobic barrier between inside and outside of cell
Hydrophilic heads help to hold at the surface of cell membranes
Forms glycolipids by combining with carbs - important on cell membranes for cell recognition
Test for lipids
Emulsion test
1) add 2ml of food sample to 5ml of ethanol
2) shake test tube to dissolve all the lipids
3) add 5ml of water and shake gently
Milky white emulsion indicates positive test & presence of a lipid
Control experiment: use water instead of the food sample, solution should remain clear
What are the monomers of proteins/polypeptides
Amino acids
Structure of amino acids
Amino group (NH^2)
Carboxylic acid group (-COOH)
Variable R group - which is a carbon connecting chain
Hydrogen atom
How many amino acids are there
20
Each determined by their differnt R groups
How are amino acids joined together
Peptide bonds formed between the carbon atom of one amino acid & the nitrogen atom of the other
Condensation reaction where water is lost/formed
-OH lost from cooh group and -H from amino group
How many amino acids are in di- and poly- peptides
Dipeptide: 2
Polypeptides: 3 or more
What’s the secondary structure of a protein
Due to the hydrogen in the -NH group having a positive charge and the -O in the C=O group having a negative charge, weak hydrogen bonds are formed.
Leads to either alpha helix or beta pleated sheets
What’s the primary structure of proteins
Polypeptide
Order, number and sequence of amino acids determine the proteins function in the end
What’s the tertiary structure of proteins
3D shape of proteins
Formed from further twisting and folding
These bonds maintain the structure:
-disulphide bridges - between sulfur and R group of the aa cysteine. These are strong and hard to break
-ionic bonds - between carboxyl and amino groups that aren’t in peptide bond. Easily broken by changes in pH
-hydrogen bonds: numerous but easily broken
What is the difference between globular and fibrous proteins
Globular - compact, involved in chemical reactions, soluble eg: enzymes
Fibrous - long and used to form fibres eg: keratin
Test for proteins
Buriet test - presence of peptide bonds
1) add equal volume of sodium hydroxide at room temp to food sample in test tube
2) add 3 drops of dilute copper sulfate solution and mix
If positive: blue to lilac/purple
What is a polysaccharide
Polymers formed by combining many monosaccharide molecules.
Glycosidic bonds are formed by condensation reactions
Why does STARCH and GLYCOGEN being large & insoluble suit their functions?
Doesn’t affect water potential so tends not to draw in water by osmosis
Does not diffuse out of cells
Why does starch and glycogen being compact suit their functions?
A lot of energy can be stored in a small space
Why does glycogen being more highly branched than starch suit it’s function?
It has more ends that can be acted on simultaneously by enzymes - more rapidly broken down to form glucose monomers which are used in respiration
This is important for animals which have a higher metabolic rate and therefore respiratory rate than plants because they are more active
What are the similarities & differences in structure between glycogen and starch ?
Starch can be unbranched or branched
Glycogen is more highly branched
Glycogen has shorter chains
Both form glycosidic bonds by a condensation reaction
Both are polysaccharides
When hydrolysed what happens to starch?
It forms alpha glucose which is both easily transported and readily used in respiration
What is the main function of cellulose?
Providing support and rigidity
How do the hydrogen bonds suit the function of cellulose?
While individual hydrogen bonds add very little to the strength of the molecule this sheer overall number of them makes a considerable contribution to strengthening cellulose 
What are cellulose molecules grouped together to form
Microfibrils which can be grouped to form fibres providing more strength
How are differences in the properties of different fats and oils determined ?
As the glycerol molecule in all triglycerides is the same the difference in properties come from variations in the fatty acids
Why does the emulsion (cloudy colour) appear in positive test for lipids ?
Due to any lipid in the sample being finely dispersed in the sample to form an emulsion.
Light passing through is refracted as it passes from oil droplets to water droplets making it appear cloudy
What are 4 other roles of lipids ?
Source of energy - twice the amount of energy is released from them than from carbs + valuable water released
Waterproofing - lipids are insoluble
Insulation - fats are slow conductors of heat and when stored beneath the body surface they help retain heat. Also act as electrical insulators in the myelin sheath
Protection - fat is often stored around delicate organs such as the kidney
What is the difference in hydrogen bonding between alpha- helix and beta pleated sheets ?
Alpha helix is INTRAmolecular
Beta pleated sheets is INTERmolecular
What are the hydrogen bonds that keep the alpha helixes together vulnerable to?
Fluctuations in pH and temperature
Describe the quaternary structure of a protein
The quaternary structure arises from the combination of a number of different polypeptide chains and associated non-protein groups into a large complex protein molecule
What is the function of a catalyst
Alter the rate of a chemical reaction without undergoing permanent changes themselves
What does the induced fit model of enzyme action propose?
That the active site forms as the enzyme and substrate interact
How does the induced fit model of enzyme action work?
The proximity of the substrate causes a change in the enzyme that forms the functional active site.
The enzyme has a certain general shape but this alters in the presence of a substrate. (induced fit)
The change in shape puts a strain on the substrate molecule which distorts particular bonds in the substrate and consequently lowers the activation energy needed to break the bond.
What is a limitation of the lock and key model for enzyme action
This model considers the enzyme, like a lock, to have a rigid structure. However scientists discovered that other molecules could bind to enzymes at sites other than the active site and alter the activity of the enzyme which suggests that the enzymes shape can be altered by a binding molecule - its structure is not rigid but in fact flexible .
What two changes are most frequently measured in enzyme-catalysed reactions ?
- The formation of products eg. volume of oxygen formed
- The disappearance of the substrate eg. starch when acted upon by amylase
Explain how the effect of temperature on enzyme action causes an increase in rate of reaction
A rise in temp increases the KE of molecules - they move more rapidly and therefore enzyme and substrate molecules come together more often in a given time.
The collisions are more effective which results in more enzyme-substrate complexes being formed
Rate of reaction increases
Explain how the effect of temperature on enzyme action eventually causes a decrease in rate of reaction
Temp rise begins to cause the hydrogen & other bonds in the enzyme molecule to break - results in the enzyme & its active site changing shape.
At first the substrate fits less easily into the active site-slows rate of reaction (happens at ~45 degrees in humans)
At some point the enzyme is so disrupted that it stops working altogether - becomes denatured
Explain the effect of pH on enzyme activity
Each enzyme has an optimum pH - a change in pH away from the optimum affects the rate of enzyme action.
How does this happen?
Change in pH alters the charges on the amino acids that make up the active site of the enzyme so substrate can’t attach and so enzyme- substrate complex can’t be formed
Depending on how significant the change in pH, it may cause the bonds maintaining the enzymes tertiary structure to break and so the active site changes shape
Explain the effect of enzyme concentration on the rate of reaction
As long as there is an excess substrate, an increase in enzyme conc leads to a proportionate increase in rate of reaction as there is more substrate than enzyme’s active sites can deal with
If substrate is limiting however, an increase in enzyme concentration will have no effect on the rate of reaction and it will stabilise at a constant level- the graph will level off
Explain the effect of substrate concentration on the rate of reaction
If the enzyme concentration is fixed and the substrate concentration is slowly increased the rate of reactions increases. This is because as more substrate is added the active sites of enzymes become filled until the point where they are at full capacity - working as fast as they can.
After that the addition of more substrate has no effect on the rate of reaction - it levels off
What are enzyme inhibitors
Substances that directly or indirectly interfere with the functioning of the active site of an enzyme and so reduce its activity
What are the two types of enzyme inhibitor
Competitive inhibitors - bind to the active site of the enzyme
Non-competitive inhibitor – bind to the enzyme at a position other than the active site
How do competitive inhibitors work?
They have a similar molecular shape to that of the substrate which allows them to occupy the active site of an enzyme.
Therefore, competitive inhibitors compete with the substrate for the available active sites of enzymes
How do non-competitive inhibitors work?
They attach themselves to the enzyme at a binding site which is not the active site. In doing so it alters the shape of the enzyme and it’s active site in such a way that substrate molecules can no longer occupy it and therefore a reaction cannot take place in the same way
How is effect of a competitive inhibitor changed by an increase in substrate concentration?
The effect of the inhibitor is reduced
How is effect of a non competitive inhibitor changed by an increase in substrate concentration?
As the substrate and the non competitive inhibitors aren’t competing for the same site, an increase in the substrate concentration does not decrease the effect of the inhibitor
Describe the structure of a nucleotide
A pentose sugar
A phosphate group
A nitrogen containing organic base (cytosine, guanine, uracil, adenine, thymine)
Describe RNA
The pentose sugar is always RIBOSE
Organic bases are adenine, guanine, cytosine and URACIL
Usually shorter than DNA
Single stranded
How was the structure of DNA discovered
In 1953, Watson and Crick worked out the structure of DNA following the pioneering work of Rosalind Franklin on X-ray diffraction patterns.
Describe base pairing in DNA
Hydrogen bonds hold the bases together
Adenine bonds to Thymine
Cytosine bonds to Guanine
(Said to be complimentary)
How is DNA a stable molecule ?
The phosphodiester backbone protects the more chemically reactive organic bases inside the double helix.
As there are 3 hydrogen bonds between cytosine-guanine, the higher the proportion of C-G pairings the more stable the DNA molecule
What is the function of DNA ?
Hereditary material responsible for passing genetic information from cell to cell and generation to generation
Due to there being 3.2 billion base pairs there almost infinite possibility of base sequences provides genetic diversity in organisms
In which ways is DNA adapted for its function?
Very stable: passes on easily with little change - most mutations are repaired so persistent ones are rare.
Joined only by hydrogen bonds: allows them to separate easily during DNA replication and protein synthesis
Extremely large : can carry immense amount of genetic info
Base pairs within the helical cylinder: genetic info is to some extent protected from being corrupted by outside chemical &physical forces
Base pairing : leads to DNA being able to replicate and to transfer information as mRNA
How is the pentose sugar numbered ?
1’ 2’ 3’ 4’ 5’ clockwise round the sugar from the point on the pentagon
What importance do the 3’ (3 prime) and 5’ (5 prime) numbering have ?
3’ has an attached hydroxyl group
5’ has an attached phosphate group
How are the strands arranged in the double helix structure
One strand runs in the 5’ to 3’ direction while the other runs in the opposite way (3’ to 5’)
The two strands are therefore said to be ANTIPARALLEL
What is the name of the process by which DNA replicates ?
Semi- conservative replication
What are the four things needed for semi conservative replication to take place?
- The four types of nucleotide each with their bases
- Both strands of the DNA molecules act as a template for the attachment of these nucleotides
- The enzyme DNA polymerase
- A source of chemical energy
Describe the steps in the process of semi conservative replication
- DNA helicase unzips hydrogen bonds holding the two strands together
- An RNA primer begins the new strand
- The exposed poly nucleotide strand acts as a template to which complimentary free nucleotides bind (complimentary base pairing)
- DNA polymerase joins nucleotides together to form ‘missing’ polynucleotide strand on each of the two original strands of DNA
- Leading strand grows continuously
- Lagging strand grows in fragments (Okazaki fragments)
- New phosphodiester bonds form between the nucleotides to make new sugar phosphate backbone
- RNA primers are removed by an enzyme and the gaps are filled with DNA
- Two new strands of DNA are formed
Why is semi conservative replication called semi conservative replication?
Each of the new DNA molecules contains one of the original DNA strands, that is, half the original DNA has been saved and built into each of the new DNA molecules
What evidence is there for the semi conservative replication
Meselsohn and Stahl devised an experiment in order to find out which of the two theories (semi conservative/ conservative) was correct.
Due to all bases in DNA containing nitrogen and there being two isotopes 14N and 15N they conducted a study.
Used DNA from E. coli bacterium
Grew bacterium in 15N medium for many generations
Transferred to 14N medium and samples removed at regular intervals (after 1, 2 and 3 generations)
DNA extracted from bacteria and suspended in a special solution
DNA suspension centrifuged
The lighter the DNA, the nearer the top it collected - results determined which theory was correct
What does ATP stand for?
Adenosine triphosphate
Describe the structure of ATP
The ATP is a phosphorylated macromolecule made from 3 parts:
- Adenine (nitrogen containing organic base)
- ribose (pentose sugar that acts as backbone)
- phosphates (chain of 3 phosphate groups)
Explain how ATP releases energy (in terms of bonding)
The bonds between the 3 phosphate groups are unstable and have a low activation energy = they are easily broken
When they break they release energy
(Usually in living organisms, only the terminal phosphate is removed)
What is the equation involving ATP producing energy ?
ATP + H2O ——> ADP + Pi + E
(Pi being an inorganic phosphate)
What type of reaction occurs to convert ATP to ADP and which enzyme is used?
As water is used to convert ATP to ADP it is a hydrolysis reaction.
Catalysed by the enzyme ATP hydrolase (ATPase)
What does ADP stand for ?
adenosine diphosphate
Explain how the synthesis of ATP is a reversible reaction
Energy can be used to add an inorganic phosphate (Pi) to ADP to reform ATP.
The reaction is catalysed by the enzyme ATP synthase.
Water is removed = condensation reaction
In what 3 ways does the synthesis of ATP from ADP occur?
- in chlorophyll containing plant cells during photosynthesis (photophosphorylation)
- in plant and animal cells during respiration (oxidative phosphorylation)
- in plant and animal cells when phosphate groups are transferred from donor molecules to ADP (substrate level phosphorylation)
Why is ATP a better immediate energy source than glucose?
- each ATP molecule releases less energy than each glucose molecule = energy for reactions is released in smaller, more manageable quantities
- the hydrolysis of ATP to ADP is a single reaction that releases immediate energy whereas the breakdown of glucose is a long series of reactions so energy release takes longer
What is a problem with ATP and how is it solved
ATP can’t be stored so has to be continuously made within mitochondria
Cells such as muscle fibres and the epithelium which require energy for movement and active transport process many mitochondria
Which 5 energy-requiring processes is ATP used for ?
Metabolic processes
Movement
Active transport
Secretion
Activation of molecules
How is ATP used in metabolic processes
Provides energy needed to build macromolecules from their basic units eg. Making starch from glucose
How is ATP used in movement
Provides energy for muscle contraction.
Allows filaments of muscle to slide past one another which shortens the overall length of the muscle fibre
How is ATP used in active transport
Provides energy to change the shape of the carrier proteins in plasma membranes which allows molecules or ions to be moved against a concentration gradient
How is ATP used in secretion
ATP is needed to form the lysosomes necessary for the secretion of cell products
How is ATP used in the activation of molecules
The inorganic phosphate produced during the hydrolysis of ATP can be used to phosphorylate other compounds in order to make them more reactive - lowers the activation energy in enzyme catalysed reactions
What are the 5 unusual properties of water
Dipolar
Hydrogen bonding
Specific heat capacity
Latent heat of vaporisation
Cohesion and surface tension
Describe the dipolar nature of water
Although the water molecule has no overall charge the oxygen atom has a slight negative one, while the hydrogen atoms have a slight positive one.
(Water has both negative and positive poles= dipolar)
Describe how water can undergo hydrogen bonding
Different poles attract so the + pole of one water molecule will be attracted to the - pole of another.
The attractive force between the opposite charges is called a hydrogen bond.
Although individually they are fairly weak, together they form important forces that cause the water molecules to stick together
Explain the specific heat capacity of water
Because water molecules bond to each other it takes more energy to separate them- boiling point is higher than expected.
More energy required it heat a certain mass of water = high specific heat capacity
Water acts as a buffer against sudden temp variations.
Describe the latent heat of vaporisation of water
Hydrogen bonding between water molecules means that a lot of energy is required to evaporate 1g of water. (Latent heat of vaporisation)
Describe the cohesion and surface tension of water
Cohesion describes the tendency of molecules to stick together
Due to hydrogen bonding water has large cohesive forces which allow it to be pulled through a tube (eg xylem vessel)
Surface tension describes when water molecules meet air they tend to be pulled back into the body of water rather than escaping.
This means that the water surface acts like a skin and is strong enough to support small organisms (eg pond skaters)
How is water important for metabolism
Breaks down complex molecules by hydrolysis and is also produced in condensation reactions
Chemical reactions take place in an aqueous environment
Water is a major raw material of photosynthesis
How is water important as a solvent
Readily dissolves substances :
-gases: such as oxygen and co2
-wastes : such as ammonia and urea
-inorganic ions : such as small hydrophilic molecules
-enzymes : reactions take place in solution
What are the other important features of water
It’s evaporation cools organisms: allows them to control their temperature
Not easily compressed: provides support
Transparent: aquatic plants can photosynthesise, light rays can penetrate the jelly like fluid that fills the eye in order to reach the retina
Where are inorganic ions found
Cytoplasm of organisms
Body fluids
Part of larger molecules
(They may be in concentrations that range from very high to very low )
What are phosphate ions used for
Storing energy in ATP
Structural role in DNA
What are hydrogen ions used for
Determining the pH of solutions and therefore the functioning of enzymes
What are sodium ions used for
Transport of glucose and amino acids across plasma membranes
Why is DNA helicase important in semi-conservative replication
Breaks down the hydrogen bonds linking pairs allowing double helix to separate and unwind so it can be read
