2.1.2 - Biological molecules Flashcards
1
Q
Define the term ‘polar’ in relation to molecules
A
Polar molecules have regions of negativity and regions of positivity
2
Q
Explain how polar molecules like water interact with each other
A
- The positive and negative regions of the molecules attract each other and form hydrogen bonds
- These bonds give water its cohesive properties - It moves as one body because the molecules are attracted to each other
- These bonds also give water its adhesive properties, its molecules are attracted to other surfaces
3
Q
What are hydrogen bonds ?
A
- Hydrogen bonds are weak intermolecular forces that form between a hydrogen atom from one molecule and either N,O or F atom from another molecule
- They break and reform between the constantly moving water molecules
4
Q
What are the unique properties of water ?
A
- High boiling point
- Becomes less dense when it freezes
- Cohesive properties
- Adhesive properties
5
Q
Due to water being a liquid at room temperature what four things does this allow it to do?
A
- It provides a habitat for living things
- Forms a major component of the tissues in living organisms
- Provides a reaction medium for chemical reaction.
- Provides a transport medium
6
Q
What is the density of water like ?
A
- Solid water has a lower density than liquid water, this is because of the hydrogen bonds formed
- As water is cooled below 4 degrees, the hydrogen bonds fix the positions of the polar molecules slightly further apart from the average distance in the liquid state
7
Q
What are the benefits of ice floating ?
A
- Aquatic organisms have a stable environment in which to live on or under throughput the winter
- Ponds and other bodies of water are insulated against extreme cold
8
Q
What is surface tension in water ?
A
- Hydrogen bonds are very cohesive, causing surface tension
- Tension causes the surface of the liquid to contract so that it is very thin but very strong
- It’s caused by attractive forces that hold the molecules of the liquid together
9
Q
Explain how the ‘skin’ of surface tension of water enables a pond skater to inhabit the surface of water
A
The skin is caused as water molecules are more strongly cohesive to each other than to air, this skin supports thepond skater.
10
Q
What is the boiling point of water like ?
A
The boiling point of water is unusually high because it has hydrogen bonds
11
Q
What does the high SHC of water mean ?
A
It takes a lot of energy to increase the temperature of water and cause it to evaporate
12
Q
What is cohesion and adhesion in water ?
A
- It moves as one mass because the molecules are attracted to each other via electrostatic forces
- Water molecules are attracted to other materials
13
Q
What does cohesion and adhesion lead to ?
A
- The acts of cohesion and adhesion result in exhibiting capillary action
- This is he process by which water can rise up a narrow tube against the force of gravity
14
Q
What are carbohydrates ?
A
Carbohydrates are groups of substances that provide energy and are used to build bodily structures
15
Q
What are the functions of carbohydrates ?
A
- Provide energy via respiration
- Used to build bodily structures
- They are a store of energy, glycogen and starch
- Used in nucleic acids, deoxyribose and ribose, these are known as pentose saccharides
16
Q
What is a Monosaccharide ?
A
- A monosaccharide is a single unit of sugar
- For example, glucose, fructose and ribose
17
Q
What is a disaccharide ?
A
- A disaccharide is when two monosaccharides link together
- For example, Lactose and sucrose
18
Q
What is a polysaccharide ?
A
- A polysaccharide is when many monosaccharides are linked together.
- For example, glycogen, cellulose and starch
19
Q
What is glucose ?
A
- Glucose molecules are polar and soluble in water, this is because of the hydrogen bonds between the hydroxyl groups and water molecules
- This means glucose is dissolved in the cytosol of the cell
- Glucose is a hexose monosaccharide due to the fact that it has six carbons
20
Q
What are the two structural variations of glucose ?
A
Alpha (α) glucose and Beta (β) glucose
21
Q
How does 𝛂 glucose differ from β glucose ?
A
- The hydroxyl group (OH) on carbon 1 is in opposite positions
- This affectsthe structure and properties of the polysaccharides when it bonds
22
Q
What is a condensation reaction ?
A
- A condensation reaction is one which forms a disaccharide
- 2 monosaccharides join together
- The two OH groups interact and bonds are broken
- A new glycosidic bond is formed
- Water is released
23
Q
How is lactose formed ?
A
- A condensation reaction between glucose and galactose
- Glucose + Galactose = Lactose
24
Q
How is maltose formed ?
A
- A condensation reaction between two glucose molecules
- Glucose + Glucose = Maltose
25
How is sucrose formed ?
- A condensation reaction between glucose and fructose
| - Glucose + Fructose = Sucrose
26
What is a hexose monosaccharide ?
A sugar that contains six carbons
27
What is a pentose monosaccharide ?
A sugar that contains five carbons
28
Which two pentose sugars are important components of biological molecules?
- Deoxyribose, present in DNA molecules
| - Ribose, present in RNA molecules
29
What are the properties and structure of starch ?
- Made of amylose (mainly, 1-4 glycosidic bonds) and amylopectin (1-4 and some 1-6 glycosidic bonds)
- Insoluble, does not create a water potential gradient
- Chemical energy store
- Compact and ideal for storage
- Easily digestible
30
What are the properties and structure of amylose ?
- Long unbranched chains of alpha glucose
- Joined by 1-4 glycosidic bonds
- Insoluble (does not create water potential gradient)
- Metabolically inactive
- Compact and ideal for storage
31
What are the properties and structure of amylopectin ?
- Long, branched chains of alpha glucose
- Joined by 1-4 glycosidic bonds (chains) and 1-6 glycosidic bonds (branches)
- 1-6 branching points occur approximately one in every 25 glucose subunits.
- Insoluble (do not affect water potential)
- Compact and ideal for storage
32
What do 1-4 glycosidic bonds cause ?
Chains
33
What do 1-6 glycosidic bonds cause ?
Branches
34
What are the benefits of coiling and branching in polysaccharides ?
- Makes them very compact which is ideal for storage.
- Allows for free ends where glucose can be added or removed quickly. This speeds up the process of storing/releasing glucose molecules required.
35
What are the properties and structure of glycogen ?
- Short, branched chains of alpha glucose
- Joined by 1-4 glycosidic bonds (chains) and 1-6 glycosidic bonds (branches)
- Compact so ideal for storage
- Insoluble
- Branching means many free ends so glucose can be released (or stored) quickly
36
What is the function of glycogen ?
- Energy store in animals
| - Stores soluble glucose until it is needed
37
What are the similarities between amylopectin and glycogen ?
- Insoluble
- Branched
- Compact so ideal for storage
38
Describe the structure and properties of cellulose
- Long, unbranched chains of beta (β) glucose
- Every alternate beta (β) glucose molecule is turned upside down.
- Forms straight cellulose chains
- Contains 1-4 glycosidic bonds
39
What are cellulose chains ?
- The cellulose chains are linked by hydrogen bonds forming strong fibres called microfibrils, microfibrils are compact
- Microfibrils join to make macrofibrils, which combine to make fibres
40
Describe the function of cellulose
- Cellulose is a fibre necessary for a healthy digestive system. This is due to the fact that it is very hard to break down.
- Cellulose provides structural support for cells in plants
- e.g. cellulose cell wall in plants
41
What is a hydrolysis reaction ?
- A hydrolysis reaction is how a disaccharide is broken down
- Addition of water to hydrolyse the disaccharide into (useable) monomers
- Reactions are catalysed by enzymes
- These are the opposite of condensation reactions that form glycosidic bonds.
42
What test is used for the presence of starch ?
The iodine test
43
Explain the iodine test
- Add iodine dissolved in potassium iodide solution to test sample
- If starch is present the colour will change from brown/orange to dark blue/black
- If no starch is present, the colour stays brown/orange
44
What test is used for the presence of protein ?
The Biuret test
45
Explain the Biuret test
- First step is to add few drops of sodium hydroxide solution this is because the solution has to be alkaline
- Next add the copper (ii) sulphate solution
- If a protein is present the solution turns purple
- If no protein is present the solution stays blue
46
What does the Biuret test really discover?
Peptide bonds in proteins
47
How is the colour formed in the Biuret test?
A complex is formed between the nitrogen atoms in a peptide chain and Cu2+ ions
48
What test is used for the presence of lipids ?
The emulsion test
49
Explain the emulsion test
- Shake the test sample which contains ethanol for about 1 minute then pour solution into cold water
- If lipid is present, solution turns milky
- If there is no lipid present the solution stays clear
- The more lipid present, the more noticeable the milky colour
50
What is a reducing sugar ?
- A sugar which can give electrons to other molecules
| - Reducing sugars include all monosaccharides and some disaccharides
51
What is used to test for reducing sugars ?
The Benedict's test, using Benedict's solution
52
Explain the Benedict's test
- Add Benedict's reagent to the sample and heat it in a water bath
- If a coloured precipitate is formed than the test is positive and there is a reducing sugar present
- Colour of precipitate changes from: blue - green - yellow - orange - brick red
- The higher the concentration of reducing sugar, the further the colour change goes
53
What causes the change in colour of the Benedict's solution?
The Cu2+ ions in the Benedict's solution reduce to Cu+ ions which give it that orange colour
54
What is another way to test for reducing sugars ?
- Reagent strips
- The advantage to reagent strips is that with the use of a colour coded chart, the concentration of the sugar can be determined
55
What is the test for non reducing sugars ?
Benedicts test
56
What must first happen to the sugar solution before it can tested for non-reducing sugars?
- It must be boiled with hydrochloric acid to hydrolyse the bonds and free up the reducing sugar group e.g. Sucrose split into glucose and fructose
57
Why is Sodium hydrogen carbonate added after adding HCl ?
To neutralise the acid
58
What are the non-reducing sugars Benedict's test results?
- Positive result, forms coloured precipitate.
- Colour changes:
- Blue - Green - Yellow - Orange - Red
- Negative result, stays blue so no sugar present
59
How can colorimetry be used to calculate the concentration of reducing sugar present ?
- A colorimeter is a piece of equipment that quantitatively measures the absorbance, or transmission, of light of a coloured solution.
- The more concentrated a solution is the more light it will absorb and the less light it will transmit.
60
What are lipids ?
- Lipids are molecules containing carbon, hydrogen and oxygen
- They are non polar and insoluble in water
61
What are the three types of lipids ?
- Triglycerides
- Phospholipids
- Sterols
62
How do u test for lipids ?
Emulsion tests
63
What is a triglyceride ?
A triglyceride is made from three fatty acids (Carboxylic Acid) and a glycerol (Alcohol)
64
What are the functions of triglycerides ?
- Protection of vital organs
- Thermal insulation
- They form the myelin sheath around some neurones, acting as electrical insulators
- As a water source from the respiration of lipids
- Components of cell membranes
65
Why are they useful for storage ?
- Can be stored in a compact way
| - They are not water soluble
66
How do triglycerides compare to carbohydrates in terms of energy ?
Triglycerides release more energy per gram
67
Why do we not use triglycerides as energy ?
Too much energy is required to break them down so it is not efficient
68
Explain the synthesis of a triglyceride
The hydroxyl groups interact, leading to the formation of three water molecules and three ester bonds between the fatty acids and the glycerol
69
Explain the hydrolysis of a triglyceride
To break down a triglyceride you have to add 3 H2O molecules to hydrolyse it
70
What is a saturated fatty acid ?
Fatty acid chains that have no double bonds present between the carbon atoms
71
What is an unsaturated fatty acid ?
Fatty acids with double bonds between some carbon atoms
72
What does a double bond cause in the chain ?
Double bond causes the molecule to kink or bend
73
Why are unsaturated fatty acids liquid at room temp ?
- The double bonds cause the molecule to bend so they can't pack closely together
- Therefore they are oils and not fats
74
What is a phospholipid ?
- Phospholipids are modified triglycerides
| - One of the fatty acid chains in a triglyceride is replaced with a phosphate group to make a phospholipid
75
How are phospholipids formed ?
A condensation reaction between a glycerol molecule, 2 fatty acids, and a phosphate group
76
What bonds are involved in the formation of a phospholipids ?
Ester bonds
77
What properties does the phospholipid head have ?
The head is charged and polar due to the phosphate ions therefore it is hydrophilic and attracts water
78
What properties does the phospholipid tail have ?
Tail is not charged and non polar due to the long chain hydrocarbons therefore it is hydrophobic and repels water
79
How do phospholipids interact with water ?
- They will form a layer on the surface with heads in the water and the tails sticking out of the water.
- They are called surfactants.
80
What is a phospholipid bilayer ?
The heads protect the tails from the water the tails point inwards and the heads point outwards
81
What does the phospholipid bilayer allow ?
- They are able to separate an aqueous environment in which cells usually exist from the aqueous cytosol within cells
- They play a key role in forming cell membranes
82
Explain the differences between phospholipids and triglycerides
- Triglycerides contain 3 fatty acids but phospholipids only contain two and a phosphate group
- Triglycerides contain 3 ester bonds but phospholipids only contain 2
- Phospholipids have a hydrophilic head
83
What are sterols ?
Sterols are another type of lipid
84
What is the structure of sterols ?
They are complex alcohol molecules based on a four carbon ring structure with a hydroxyl group at one end
85
Where are the sterols manufactured ?
They are manufactured in the liver and intestines
86
What are the functions of sterols ?
- Adds stability to the cell membrane
- Regulates fluidity by keeping the membrane fluid at low temperatures and stopping them becoming too fluid at high temperatures
- Used to make steroid hormones
87
How does cholesterol sit in phospholipid bilayers?
With the hydroxyl group in contact with the phosphate head
88
Which part of the sterol is hydrophilic ?
The hydroxyl group
89
Which part of the sterol is hydrophobic ?
The four carbon ring structure and the rest of the body
90
What are the basic units of proteins ?
Amino acids
91
How many common amino acids are there ?
- There are 20 common amino acids in the body
| - There are 3.2 million different ways they could join and bond together
92
What is a special feature of amino acids ?
- They are amphoteric
| - They act as a pH buffer, helping to stabilise the pH of your blood
93
Why are amino acids able to be amphoteric ?
The reason they can act as a buffer is because if the blood is not acidic enough the hydroxyl group can let a hydrogen ion go. If the blood is too acidic its got too many hydrogen ions, the amine group can take in some of these hydrogen ions.
94
What are the functions of proteins ?
- Enzymes
- Signal; hormone proteins
- Structural; keratin and collagen
- Contractile; spindle fibres, actin and myosin in muscles
- Storage; albumin present in eggs and casein present in milk
- Transport; haemoglobin and myoglobin
- Defensive; antibodies
95
What type of reaction occurs to form a protein from 2 amino acids?
Condensation
96
What catalyses the reaction of two amino acids ?
Peptidyl transferase
97
What is produced in the reaction of two amino acids ?
A dipeptide and water
98
What type of bond is formed from the synthesis of a protein ?
Peptide bond
99
Between which parts of the amino acid molecules does the condensation reaction between two amino acids occur?
The carboxyl group of one amino acid and the amine group of another amino acid
100
What is the primary structure of a protein ?
The sequence of amino acids
101
What type of bonding holds the primary structure of a protein together?
Peptide bonds
102
What shape is the primary structure of a protein?
Linear
103
What forms the secondary structure of a protein?
The folding of the primary structure
104
What type of bonds hold together the secondary structure of a protein?
Hydrogen bonds
105
In the secondary structure, what do hydrogen bonds form between?
- Between a hydrogen (H) atom and another electronegative atom bearing a lone pair of electrons
- Hydrogen and either Oxygen, Nitrogen or Fluorine
106
What are the two possible shapes of the secondary structure?
- Beta pleated sheet is when the polypeptide chains lie parallel to one another. Hydrogen bonds hold it together.
- Alpha helix is formed due to the hydrogen bonds pulling the amino acid chains together
107
Between which amino acids do the hydrogen bonds form?
The hydrogen bonds form with the fourth amino acid along the chain.
108
What is the tertiary structure formed by?
The folding of the secondary structure
109
Why do proteins fold at the tertiary level of structure?
Interactions between the R - groups
110
What are the 4 types of bond formed at the tertiary level of structure?
- Hydrogen bonds
- Ionic bonds
- Disulphide bonds
- Hydrophobic and hydrophilic interactions
111
What do ionic bonds form between?
Oppositely charged ions
112
What do hydrogen bonds form between?
Between a hydrogen (H) atom and another electronegative atom bearing a lone pair of electrons
113
What do disulphide bridges form between?
Sulphur atoms contained within separate R groups
114
What do hydrophobic and hydrophilic interactions form between?
Polar and non polar R - groups
115
What forms the quaternary structure?
- Formed by the interaction of more than one tertiary protein
- Two or more tertiary proteins being held together by different bonds
116
What type of bonds holds together the quaternary structure?
- Ionic
- Hydrogen
- Disulphide
- Hydrophobic and Hydrophilic interactions
117
Explain the breakdown of peptides
- Water molecule is used to break the peptide bond in a hydrolysis reaction, reforming the amine and carboxylic acid group
- Protease enzymes catalyse the reverse reaction - turning peptides back into their constituent amino acids
118
What is a globular protein?
Spherical, water soluble protein
119
What are globular proteins used for ?
- Essential for regulating processes such as :
| - Chemical reactions, immunity and muscle contractions; along with many others
120
Give 3 characteristics of globular proteins
- Compact
- Water soluble
- Roughly spherical
121
Why are globular proteins water soluble ?
- Hydrophilic R-groups are on the outside, this allows for them to be soluble in water
- The tertiary structure is folded so that the hydrophobic R-groups are kept away from the aqueous environment
122
What are some examples of globular proteins ?
- Insulin
- Haemoglobin
- Catalase
123
What is the function of insulin ?
- Hormone involved in the regulation of blood glucose concentration.
- Stored as energy for later use.
- When there is a high glucose concentration in the blood, insulin tells the body to store leftover glucose in the liver
124
Where is insulin produced ?
Produced in the pancreas
125
Why is it beneficial for insulin to be water-soluble?
Hormones are transported in the blood so must be water soluble
126
What are conjugated proteins ?
Conjugated proteins are globular proteins that contain a prosthetic group
127
What is a prosthetic group ?
A non protein component
128
State some examples of prosthetic groups
- Haem groups, include iron (II) ions
- Different metal ions
- Vitamin molecules
129
Define a simple protein
A simple protein is one without a prosthetic group
130
Give 2 examples of conjugated proteins
- Haemoglobin
| - Catalase
131
What is the function of haemoglobin ?
- Carries oxygen around the body in red blood cells
- Carries it from the lungs to the cells that need it
- Stores, transports and releases oxygen
132
What is haemoglobin made up of ?
- 4 subunits
- 2 alpha helixes
- 2 beta pleated sheets
133
What prosthetic group does each subunit of haemoglobin contain?
Haem group
134
What is a haem group ?
It is a prosthetic group that contains Iron (II) ions
135
What is the function of the haem groups in haemoglobin ?
The iron (II) ions in haem are able to combine reversibly with an oxygen molecule which allows haemoglobin to transfer oxygen
136
What is the function of catalase ?
- Break down of hydrogen peroxide which is otherwise harmful to cells
- Protects the cell from oxidative damage
137
What is catalase made up of ?
- It is made up of 4 tetrahedral polypeptide chains, each of which have a haem group
138
What prosthetic group does catalase include ?
Haem group
139
What is the function of haem groups in catalase ?
It allows the iron (II) ions to interact with hydrogen peroxide and speed up its breakdown
140
What are fibrous proteins ?
- They are long, insoluble, structural proteins
| - This is because they have a high amount of amino acids
141
How does the repetitive amino acid sequences affect the properties of fibrous proteins?
- Gives them more organised structures
| - Makes strong molecules that do not fold into complex 3D shapes
142
Give 3 examples of fibrous proteins
- Keratin
- Collagen
- Elastin
143
Where is Keratin found ?
Keratin is found mainly in hair, skin and nails
144
Which amino acid does keratin contain in a high proportion?
Cysteine, contains sulphur
145
What type of bonding occurs in keratin ?
Disulphide bonds
146
What does the amount of disulphide bonds determine ?
- It determines the flexibility, the fewer bonds the more flexible it is
- Hair is more flexible compared to nails because it has fewer bonds compared to nails
147
What does the high amount of sulphur lead to in keratin ?
It makes it insoluble, inflexible and strong
148
Where is Elastin found ?
In the walls of blood vessels and lungs
149
What makes up elastin ?
- Quaternary structure made from many molecules called tropoelastin
- This makes a very large insoluble and stable, cross linked structure.
150
What is the function of elastin ?
Elastin gives structures flexibility to expand when they need to and then also return back to their original position
151
Why is it beneficial for tissues to contain elastin?
It confers strength and elasticity
152
Where is collagen found ?
In the skin, tendons, ligaments, and nervous system
153
What is the structure of collagen ?
All forms of collagen are made up of three polypeptides wound together in a long and strong rope-like structure
154
What property does collagen have ?
- Long and flexible under low stress
| - Insoluble
