Biological Molecules Flashcards
• Biological molecules • Nucleic acids
What is a monomer?
A smaller unit from which larger molecules are made
What are polymers made from?
Repeating monomer units
What are three examples of monomers?
Monosaccharides
Amino acids
Nucleotides
What are four examples of polymers?
Polysaccharides Proteins Deoxyribonucleic Acid (DNA) Ribonucleic Acid (RNA)
What is a condensation reaction?
The formation of a chemical bond between two molecules that involves the elimination of a water molecule
What is hydrolysis?
A reaction, involving the use of a water molecule, which breaks a chemical bond between two molecules
What are carbohydrates made from?
Monosaccharides
What is maltose made from?
Glucose + Glucose
What is sucrose made from?
Glucose + Fructose
What is lactose made from?
Glucose + Galactose
How are polysaccharides formed?
By the condensation of many glucose units
How many isomers does glucose have?
2
What are glucose’s isomers?
Beta- and alpha- glucose
What is glycogen formed by?
The condensation of alpha-glucose
What is starch formed by?
The condensation of alpha-glucose
What is cellulose formed by?
The condensation of beta-glucose
Why are polysaccharides suitable storage molecules?
They are large and therefore insoluble
How do you test for starch?
Potassium iodide
During the potassium iodide test, what will happen if starch is present?
Colour change from yellow to blue/black
What are some examples of reducing sugars?
All monosaccharides Some disaccharides (such as maltose)
What is the test for reducing sugars?
Benedict’s Test
What do you use in the test for reducing sugars?
Benedict’s reagent
What is Benedict’s reagent?
An alkaline solution of copper (II) sulphate
What is the positive result for the reducing sugars test?
A red precipitate [copper (I) oxide] formed
What is a requirement for Benedict’s test?
Food tested has to be in liquid form or dissolved in water
What bond is formed in the condensation reaction of glucose?
Glycosidic bond
What happens if the glycosidic bond in a disaccharide is broken?
The constituent monosaccharides are released
What is required for hydrolysis?
A water molecule
What is an example of a non-reducing sugar?
All polysaccharides Some disaccharides (such as sucrose)
How do you test for a non-reducing sugar?
Test with Benedict’s reagent, if negative result then
Add dilute hydrochloride acid
Add sodium hydrogencarbonate
Retest with Benedict’s reagent
When testing for non-reducing sugars why do you use hydrochloric acid?
To hydrolyse any polysaccharide or disaccharide present into its constituent monomers
Monosaccharides are reducing sugars
Why do you have to add sodium hydrogencarbonate when testing for non-reducing sugars?
To neutralise the hydrochloric acid
Benedict’s reagent doesn’t work in acidic conditions
How is starch commonly found?
In small grains
Where is starch found?
Many parts of plants
Is starch ever found in animal cells?
No, only in plant cells
What are the two forms of starch?
Amylose and amylopectin
What glycosidic bonds does amylose have?
1,4
What glycosidic bonds does amylopectin have?
1,4 and 1,6
Is amylose a straight or branched chain?
Straight
Is amylopectin a straight or branched chain?
Branched
Why is amylopectin a good energy source?
The branched ends can be acted on simultaneously by enzymes which means that glucose monomers can be released rapidly
Why is amylose a good storage molecule?
Arranged in a tight helix held together by hydrogen bonds between -OH groups
Tight helix means it is very compact
Lots can fit in a small space
What colour does amylose go when potassium iodide is added?
Dark blue / black
What colour does amylopectin go when potassium iodide is added?
Brick red / brown
Where is glycogen found?
Animals and bacteria
Is glycogen ever found in plants?
No
Does glycogen have longer or shorter chains than starch?
Shorter
Is glycogen a straight or branched chain?
A highly branched chain, more so than starch
Where is glycogen stored in animals?
Mainly in the muscles and liver
How is glycogen stored in animals?
As small grains
Why is glycogen more highly branched than starch?
For a more rapid release of glucose which is needed for respiration. More important to animals as they have a higher metabolic and respiratory rate than plants.
Is cellulose a straight or branched chain?
Cellulose is a straight, unbranched chain
How is cellulose arranged?
Chains run parallel to one another, allowing hydrogen bonds to form cross linkages to adjacent chains
Why does cellulose have good structural stability?
Large quantity of hydrogen bonds hold parallel chains together
What are cellulose molecules grouped together to form?
Microfibrils
What are microfibrils grouped together to form?
Fibres
Where is cellulose commonly found?
Plant cell walls
How does the cellulose cell wall impact osmotic activity?
It prevents the cell from bursting as water enters it via osmosis
How does the cellulose cell wall prevent osmotic rupture?
By exerting an inward pressure that stops any further influx of water.
What occurs as a result of the inward pressure exerted by the cellulose cell wall in plants?
Living plants cells are turgid and push against each other, making the non-wood parts of the plant semi-rigid.
Why is it important to maintain the turgidity in stems and leaves?
To provide the maximum surface area for photosynthesis
Why do cellulose molecules form long, straight, unbranched chains?
They are made of beta-glucose
What do Lipids contain?
Hydrogen
Carbon
Oxygen
Do lipids have a higher or lower proportion of oxygen to carbon and hydrogen than carbohydrates?
Lower
What are lipids insoluble in?
Water
What are lipids soluble in?
Organic solvents such as alcohol and acetone
What are the main two groups of lipids?
Triglycerides
Phospholipids
What are the roles of lipids?
Cell membrane Energy source Waterproofing Insulation Protection
How do lipids act as a source of energy?
When oxidised, lipids provide over twice the energy as the same mass of carbohydrates
What do lipids release when oxidised?
Water
How do lipids act as waterproofing in plants and insects?
Plants and insects have waxy, lipid cuticles that conserve water
How do lipids act as waterproofing in mammals?
Mammals produce an oily secretion from the sebaceous glands in the skin
How do lipids act as insulation?
Lipids are slow conductors of heat
When stored beneath the body surface they help to retain heat
Where do lipids act as electrical insulators?
In the myelin sheath around nerve cells
How do lipids act as protection?
Lipids are often stored around delicate organs (such as the kidney)
What are triglycerides made of?
3 fatty acids
Glycerol
How are the parts of a triglyceride combined?
Each fatty acid forms an ester bond with glycerol in a condensation reaction
What does hydrolysis of a triglyceride produce?
Glycerol
3 fatty acids
What group do all fatty acids have?
A carboxyl group (-COOH)
Why is the low mass to energy ratio (of lipids) beneficial to animals?
It reduces the mass they have to carry as they move around which conserves energy
Why are triglycerides insoluble?
They are large non-polar molecules
Why are triglycerides important for organisms living in dry desert environments?
Triglycerides have a high ratio of hydrogen to oxygen atoms, so release water when oxidised
What does saturated mean?
No double bonds between carbon atoms
What does mono-unsaturated mean?
One double bond between carbon atoms
What does poly-unsaturated mean?
More than one double bond between carbon atoms?
Why are unsaturated molecules often liquids at room temperature?
The double bonds cause the molecule to bend so they can’t pack as closely together
What are phospholipids made of?
2 Fatty acids
Glycerol
Phosphate molecule
What two parts can a phospholipid be split into?
Hydrophilic head
Hydrophobic tail
Are phospholipids polar or non-polar?
Polar
What does hydrophobic mean?
Water hating
What does hydrophilic mean?
Water loving
What can phospholipids form that are important for cell recognition?
Glycolipids
What forms a glycolipid?
Phospholipid + Carbohydrate
What is the test for lipids?
The emulsion test
How do you carry out the emulsion test?
Take a dry and grease free test tube
Add 5ml of ethanol to 2ml of test sample
Shake mixture to dissolve any lipid present
Add 5ml of water and shake gently
What indicates a lipid is present during the emulsion test?
Cloudy white colour / cloudy white emulsion
What should you do as a control during the emulsion test?
Repeat the procedure using water instead of the test sample, the final result should be clear
What causes the cloudy colour in the emulsion test?
Lipid in sample is finely dispersed throughout water to form an emulsion
Light is refracted through the emulsion as it passes from oil droplets to water droplets
What monomer forms a polypeptide?
Amino acids
What can polypeptides be combined to form?
Proteins
What four groups are attached to the central carbon atom in an amino acid?
Amino group -NH2
Carboxyl group -COOH
Hydrogen atom -H
R (side) group
What is the R (side) group in an amino acid?
A variety of different chemical groups
Do all amino acids have the same R (side) group?
No, each amino acid has a different R (side) group
By what process do amino acids combine to form polypeptides?
Condensation
What parts of an amino acid are involved in the formation of a polypeptide via condensation?
An -OH from the carboxyl group of one amino acid
An -H from the amino group of another amino acid
What bond joins adjacent amino acids?
Peptide bond
Where does a peptide bond form?
Between the carbon atom of one amino acid and the nitrogen atom of another amino acid
How can a peptide bond be broken?
Hydrolysis
What is polymerisation?
A process by which a series of condensation reactions allow many amino acid monomers to be joined together to form a polypeptide
What forms the primary structure of any protein?
The sequence of amino acids in a polypeptide chain
How many naturally occurring amino acids are there?
20 (these occur in all living organisms)
What does the primary structure of a protein determine?
The ultimate shape and structure of the protein
What bonds form in the secondary structure of proteins?
Hydrogen bonds
Where do hydrogen bonds form in the secondary structure of proteins?
Between the -NH and -C=O groups on either side of every peptide bond
What do the hydrogen bonds in the secondary structure of a protein cause?
The long polypeptide chain to be twisted into a 3D shape
What is the tertiary structure of proteins?
The twisting and folding of the secondary structure to give the complex, and more specific, 3D structure of each protein
What bonds form in the tertiary structure of proteins?
Disulfide bridges
Ionic bonds
Hydrogen bonds
What control where bonds occur in the tertiary structure of a protein?
The primary structure of a protein
Where do ionic bonds form in the tertiary structure of a protein?
Between any carboxyl and amino groups that are not involved in forming peptide bonds
What easily breaks ionic bonds?
Changes in pH
What is the primary structure of a protein?
The sequence of amino acids found in its polypeptide chains
What is the quaternary structure of proteins?
Multiple polypeptide chains linked in various ways
What may also be associated with the quaternary structure of proteins?
A prosthetic group (non-protein group)
What determines the 3D shape of a protein?
The sequence of amino acids (primary structure)
What is the test for proteins?
Biuret test
How does the ‘Biuret test’ test for proteins?
Detects peptide bonds
How do you carry out the Biuret test?
Add an equal volume of sodium hydroxide to the test sample (at room temperature)
Add a fwe drops of copper (II) sulfate solution (0.05%) and mix gently
In the Biuret test, what indicates the presence of a peptide bond?
A purple colour
What is the negative result in the Biuret test?
The solution remains blue
What are the two basic types of protein?
Fibrous proteins
Globular proteins
What are the function of fibrous proteins?
Structural functions
What are the functions of globular proteins?
To carry out metabolic functions
What type of proteins are enzymes?
Globular
How do enzymes act as catalysts?
By lowering activation energy
Why are enzymes necessary to sustain life as we know it?
They allow reactions to take place at a lower temperature than normal which means some metabolic processes can occur rapidly at human body temperature
What would happen without enzymes?
Metabolic processes and reactions would proceed to slowly to sustain life as we know it
What does an enzyme form with a complementary substrate molecule?
Enzyme-substrate complex
Where does the substrate bond to the enzyme?
Active site
How is the substrate molecule held within the active site?
Temporary bonds form between certain amino acids on the active site and certain groups on the substrate molecule
What model is used to represent enzyme action?
The induced fit model
What does the induced fit model of an enzyme suggest?
The active site forms as the enzyme and substrate interact
How is a functional active site formed?
A change in the enzyme caused by the proximity of the substrate molecule
What does the induced fit model propose about enzyme shape?
An enzyme has a certain general shape, but this alters in the presence of a substrate molecule
How do enzymes lower activation energy?
By changing shape which puts strain on the substrate molecules
This strain distorts certain bonds in the substrate molecule which results in less energy being needed to break the bond
What is an example of a change in an enzyme’s environment?
Collision with a substrate molecule
What is the result of a change in an enzyme’s environment?
Alteration of the enzyme’s shape
What was a limitation of the lock and key model (for enzymes)?
It suggested enzymes were rigid structures, when they are actually flexible
What two things must an enzyme have or do in order to act as a catalyst?
Come into physical contact with the substrate
Have an active site which fits the enzyme
What two things are often measured to calculate the rate of reaction?
Product formation
Substrate disappearance
How can increasing temperature increase the rate of reaction?
Molecules have more kinetic energy so collide more, this means that more enzyme-substrate complexes are formed
How can increasing temperature decrease the rate of reaction?
Rising temperature causes the hydrogen (and other) bonds in the enzyme to break
This alters the shape of the active site so substrate fits less easily (hence rate of reaction is slowed)
If temperature keeps increasing enzyme becomes denatured and can no longer bond to substrate
What is the best temperature for a specific enzyme known as?
Optimum temperature
What is roughly the optimum temperature for human enzymes?
40 degrees
Why might human body temperature have evolved to be 37 degrees when most human enzymes have an optimum temperature of 40 degrees?
Advantages offset by additional energy required to maintain higher temperature
Other proteins may be denatured
A further rise in temperature (e.g. during illness) may cause enzymes to denature
How is the pH of a solution calculated?
pH = -log10[H+]
What is the pH of a solution with [H+} concentration of (1x10^-9) ?
pH 9
How can a slight change in pH impact enzyme activity?
A change in pH alters charges on the amino acids that make up the active site meaning enzyme-substrate complexes no longer form
How can a significant change in pH impact enzyme activity?
It may cause the bonds in the tertiary structure to break, therefore the active site changes shape
Are pH fluctuations in an organism more likely to reduce and enzyme’s activity or denature it?
Reduce enzyme activity as pH fluctuations within an organism tend to be small
What are two types of enzyme inhibitors?
Competitive
Non-competitive
Where do competitive inhibitors bind?
Active site
Where do non-competitive inhibitors bind?
Allosteric site
What determines the impact of a competitive inhibitor?
The different in concentration of the competitive inhibitor and the substrate
Why can a competitive inhibitor bind to the active site?
The competitive inhibitor is of a similar shape to the substrate molecule
How do competitive inhibitors reduce the rate of reaction?
By reducing the rate at which enzyme-substrate complexes form
How do non-competitive inhibitors reduce the rate of reaction?
Preventing enzyme-substrate complexes from forming as enzyme no longer complementary to substrate
Does concentration of the substrate have an impact on the effect of a non-competitive inhibitor?
No
Why do non-competitive inhibitors reduce the rate of reaction?
By binding to the allosteric site they cause the enzyme to change shape so it no longer has an active site that is complementary to the substrate
What is a metabolic pathway?
A series of reactions in which each step is catalysed by an enzyme
What does DNA stand for?
Deoxyribonucleic acid
What does RNA stand for?
Ribonucleic acid
What are nucleotides made up of?
Pentose sugar
Phosphate group
Nitrogen-containing organic base
What is the base ‘C’?
Cytosine
What is the base ‘G’?
Guanine
What is the base ‘A’?
Adenine
What is the base ‘T’?
Thymine
What is the base ‘U’?
Uracil
What is a DNA nucleotide made up of?
Deoxyribose sugar
Phosphate group
One of either cytosine, guanine, adenine, or thymine
What is a single RNA nucleotide made up of?
Ribose sugar
Phosphate group
One of either cytosine, guanine, adenine, or uracil
What bond is formed between the phosphate group and pentose sugar of adjacent nucleotides?
Phosphodiester bond
What is the structure of RNA?
Single chain
Relatively short polynucleotide
What are the three functions of RNA?
Transfer of genetic information from DNA to ribosomes
Forming part of ribosomes
Protein synthesis
What is the structure of DNA?
Two polynucleotide chains
Extremely long strands
How are the two DNA strands joined?
Hydrogen bonds form between complementary base pairs
What are the complementary base pairs?
Adenine - thymine
Cytosine - guanine
How many hydrogen bonds form between adenine and thymine?
2
How many hydrogen bonds form between cytosine and guanine?
3
What is the structure of DNA said to be?
A double helix
What do the deoxyribose and phosphate group form in DNA?
A structural backbone
What three scientists were important in discovering the structure of DNA?
James Watson
Francis Crick
Rosalind Franklin
Why is DNA a stable molecule?
Phosphodiester backbone protects organic bases inside the double helix
Hydrogen bonds link complementary base pairs
Why does a higher proportion of G-C pairs increase the stability of a DNA molecule?
3 hydrogen bonds between guanine and cytosine
What provides genetic diversity within organisms?
The almost infinite variety of sequences of bases in a DNA molecule
How many base pairs are there in a typical mammalian cell?
Roughly 3.2 billion
How is DNA adapted to its function?
Stable and rarely mutates
Strands only joined by hydrogen bonds so can separate during replication
Large so carries lots of genetic information
Genetic information protected by phosphodiester backbone
Base pairings means DNA can replicate and transfer information as mRNA
How does DNA replicate?
Semi-conservative replication
What are the four requirements for semi-conservative replication of DNA?
Four types of nucleotide must be present with their bases (A,C,T,G)
DNA polymerase must be present
DNA helicase must be present
Source of chemical energy required to drive process
What does DNA helicase do in semi-conservative replication?
Breaks hydrogen bonds between complimentary base pairs
‘unzips genes’
Why is it called semi-conservative replication?
Each original DNA strand acts as a template to which free nucleotides are attached
New DNA molecule contains 1 original and 1 new strand
What does DNA polymerase do in semi-conservative replication?
Joins nucleotides together via a condensation reaction (forms the phosphodiester bonds on the new strand)
What are the two strands called in semi-conservative replication?
Leading strand
Lagging strand
What is the leading strand?
The original strand of DNA that is continuously acted on by DNA polymerase
What is the lagging strand?
The original strand of DNA that isn’t continuously acted on by DNA polymerase
Why is there a leading and lagging strand in DNA replication?
DNA polymerase has a specific active site that only works in one direction
DNA strands are anti parallel so enzyme has to work in opposite directions
What word can be used to describe the opposite arrangement of nucleotides in the two strands of a DNA molecule?
Anti parallel
What two methods of DNA replication were proposed but later rejected?
Dispersive
Conservative
What is ATP?
A phosphorylated macromolecule
What does ATP stand for?
Adenosine triphosphate
What is ATP made up of?
Adenosine
Ribose
A chain of 3 phosphates
What enzyme catalyses ATP synthesis?
ATP synthase
What is the role of ATP?
Temporary energy source
Why is ATP a good energy source?
Energy released in smaller, more manageable, quantities
Single reaction to release immediate energy
What is ATP hydrolysed to?
ADP
What is released via the hydrolysis of ATP to ADP?
Energy
Where is ATP made?
Mitochondria
Can ATP be stored?
No, it has to be continuously produced
What processes require ATP?
Metabolic processes Movement Active transport Secretion Activation of molecules
Why do metabolic processes require ATP?
ATP provides the energy needed to build macromolecules from their basic units
Why does movement require ATP?
ATP provides the energy for muscle contraction
Why does muscle contraction require ATP?
ATP provides the energy for the filaments of muscle to slide past one another and therefore shorten the overall length of the muscle fibre
Why does active transport require ATP?
ATP provides the energy to change the shape of carrier proteins in plasma membranes
Why is ATP required for secretion?
ATP is needed to form the lysosomes necessary for the secretion of cell products
Why is ATP required for the activation of molecules?
The inorganic phosphate released during the hydrolysis of ATP can be use to phosphorylate other compounds in order to make them more reactive (thus lowering activation energy)
What is an example of ATP assisted molecule activation?
The addition of phosphate to glucose molecules at the start of glycosis
Although water has no overall charge, what is it still described as?
Dipolar
Why is water a dipolar molecule?
Oxygen atom has slight negative charge
Hydrogen atoms have slight positive charge
Molecule has both positive and negative poles
Why is the high specific heat capacity of water important?
It acts as a buffer for sudden temperature variations
Why is evaporation of water via sweat an effective method of cooling down?
Water has a high latent heat of vaporisation (requires lots of energy to evaporate)
Why is surface tension in water important?
Allows water to support small organisms (e.g. pond skaters)
What is cohesion?
The tendency of molecules to stick together
Why are the large cohesive forces of water important?
Allows it to be pulled up a tube, such as the xylem vessel in plants
How is water used in metabolism?
Used to break down complex molecules in hydrolysis
Chemical reactions take place in an aqueous environment
Required for photosynthesis
Water dissolves many other substances so what is it often called?
Universal solvent
Why is water important as a solvent?
Readily dissolves other substances such as:
gases (oxygen, carbon dioxide)
wastes (ammonia, urea)
inorganic ions and small hydrophilic molecules (amino acids, monosaccharides, ATP)
enzymes whose reactions take place in solution
Why is it important that water isn’t easily compressed?
Provides support in hydrostatic skeletons and turgor pressure
What organisms rely on turgor pressure?
Herbaceous plants
What is an example of an organism with a hydrostatic skeleton?
Earthworm
What is the role of iron ions?
Oxygen transport in haemoglobin
What are the roles of phosphate ions?
DNA structure
Storing energy in ATP
What is the role of hydrogen ions?
Determining pH of solutions (and therefore enzyme function)
What is the function of sodium ions?
Transport of glucose and amino acids across plasma membranes
