-Module 2; Biological molecules Flashcards
1
Q
Structure of water
A
One atom of oxygen joined to two hydrogens by a covalent bond.
H’s shared electrons are pulled to the oxygen atom, causing each H to be slightly positive.
Oxygen is left slightly negative.
This makes water a polar molecule, a dipole.
2
Q
What are the features of hydrogen bonding between water molecules?
A
The slightly negative charge on the oxygen atom is attracted to and forms a hydrogen bond with the slightly positive charge of a hydrogen on another water molecule.
We use the delta sign to show slightly negative and slightly positive.
3
Q
What are the 5 main properties of water?
A
1- High specific heat capacity
2- Cohesive and adhesive
3- Hight latent heat of vaporisation
4- Lower density when solid
5- Good solvent
4
Q
What is meant by a high specific heat capacity of water and what is the benefit of this?
A
SHC is the energy needed to raise the temperature of a gram of a substance by 1 degree.
H bonds between water molecules can absorb a lot of energy.
Water has a high SHC.
Important bc large fluctuations in temp are not good for aquatic organisms.
5
Q
What is meant by High latent heat of vaporization and why is it important?
A
Lots of energy is needed to break the bonds between water molecules to change water from a liquid to a gas. This makes water an excellent coolant.
6
Q
Roles of water as a coolant.
A
Sweat evaporates, carries heat away.
Plants transpiration, water evaporates from leaves and carries heat away.
Temperature buffer for chemical reactions in prokaryotes and eukaryotes.
Proper function of enzymes- active in a narrow temp range.
7
Q
What is cohesion in water?
A
Cohesion is the attraction between water due to hydrogen bonding.
8
Q
What are the roles of water being cohesive?
A
Transport
Transpiration
Blood
Phloem
Surface tension (provides habitat)
9
Q
Why is surface tension formed?
A
Water molecules are more attracted to each other than the air.
10
Q
How do hydrogen bonds behave in water related to cohesion?
A
They are relatively weak so break and reform constantly, however they occur in such large numbers that water remains cohesive.
11
Q
What is adhesion?
A
The attraction between a water molecule and another polar molecule.
12
Q
What are the roles of cohesion and adhesion together?
A
The combination of the two is capillary action, this is what allows water to move through the xylem tubes.
13
Q
Why does water have a lower density when solid?
A
As water changes state from liquid to solid, each water molecule forms four hydrogen bonds to other water molecules, creating a hexagonal lattice structure. This makes ice less dense than liquid water and is why ice floats.
14
Q
Why is water being less dense when solid than liquid important?
A
Ice forms a protective barrier which reduces the rate of heat loss and makes the environment more stable for aquatic organisms.
15
Q
How does water dissolve substances?
A
Water is polar and therefore the slightly positive end of water will be attracted to negative ions and vice versa. Water molecules surround each ion and dissolve the substance.
16
Q
Why is it important that water is a good solvent for living organisms?
A
Transport of molecules and ions in living organisms (blood/phloem)
Ions can dissolve in water in blood and are important in the regulation of pH and water balance.
Most chemical reactions take place in a solution.
17
Q
What substances dissolve in water?
A
Ions and polar molecules.
To identify these, look for -OH and -SH groups in chemical structures.
18
Q
Why is it useful to organisms that water is a liquid at room temp?
A
Effective transport medium, eg, blood/phloem.
Habitat for aquatic organisms.
Medium for chemical reactions.
19
Q
What are the roles of carbohydrates?
A
Energy storage (starch)
Energy source (glucose)
Structural (cellulose)
20
Q
What are the molecules in carbohydrates?
What ratio are they usually in?
A
Carbon, hydrogen, oxygen.
They are usually in the ratio of C:H:O is 1:2:1.
21
Q
What is a single sugar unit called? What about two and more?
A
Monosaccharide, disaccharide, polysaccharide.
22
Q
What are monomers?
A
They are small, basic units like monosaccharides.
23
Q
What are polymers?
A
Polymers are large, complex, molecules composed of long chains of monomers joined together, eg cellulose, starch and proteins.
24
Q
What are the structural features of glucose of a monosaccharide?
A
Glucose has 6 carbon atoms and is therefore a hexose monosaccharide.
Has the formula C6H12O6.
Two forms fo structural isotopes (alpha and beta)
25
Draw a glucose monosaccharide.
/...
26
What is the difference between alpha and beta glucose?
Alpha glucose the hydroxyl group at carbon 1 points down.
Opposite for beta.
27
What are the features of fructose?
Pentose sugar.
It is very sweet and soluble and is the most common sugar in nectar and fruit.
Fructose is sweeter than glucose which is sweeter than galactose.
28
What are the features of galactose?
It is not as soluble as glucose and has an important role in the production of glycolipids and glycoproteins.
29
What are pentose monosaccharides?
They contain 5 carbon atoms, example deoxyribose and ribose.
30
How are disaccharides formed between two alpha glucose?
When two alpha glucose are side by side, the two hydroxyl groups react. When this happens, bonds are broken and new bonds are formed in different places forming new molecules. The bond is formed between carbon 1 and carbon 4. This means it is a glycosidic 1-4 bond. The reaction is a condensation reaction.
31
What are the enzymes involved in hydrolysis?
Hydrolase enzymes.
32
How is alpha lactose formed?
Beta galactose and alpha glucose with a beta 1-4 glycosidic bond directed upwards.
33
How is beta lactose formed?
Beta galactose + beta glucose joined with a beta glycosidic bond.
34
How is sucrose formed?
Alpha glucose + beta fructose
35
What are the 3 important disaccharides to learn and what are they made up of?
Maltose is made up of two glucose.
Lactose is made up of glucose and galactose.
Sucrose is made of glucose and fructose.
36
Why are the 5 key features of a polysaccharide energy storage molecule?
Compact - energy dense.
Insoluble - would not affect the water potential of the cell.
Easy to add glucose to - condensation reaction
Easy to remove glucose from - hydrolysis
Metabolically inactive
37
How is starch formed and what is it's use?
Glucose is produced during photosynthesis and is converted to and stored in the chloroplasts and in membrane bound starch grains of plant cells. Used as a source of energy for the plant.
38
What is the structure of starch?
Starch is a polysaccharide made up of many alpha glucose molecules.
There are two kinds of glycosidic bonds that can form between the glucose molecules which allows two slightly different structural units to be formed; amylose and amylopectin.
39
What are the features and structure of amylose?
Amylose makes up 30% of starch.
It is a long unbranched chain of a-glucose connected by 1-4 glycosidic bonds only.
It coils into a compact helix which is then held in place by hydrogen bonds.
The OH groups are arranged to the inside of coil, making amylose less soluble as these are the groups that would H-bond with water.
40
What are the features and structure of amylopectin?
Makes up 70% of starch.
Chains of alpha-glucose connected by 1-4 glycosidic bonds to form helical shapes.
Approx every 25 glucose, a 1-6 glycosidic bond forms by condensation, creating a branch.
Highly branched structure has multiple sites for hydrolysis allowing glucose to be removed quickly.
41
Where is glycogen found and what is it's function?
It is stores in small granules, particularly in the muscles and the liver.
It is used as an energy storage molecule by animals and fungi.
42
What is glycogen's structure?
It is made of alpha glucose.
Branch points every 10th residue and are 1-6 glycosidic bonds.
43
Why do animals use glycogen not starch?
Glycogen is coiled making it more compact for easier storage.
It is highly branched and so easier access to free ends where hydrolysis takes place, means glucose can be released quickly.
Plants are immobile and animals are active so need a lot more energy.
44
Why is it important that glucose is stored and not always freely available in the blood or phloem?
Glucose is soluble. Too much glucose will lower the water potential of the blood, causing water to move out of cells by osmosis.
45
What is the structure of cellulose?
Cellulose is made up of long, unbranched chains of B glucose.
The hydroxyl groups on carbon 1 and 4 are too far apart.
Alternate B glucose molecules must be inverted so that they are close enough to form a 1-4 glycosidic bond.
It is a straight chain molecule.
46
How many cellulose chains bind together to form a microfibril?
60-70.
47
How many microfibrils bundle together to form macrofibrils? How do they form cell walls?
Up to 400. They are embedded in pectin to form cell walls. They criss cross in all directions for tensile strength.
48
What is the function of cellulose?
Makes up the cell wall to give the cell tensile strength.
It prevents the cell bursting when turgid and protects the cell membrane.
The cell wall is fully permeable due to space between macrofibrils.
It is insoluble and inert.
49
What are the functions of lipids?
They are an energy source, can be used in respiration (2x energy per gram than glucose).
Water source.
Energy store, insoluble in water so doesn't affect water potential.
Thermal insulation
Stores fat soluble vitamins (adipose tissue stores A,D,E and K).
Buoyancy.
Cushoning.
Membrane protection.
Hormone production.
Electrical impulse insulation.
Waterproofing.
50
What elements are lipids made up of?
Carbon, hydrogen and oxygen.
51
What does it mean that lipids are macromolecules?
They are complex molecules with a relatively large molecular mass.
This means they don't form polymers as they are not monomers.
52
Are lipids polar? What dies this mean for it's solubility?
No, they have an even distribution of electrons in the outer orbitals where the bonds form.
Therefore they are insoluble.
53
What is the structure of triglycerides?
They are made by combining one glycerol molecule with three fatty acids.
The glycerol is a member of the alcohol group and acts as the backbone.
54
What group do fatty acids belong to? Why?
Carboxylic acids because they have carboxyl groups (-COOH) with a hydrocarbon chains attached.
55
How do the glycerol and the 3 fatty acids join?
They both have hydroxyl groups (-OH).
The hydroxyl groups interact, leading to the formation of three water molecules and three bonds between glycerol molecule.
These are called ester bonds.
56
What kind of reaction breaks down triglycerides?
Hydrolysis.
57
What are saturated fatty acids?
Fatty acids with no double bonds between carbon atoms.
They have formed the maximum number of bonds with hydrogen atoms, they are a straight chain.
58
What is an unsaturated fatty acid?
A fatty acid with double bonds between some of the carbon atoms.
If it is only one double bond it is monounsaturated, if it is more than two it is polyunsaturated.
Double bonds cause the molecule to kink or bend.
59
Are saturated an unsaturated fats liquid or solid at room temp?
Saturated are solid.
Unsaturated are liquid.
60
What kind of fats are better for human consumption? How is coronary heart disease caused?
Plant contain unsaturated triglycerides (oils) which tend to be healthier for humans than saturated fats (solid).
Excess saturated fats can lead to coronary heart disease, however evidence is unconclusive.
61
Why are triglycerides ideal as storage molecules?
They are insoluble.
They release twice as much energy per gram as glucose.
Don't affect water potential of cells.
Triglycerides bundle together to form insoluble droplets in cells with the hydrophobic tails inwards and the hydrophilic heads outwards allowing them to be transported in an aqueous envrionment.
62
What is the ratio of CHO in a triglyceride?
1:2:<1. Much less oxygen in lipids than carbohydrates.
63
What are phospholipids?
They are modified triglycerides that contain phosphorus and two fatty acid chains. (diglycerides)
64
How is phosphate formed?
Phosphoric acid. Hydrogen ions dissociate which is why it's an acid.
When this happens phosphate forms which is a negatively charged ion.
65
How are phospholipids formed?
One of the fatty acid chains in a triglyceride molecule is replaced with a phosphate group.
This is a condensation reaction with the release of a water molecule.
66
How do the phosphate heads of phospholipids interact with water?
They are charged and is therefore attracted to water so is hydrophilic and water loving.
67
How do the fatty acid tails interact with water?
Fatty acids aren't polar and therefore aren't soluble in water.
They are referred to as hydrophobic and water hating.
68
What is a molecule with both hydrophobic and hydrophilic portions called?
Amphipathic.
69
How does a phospholipid's structure act in water?
Their hydrophobic and hydrophilic structure causes them to form a layer on the surface of the water with phosphate heads in the water and fatty acid tails sticking out.
Because of this they are called surfactants (surface active agents)
70
What is a micelle?
The structure fats take on when submerged in water.
71
How does a phospholipid's structure lead to it's function?
They form a double layer called a bi-layer.
The centre of the bi-layer is hydrophobic so water soluble substances cannot easily pass through.
72
How is a membrane fluid and flexible?
Phospholipids are free to move around in their bi-layer .
73
What molecules are able to pass through a bi-layer?
Small and non-polar molecules.
74
What is a sterol? (AKA steroid alcohols)
A type of lipid found in cells, but not fats or oils.
They have a different structure - they are complex ring structures with a hydroxyl group (OH) at one end.
Amphipathic in nature.
Hydroxyl group is polar and therfore hydrophilic and the rest of the molecule is hydrophobic.
75
What is cholesterol? What are it's features?
It is a sterol.
Primarily produced in liver and intestines.
Cholesterol is important in the formation in cell membranes.
They are flattened in shape and fit between phospholipids and increases the packing of the membrane, making it more rigid.
Hydroxyl group arranged to the outer edge.
Cholesterol increases fluidity at low temps and decreases fluidity at high temps.
76
What is the test for lipids?
Emulsion test.
Lipids dissolve in ethanol because ethanol has a non-polar ethyl group.
Dissolved lipid added to pure water.
A white cloudy emulsion appears on the surface.
77
How are sugars classed as reducing or non-reducing?
Sugars are classed as reducing or non-reducing based on their ability to act as a reducing agent during the Benedict's test.
A reducing agent donates (loses) electrons during a redox reaction and is itself oxidised.
78
What kind of sugars are reducing? What tests detect them?
Monosaccharides and some disaccharides. Their presence is detected by the Benedict's test.
79
What are the stages of the Benedict's test for reducing sugars?
Stage 1 - benedict's solution contains copper (II) sulfate, sodium citrate and sodium carbonate. The Cu2+ ions give it a clear blue colour. Usually 2cm^3 of the benedict's solution is added to 2cm^3 of the solution to test.
Stage 2 - When heated in the presence of a reducing sugar, the Cu2+ ions are reduced to Cu+ ions in the form of copper(I) oxide, which forms a brick red precipitate.
Stage 3 - The colour of the precipitate indicates the relative concentration of reducing sugar. A clear blue colour is a negative result, but a non-reducing sugar may still be present.
80
How do you perform the semi-quantitative benedict's test?
If you add benedict's in excess the intensity of the red colour is proportional to the concentration of sugar.
The reaction mixture will appear green if only a little precipitate is formed and fully red if a lot of precipitate is formed.
81
How do you perform Benedict's test for non-reducing sugars?
Non-reducing sugars like sucrose must first be hydrolysed to glucose and fructose by adding dilute hydrochloric acid.
The solution is then boiled and the acid is neutralised by adding sodium hydrogencarbonate.
Benedict's solution can then be added.
Once Benedict's solution is added and the sample is heated, a change in colour will indicate that a reducing sugar is present.
82
How is the iodine test for starch carried out?
A few drops of iodine or potassium iodide are added to the sample.
If starch is present, the solution will turn a blue-black colour.
83
What is the biuret test for proteins?
A few drops of biuret - blue copper (II) sulfate (containing Cu2+ ions) and sodium hydroxide - are added to the solution. The test tube is shaken after every drop.
The solution will turn a purple/violet colour in the presence of peptide bonds. This does not conclusively prove a protein is present, but protein is the most likely substance.
The purple/violet colour is due to Cu2+ ions bonding to adjacent pairs of -CO-NH- groups in peptide bonds. A more intense colour indicates more peptide bonds are present.
84
What are the 4 roles of proteins?
Stuctural - proteins are the main components of body tissues, such as muscle, skin, ligaments and hair.
Catalytic - all enzymes are proteins, catalysing many biochemical reactions.
Signalling - many hormones and receptors are proteins.
Immunology - all antibodies are proteins.
85
What is the basic structure of an amino acid?
An amino acid is made up of the elements C,H, O, N and S.
Amino/amine group, R group and carboxyl group.
86
What does the R group on amino acids do?
The R group is what determines the amino acid, it is the only thing that is different on amino acids.
Some R groups are complex ring structures.
87
What is the R group on an amino acid?
The R group represents a side chain from the central alpha carbon. It can be anything from a single hydrogen to a complex ring structure. It can be polar/non-polar/hydrophobic/hydrophilic.
88
How many amino acids are in our body?
How many are non-essential?
How many are essential and how are they obtained?
How many are conditionally essential?
20 found in our body.
5 said to be non-essential as our body can make them from other amino acids.
9 are essential.
6 are conditionally essential as they are only required by infants and growing children.
89
What role do amino acids play as buffers?
When in water the amino group and carboxyl acids can ionise.
NH2 becomes NH3+ and COOH becomes COO-.
This means the molecule has amphoteric properties (acidic and basic)
By accepting and releasing H+ ions, amino acids can regulate changes in pH which means they behave as pH buffers.
90
What is a buffer?
A buffer is a substance that resists large changes in pH.
91
What are peptides?
How do they form proteins?
Amino acids are monomers which come together to form peptides which are polymers.
One or more polypeptides come together to form a protein.
92
What are proteins in molecular terms?
They are complex macromolecules and have specific biological functions.
93
What molecules do all proteins contain?
C, O, H, N
94
What is a peptide bond?
It is a covalent bond, the making of a peptide bond involves a condensation reaction and the breaking involves a hydrolysis reaction. Protease enzymes catalyse this reaction.
The reactions are the same as in glucose but a peptide bind is formed instead.
95
How is a polypeptide chain formed?
More amino acids are added to a dipeptide.
96
How many polypeptide chains does a protein consist of in it's highly specific 3D shape?
One or more polypeptide chains folded.
97
How many levels of structure are there in a protein?
Up to 4, primary, secondary, tertiary and quaternary.
98
What is the primary structure of a protein?
The sequence of amino acids in a polypeptide chain.
Different proteins have different sequences of amino acids in their primary structure.
99
What is the secondary structure of proteins?
The chain of amino acids twists into one of two structures, alpha helixes and beta pleated sheets. Both can exist in a single polypeptide.
100
How are alpha helixes formed?
H bonds form between the -NH and -CO groups of the amino acids - not the R groups.
This causes the chain to be pulled into a coil shape called am alpha helix.
101
How are beta pleated sheets formed?
They fold very slightly in a zig-zag structure.
H bonds between -NH groups of one amino acid and the -CO group of another strand hold the sheets together.
H bonds are relatively weak but lots are formed which makes these stable structures at optimum temperature and pH.
102
What are the tertiary structures of a protein?
Ionic bonds - attractions between negatively charged and positively charged R groups.
Disulfide bonds - two cysteine amino acids that bond between two sulfur atoms.
Hydrophilic and hydrophobic interactions.
Hydrogen bonds - weak bonds between slightly positive and slightly negative R groups.
103
How do hydrophobic and hydrophilic interactions affect tertiary protein structure?
Proteins are assembled in aqueous environment.
This affects how protein folds as R group that are hydrophobic orientate inside and hydrophilic outside.
104
What is the quaternary structure of a protein?
Several different polypeptide chains come together to form the quaternary structure, each tertiary structure polypeptide is a subunit.
They are held together with bonds.
Not all proteins have a quaternary structure. For some, the tertiary structure is the final 3D arrangement.
105
How are peptides broken down?
Proteases catalyse the hydrolysis reaction which turns peptides into their constituent amino acids.
A water molecule is used to break the peptide bond reforming the amino group and carboxyl group.
106
What are fibrous proteins?
They are long, insoluble proteins that don't fold.
They have a high proportion of amino acids with small hydrophobic R groups.
Long polypeptide chains run parallel to one another and H bonds form crosslinks between them.
Stong- provide structural strength.
107
What kind of protein is keratin and what are it's functions?
It is a fibrous protein.
It is found in hair, claws, hooves, scales, feathers, fur, nails etc.
It can be flexible )skin) or hard (nails)
Has a large proportion of the sulfur-containing amino acid cysteine - strong disulfide bonds form inflexible and insoluble molecules.
Waterproof.
Degree of disulfide bonds determines flexibility.
108
What type of protein is elastin and what are it's functions?
Fibrous
It is made from stretchy molecules called tropoelastin, found in elastic fibres.
Cross-linking and coiling make elastin strong and extensible.
Elastic fibres are present in blood vessels, alveoli, bladder, stomach and skin.
It allows blood vessels to withstand the pressure of blood travelling through them.
109
What type of protein is collagen and what is it's function?
Fibrous.
Connective tissue in skin, tendons, ligaments and nervous system.
Bones are made from collagen and then reinforced with calcium phosphate.
Provides mechanical strength and flexibility and is not stretchy.
Made of 3 polypeptides wound together in a long, rope like structure.
Every 3rd amino acid is a glycine which allows close packing of the helix.
H bonds form between polypeptides.
110
What are the features of a globular protein?
Usually spherical, tightly folded polypeptide chains.
Hydrophobic groups are on the inside and hydrophilic groups are on the outside.
Hydrophilic groups associate with water molecules making many soluble in water.
111
What is a prosthetic group on a protein?
A conjugated protein is one that is chemically bonded to a non-protein part called a prosthetic group (can be a carbohydrate or mineral etc).
The extra component is essential to the function of the molecule.
EG haemoglobin, the haem group contains an iron ion.
112
What type of protein is haemoglobin and what is it's structure and function?
Globular.
It is the red, oxygen-carrying pigment in red blood cells.
Each of the 4 subunits contains a haem prosthetic group that holds an iron ion.
The iron ion binds reversibly with oxygen and this is how oxygen is transported. When oxygen combines with iron the shape of the pigment changes and the protein is called oxyhaemoglobin.
113
What type of protein is insulin and what is it's structure and function?
Globular.
It is a hormone.
Involved in regulating blood glucose concentration.
Soluble.
Precise shape to fit into specific membrane receptors.
Insulin has two polypeptide chains that fold into tertiary structure and are then joined by disulfide bonds.
114
What type of protein is catalase and what is it's structure and function?
Globular.
Catalyse is an enzyme which interacts with hydrogen peroxide to speed up it's breakdown into water and oxygen.
It is a quaternary protein with 4 haem prosthetic groups. There are iron II ions in the prosthetic groups which allow the interaction with hydrogen peroxide.
115
What type of protein is pepsin and what is it's structure and function?
Pepsin is an enzyme that digests protein in the stomach.
Single polypeptide chain of 327 amino acids.
Some of pepsin’s amino acids have acidic R-groups which makes it stable in acidic environments.
The tertiary structure is also held together by H bonds and 2 disulfide bridges.
