Biological Molecules Flashcards
(100 cards)
1
Q
Why are biological molecules important for scientists ?
A
All life on Earth shares a common chemistry, which suggests all life has a common ancestor
2
Q
What does sharing a common chemistry mean ?
A
The cells of all living organisms contain only a few groups of carbon-based compounds (monomers) that act similarly
3
Q
What is a monomer ?
A
Smaller units from which larger molecules are made
4
Q
What is a polymer ?
A
Molecules made from a large number of monomers joined together
5
Q
What is the monomer of DNA/RNA and why is it important ?
A
Nucleotides. They are important as they contain the genetic code for protein production
6
Q
What is the monomer of carbohydrates and why is it important?
A
Monosaccharides. They are important as they are respiratory substrates and help form cell wall and plasma membrane structures
7
Q
What is the monomer of proteins and why are they important ?
A
Amino acids. They are important because they form cell structures, enzymes, chemical messengers and blood components
8
Q
What are the monomers of lipids and why are these important ?
A
Fatty acids, glycerol, (phosphate). They are important because they form the bilayer of plasma membrane, some hormones and respiratory substrates
9
Q
What is a condensation reaction ?
A
The joining of two molecules together with the formation of a chemical bond, involving the elimination of a molecule of water
10
Q
What is a hydrolysis reaction ?
A
Breaking of a chemical bond between two molecules involving the use of water
11
Q
Name some examples of monosaccharides
A
Glucose, fructose, galactose
12
Q
What does a condensation reaction between two monosaccharides form ?
A
A glycosidic bond
A disaccharide
13
Q
Maltose monomers ?
A
Glucose + glucose
14
Q
Sucrose monomers ?
A
Glucose + fructose
15
Q
Lactose monomers ?
A
Glucose + galactose
16
Q
What is an isomer ?
A
Molecules with the same molecular formula but atoms connected in a different way
17
Q
What are the two glucose isomers ?
A
Alpha glucose (hydrogen atoms at the top) and beta glucose (hydrogen atom and hydroxide atoms at the top)
18
Q
What is a reducing sugar ?
A
Sugars that can donate electrons causing the carbonyl group to become oxidised
19
Q
What is the test for reducing sugars ?
A
- Crush the sample and add into a test tube
- Add 5cm3 of Benedict’s reagent to test tube
- Heat up test tube using a water bath for five minutes
- Colour change from blue to green/yellow/orange/brick red if positive test as precipitate formed based on sugar concentration
20
Q
How can the test for reducing sugars be made more accurate ?
A
- Filter the precipitate and weight it
- Remove the precipitate and use a colorimeter to measure the Benedict reagent’s absorbance
21
Q
What is the test for non-reducing sugars ?
A
- Crush sample and place in a test tube
- Add 5cm3 of dilute hydrochloric acid and heat in a water bath
- Neutralise solution using sodium hydrogen carbonate
- Carry out the Benedict reagents test
22
Q
What is a polysaccharide ?
A
Polymers formed by many monosaccharides joined by glycosidic bonds in a condensation reaction
23
Q
Name some examples of polysaccharides ?
A
Glycogen, amylose, amylopectin (alpha glucose), cellulose (beta glucose)
24
Q
What is the function of glycogen ?
A
Storage for excess glucose in animal and fungal cells that can be used for respiration, releasing ATP
25
Where is glycogen usually found in animal cells and why ?
Liver and muscle cells due to the high cellular respiration rate
26
Describe the structure of glycogen?
Long branched chains of alpha glucose with glycosidic bonds present between 1,4 and 1,6. It has many side branches
27
What are the benefits of the structure of glycogen?
Branched shape makes it more compact to store more glucose molecules for its size
More free ends for monomers to be added/removed for more rapid hydrolysis and condensation via enzymes (essential for rapid ATP release when there is high cellular respiration demand)
Insoluble so doesn't affect water potential and cause cell to burst (due to large size)
28
What is the function of starch ?
Storage for excess glucose in plant cells in the form of small granules in plastids, and storage molecules in plants such as bulbs and tubers
29
Describe the structure of starch ?
It is made up of two polymers : amylose (10-30% starch) and amylopectin (70-90% starch)
30
Describe the structure of amylose ?
Unbranched helix shape of alpha glucose with 1,4 glycosidic bonds. Hydrogen bonds cause the helix shape
31
What is the benefit of amylose’s structure ?
It makes starch very compact due to its helical shape so more of the glucose monomer can be stored in a smaller space for later use.
It is also insoluble which means that it does not affect water potential, which would cause the cell to burst (due to large size)
32
What is the structure of amylopectin ?
Long, branched structure of alpha glucose with glycosidic bonds present between 1,4 and 1,6
33
What is the benefit of the structure of amylopectin ?
Similarly to glycogen, having many free ends means more rapid hydrolysis and condensation enzyme reactions for cellular respiration and added storage
It is also compact and insoluble (as it is so large)
34
What is the function of cellulose ?
It is the structural support in plant cell walls to provide the plant with strength. It also allows the exchange the of substances in and out of the cell
35
What is the structure of cellulose ?
Long, unbranched chains of beta glucose with 1,4 glycosidic bonds present. These are straight chains due to the inversion of every adjacent B-glucose monomer
36
What is the benefit of the structure of cellulose ?
Inversion of beta glucose and straight unbranched chains means many hydrogen bonds form between adjacent parallel microfibril chains. A large number of hydrogen bonds provides high tensile strength and rigidity for the fibrils so the cell can withstand turgor pressure
It is also freely permeable for water and other substance to enter and exit the cell
37
What is the test for starch ?
1. Add a few drops of iodine dissolved in potassium iodide solution to sample
2. A positive test will show a colour change from browny-orange to dark blue/black
38
What are the two groups of lipids ?
Triglycerides and phospholipids
39
Describe the structure of triglycerides?
Contain one glycerol bonded to three fatty acids in 3 condensation reactions, forming 3 ester bond and 3 molecules of water. Triglycerides vary in property due to fatty acids R groups. They are non-polar as electrons are shared equally
40
Describe the structure of phospholipids ?
One glycerol molecule, two fatty acids and a phosphate containing group joined together in 3 condensation reactions, releasing three molecules of water. They are polar due to the phosphate-containing group
41
Describe the qualities of a fatty acid ?
Non-polar
Hydrophobic (not soluble in water)
Can be saturated or unsaturated
42
What are the differences between a molecule that is saturated and a molecule that is unsaturated ?
A saturated molecule has no double bond between any carbon atoms (all single bonds),
an unsaturated molecule has a carbon-carbon double bond (so some carbon atoms are not fully saturated with hydrogen)
Saturated molecules are solid at room temperature whereas unsaturated molecules are usually liquid because they cannot pack closely together
43
What is the main function of triglycerides and how does it’s structure benefit ?
Energy storage molecules. The long hydrocarbon chain of glycerol has many C-H bonds and little oxygen so it is highly reduced, causing oxidation to break bonds and release ATP during respiration (which also provides a source of water) . They have a higher energy per gram than carbohydrates due to their lower mass to energy ratio
44
What are the other functions of lipids and how does their structure help ?
They are hydrophobic (non-polar) so do not cause osmotic water uptake in cells. They are used as waterproofing for this reason.
Fats are slow conductors of heat so when stored beneath the body surface, they help retain heath (insulation)
They also act as protection
45
What is the main function of phospholipids and how does their structure benefit ?
They form the bilayer of cell membranes. As they have hydrophobic tails and hydrophobic heads, they form a hydrophobic core which acts as a barrier to water soluble molecules.
46
How does the structure of phospholipids affect the plasma membrane
The phosphate heads form H-bonds with water to allow compartmentalisation
Weak hydrophobic interactions hold proteins in place but they can still move around
More saturated fats = less fluidity
47
How does a reducing sugar cause a colour change in Benedict's solution ?
The Benedict's solution contains Cu2+ ions which are blue. When the reducing sugar donates an electron, this causes the Cu2+ ion to be reduced and form a Cu+ ion, which is red.
48
How does a colorimeter work with the reducing sugar test ?
You would filter out the precipitate and then add the solution in cuvettes inside of the colorimeter. Then, you pass red light through the solution as that is the colour that is most absorbed by blue light as they are on opposite ends of the spectrum.
49
What is the relationship between light transmitted and the concentration of a reducing sugar when using a colorimeter ?
The greater the light transmitted, the greater the concentration of the reducing sugar as there are less Cu2+ ions in solution, so it is a paler blue and absorbs less red light
50
What does a condensation reaction between two amino acids form ?
A molecule of water
A dipeptide
A peptide bond between the C of the carboxyl group and the N of the adjacent amine group
51
What does a condensation reaction between more than two amino acids form ?
A molecule of water
A polypeptide
Peptide bond between the C of the carboxyl group and the N of the adjacent amine group
52
What is a protein made up of ?
One or more polypeptides
53
Describe the structure of an amino acid ?
It contains an amine group on the left (NH2), a carboxyl group to the right (COOH), and an R group on the top.
The carboxyl group is acidic whereas the nitrogen-containing amine group acts as a base (can accept H+ ion from acid)
54
What is an R group and why are these important for amino acids ?
They are also known as the variable group as they determine the identity of an animo acid out of a bank of twenty naturally occurring amino acids. All of these groups other than glycine are carbon-containing.
55
Describe the primary structure of a protein ?
Sequence of amino acids in the polypeptide chain (peptide bonds only)
56
Describe the secondary structure of a protein ?
Hydrogen bonds form between strongly polar R groups in the amino acids, causing the peptide chain to either
1. Coil up and form alpha-helix shape (forms between every fourth peptide bond)
2. Fold to form beta pleated sheet (formed between parallel peptide bonds)
57
Describe the tertiary structure of a protein ?
1. More hydrogen bonds form between strongly polar R groups
2. Ionic bonds between positive amine group and negatively- charged R groups (between oppositely charged parts on the molecule)
3. Disulphide bridges also form between cysteine molecules when their sulphur atoms bond. They help with stabilisation.
58
Describe the quaternary structure of a protein ?
Two or more polypeptide chains working together as a functional macromolecule. Each polypeptide is referred to as a subunit.
59
Outline the test for proteins, and describe the qualitative results for a positive test ?
1. Crush food sample and place in a test tube.
2.Make sample alkaline by adding a few drops of sodium hydroxide
3. Add 5cm3 of copper (II) sulphate solution
4. In a positive test, there will be a colour change from blue to lilac
60
What are the four main biological roles of proteins ?
1.Structural proteins (e.g collagen, keratin, silk)
2. Transport proteins(e.g. carrier and channel proteins)
3. enzymes (e.g. protease, amylase, lipase)
4. antibodies
61
Describe the structure of structural proteins ?
Long polypeptide chains parallel to each other with cross links
62
Describe the structure of enzymes ?
Spherical shape due to tight folding of polypeptide chain
63
Describe the structure of transport proteins ?
Made up of hydrophobic and hydrophilic interactions between amino acids that cause them to fold up into channels
64
Describe the structure of antibodies ?
Made up of two light (short) and two heavy (long) polypeptide chains. These contain variable regions within the chains that differ greatly
65
Describe the structure of globular proteins ?
Spherical shape caused by tightly folded peptide chains (can cause specific shapes). They have the hydrophobic R groups oriented towards the centre and the hydrophilic R groups pointing outwards to make them soluble in water.
66
Describe the structure of fibrous proteins ?
Parallel peptide chains held together by strong cross links due to strong hydrogen bonds (repetitive amino acids). This forms long, rope-like structures, which makes it strong and have a high tensile strength. It has a large number of hydrophobic R-groups, making it insoluble in water.
67
What is a microfibril ?
Parallel cellulose chains grouped together
68
What is a macrofibril?
Many parallel microfibrils grouped together
69
What is a fibril ?
Many parallel macrofibrils grouped together
70
What are the two types of unsaturated a molecule can be ?
Mono-unsaturated (only one carbon-carbon double bond)
Polyunsaturated (more than one carbon-carbon double bond)
71
What is an enzyme ?
A protein that speeds up the rate of a chemical reaction by acting as a biological catalysts (for both cellular, respiration, and whole organism reactions, digestion)
72
How does an enzyme work ?
Each enzyme lowers the activation energy of the reaction it catalyses.
73
What is the activation energy ?
The minimum energy that particles must collide with for a reaction to be successful
74
Does an enzyme affect the enthalpy change of a reaction ?
No, it only lowers activation energy. The energy of the products and the reactants remain the same
75
What are the two types of reactions an enzyme catalyses ?
Catabolic reactions (hydrolysis of a larger molecule into smaller products)
Anabolic reactions (condensation reactions of smaller monomers into larger product)
76
How does an enzyme lower the activation energy of a catabolic reaction ?
The enzyme molds around the substrate so that it strains the bonds in the substrate. This allows the substrate to be broken more easily into products
77
How does an enzyme lower the activation energy of an anabolic reaction ?
The enzyme molds around the substrates which reduces any repulsion between the molecules. This makes it easier for the substrates to join together and form products.
78
What does the lock and key theory state ?
An enzyme has an active site that is complimentary to the substrate. The substrate binds to the active site, and the enzyme catalyses the reaction. The products are released and the enzyme remains unchanged
79
What does the induced fit model suggest about enzyme activity ?
The induced fit model suggests that the enzyme has an active site that is similar to the substrate. As the substrate approaches the enzyme, the active site's tertiary structure changes as temporary bonds form. This causes the active to become complementary and mold around the substrate, forming an enzyme-substrate complex. The enzyme releases the products and returns to its resting shape.
80
Why are enzymes specific ?
Enzymes are specific because their primary structure (sequence of amino acids) determines where bonds form in the secondary and tertiary structures. This determines the folding of the protein and the shape of the enzyme's active site. This makes the active site of an enzyme complimentary to one type of substrate.
81
What happens to the activity of an enzyme if its active site is altered ?
The active site will no longer be complimentary to the substrate, so no enzyme-substrate complexes will be able to form. Therefore, no reactions can occur, which causes the rate of reaction to become slower
82
What factors affect the activity of an enzyme ?
temperature
pH
concentration of substrate
concentration of enzyme
presence of inhibitors
83
What word is used to describe the best conditions for enzyme activity ?
Optimum
84
How does increasing the temperature (up to the optimum) affect enzyme activity ?
Increasing the temperature increases the average kinetic energy of the particles. This means that particles are more likely to collide, increasing the frequency of successful collisions forming enzyme-substrate complexes. This means more reactions are catalysed for, increasing the rate of reaction
85
How does increasing the temperature (past the optimum) affect enzyme activity ?
Increasing the temperature increases the average kinetic energy of enzymes, which causes the hydrogen bonds in the tertiary structure to break. This causes the shape of an enzyme's active site to also change. This means the active site is no longer complementary to the substrate and no enzyme-substrate complexes can form. This causes the rate of reaction to become slower
86
How does pH (not optimum) affect enzyme activity ?
low pH = H+
high pH = OH-
An increase in these ions causes the reaction solution to become charged. This can break H bonds and ionic bonds in the tertiary structure to break at extreme concentrations. This alters the shape of the active site (enzyme is denatured) so no enzyme-substrate complexes can form.
87
How does substrate concentration (before point of saturation) affect enzyme activity ?
The likelihood of enzyme-substrate complexes formin increases, so more reactions can be catalysed for. This means that the rate of reaction increases
88
How does substrate concentration (after the point of saturated) affect enzyme activity ?
All active sites are saturated meaning that excess substrate have no free active sites to form enzyme-substrate complexes with. This means that the rate of reaction remains constant from this point
89
How does enzyme concentration (before point of saturation) affect enzyme activity ?
As enzyme concentration increases, the number of available active sites also increases. This increases the likelihood of enzyme-substrate complexes forming, which therefore increases enzyme activity
90
How does enzyme concentration (past the point of saturation) affect enzyme activity ?
As enzyme concentration increases, enzyme activity remains constant. This is because the maximum number of enzyme-substrate complexes form, which means that excess enzymes have no effect on the rate of reaction.
91
What are the two types of inhibitors ?
Competitive and non-competitive inhibitors
92
How do inhibitors affect the rate of an enzyme-catalysed reaction ?
An inhibitor reduces the rate of an enzyme-catalysed reaction
93
How do competitive inhibitors reduce the rate of an enzyme-catalysed reaction ?
Competitive inhibitors have a similar shape to the substrate meaning that they are able to enter the enzyme's active site and occupy the active site temporarily. This reduces the available active sites of the substrate, reducing the number of enzyme complexes forming. This, therefore, reduces the rate of reaction.
94
How can we reduce the effect of competitive inhibitors ?
We can increase the concentration of substrate. This is because it reduces the likelihood of the inhibitor entering the enzyme's active site, so increases the frequency of enzyme-substrate complexes forming. This reduces the effect of the inhibitor.
95
What is Vmax ?
Point of a graph of a factor against the rate of an enzyme-catalysed reaction where the maximum number of enzyme-substrate complexes have formed.
96
How does a non-competitive inhibitor reduce the rate of an enzyme-catalysed reaction ?
A non-competitive inhibitor binds to an allosteric site on the enzyme (site that is not the active site of an enzyme). This causes a permanent change in the tertiary structure of the enzyme, which causes a change in the shape of the active site. This means the enzyme's active site is no longer complementary to the substrate so no enzyme-substrate complexes can form.
97
Does increasing the concentration of substrate reduce the effect of no-competitive inhibitors ?
No. This is because the enzyme is permanently damaged, meaning that it can no longer catalyse any reactions or form enzyme-substrate complexes, even if we increase the substrate concentration.
98
Give some examples of useful inhibitors and whether they are competitive or non-competitive ?
Ethanol - competitive inhibitor of dehydrogenase (prevents ethylene glycol hydrolysis from antifreeze)
Penicillin - competitive inhibitor of the enzyme that produces bacterial cell walls (used to treat infections)
Allopurinol - competitive inhibitor of xanthine oxidase to prevent uric acid build up in the body (can cause gout)
99
Give some examples of dangerous inhibitors and whether they are competitive or non-competitive ?
Snake venom - phosphodiesters act as competitive inhibitors to heart and circulatory system specific enzymes, causing blot clots and lowered blood pressure. Treatment is antivenom (bind to inhibitors)
Cyanide - non-competitive inhibitor of respiratory enzyme cytochrome oxidase, so ATP cannot form. Treatment sodium thiosulfate and sodium nitrate as they catalyse the reaction of cyanide into thiocyanide
100
Outline a method for the test for lipids ?
1. Crush sample and place in a test tube
2. Add a few drops of ethanol to the test tube and shake the test tube
3. Add a few drops of water to the test tube
4. Positive test - white emulsion will form
