Biological Molecules Flashcards
1
Q
Are carbon atoms readily able to form bonds with other carbon atoms
A
Yes
2
Q
What do all molecules of life contain
A
- carbon backbone (which other atoms can attach onto)
- Attached functional groups
3
Q
What are carbon containing molecules known as
A
Organic molecules
4
Q
What is a monomer
A
The individual molecules that make up chains/polymers
5
Q
Give 3 examples of monomers
A
- monosaccharides
- amino acids
- nucleotides
6
Q
Give 3 examples of polymers
A
- Proteins
- Carbohydrates
- Nucleic acids
7
Q
What is the basic monomer unit in carbohydrates
A
Saccharide (sugar)
8
Q
What is a single monomer in a carbohydrate called
A
Monosaccharide
9
Q
What is a pair of monosaccharides combined called
A
Disaccharide
—> larger numbers would be called polysaccharides
10
Q
Descibe what a monosaccharide is and what the general formula of a monosaccharide is
A
- sweet tasting soluble substance
- C(H20)n
11
Q
Give examples of monosaccharides
A
- glucose
- galactose
- fructose
12
Q
What is glucose and its general formula
A
- hexose (6-carbon)
- C6 H12 O6
13
Q
What is a reducing sugar
A
- a sugar that can donate electrons to (or reduce) another chemical
—> all monosaccharides and some disaccharides (e.g. maltose) are reducing sugars
14
Q
What is the test for a reducing sugar
A
The Benedict’s test
15
Q
How do you know if a reducing sugar is present
A
- reducing sugar is heated with Benedict’s reagent
- forms an insoluble red precipitate of copper (I) oxide
16
Q
How do you carry out the test for reducing sugars
A
- Add 2cm3 of the food sample to be be tested to a a test tube
- (if sample isn’t in liquid form, you have to grind it up in water)
- Add an equal volume of Benedict’s reagent
- Heat mixture in a gently boiling water bath for 5 mins
- if reducing sugar is present = solution goes orange-brown
17
Q
What is Benedict’s reagent
A
alkaline solution of copper (II) sulfate
18
Q
Give 3 examples of pairs of monosaccharides that form disaccharides
A
- glucose + glucose = maltose
- glucose + fructose = sucrose
- glucose + galactose = lactose
19
Q
What happens when monosaccharides join
A
- molecule of water is removed, this reaction is called condensation reaction
- Forming a bond called: Glycosidic bond
20
Q
What happens when water is added to a disaccharide under suitable conditions, and what is this called
A
- it breaks the glycosidic bond
- releasing the constituent monosaccharides
- this is called hydrolysis (addition of water that causes breakdown)
21
Q
What are non reducing sugars
A
- other disaccharides (like sucrose)
- They don’t change colour of Benedict’s reagent when they are heat with it
22
Q
How can you detect a non reducing sugar
A
- it needs to be hydrolysed into its monosaccharide components by hydrolysis
23
Q
Describe the process for detecting non reducing sugars
A
- if not liquid = ground up in water
- add 2cm3 of food sample to 2cm3 of Benedict’s in a test tube — then filter
- put in a gently boiling water bath for 5 mins
- If it doesn’t change colour (remains blue) then reducing sugar isn’t present
- add 2cm3 of food sample to 2cm3 of dilute hydrochloric acid in a test tube and place in gently boiling water bath for 5 mins
- dilute hydrochloric acid will hydrolyse any disaccharide present into its monosaccharide components
- slowly add sodium hydrogencarbonate solution to the test tube = neutralise acid (Benedict’s less effective in acidic cond.)
- test with pH paper to check solution is alkaline
- retest for solution with Benedict’s again
- if non reducing in original sample = orange brown (due to reducing sugars being produced by the hydrolysis of non-reducing sugar)
24
Q
How are polysaccharides formed
A
- these polymers are formed by combining many monosaccharide molecules together
- these monosaccharide molecules are joined by glycosidic bonds, formed through condensation reactions
25
What is one of the uses of polysaccharides
- they are very large molecules and insoluble
—> suitable for storage
- some polysaccharides (cellulose) are used to give structural support to plant cells
26
What happens when polysaccharides are hydrolysed
- break down into disaccharides or monosaccharides
27
Is starch a mono/di/polysaccharide
- polysaccharide (can be found as small granules or grains in plants, e.g. starch grains in chloroplasts)
28
How is starch formed
- joining 200-100 000 α-glucose molecules by glycosidic bonds in a series of condensation reactions
29
Is starch easy to detect? How can it be detected
- yes
- it can be detected by the change of colour of the iodine in potassium iodine solution
- yellow —> blue-black
30
What are the different steps for testing for starch
- carry out at room temp
- place 2cm3 of the sample being tested into a test tube (or 2 drops into a depression on a spotting tile)
- add 2 drops of iodine solution
- shake/stir
- if starch is present it will go blue-black
31
What is starch and where can it be found
- polysaccharide
- found in many parts of the plant: form of small grain
- large amounts occur in seeds and storage organs (such as potato tubers)
32
What is starch’s role in most diets
Major energy source
33
Describe the structure of starch
- 20% made from Amylose (alpha helix straight chain)
- 80% made from Amylopectin (branched)
34
What is the main role for starch
Energy storage
35
Why is starch especially suited for energy storage
- insoluble: doesn’t affect water potential, so water isn’t drawn into the cells by osmosis
- large molecule: won’t diffuse out our cells
- compact: lots can be stored in small spaces
36
Where is starch found in animal cells
- it’s not
- instead a similar polysaccharide called glycogen, serves the same role
37
Where is glycogen found in plant cells
- it’s not
- found in animals and bacteria instead
38
Describe glycogen’s structure
- very similar to starch
-but—> shorter chains and is more highly branched than amylopectin
—because—> animals have a higher metabolic rate
39
Why is glycogen sometimes called ‘animal starch’
- its the major carbohydrate storage product of animals
40
How is glycogen stored in animals
- stored as small granules mainly in muscles and the liver
41
Describe the mass of carbohydrate that is stored in glycogen and why
- small
—> because fat is the main storage molecule in animals
42
What about glycogen’s structure makes it suitable for storage
- insoluble: doesn’t draw water into cells by osmosis AND doesn’t diffuse out of cells
- compact: lots can be stored in a small space
- More highly branched than starch: each end can be acted on by enzymes simultaneously
—> therefore rapidly broken down to form glucose monomers, which are used in respiration
——> important to animals who have a higher metabolic rate than plants because they are more active.
43
How does cellulose differ from starch and glycogen
- made up of monomers of beta glucose (rather than alpha glucose)
- this small variation produces fundamental differences in the structure and function of this polysaccharide
44
Describe structure of cellulose
- straight unbranched chains
- Alternate glucose molecules are inverted
- the chains run parallel to each other, allowing hydrogen bonds to form cross-linkages between adjacent chains (microfibrils)
- sheer overall number of hydrogen bonds make it incredibly strong, hence why its a valuable structural material
- fully permeable: allows movement of water and numerous substances to and from membrane
45
What structure can cellulose molecules form when grouped together
- microfibrils
- which in turn are arranged in parallel groups called fibres
46
Why is cellulose important to plant cells
- Strengthen cell wall and provides rigidity to the plant cell
- which then prevents the cell from bursting as water enters it by osmosis
47
How does cellulose prevent cells from bursting from osmosis
- exerting an inward pressure pressure that stops any further influx of water
- therefore living plant cells are turgid and push against one another, making non-woody parts of the plant semi-rigid
- which is especially important in maintaining stems and leaves in a turgid state
- so that they can provide the max surface area for photosynthesis
48
Why is the structure of cellulose suited to its function of providing support and rigidity
- made up of beta glucose = form long straight unbranched chains
- these cellulose molecular chains run parallel to each other and are crossed linked by hydrogen bonds which add COLLECTIVE STRENGTH
- these molecules are grouped to form microfibrils which in turn group to form fibres: all of which provide more strength.
49
Polymerisation
The process of making a polymer
50
Condensation
Chemical process in which two molecules combine to form a more complex one with the elimination of a simple substance, usually water. Many biological polymers (e.g. polysaccharides, polypeptides) are formed by condensation.
51
Hydrolysis
The breaking down of large molecules into smaller ones by the addition of water molecules.
52
Carbohydrates
Compounds made from carbon, hydrogen and oxygen. Either monosaccharides, disaccharides and polysaccharides.
53
Monosaccharide
A single molecule of sugar e.g. glucose
54
Organic molecule
Molecules containing carbo, hydrogen and oxygen that can be found in living things; four types are carbohydrates, proteins (chain of amino acids), lipids, and nucleic acids
55
Disaccharide
Made up of two sugar units joined by a condensation reaction. Monosaccharides are joined by a glycosidic bond.
56
Polysaccharide
Made of many sugar units that are formed by a condensation reaction. Monosaccharides are joined by a glycosidic bonds. For example starch, glycogen, cellulose and chitin.
57
Glucose
C6H12O6 - a single sugar which is used to release energy (ATP) in respiration.
58
Reducing sugar
A sugar that serves as a reducing agent. All monosaccharides are reducing sugars along with some disaccharides e.g lactose and maltose
59
Glycosidic bond
Bond between each subunits of monosaccharide, bond is found in disaccharides and polysaccharides.
60
Non-reducing sugar
A sugar which cannot serve as a reducing agent. An example is sucrose. This is a disaccharide
61
Non-reducing sugar test
Following a negative reducing sugars test.
- Heat the solution with HCl to hydrolyse the non-reducing sugar into it's monosaccharides.
- Then perform the Benedict's test again.
- If you get a positive result after hydrolysis then a non-reducing sugar is present.
62
Starch
A polysaccharide found in plant cells made up of alpha-glucose - comprised of amylose (alpha-1,4 glyosidic bonds) and amylopectin (alpha-1,4- and alpha-1,6-glyosidic bonds)
63
Glycogen
A highly branched polysaccharide made up of alpha-glucose found in animal cells (alpha-1,4- and alpha-1,6-glyosidic bonds).
64
Cellulose
A polysaccharide made up of beta-glucose found in plant cells (beta-1,4-glycosidic bonds).
65
Alpha Glucose
An isomer of glucose that can bond together to form starch or glycogen. Hydroxyl group is found below carbon 1
66
Beta glucose
An isomer of glucose that can bond together to form cellulose. Hydroxyl group is found above carbon 1
67
Isomer
Alpha and Beta glucose. Resulting in formation of structurally different molecules. Such as Starch (alpha) and Cellulose (beta)
68
Ribose
the pentose monosaccharide present in RNA molecules.
69
Deoxyribose
Pentose monosaccharide present in DNA
70
Lactose
A disaccharide made up of glucose and galactose
71
Sucrose
a disaccharide made of glucose and fructose
72
Maltose
a disaccharide formed when two glucose monomers join together.
73
Amylose
- un branched, made up of alpha glucose molecules joined by alpha 1-4 glycosidic bonds
74
Amylopectin
- Highly branched, made up of alpha glucose molecules joined by a alpha 1-4 glycosidic bond with some alpha 1-6 branches
75
Describe structure of Amylopectin
- branched forms has many ends = each end can be acted on by enzymes simultaneously = glucose monomers are released very rapidly
- it can be hydrolysed to release alpha glucose at a faster rate
76
Describe the structure of Amylose
- forms a helix structure: alpha helix
- few branch ends and highly compact: so good for storage of glucose
—> however bad for release of glucose as hydrolysis occurs at ends, so its a slow release
77
Draw an alpha glucose linked with another
78
What are the characteristics that all lipids share
- contain carbon, hydrogen, oxygen
- proportion of oxygen, carbon, hydrogen is smaller than in carbohydrates
- insoluble in water
- soluble in organic solvents (such as alcohols and acetone)
79
What are the main groups of Lipids
- Triglycerides (fats and oils)
- Phospholipids
80
What are the functions of Lipids
- Phospholipids contribute to the flexibility of membranes
and
the transfer of lipid-soluble substances across them
- source of energy
- waterproofing
- insulation
- protection
81
Why does Lipids make a good source of energy
- when oxidised: lipids provide more than twice the energy carbohydrates do and release valuable water
82
Why are lipids good for waterproofing, and where is this used
- insoluble in water = waterproof
- in plants + insects: waxy lipid cuticles that conserve water
- Mammals: produce oily secretion from the sebaceous glands in the skin
83
Why are lipids good for insulation
- Fats are slow conductors of heat
- when stored beneath the body surface = retain body heat
- ALSO act as electrical insulators in the Myelin sheath around nerve cells
84
Why are Lipids good for protection
Fat is often stored around delicate organs, such as the kidney
85
At 10-20 degrees (room temp) what state are fats and oils at
- fat = solid
- oil = liquid
86
Why are Triglycerides called this
they have 3 (tri) fatty acids combined with glycerol (Glyceride)
87
What happens to each fatty acid and the glycerol during a condensation reaction
- each fatty acid forms an ester bond with glycerol
88
What is produced from hydrolysis of a triglyceride
Glycerol + 3 fatty acids
89
Glycerol + 3 fatty acids —>
triglyceride + 3 water
90
Where do the differences in all triglycerides come from
- variations in the fatty acids. There’s over 70 different fatty acids
- not glycerol molecule because its always the same one in all triglycerides
91
What do all Fatty acids have in common
They all have a carboxyl (—COOH) group with a hydrocarbon chain attached
92
Why would a fatty acid be called saturated
- If the carbon chain has no carbon-carbon double bonds
- described as saturated
- because all carbon atoms are linked with the maximum number of hydrogen atoms
- they are saturated with hydrogen atoms
93
When would you call a fatty acid mono-unsaturated
If a single double bond is present
94
When would you call a fatty acid polyunsaturated
If more than one double bond is present
95
How does the structure of triglycerides relate to their properties
- high ratio of energy-storing carbon-hydrogen bonds to carbon atoms = good energy store
- low mass to energy ratio = good storage molecules
—because—> can be stored in small volumes —good—> reduces mass that animals need to carry when they move around
- large, non-polar molecules = insoluble = storage doesn’t affect osmosis in cells or the water potential of them
- high ratio of hydrogen to oxygen atoms = release water when oxidised = source of water
—Good—> for organisms that live in deserts.
96
What makes phospholipids different to lipids
1 of the fatty acid molecules is replaced by a phosphate molecule
97
Are phospholipids hydrophobic
- fatty acid molecules repel water molecules (hydrophobic)
- phospholipids don’t have fatty acid
- therefore it attracts water (hydrophilic)
98
What 2 parts is a phospholipid made from
- a hydrophilic ‘head’: interacts with water (is attracted to it) but not with fat
- a hydrophobic ‘tail’: which orients itself away from water but mixes readily with fat
99
What happens when phospholipid molecules are placed in water
- they are polar molecules
- they position themselves so that the hydrophilic heads are as close to the water as possible
- and the hydrophobic tails are as far away as possible
100
How does the structure of Phospholipids relate to their properties
- polar molecules: in aqueous environment, phospholipids form a bilayer within cell-surface membranes. Resulting in a hydrophobic barrier forming between the inside and outside of a cell
- hydrophilic phosphate ‘heads’ of phospholipid molecules help to hold at the surface of the cell-surface membrane
- phospholipid structure = can form glycolipids by combining with carbohydrates within the cell-surface membrane. These glycolipids are important in cell recognition
101
How do you test for lipids + name
Emulsion test
- dry and grease-free test tube
- add 2cm3 of sample being tested to test tube. Add 5cm3 of ethanol
- shake the tube thoroughly to dissolve any lipid in sample
- Add 5cm3 of water and gently shake
- clear —> cloudy-white means presence of lipid
102
What’s the control for the test for lipids
- repeat procedures using water instead of sample
- the final solution should remain clear
103
Why does the solution go cloudy if lipid is present
- due to any lipid in the sample being finely dispersed in the water to form an emulsion
- light passing through this emulsion is refracted as it passes from oil droplet to water droplet
- making it appear cloudy
104
What are the basic monomer units which combine to make up a polymer called a polypeptide
Amino acids
105
What do you get if you combines polypeptides
Proteins
106
How many amino acids occur in all living organisms, what does this suggest?
- 20 (of the 100 that’ve been identified) occur naturally in protein
- the same 20 live in organisms
- this provides indirect evidence for evolution
107
What do all amino acids have in common
Every amino acid has a central carbon atom to which are attached 4 different chemical groups:
- amino group
- carboxyl group
- hydrogen group
- R (side) group
108
Describe the amino group attached to the central carbon atom in amino acids
- (—NH2)
- a basic group from which the amino part of the name amino acid is derived
109
Describe the carboxyl group attached to the central carbon atom in amino acids
- (—COOH)
- an acidic group which gives the amino acid the acid part of its name
110
Describe the hydrogen atom attached to the central carbon atom in amino acids
- (—H)
- its literally just a hydrogen atom
111
Describe the R (side) group attached to the central carbon atom in amino acids
- its a variety of different chemical groups
- Each amino acid has a different R group
- These 20 naturally occurring amino acids only differ in their R (side) group
112
Draw the general structure of an amino acid
113
How is a dipeptide formed
- Condensation reaction (water formed by combining —OH from carboxyl group and —H from amino group)
- the two amino acids become linked by a new peptide bond
- peptide bond is between the carbon atom of one amino acid and the nitrogen atom of the other
- forming a dipeptide
114
How is a peptide bond broken
Hydrolysis (addition of water)
115
How is polypeptide formed
- through a series of condensation reactions, many amino acid monomers are joined together in a process called polymerisation
- resulting in a chain of hundred of amino acids = polypeptide
116
What forms the structure of any protein
- Depending on the sequence of amino acids in a polypeptide chain
- it forms the primary structure of any protein
117
What determines the shape and hence function of a protein
- The combination of the 20 naturally occurring amino acids in the sequence
- the different sequences result in different structures
- there is a near limitless No. of possible combinations
118
What might happen if a change happens in just a single amino acid in the sequence
- Lead to a change in the shape of the protein
- and may stop carrying out its function
119
What is a protein made out of
- a simple protein may consist of a single polypeptide chain
- but others can be made up of multiple
- polypeptides are the primary structure of proteins
120
Describe the charge of the hydrogen in the (—NH) group in a polypeptide
Positive
121
Describe the charge of the oxygen in the (—C==O) group in a polypeptide
Negative
122
Where are the hydrogen bonds formed in a polypeptide
- positive charge of H in —NH group
- negative charge of O in —C==O group
- readily forms a weak bond, called hydrogen bonds
- this is the secondary structure of proteins
123
What does the hydrogen bonds in a polypeptide influence
- it can cause the long polypeptide chain to be twisted into a 3D shape such as a coil (alpha helix)
124
What is the tertiary structure of proteins
When alpha helices of the secondary protein structure are twisted and folded even more to give complex, and often specific, 3D structure of each protein
125
What are the 3 different bonds that help maintain the tertiary structure of proteins, what is dependent on where these bonds occur
where they occur depends on the primary structure of the protein
- disulphide bridges
- ionic bonds
- hydrogen bonds
126
Describe the disulphide bridges that maintain the tertiary structure of proteins
strong = not easily broken
127
Describe the ionic bonds that maintain the tertiary structure of proteins
- formed between any carboxyl and amino groups that aren’t involved in forming peptide bonds
- weaker than disulphide bonds and
- easily broken by changes in pH
128
Describe the hydrogen bonds that maintain the tertiary structure of proteins
- numerous
- however = easily broken
129
What allows each protein to be recognised by other molecules
- their structure = how they function
- this makes each protein distinctive
- allowing it to recognise and be recognised by other molecules
- therefore it can interact with then m in a very specific way
130
What is the primary structure of a protein
- the sequence of amino acids found in its polypeptide chains
- sequence = its properties + shape
131
How did we find out about the primary structure of proteins
following the elucidation of the amino acid sequence of insulin by Frederick Sanger in 1954
132
What is the secondary structure of a protein
- the shape which the polypeptide chain forms AS A RESULT OF hydrogen bonding
- this is most often a spiral (known as an alpha helix)
- although other configurations occur
133
What is the tertiary structure of a protein
- its due to the bending and twisting of the polypeptide helix into a compact 3D structure
- All 3 types of bond, contribute to the maintenance of the tertiary structure
134
What is the quaternary structure of a protein
it arises from the combination of a number of different polypeptide chains and associated non-protein (prosthetic) groups into a large, complex protein molecule, e.g. haemoglobin
135
What are prosthetic groups
- non-protein
- e.g. iron-containing haem group in haemoglobin
136
What test is used for testing for proteins
Biuret test —> detects the peptide bond
137
How is the Biuret test performed
- place sample of solution in test tube
- add equal volume of sodium hydroxide solution (at room temp)
- add a few drops of very dilute (0.05%) copper (II) sulfate solution
- mix gently
- blue —> purple = peptide bonds, hence presence of protein
138
What are the 2 basic types of proteins
- Fibrous proteins (e.g. collagen). = they have a structural function
- Globular proteins (e.g. enzymes and haemoglobin) = carry out metabolic functions
139
Describe the structure of Fibrous proteins, + examples
- Form long fibres
- Repetitive sequence of amino acids
- e.g. Myosin (in Muscles), Keratin (hair + nails) and collagen (in skin + ligaments/tendons)
140
Describe the structure of collagen in terms of primary, secondary, ….
- Primary structure is an un branched polypeptide chain
- in the secondary structure the polypeptide chain is very tightly wound
- it has lots of amino acid, glycine helps close packing
- in the tertiary structure the chain is twisted into a second helix
- the quaternary structure is made up of 3 such polypeptide chains wound together in the same way as individual fibres are wound together in a rope
141
Where is collagen found
- in Tendons
- Tendons join muscles to bones
- when a muscle contracts the bone is pulled in the direction of the contraction
142
Explain why the quaternary structure of collagen makes it a suitable molecule for a tendon
- it has 3 polypeptide chains wound together to form a strong, rope-like structure
- which has strength in the direction of pull of a tendon
143
How are the individual collagen peptide chains in the fibres held together
By the bonds between the amino acids of adjacent chains
144
Suggest how the cross-linkages between the amino acids of polypeptide chains increase the strength and stability of a collagen fibre
Prevents the individual polypeptide chains from sliding past one another and so they gain strength because they act as a single unit
145
Describe the ends of each collagen molecule
The points where one collagen molecule ends and the next begins are spread throughout the fibre rather than all being in the same position along it
146
The points where one collagen molecule ends and the next begins are spread throughout the fibre. Explain why this arrangement of collagen molecules is necessary for the efficient functioning of a tendon.
- The junctions between adjacent collagen molecules are points of weakness.
- If they all occurred at the same point in a fibre, this would be a major weak point at which the fibre might break
147
What are the properties of globular proteins
- Easily water soluble
- tertiary structure is critical to function
- Polypeptide chains folded into a spherical shape
148
What is the functions of globular proteins
- Catalytic, e.g. enzymes
- Regulatory, e.g. hormones (insulin)
- Transport, e.g. haemoglobin
- Protective, e.g. immunoglobulins (antibodies)
149
What are the properties of fibrous proteins
- water insoluble
- very tough physically: may be supple or stretchy
- Parallel polypeptide chains in long fibres or sheets
150
What are the functions of fibrous proteins
- Structural role in cells and organisms, e.g. collagen in connective tissues, skin and blood vessel walls
- contractile, e.g. myosin actin
151
What do many colleges molecules form
- They can form fibrils from the covalent cross links between the collagen molecules
- these fibrils can then group together to form larger fibres
152
What is allows tissue to resume their shape after stretching
- the fibrous proteins contain elastin = elastic properties
153
Give 3 examples of globular proteins
- insulin
- RuBisCo
- Haemoglobin
154
What is insulin
- globular protein
- a peptide hormone involved in the regulation of blood glucose
- composed of 2 peptide chains (A and B chain) which are linked together by 2 disulphide bonds
155
What is RuBisCo
- Globular protein
- large multi-unit enzyme found in green plants and catalyses the first step of carbon fixation in the Calvin cycle
- It consists of 8 large (L) and 8 small (S) subunits arranged as 4 dimers
- It’s the most abundant protein on Earth
156
How does the shape of a catalytic protein (enzyme) relate to its functional role
The spherical shape helps form the active site
157
What is Haemoglobin
- oxygen transporting protein found in vertebrate red blood cells
- 1 haemoglobin molecule consists of 4 polypeptide chains (2 identical alpha chains and 2 identical beta chains)
- each polypeptide subunit contains a non-protein prosthetic group, and iron-containing haem group, which binds oxygen
158
What is keratin
- fibrous protein
- found in hair, nails, horns, outer layer of skin, etc
- the polypeptide chains of keratin are arranged in parallel sheets held together by hydrogen bonding
159
Which protein is always in a solution, globular or fibrous
Globular - its soluble
160
Summarise the roles of Globular and fibrous proteins
- Globular = metabolic functions
- Fibrous = structural role
161
Describe the structure of Collagen
- made of 3 identical alpha helix polypeptide chains wound around each other to form a triple helix
- in each polypeptide chain, every 3rd amino acid is glycine (glycine is so small it allows 3 polypeptides to pack closely together)
- the 3 chains are held together by hydrogen bonds
- the collagen molecules cross link y through covalent bonds to form fibres, which give collagen its great strength
162
What is Denaturation of Proteins
When a protein unfolds and loses its 3D shape (denatures), and then also loses its function
163
What happens during denaturation of Proteins and what might cause it + what happens to active site as a result
- hydrogen binds are disrupted. Tertiary shape of protein changes
- caused by shifts in pH, temp, exposed to detergents or salts
- this can effect the charge of the active site
164
What happens when a protein is denatured due to temp change
- Heating protein = increase the kinetic energy in the molecules
- lead to: atoms vibrating = some of the bonds holding the tertiary shape together (which are quite weak, break. E.g. hydrogen bonds might break)
- lead to: tertiary structure unravelling
- lead to: change in tertiary structure (protein will be permanently denatured)
165
What is an enzyme
- globular protein that acts as catalyst
166
What do catalysts do
- alter the rate of a chemical reaction without undergoing permanent changes themselves
- They can be reused repeatedly, therefore effective in small amounts
- they lower activation energy
167
What conditions must be satisfied for a natural reaction to occur
- molecules must collide with sufficient energy to alter the arrangement of their atoms to form the products
- the free energy of the products must be less than that of the substrates
- activation energy (minimum amount of energy needed to activate the reaction)
168
How do enzymes work in relation to energy levels
- They lower the activation energy
- allows metabolic processes to occur rapidly
169
What is the active site
- specific functional region of an enzyme
- made up of relatively small number of amino acids
- forms a small depression within the enzyme molecule
170
What is a scientific model
How scientists explain their observations through representations of how they work
171
What does the induced fit model of enzyme action propose
- The active site forms as the enzyme and substrate interact
- The proximity of the substrate leads to a change in the enzyme that forms the active site
172
What happens to an enzyme when in the presence of a substrate (induced fit model of enzyme)
- Enzymes have a certain general shape, but it can alter in the presence of the substrate
- As it changes shape, the enzyme puts a strain on the substrate molecule
- this strain distorts a particular bond or bonds in the substrate and consequently lowers the activation energy needed to break the bond.
173
174
What is the Lock and key model of enzyme action
- enzymes work in the same way a key operates with a lock
- enzymes are specific
- substrate will only fit the active site of one particular enzyme
- therefore the shapes of the substrate (key) exactly fits the active site of the enzyme (lock)
175
Describe one limitation of the lock and key model of enzyme action
- the enzyme (lock) is considered to be a rigid structure
- however other molecules can bind to enzymes at site other than the active site
- in doing so, they alter the activity of the enzymes
- suggesting that: enzyme’s shape was altered by other molecule
- suggesting that the structure isn’t rigid, but flexible
176
Explain why the induced fit model is a better explanation of enzyme action than the lock and key model
- It more clearly matched current observations such as enzyme activity being changed when molecules bond at places other than the active site.
- This suggests that enzyme molecules change shape when other molecules bind to them
177
Activation energy
Energy required to bring about a reaction
178
Substrate
A substance that is acted on or used by another substance or process. Fits into the active site of an enzyme.
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Active site
A group of amino acids that makes up the region of an enzyme into which the substrate fits in order to catalyse a reaction.
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Enzyme-substrate complex
The intermediate formed when a substrate molecule interacts with the active site of an enzyme.
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Induced fit
A mechanism of interaction between an enzyme and a substrate. As the substrate fits into the active site the active site of the enzyme changes shape in order to allow an enzyme-substrate complex to be formed.
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pH
- A figure expressing the acidity or alkalinity of a solution on a logarithmic scale on which 7 is neutral, lower values are more acidic and higher values are more alkaline.
- formula: pH = -log10[H+].
- A hydrogen ion [H+] concentration of 1x10-9 = pH of 9
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Inhibitor
- A substance which directly/indirectly interferes with the functioning of the active site of an enzyme
- so reduces its activity
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Competitive inhibitor
A form of inhibitor which binds to the active site of the enzyme preventing the binding of substrate.
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Non-Competitive Inhibitor
A form of inhibitor which does not bind at the active site of the enzyme which prevents the binding of substrate.
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Which type of bond is principally responsible for holding the α-helix shape of a protein secondary structure?
Hydrogen
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Students were asked to highlight only the R groups of two ring-shaped amino acids.
Which pair of diagrams are correct for both amino acids?
Write the letter for the correct pair below
D
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How is bond X formed
Condensation
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Haemoglobin consists of two alpha chains and two beta chains. Approximately 5% of all humans have one amino acid in the beta chain that has been changed, affecting the structure and stability of haemoglobin.
Which of the levels of protein structure could be changed in the haemoglobin of these humans?
primary, secondary, tertiary and quaternary
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In unsaturated lipid molecules, where are double bonds located?
Within fatty acids only
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The first step in the test for a lipid is to add ethanol or propanone. What does this step do?
dissolve the lipid
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What is the characteristic of saturated lipids which distinguishes them from unsaturated lipids?
they have no carbon-carbon double bonds
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An amino acid has the structure shown in the picture. Which two of the groups, 1-4, combine to form a peptide link?
1 and 3
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Polysaccharides are synthesised in plants by which process
Condensation
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Which one of these molecules does not contain nitrogen?:
- Protein
- DNA
- nucleotides
- triglycerides
-triglycerides
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what do coenzymes do to enzyme activity
- Coenzymes assist enzymes in turning substrates into products
- e.g. Vitamins
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what are EXTRACELLULAR ENZYMES
- These are produced by cells but achieve their effects outside them, ie are secreted from the cells.
- They would be secreted directly onto the substrate or into a lumen through which the substrate passes eg mammalian alimentary canal.
- Some enzymes are released in an inactive form as a PRECURSOR
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what are INTRACELLULAR ENZYMES.
- Such enzymes are produced and act at the same site, ie within the cell itself.
- These molecules may be uniformly distributed within the cell, or may be compartmentalised (held within specific organelles such as lysosomes) or membrane bound.
- This allows the cell to specialise certain functions in certain areas.
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what are HYDROLASES
- Such enzymes can catalyse either hydrolysis or condensation reactions
- These reactions are the inverse of one another and the direction of action depends on the conditions (eg pH etc).
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what are the 3 examples of hydrolases
- CARBOHYDRASES: act on carbohydrates eg sucrase, maltase, amylase.
-ESTERASES: act on organic esters, eg lipases
- PROTEASES: these act on the peptide linkages ie -C.O-NH-
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describe the structure of a protease
- sub-divided into:
- ENDOPEPTIDASES which attack internal linkages within the polypeptide molecules splitting them into peptides
- EXOPEPTIDASES which attack the terminal peptide bonds forming amino acids (amino-peptidases work from the N-terminal end of the chain, carboxyl-peptidases work from the C-terminal end).
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what are OXIDOREDUCTASES (DEHYDROGENASES
- These catalyse reactions involving the oxidation of substrates by transferring hydrogen from the substrates to another molecule that is termed the hydrogen acceptor (or CO-ENZYME).
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what are some examples of dehydrogenases
- NAD (nicotinamide adenine dinucleotide)
- FAD (flavin adenine dinucleotide).
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what are PHOSPHORYLASES
- These catalyse reactions in which a polymer is hydrolysed back to monomer units with the addition of phosphate groups.
- This means that the monomers retain a high internal energy and are prevented from leaving the cell,
- eg starch may be hydrolysed into glucose-6-phosphate. These enzymes may also transfer inorganic phosphate form one substrate to another.
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what are TRANSFERASES
- these enzymes transfer groups from one substrate to another, in this case amine groups from one molecule to another which is important in amino acid synthesis.
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what are ISOMERASES
- These catalyse the change from one isomeric form to another
- eg phosphohexoisomerase converts glucose-6-phosphate to fructose-6-phosphate.
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what 2 conditions must be met for an enzyme to work
- come into physical contact with its substrate
- have an active site which fits the substrate
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what 2 changes do we measure for when we are investigating enzyme activity
- formation of products
- disappearance of substrate
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Describe why a graph measuring formation of oxygen due to the action of catalase on hydrogen peroxide would look like this
- At first: lots of substrate but no product
- therefore: easy for substrate molecules to be in contact with empty active sites on enzyme molecules
- Then: all active sites are filled = substrate is rapidly broken down = increase in amount of product
- as reaction proceeds = less substrate, more product
- therefore: difficult for substrate molecules to come in contact with enzyme molecules (because fewer substrate molecules + product molecules might 'get in the way' of the active site)
- therefore: takes longer to be broken down and form product (why graph 'tails off')
- continues till so little substrate = its conc. can't be measured
- therefore: graph flattens out (substrate is used up = no new products can be produced)
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how do we measure rate of change on a curve
draw a tangnent
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are the active site and substrate the same shape
NO!!!!, they're complementary
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what is the effect of temp on enzyme action
- more temp = higher kinetic energy
- move around more rapidly + collide more often
- therefore substrate and enzyme molecule come together more often in a given time
- therefore there's more effective collisions = increased rate of reaction
- lower temps = slower rate of reaction
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what is the effect on enzyme action if temp is too high
- too much vibration, causing hydrogen + other weak bonds in enzyme molecule to break
- this changes the enzyme's active site
- at first: substrate fits into active site less easy (slowing rate of reaction)
- eventually enzyme is so disrupted that it stops working altogether (denaturation)
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Many enzymes in the human body have an optimum temp of about 40'C. Our body temps have evolved to be 37'C. Why might this be the case?
- although higher body temp = increased metabolic rate
- the advs are offset by the additional energy (food) that would be required to maintain this higher temp
- other proteins, apart from enzymes, may be denatured at higher temps
- when our body temp rises naturally (illness) it might rise even further = denaturing enzymes
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How does pH affect how an enzyme works
- pH change = alters the charges on the amino acids that make up the active site of the enzyme
- depending on significance of pH change, causes bonds maintaining the enzyme’s tertiary structure to break = active site changes shape
- Therefore: substrate can’t attach to active site = enzyme substrate complex can’t be formed
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Describe what the arrangement of the active site is determined by and how a change in pH might affect this
- active site is determined by hydrogen and ionic bonds between —NH2 and —COOH groups of the polypeptides that make up the enzyme
- the change in the H+ ions affect this bonding, causing the active site to change shape.
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Describe pH fluctuations in human body
- pH fluctuations are usually small
- this means they are far more likely to reduce an enzyme’s activity (not denature it)
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What happens if you increase the concentration of enzymes in a reaction
- as long as there’s excess of substrate = increase in rate of reaction
- However, when there’s no more excess of substrate = increasing numbers of enzyme concentration will have no effect on rate of reaction
- because the substrate is limiting = graph will level off
- because available substrate is decreasing = decreasing amount of reactions happening
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Explain what is happening at each of the points, demonstrated in the 3 graphs
Graph 1: low enzyme conc.
- There are too few enzyme molecules to allow all substrate molecules to find an active site at one time
- Rate of reaction = half the maximum possible for No. of substrate molecules available
Graph 2: intermediate enzyme conc.
- 2x as many enzyme molecules = all substrate molecules can occupy an active site at the same time
- rate of reaction has doubled to its maximum because all actives sites are filled
Graph 3: high enzyme conc.
- addition of further enzyme molecules = no effect
- because there’s already enough active sites to accommodate available substrate molecules
- therefore no increase in rate of reaction
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Explain what is happening at each of the points, demonstrated in the 3 graphs
Graph 1: low substrate conc.
- too few substrate molecules to occupy all the available active sites
- rate of reaction = half the maximum possible for the No. of enzyme molecules available
Graph 2: intermediate substrate conc.
- 2x as many substrate molecules available = all active sites occupied at one time
- rate of reaction doubles to maximum because all active sites occupied at one time
Graph 3: high substrate conc.
- addition of further substrate molecules = no effect because all active sites are already occupied at one time
- therefore no more increase in rate of reaction
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How does a competitive inhibitor’s structure relate to its function
- competitive inhibitors have a molecular shape similar to that of the substrate
- allowing them to occupy the active site of an enzyme
- therefore they compete with the substrate for the available active sites
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What happens to rate of reaction when conc. of competitive inhibitors are increased
- enzyme activity decreases because competitive inhibitors get in the way of the substrate molecules
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Are competitive inhibitors permanently bound to the active site
No, when it leaves another molecule can take its place
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Give an example of competitive inhibition
- occurs with important respiratory enzyme that acts on succinate
- competitive inhibitors have similar shape to succinate = can easily combine with the enzyme and blocks succinate from combining with the enzyme’s active site
- another is the inhibition of the enzyme transpeptidase by penicillin
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How do non-competitive inhibitors work
- bind to other part of enzyme (that isn’t active site)
- upon attaching to enzyme, alters shape of enzyme, thus the shape of the active site
- therefore substrate molecules can’t bind = enzyme can’t function
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How does increasing substrate molecules increase/decrease the effect of the inhibitor
- doesn’t because they don’t compete with substrate molecules for the active site
- increasing substrate molecules doesn’t decrease the effect of the inhibitor
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What is a metabolic pathway
A series of reactions in which each step is catalysed by an enzyme
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How many metabolic pathways are there in a single cell
Hundreds
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Describe the metabolic pathways that you’d find in a single cell
- not all haphazard, but highly structured
- enzymes that control these pathways are often attached to the membrane of a cell organelle in a very precise sequence
- inside each organelle = optimum conditions for enzyme functions
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in order to keep steady concentration of a particular chemical in a cell, what is done?
- The same chemical often acts as an inhibitor of an enzyme at the start of the reaction
- this is one of the ways how optimum conditions for enzyme activity is kept within a cell
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What happens if for some reason, the concentration of end product increases above normal
- There will be greater inhibition of enzyme A
- as a result, less end product will be produced and its concentration will return to normal
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What happens if the concentration of the end product falls below normal
- there will be less of it to inhibit enzyme A
- consequently, more end product will be produced and, again, its concentration will return to normal
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What is end-product inhibition
- a form of negative feedback for regulation of metabolic pathways, where the final product in a series of reactions causes an inhibitory effect in an earlier step in the sequence.
- this type of inhibition is usually non-competitive
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what does the value 'Q10 (the ten is little) = 2' tell us
- the rate of reaction doubles when the temperature of the reaction is increased by 10°C.
- most enzyme mediated reactions have this value
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what does the value 'Q10 = 3' tell us
indicates the reaction triples with a 10°C increase
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where are enzymes made in the cell, and where can they work
- made inside cells
- but can function either: intracellular or extracellular
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what does it mean if an enzyme functions intracellular
- they function inside cells
- e.g. lysins (respiratory enzymes)
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what does it mean if an enzyme functions extracellular
- functions outside of cell
- e.g. digestive enzymes in the alimentary canal
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what is pH
- A measure of hydrogen ion concentration
- higher the conc. = the lower the pH
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which enzyme has an optimum pH of 2
pepsin (protease) found in stomach
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what happens if pH is too low
- Small changes in pH outside the optimum can cause small reversible changes in the enzyme structure and results in inactivation.
- The R groups on the amino acids are affected by free hydrogen ions and hydroxyl ions.
- In the formation of the ESC the charges on the active site must match those on the substrate. (If the active site has for example too many Hydrogen ions the active site and the substrate could repel each other) .
- The time taken for the reaction to occur will be longer than the at the optimum. There will be fewer successful collisions and therefore fewer ESC formed.
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describe what happens for enzymes when pH is optimum
- The charges of the active site will be complementary to the charges on the substrate.
- The number of successful collisions between enzyme and substrate will be at its greatest and so there will be more E-S complexes formed.
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describe what happens to enzymes when pH is too high
- Extremes in pH can denature an enzyme.
- Hydrogen ions can interfere with Hydrogen bonds and ionic bonds causing them to break.
- The tertiary 3D globular shape of the enzyme will then be altered which will alter the shape of the active site.
- Fewer E-S complexes will form and the time taken for the reaction to occur will increase.
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what is the turn over number
The number of substrate molecules that one molecule of enzyme can turn into products in one minute is called the turnover number
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what is a catabolic reaction
- Breakdown of larger molecules to smaller ones
- e.g. digestion of food
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what is an anabolic reaction
- Larger molecules are made from smaller ones
- e.g. building glycogen
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what is the definition of rate
how fast something occurs in a particular time
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what are the 5 factors that affect enzyme activity
- Temp
- pH
- conc. of enzymes
- conc. of substrate
- presence of inhibitors
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on a rate of reaction graph, what does Vmax stand for
maximum rate of reaction
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on a rate of reaction graph, what does Km stand for
the concentration of substrate which permits the enzyme to achieve half Vmax.
250
describe an enzyme with a high Km
- has a low affinity for its substrate,
- and so requires a greater concentration of substrate to achieve Vmax
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