Biological Molecules Flashcards
(185 cards)
1
Q
What is covalent bonding?
A
Where atoms share a pair of electrons in their outer shells. As a result, the outer shell of both atoms is filled and a more stable compound, called a molecule is formed
2
Q
What is an ion?
A
Electrically charged particle, formed when atoms lose or gain electrons
3
Q
The loss of an electron leads to
A
The formation of a positive ion e.g. H+
4
Q
The gain of an electron leads to
A
The formation of a negative ion e.g. cl-
5
Q
More than one electron may be
A
Lost or received e.g. loss of 2 electrons from a calcium atom forms ca2+
6
Q
Ions may be made up of more than one type of
A
Atom
7
Q
Certain molecules known as monomers can be linked together to form
A
Long chains
8
Q
Long chains of monomer sub-units are called
A
Polymers
9
Q
What is the process by which polymers are formed?
A
Polymerisation
10
Q
In the formation of polymers by polymerisation in organisms, each time a new sub-unit is attached a molecule of what is formed?
A
Water
11
Q
What is a condensation reaction?
A
Chemical process in which 2 molecules combine to form a more complex one with the elimination of a water molecule
12
Q
What is a hydrolysis reaction?
A
The breaking down of large molecules into smaller ones by the addition of water molecules
13
Q
Metabolism definition
A
All the chemical processes that take place in living organisms are collectively called the metabolism
14
Q
The mole is the SI unit for measuring
A
The amount of substance and is abbreviated to mol
15
Q
Moles =
A
Mass/mr
16
Q
Lipids are a varied group of substances that share what characteristics?
A
- consist of carbon, hydrogen and oxygen
- the proportion of oxygen to carbon and hydrogen is smaller than in carbohydrates
- insoluble in water
- soluble in organic solvents such as alcohol and acetone
17
Q
The main groups of lipids are
A
Triglycerides and phospholipids
18
Q
What are the roles of lipids?
A
- phospholipids contribute to the flexibility of membranes and the transfer of lipid-soluble substances across them
- source of energy- when oxidises, lipids produce more than twice the energy as the same mass of carbohydrates and release valuable water
- waterproofing- lipids are insoluble in ways and therefore used as waterproofing- both plants and insects have waxy, lipid cuticles that conserve water
- insulation- fats are slow conductors of heat and when stored beneath the body surface, help to retain body heat. They also act as electrical insulators in the myelin sheath around nerve cells
- protection- fat is often stored around delicate organs, such as the kidneys.
19
Q
Fats are ____ at room temperature whereas oils are liquid
A
Solid
20
Q
Triglycerides are called so because they have
A
Three (tri) fatty acids combined with glycerol (glycerides)
21
Q
What bond does each each fatty acid form with glycerol in a condensation reaction?
A
Ester bond
22
Q
As the glycerol molecule in all triglycerides is the same, the difference in properties of different fats and oils come from variation in
A
The fatty acids
23
Q
There are over 70 different fatty acids and all have a
A
Carboxyl group (-COOH) group with a hydrocarbon chain attached
24
Q
Are fatty acids hydrophobic or hydrophilic?
A
Hydrophobic
25
If the hydrocarbon chain has no carbon-carbon double bonds, the fatty acid is described as
Saturated
26
If there is a single carbon to carbon double bond the fatty acid is described as
Mono-unsaturated
27
If the hydrocarbon chain has carbon-carbon double bonds, the fatty acid is described as
Saturated
28
Triglycerides are non-___ molecules
Polar
29
How is the structure of triglycerides related to their properties?
- triglycerides have a high ratio of energy-storing carbon-hydrogen bonds to carbon atoms and are therefore an excellent source of energy
- triglycerides have a low mass to energy ratio = good storage molecule because lots of energy can be stored in a small volume; this is especially beneficial for animals as it reduces the mass they have to carry as they move around
- being large, non-polar molecules, triglycerides are insoluble in water. As a result, their storage does affect osmosis in cells or the water potential of them
- as they have a high ratio of hydrogen to oxygen atoms, triglycerides release water when oxidised and therefore provide and important source of water, especially for organisms living in a dry desert
30
Phospholipids are compromised of glycerol combined with
2 fatty acids and a phosphate molecole
31
Whereas fatty acid molecules repel water (hydrophobic) phosphate molecules are
Hydrophilic
32
Phospholipids are made up of 2 parts:
- hydrophilic phosphate head (interacts with water)
| - hydrophobic tails (orient away from water) - long chain of hydrocarbons (but mixes readily with fat)
33
Phospholipids are ___ molecules
Polar
34
Explain what happens when phospholipids are placed in water
They position themselves so that they hydrophilic heads are as close to the water as possible and the hydrophobic tails are as far away from the water as possible
35
How is the structure of phospholipids related to their properties?
- phospholipids are polar molecules, having a hydrophilic phosphate head and a hydrophobic tail of 2 fatty acids- this means that in an aqueous environment, phospholipids form a bilayer within cell-surface membranes. As a result, they hydrophobic barrier is formed between the inside and the outside of a cell
- phospholipid structure allows them to form glycolipids by combining with carbohydrates within the cell-surface membrane- these glycolipids are important in cell recognition
36
What is the test for lipids?
Emulsion test
37
Describe the emulsion test
- take a completely dry, grease-free test tube
- to 2cm (cubed) of the sample being tested, add 5cm (cubed) of ethanol
- shake the the tube thoroughly to dissolve any lipid in the sample
- a cloudy-white colour indicates the presence of a lipid
- as a control, repeat the procedure using water instead of the sample; the final solution should remain clear
38
Why is a cloudy colour formed if a lipid is present in the emulsion test?
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 droplets to water droplets, making it appear cloudy
39
Organisms that move e.g. animals and parts of organisms that move e.g. some plant seeds use lipids rather than carbohydrates as an energy storage. Suggest a reason for this
Lipids provide more than twice as much energy as carbohydrates when oxidised. If fat is stored, the same amount of energy can be provided for less than half the mass; it is therefore a lighter storage product
40
Amino acids are the basic monomer units which can combine to make up a polymer called
A polypeptide
41
Polypeptides can be combined to form
Proteins
42
About 100 amino acids have been identified, __ of which naturally occur in proteins
20
43
The fact that the same 20 amino acids occur in all living organisms is indirect evidence for
Evolution
44
Describe the structure of an amino acid
- central carbon atom surrounded by 4 groups
- amino group (NH(2))
- carboxyl group (-COOH)- an acidic group which gives the amino acid the acid part of its name
- hydrogen atom
- R group- variable region
45
The R group of an amino acid can be a variety of
Different chemical groups
46
The 20 naturally occurring amino acids only vary in their
R group
47
2 amino acids are linked together through what bond?
Peptide bond- formed form a condensation reaction
48
How is the water made in a condensation reaction between two amino acids?
Combining -OH from carboxyl group of one amino acid with an -H from the amino group of another amino acid
49
Two amino acids are linked together by a peptide bond between
The carbon atom of one amino and nitrogen atom of another
50
Through a series of many condensation reactions, many amino acid monomers can be joined together in a process called
Polymerisation
51
The sequence of amino acids in a polypeptide chain forms
The primary structure of any protein
52
The sequence of amino acids in a polypeptide chain which forms the primary structure is determined by
DNA
53
The primary structure of a protein determines
The protein's shape and hence its function
54
A change in just a single amino acid in the primary sequence can lead to a change in
The shape of a protein, stopping it from carrying out its function I.e. a protein's shape is specific to its function and changing its shape will make it function differently
55
Ultimately, the secondary structure of a protein is
The shape which the polypeptide chain forms as a result of hydrogen bonding
56
How are the hydrogen bonds formed in the secondary structure?
- the linked amino acids that make up a polypeptide possess both -NH and -C=O groups on either side of every peptide bond
- the hydrogen of -NH group = overall positive charge
- O of the -C=O = overall negative charge
- these 2 groups readily form hydrogen bonds
57
What do the hydrogen bonds of the protein's secondary structure cause?
Hydrogen bonds cause the polypeptide chain to be twisted into a 3D shape such as the coil known as a-helix
58
What is the tertiary structure of a protein?
The a-helicases of the secondary protein structure can be twisted and folded even more to give a complex and often specific 3D structure of each protein
59
Tertiary structure is maintained by which bonds?
- disulfide bridges- fairly strong therefore not easily broken
- ionic bonds- weaker than disulfide bridges and easily broken by changes in PH
- hydrogen bonds- numerous but easily broken
60
What is the test used to test for proteins?
Buiret test detects peptide bonds
61
How is the buriet test carried out?
- place a sample of the solution to be tested in a test tube and add an equal volume of sodium hydroxide solution at room temperature
- add a few drops of very dilute copper sulfate solution and mix gently
- a purple colouration indicates the presence of peptide binds and hence a protein.
- if no protein is present, the solution remains blue
62
What are the 2 types of proteins?
Fibrous and globular
63
Fibrous proteins such as collagen have
Structural functions
64
Globular proteins such as enzymes and haemoglobin carry out
Metabolic functions
65
Fibrous proteins form long chains which run
Parallel to one another
66
Fibrous proteins form long chains which run parallel to one another, how are these chains linked?
By cross-bridges and so form very stable molecules
67
Describe collagen's molecular structure
- primary structure is an unbranched polypeptide chain
- in the secondary structure, the polypeptide chain is tightly wound
- lots of the amino acid glycine keeps close packing
- in the tertiary structure, the chain is twisted into a second helix
- its quaternary structure is made up of 3 such polypeptide chains wound together (in the same way as individual fibres are wound in a rope)
68
Collagen is found in
Tendons
| Tendons join muscles to bones. When a muscle contracts the bone is pulled in the direction of the contraction
69
The quaternary structure arises from
The combination of a number of different polypeptide chains and associated non-protein (prosthetic) groups into a large, complex molecule
70
It is the 3D shape of a protein that is important when it comes to how
It functions
71
Explain why the quaternary structure of collagen makes it a suitable molecule for a tendon?
The individual collage polypeptide chains in the fibres are held together by binds between amino acids of adjacent chains
72
Suggest how cross-linkages between the amino acids of polypeptide chains increases the strength and stability of the collagen fibre
The point where one collagen molecule ends and the next begins are spread throughout the fibre rather than all being in the same position along it
73
Carbohydrates are carbon molecules combined with
Water (hydrate)
74
Carbon-containing molecules are what kind of molecules?
Organic molecules
75
What is the basic monomer unit of carbohydrates?
Monosaccharides
76
Two monosaccharides combine to make
Disaccharides
77
Are monosaccharides soluble and sweet-tasting?
Yes
78
What is the general formula for monosaccharides?
(CH(2)O)n where n can be any number from 3-7
79
What are the 3 monosaccharides?
Glucose, galactose and fructose
80
Glucose has 2 isomers which are
alpha glucose and beta glucose (molecules with same molecular formula but with the atoms connected in different ways)
81
Draw alpha glucose and beta glucose
Refer to kerboodle/Google
82
All monosaccharides and some disaccharides such as maltose and lactose are
Reducing sugars
83
Reduction is a chemical reaction involving the gain of electrons or hydrogen. A reducing sugar is therefore
A sugar that can donate electrons to (or reduce) another chemical, in this case, Benedict's reagent
84
What is the name of the test used to test for reducing sugars?
Benedict's test
85
Describe the Benedict's test
1- add Benedict's reagent (blue) to a sample in liquid form and heat in a water bath that's been brought to boil for 5 minutes
2- if the test is positive, it will form a coloured precipitate (solid particles suspended in the solution). Blue--green--yellow--orange--brick red
3- the higher the concentrating of reducing sugar, the further the colour goes (can use to compare the amount of reducing sugar on different solutions), but a more accurate way to do this is to filter and weigh the precipitate.
86
If the result of the Benedict's test is negative there could still be a non-reducing sugar present. Explain the test you would use
1- first you have to break them down into monosaccharides- you do this by getting a new sample of the test solution adding dilute hydrochloric acid carefully heating it in a water bath that's been brought to boil
2- you can then neutralise it with sodium hydrogencarbonate then carry out the Benedict's test like you would on a reducing sugar
3- positive result= cloudy precipitate
- negative result= stay blue (contains no sugar reducing or non reducing)
87
Large molecules often contain carbon. Explain why this is
Carbon atoms readily link to one another to form a chain
88
Give examples of 3 disaccharides
- maltose = X2 (a) glucose
- sucrose= glucose and fructose
- lactose= glucose and galactose
89
Condensation reactions join
Monosaccharides together
90
What kind of bond forms between two monosaccharides
Glycosidic, creating a disaccharide
91
Polymers are formed by combining together many
Monosaccharide molecules
92
As polysaccharides are very big molecules they are
Insoluble
93
Monosaccharides and disaccharides are soluble and sweet tasting whereas polysaccharides are
Insoluble
94
Give some examples of polysaccharides
- starch (a mixture of 2 polysaccharides of (a) glucose: amylose and amylopectin
- glycogen (alpha glucose)
- cellulose (long unbranched chains of beta-glucose)
95
Starch is the main energy store material in
Plants
96
Cells get energy from glucose and plants store excess glucose as
Starch
97
When a plant needs more glucose for energy, it breaks down starch to release
Glucose
98
Starch is a mixture of 2 polysaccharides of (a) glucose: amylose and amylopectin. Describe amylose
Amylose is a long unbranched chain of (a) glucose- the angles of the glycosidic bonds give it a coiled structure that makes it compact so is ideal for storage as you can fit more into a small space
99
Describe amylopectin
Is a long branched chain of (a) glucose- its side branches allow the enzymes that break down the molecule to get at the glycosidic bonds easily so glucose can be released quickly
100
How does the structure of starch make it adapted to being an energy storage molecule?
- insoluble in water = doesn't affect water potential so water is not drawn in by osmosis which would make them swell= ideal for storage
- large and insoluble = doesn't diffuse out of cell
- compact
- when hydrolysed forms a-glucose which is both easily transported and readily used in respiration
101
Starch is never found in animal cells. Instead, a similar polysaccharide called ______ serves the same role
Glycogen
102
What is the test for starch called?
The iodine test
103
Describe how you would carry out the iodine test
If you do any experiment on starch and want to find out if any is left, you need the iodine test:
- add potassium iodine solution to the test sample
- if there is any starch present the sample changes from browny-orange to a dark blue-black colour
104
What is glycogen?
Polysaccharide of alpha glucose and is the major carbohydrate storage product of animals- found in animal and bacteria cells but never plant cells. It is very similar in structure to starch but has shorter chains and more highly branched (often referred to as 'animal starch') as its the major carbohydrate storage product of animals
105
How is glycogen stored?
In animals, stored as small granules mainly in the muscles and the liver
106
The mass of carbohydrate that is stored is relatively small as
Fat is the main storage molecule on animals
107
How does glycogen's structure suit it for storage?
- insoluble = doesn't draw water in by osmosis
- insoluble= doesn't diffuse out of the cell
- compact = lots can be stored in a small space
- more highly branched than starch = more ends can be acted on by enzymes = rapidly hydrolysed to form glucose monomers, respiration substrates --> important to animals which have a higher metabolic rather than plants as they're more active
108
What is cellulose?
A polysaccharide of beta glucose and is a major component of cell walls
109
Describe the structure of cellulose
Differs from starch and glycogen in one major respect: made of monomers of beta glucose; rather than forming a coiled chain like starch, cellulose has straight unbranched chains that run parallel to one another allowing hydrogen bonds between hydroxyl (-OH groups) to form cross-linkages between adjacent chains
110
Are the individual hydrogen bonds in cellulose strong?
Each hydrogen bond adds very little to the strength of the molecule, the sheer overall number of them makes a considerable contribution to the strengthening of cellulose, making it the valuable structure it is
111
Cellulose molecules are grouped together to form
Microfibrils which in turn, are arranged into parallel groups called fibres
112
Cellulose is a major component of cell walls and provides rigidity to the plant cell. Cellulose cell wall also prevents the cell bursting as water enters it by osmosis- explain how
Does this by exerting an inward pressure that stops any further influx of water. As a result, living plant cells are turgid and push against one another making non-woody parts of the plant semi-rigid; this is especially important in maintaining stems and leaves in a turgid state so they can provide max surface area for photosynthesis
113
What is an enzyme?
Globular protein that acts as a catalyst lowering the activation energy of biochemical reactions, without undergoing permanent changes itself
114
Sucrose + water ----> glucose + fructose
(Substrates) (Products)
For reactions like this to take place naturally, a number of conditions must be satisfied:
1- sucrose and water molecules must collide with sufficient energy to alter the arrangement of their atoms to form glucose and fructose
2- the free energy (energy of a system that is available) of the products must be less than that of the substrates (sucrose and water)
3- many reactions require an initial amount of energy to start. The minimum amount of energy needed to activate the reaction in this way is called the activation energy
115
Enzymes can be use repeatedly therefore
They're effective in small amounts
116
As enzymes lower activation energy
reactions can take place at a lower temperature than normal which enables some metabolic processes to occur rapidly at the human body temperature of 37 degrees Celsius (which is relatively low in terms of chemical reactions)- without enzymes, these reactions would take place too slowly to sustain life as we know it
117
Describe the structure of enzymes
- enzymes being globular proteins have a specific 3-D shape that is a result of their sequence of amino acids (primary structure)
- a specific region of the enzyme is functional= active site made up of a relatively small number of amino acids- the active site forms a small depression within the much larger enzyme molecule
- the molecule on which the enzyme acts is the substrate; this fits neatly into the active site (depression) forming an enzyme-substrate complex --> the substrate molecule is held within the active site by bonds that temporarily form between certain amino acids of the active site and groups on the substrate molecule
118
What does the induced fit model of enzyme action propose?
That the active site forms as the enzyme and substrate interact- the enzyme is flexible and can mould itself around the substrate. As the enzyme changes shape, the enzyme pulls a strain on the substrate molecule and this strain distorts a particular bond or bonds in the substrate and consequently lowers the activation energy needed to break the bond
NOTE: substrate does not ha e to be the same shape as the active site, just a complementary shape
119
Outline why changing one of the amino acids that make up the active site could prevent the enzyme from functioning
The changed amino acid may no longer bind to the substrate which will then not be positioned correctly, if at all, in the active site meaning preventing enzyme-substrate complexes from forming
120
Why are enzymes effective in small amounts?
They're not used up in reactions so can be used repeatedly
121
Why may changing certain amino acids not part of the active site prevent the enzyme from functioning
The change amino acid may be one that forms hydrogen bonds with another amino acid- if the new amino acid does not form hydrogen bonds the tertiary structure of the enzyme will change, including the active site, so the substrate may no longer fit and enzyme-substrate complexes cannot be formed
122
What does the lock and key model of enzyme action propose?
- earlier model of enzyme action proposes that enzymes work in the same way as a key operates a lock- the shape of the substrate (key) exactly fits the active site of the enzyme (lock), and so a substrate will only fit the active site of one particular enzyme- this supported by the observation that enzymes are specific in the reactions they catalyse.
123
What's a limitation of the lock and key model?
The model proposes that enzymes are a rigid structure, like a lock. However, scientists have observed that other molecules could bind to the sunken ay sites other than the active site (allosteric site); in doing so, they altered the activity of the enzyme. This suggested that the enzyme's shape was nei for altered by the binding molecule so the structure was not rigid, but flexible
= induced fit model proposed as it better fitted observations
124
Why is the induced fit model a better explanation?
More clearly matches current observations such as enzyme activity being changed when molecules bind to sites other than the active site (allosteric site). This suggests the enzyme molecule must change shape when other molecules bind to them = not a rigid structure
125
How is the structure of cellulose different from the structure of starch?
1- starch = alpha glucose
- cellulose = beta glucose
2- starch = branched
- cellulose= un-branched
3- starch= no microfibrils
- cellulose= microfibrils
4- starch= all glucose monomers same way up
- cellulose = monomers upside down
126
For an enzyme to work:
- must come into contact with substrate
| - have an active site that fits the substrate (complementary)
127
To measure the progress of enzyme-catalysed reactions, the two changes most frequently measured are:
1- the formation of the products of the reaction e.g. the volume of oxygen produced when the enzyme catalase acts on hydrogen peroxide
2- the disappearance of the substrate e.g. the reduction in the concentration of starch when it is acted upon by amylase
128
Explain the effect of temperature on enzyme action
-As the rise in temperature increases the kinetic energy of the molecules. In an enzyme-catalysed reaction this means that the enzyme and the substrate molecules come together much more often in a given time- overall, there are more effective collisions resulting in more enzyme-substrate complexes forming
129
Draw a graph of the effect of temperature on enzyme action
Look at kerboodle
130
Explain the shape of the graph that shows the effect of temperature on enzyme action
- molecules have more kinetic energy so enzymes and substrates in contact more often so more effective collisions in a given time = more enzyme-substrate complexes formed
- shown on a graph this gives a rising curve.
However, the temperature rise also causes the hydrogen bonds and other bonds in the enzyme to break that hold the enzyme's tertiary structure, resulting in the enzyme including its active site changing shape. The substrate fits less easily into the active site, slowing the rate of reaction (for human enzymes this may being at temperatures around 45 degrees Celsius)
- at some point, around 60 degrees Celsius, the enzyme is so disrupted that it is said to be denatured, a permanent change that once occurred, means the enzyme cannot function again. Shown on a graph, the rate of this reaction follows a falling curve
131
Different enzymes have different optimum temperatures some work fastest at around 10 degrees Celsius while others continue to work rapidly at around 80 degrees Celsius for example,
Enzymes used in biological washing powders and in the polymerase chain reaction
132
Many enzymes in the human body have an optimum temperature of around 40 degrees Celsius. Our body temperatures have however evolved to be 37 degrees Celsius and this may be due to:
- other proteins as well as enzymes may be denatured at higher temperatures
- at higher temperatures, any further rise in temperature e.g. during illness may denature enzymes
- although the higher body temperature would increase the metabolic rate slightly, the advantages are offset by additional energy (food) that would be needed to maintain the higher temperature
133
Different species of birds and mammals have different body temperatures. Many birds for example, have a normal body temperature at around 40 degrees Celsius because
they have a high metabolic rate for the high energy requirement for flight
134
The PH of a solution is a measure of
its hydrogen ion content
135
Every enzyme has an optimum PH- the PH of a solution is calculated using the formula:
PH= -log(10)[H+]
Below 10
A hydrogen ion concentration of 1X10(-9)
Above 10
therefore has a PH of 9
136
how does the ph affect how enzymes work?
- a change in PH alters the charges on the amino acids that make up the active site of the enzyme. As a result, the substrate can longer 'fit'/attach into the active site so an enzyme-substrate complex cannot be formed
- depending on how significant the change in PH is, it may cause the hydrogen bonds maintaining the enzyme's tertiary structure to be distorted/break- the active site therefore changes shape so the substrate is no longer complementary to the active site and enzyme-substrate complexes cannot be formed
137
PH fluctuations inside organisms are normally very small meaning that they're far more likely to reduce an enzyme's activity than
Denature it
138
What does the graph look like for the effect of PH on enzyme activity?
Narrow bell-shaped curve
139
Explain the effect of enzyme concentration on rate of reaction?
- As long as there is an excess of substrate, an increase in the amount of enzyme leads to a proportional increase in the rate of reaction (graph will initially show a proportionate increase) as there are currently more substrates than the enzymes can deal with, I.e. surplus of substrate
- if the enzyme concentration is increased, some of the excess substrate can now be acted upon and the rate of reaction will increase
- if however the substrate is limiting (there is not a sufficient supply to all the enzyme's active sites), then any increase in enzyme concentration will have no effect on the rate of reaction. The rate of reaction will therefore stabilise at a constant level (graph will level off) as all the existing substrate is being used up
140
What does the graph look like for the effect of enzyme concentration on rate of reaction?
Refer to kerboodle
141
Explain the effect of substrate concentration on the rate of reaction?
- if the conc of enzymes is fixed and the substrate conc slowly increased, the rate of reaction increases in proportion to the conc of substrate- this is because, at low substrate conc, the enzyme molecules have only a limited number of substrate molecules to collide with, and so the active sites of the enzymes are not working to their full capacity. As more substrate is added, the active sites gradually become filled, until all the active sites all the enzymes are working as fast as they can = rate of reaction as its maximum. After that, the addition of substrate will have no effect on the rate of reaction I.e. when there is excess of substrate the reaction levels off
142
What does the graph look like for the effect of substrate concentration on rate of reaction?
Same as graph got effect of enzyme concentration
143
Explain how enzyme's properties relate to their tertiary structure
1- enzymes are very specific- they usually catalyse only one reaction e.g. maltase only hydrolyses maltose
2- this is because only one complementary substrate will fit into the active site
3- the active site's shape is determined by the enzyme's tertiary structure (determined by its primary structure)
4- each different enzyme has a different tertiary structure and so a different shaped active site- if the substrate isn't a complementary fit,an enzyme-substrate complex cannot be formed and the reaction won't be catalysed
5- if the enzyme's tertiary structure is altered in any way, the shape of its active site will change, so the complementary substrate will no longer be able to carry out its function
6- the tertiary structure of the enzyme may be altered by changes in PH or temperature
7- the primary structure (amino acid sequence) of a protein is determined by a gene- if a mutation occurs in that gene, it could change the tertiary structure of the enzyme produced
144
What are enzyme inhibitors?
Substances that directly or indirectly interfere with the functioning of the active site of an enzyme and so reduce its activity
145
What are the 2 types of enzyme inhibitors?
- competitive inhibitors: bind to them active site of the enzyme
- non-competitive inhibitors: bind to the enzyme at a position other than its active site (allosteric site)
146
How does a competitive inhibitor work?
- competitive inhibitor molecules have a similar shape to that of the substrate molecule, allowing them to occupy the active site of the enzyme = they compete with substrate for available active sites
- how much of the enzyme is inhibited depends on the relative concentrations of the inhibitor and the substrate
- if there's a high concentration of the inhibitor, it'll take up nearly all the active sites and hardly any of the substrate will get to the enzyme
- but if there's a higher concentration of substrate then the substrate's chances of getting to an active site before the inhibitor will increase; so increasing the concentration of substrate will increase the rate of reaction up to a point
147
Competitive inhibitors are not permanently bound to the active site of the enzyme? True or false?
True
148
How does a non-competitive inhibitor work?
- non-competitive inhibitors attach themselves to the enzyme at a binding site that is not the active site (allosteric site)
- upon attaching to the enzyme, the inhibitor alters the shape of the enzyme and thus its active site in such a way complementary substrates can no longer occupy it and so the enzyme cannot function
- they don't compete with the substrate molecule to bind to the active site because they are a different shape
- as the substrate and inhibitor are not competing for the same site, an increase in substrate concentration does not decrease the effect of the inhibitor and won't make any difference to the reaction rate- enzyme activity will still be inhibited
149
What's an example of a competitive inhibitor?
Penicillin- inhibits the enzyme transpeptidase
150
What is ATP?
Adenosine triphosphate is a nucleotide derivative found in all living organisms which is produced in respiration and is important in the transfer of energy
151
Describe the structure of ATP
The ATP is a phosphorylated macromolecule and consists of 3 parts:
1: adenine- a nitrogen-containing organic base
2: ribose- a sugar molecule with a 5-carbon ring structure (pentose sugar)
3: phosphates- a chain of 3 phosphate groups
- it is known as a nucleotide derivative because it's a modified form of a nucleotide
152
Plant and animal cells release energy from glucose (respiration) but a cell can't
Get its energy directly from glucose. So, in respiration, the energy released from glucose is used to make ATP. Once ATP is made, it diffuses to the part of the cell that needs energy
153
How is energy stored in ATP and what is the equation for the hydrolysis of ATP?
The bonds between the phosphate groups are unstable and so have a low activation energy, which means they're easily broken; when they do break, they release a considerable amount of energy. Usually in living cells, it is only the terminal phosphate that is removed according to the equation:
ATP+ H(2)O ---> ADP + P(i) + E
(Adenine diphosphate)
(Inorganic phosphate)
(energy)
ATP hydrolysis can be 'coupled' to other energy-requiring reactions in the cell- this means the energy released can be used directly to make the couples reaction happen, rather than being lost as heat
The released inorganic phosphate can also be put to use- it can be added to another compound (phosphorylation), which often makes the compound more reactive
154
The conversion of ATP to ADP is
A reversible reaction and therefore energy can be used to add an inorganic phosphate to ADP to re-form ATP
155
The synthesis of ATP is catalysed by what enzyme?
ATPsynthase in a condensation reaction
156
The synthesis of ATP from ADP involves the addition of a phosphate molecule to ADP, it occurs in 3 ways:
1- photophosphorylation: in chlorophyll-containing plant cells during photosynthesis
2- oxidative phosphorylation: in plant and animal cells during respiration
3- substrate-level phosphorylation: in plant and animal cells where phosphate groups are transferred from donor molecules to ADP
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Why is ATP often referred to as the immediate energy source?
The same feature that makes ATP a good energy donor, the instability of its phosphate bonds, is also a reason why it is not a good long-term energy store- fats and carbohydrates such as glycogen serve this purpose much better. ATP is therefore the immediate energy source of a cell. As a result, cells do not store large quantities of ATP, but rather just maintain a few seconds' supply
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Why is it not a problem that cells do not store large quantities of ATP?
ATP is rapidly re-formed from ADP and P(i) and so a little goes a long way
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Why is ATP a better immediate energy source than glucose?
- each ATP molecule releases less energy than each glucose molecule and so the energy for reactions is released in smaller, more manageable amounts than glucose
- the hydrolysis of ATP to ADP is a single step reaction that releases immediate energy, whereas the breakdown of glucose is a long series of reactions and therefore the energy release takes longer
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ATP cannot be stored and so has to be continuously made within the
Mitochondria of cells that need it. Cells such as muscle fibres, and the epithelium of the small intestine which require energy for movement and active transport, possess many large mitochondria
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ATP is used in energy-requiring processes in cells including:
- metabolic processes: ATP provides the energy needed to build up macromolecules from their basic units- for example, making starch from glucose or polypeptides from amino acids
- movement: ATP provides the energy for muscle contraction. In muscle contraction, ATP provides the energy for the sliding filament theory
- active transport: ATP provides the energy to change the shape of carrier proteins in plasma membranes, allowing molecules or ions to be moved against a concentration gradient
- secretion: ATP is needed to form the lysosomes necessary for the secretion of cell products
- activation of molecules: the inorganic phosphate released during the hydrolysis of ATP can be used to phosphorylate other compounds in order to make them more reactive, thus lowering the activation energy in enzyme-catalysed reactions- for example, the addition of phosphate to glucose molecules at the start of glycolysis
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Explain the structure of water molecules
- a molecule of water is one atom of oxygen (O) joined to two atoms of hydrogen H(2) by shared electrons
- because the shared negative hydrogen electrons are pulled towards the oxygen atom, the other side of each hydrogen atom is left with a slight positive charge
- the unshared negative electrons
- this makes water a polar molecule- partial negative charge (δ-) i.e. delta negative on one side and partial positive charge (δ+) on the other side
- the slightly negatively-charged oxygen atoms attract the slightly positively-charged hydrogen atoms of other water molecules
- this attraction = hydrogen bonding
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Water's unusual properties are due to
Its dipolar nature and the subsequent hydrogen bonding this allows
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Although each hydrogen bond between the slightly negatively-charged oxygen atoms and the slightly positively-charged hydrogen atoms (1/10 of the strength of a covalent bond) together they form
Important forces that cause the water molecules to 'stick' together- giving water its unusual properties
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One water molecule consists of two hydrogen atoms _______ bonded to a oxygen atom
Covalently
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What is a hydrogen bond?
Chemical bond formed between the positive charge of a hydrogen atom and the negative charge on another atom of an adjacent molecule
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Explain why water is vital to living organisms
1- water makes up about 80% of a cell's contents
2- water is a metabolite in lots of important metabolic reactions including condensation and hydrolysis reactions
3- water is a solvent (some substances dissolve it)
- most metabolic reactions take place in solution e.g. in cytoplasm of eukaryotic and prokaryotic cells (so water is pretty essential)
4- water molecules are very cohesive I.e. they 'stick' together which helps water transport in plants as well as transport in other organisms
5- not easily compressed = provides support e.g. the hydrostatic skeleton of animals such as Earth worms
6- transparent = aquatic plants can photosynthesis and rays of light can penetrate the 'jelly-like' fluid that fills the eye and so reaches the retina
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What are the useful properties of water?
```
1- important metabolite
2- high latent heat of vaporisation
3- specific heat capacity of water
4- good solvent
5- strong cohesion between molecules
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Explain why water is an important metabolite
- many metabolic reactions involve a condensation or hydrolysis reaction
- water is used to break down more complex molecules by hydrolysis e.g. proteins to amino acids
- energy from ATP is released through a hydrolysis reaction
- a condensation reaction also releases a molecule of water as a new bond is formed e.g. peptide bond between two amino acids
- water also major raw material in photosynthesis
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Explain why water has a high latent heat of vaporisation and why it's useful for humans?
1- takes a lot of energy to break the hydrogen bonds between water molecules
2- so water has a high latent heat of vaporisation- a lot of energy is used up when water evaporated
3- evaporation of water such as sweat in mammals is therefore a very effective means of cooling because body heat is used to evaporate the water
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Explain specific heat capacity of water and how this means water can buffer changes in temperature; how is this important to organisms?
- the hydrogen bonds between water molecules can absorb a lot of energy = water has a high specific heat capacity- it takes a lot of energy to heat it up = boiling point of water higher than expected
- this is useful for living organisms as it means that water doesn't experience rapid temperature changes = makes water a good habitat because the temperature under water is likely to be more stable than on land- the water inside living organisms also remains at a fairly stable temperature = helps maintain constant internal body temperature
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Explain why water is a good solvent
- a lot of important substances in metabolic reactions are ionic (e.g. salt) meaning they're made up from one positively charged atom or molecule and one negatively charged atom or molecule (e.g. salt is made from a positive sodium ion and a negative chloride ion)
- as water is a polar molecule, the positive end of a water molecule will be attracted to the negative ion and the negative end of a water molecule will be attracted to the positive ion = ions will be totally surrounded by water molecules I.e. they'll dissolve
- so water's polarity makes it a good solvent
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What substances does water readily dissolve?
- gases e.g. carbon dioxide
- wastes e.g. ammonia and urea
- inorganic ions and small hydrophilic molecules e.g. amino acids, monosaccharides and ATP
- enzymes whose reactions take place in solution
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Explain why there is strong cohesion between water molecules and why this is important for living organism?
- cohesion is the attraction between molecules of the same type e.g. two water molecules- water molecules are cohesive because they tend to 'stick' together due to their dipolar nature
- strong cohesion helps water to flow making it great for transporting substances e.g. it's how water travels in columns up the xylem (tube-like transport cells) in plants
- strong cohesion also means that water has a high surface tension when it comes into contact with air; this is the reason why sweat forms droplets which evaporate from the skin to cool and organism down. It is also the reason that pond skaters and some other insects can 'walk' on the surface of a pond
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Draw a water molecule
Check camera roll
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An ion is an electrically charged particle, formed when atoms lose or gain electrons. What is an ion with a positive charge called?
Cation
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An ion is an electrically charged particle, formed when atoms lose or gain electrons. What is an ion with a negative charge called?
Anion
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With a few expeditions to the rule, an inorganic ion is an that doesn't contain
Carbon
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There are inorganic ions in solution, in the cytoplasm of cells, and in the body fluids of an organism. Each ion has a specific role depending on
Its properties; an ion's role depends on whether it is found in high or low concentrations
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What are some inorganic ions?
- iron irons (important part of haemoglobin)
- hydrogen ions (determine PH)
- sodium ions (help transport glucose and amino acids across membranes)
- phosphate ions are an essential component of ATP and DNA
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Explain why iron ions are an important part of haemoglobin?
- haemoglobin is a large globular protein that carries oxygen around the body in the (erythrocytes)
- it is made up of 4 different polypeptide chains each with an iron ion (Fe2+) in the centre
- it is the iron ion that actually binds to the oxygen in haemoglobin; so it's a pretty key component
- when oxygen is bound the Fe2+ ion temporarily becomes an Fe3+ ion, until oxygen is released
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How do hydrogen ions determine PH?
PH is calculated based on the concentration of hydrogen ions in the environment. The more hydrogen ions present, the lower the PH (and the more acidic the environment)
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How do sodium ions help transport glucose and amino acid across membranes?
- glucose and amino acids need partial help crossing cell membranes
- a molecule of glucose or an amino acid can be transported into a cell, across the cell-surface membrane, alongside sodium ions- co-transport
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Explain why phosphate ions are an essential component of ATP and DNA?
- when a phosphate ion is attached to another molecule, it's known as a phosphate group
- DNA, RNA and ATP all contain phosphate groups
- it's the bonds between the phosphate groups that store energy in ATP
- the phosphate groups in DNA and RNA allow nucleotides to join up to form polynucleotides
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What would happen without water's hydrogen bonding?
Water would be a gas (water vapour) at the temperatures commonly found on Earth and life as we know it would not exist
