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bio mol Flashcards

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1
Q

Describe the chemical structure of water

A
  • -Small molecule,
  • 2 hydrogen atoms, 1 oxygen atom bonded covalently -
  • Where the electrons are not shared equally so that the oxygen has a slight negative charge and the hydrogen has a slight positive charge: called dipole/ is polar
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2
Q

What makes water a good solvent?

A
  • Polar nature of water (with slightly positive and negative charges)
  • allows molecules to have electrostatic attraction to the charged parts of the solute molecule
  • water molecules surround It and separate It from the rest of the molecule, forming an aqueous solution
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3
Q

Give an example of where water being a good solvent is beneficial.

A
  • -Good **transport medium **
  • Dissolve molecules e.g ions, bio molecules and gases (react with water’s charges) -
  • Forms aqueous solutions
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4
Q

Why is water liquid at biological temperatures?

A
  • Small Polar molecules that hold each other together with Intermolecular forces are stronger than other Intermolecular forces - which Require more energy to be broken.
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5
Q

Why is it important that water is liquid at biological temperatures?

A

This allows water to be the medium of chemical reactions where it is the optimum temperature for enzymes in cells.

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6
Q

Why is water cohesive?

A
  • water molecules are dipole so the slight negative charge of the oxygen is attracted to the slight positive charge of the hydrogen in other water molecules.
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7
Q

Why is the cohesion of water important?

A
  • Water can travel up fine xylem vessels in the transpiration stream
  • Pulling force created when water evaporates from the stoma is enacted on the molecules that are ‘stuck’ together,
  • **pressure gradient **created,
  • water moves down pressure gradient
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8
Q

Is water adhesive?

A
  • Adhesive to other Polar/charged surfaces
  • Polarity allows It to form electrostatic attraction
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9
Q

Why is there surface tension in water?

A
  • Intermolecular forces between water molecules stronger than the intermolecular forces between water and air molecules -
  • Surfaces of water contracts so can resist force applied to it (Organisms like pond-skater to move on water, surface tension resists wei
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10
Q

What are the freezing properties of water and how does it allow organisms to survive?

A
  • Below 4 degrees c, water is less dense and rises to the surface.
  • Water freezes, it forms a **semi-crystalline **network which is dense and floats.
  • Winter months- bodies of water don’t freeze completely -
  • Aquatic life can survive, move, nutriate, reproduce u
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11
Q

Why are the freezing properties of water important?

A
  • When body of water freezes over, bottom is still insulated.
  • Never freezes entirely, aquatic life can survive during winter
  • aquatic life still able to metabolise, be nourished etc.
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12
Q

Why does water flow?

A

hydrogen bonds between water molecules continuously made and broken.

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13
Q

Why does water have a high specific heat capacity of 4.2 J and a high latent heat of vapourisation?

A
  • hydrogen bonds between water molecules stronger than most
  • Require more energy to be broken for kinetic energy to increase or to undergo a change of state
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14
Q

Why is the high specific heat capacity of water important?

A
  • allows for stable environment in aquatic habitats
  • habitats near bodies of water -stable environment for enzymes to perform optimally
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15
Q

Why is the high latent heat of vaporisation of water important?

A
  • bonds break, release lots of kinetic energy
  • When water vapour is released, kinetic energy/temperature of host decreases- **cooling effect **
  • plants: evaporation from mesophyll, diffusion through stoma
  • animals: body sweat, release at skin surface.
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16
Q

Why is water necessary for the metabolism?

A

Involved in many chemical reactions -E.g bond breaking in hydrolysis in digestion in animals, source of H+ in plant photosynthesis

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17
Q

What does it mean for organisms to be carbon based?

A

Backbone to organic molecules that form organisms

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18
Q

What are the 4 main types of biological molecules?

A

Macromolecules: Carbohydrates, lipids, proteins, nucleic acids (all have carbon skeletons).

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19
Q

Which elements make up carbohydrates?

A

Carbon, hydrogen, oxygen

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20
Q

Which elements make up lipids?

A

Carbon, hydrogen, oxygen

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21
Q

Which elements make up proteins?

A

Carbon, hydrogen, oxygen, nitrogen, sulfur

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22
Q

Which elements make up nucleic acids?

A

Carbon, hydrogen, oxygen, nitrogen, phosphorus

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23
Q

Monomer: monosaccharide?

A

Polymer: polysaccharides

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24
Q

Monomer: Amino acid

A

Polymer: Polypeptides

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25
Q

Monomer: nucleotides

A

Polymer: Polynucleotides

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26
Q

Why don’t lipids form polymers?

A

Non- repeating pattern -Different base units

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27
Q

Define condensation

A

Reaction- smaller molecules (monomers) combine to form more complex molecule (polymer) -with removal of water.

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28
Q

How is water formed in a condensation reaction?

A

-Hydroxyl (-OH) from one monomer + the hydrogen (H) from another monomer are removed when the monomers bond together

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29
Q

Define hydrolysis

A

Reaction: complex molecule (a polymer) is broken down into smaller molecules (monomers) -with the addition of water.

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30
Q

Why is water required in hydrolysis?

A

-Pull apart the monomers as the hydroxyl (-OH) joins to one monomer and one hydrogen (H) joins to another monomer.

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31
Q

Why are condensation and hydrolysis reactions used?

A

To build up and break down all biological molecules.

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32
Q

What is the formula of a triose?

A

C3H6O3 e.g glyceraldehyde

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33
Q

What is the formula of a tetrose?

A

C4H8O4

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34
Q

What is the formula of a pentose?

A

C5H10O5 e.g ribose

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35
Q

What is the formula of a hexose?

A

C6H12O6 e.g glucose

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36
Q

Name 3 common hexose

A

fructose, galactose, glucose

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37
Q

What properties of glucose allow it to be involved in and control the rate of respiration?

A
  • The molecules are small so easily transported in carrier proteins,
  • they are soluble so are easily transported.
  • They are less reactive, their breakdown must be controlled by specific enzymes.
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38
Q

What are the two isomers of glucose?

A

Alpha glucose and beta glucose

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39
Q

Where is ribose found?

A

In Ribonucleic acid (RNA) and in ATP.

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40
Q

How are disaccharides produced?

A

The condensation reaction between two monosaccharides that forms a glycosidic bond between them.

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41
Q

How is maltose produced and what is its function?

A

a condensation Reaction between two alpha glucose molecules. - Maltose is found in seeds, which needs energy for germination.

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42
Q

How is sucrose formed and what is its function?

A

A condensation reaction between alpha glucose and fructose. Present in plants, it is produced in photosynthesis and is transported via the phloem, providing sugars to the rest of the plant for respiration.

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43
Q

How is lactose formed and what is its function?

A

condensation Reaction between alpha glucose and galactose -It is found It mammalian milk to provide energy for infant mammals

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44
Q

Describe the formation of a glycosidic bond.

A

When any polysaccharide is formed and monosaccharides join together in a condensation reaction, an OH molecule and a H atom are removed, producing water and a **covalent glycosidic bond **takes its place.

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45
Q

How are disaccharides broken down into monosaccharides?

A

hydrolysis Reaction, requires water -break the glycosidic bond, adding an OH molecule and a H atom to form two monosaccharides.

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46
Q

Describe the components of starch.

A

Starch consists of amylose and amylopectin: - Amylose is a long chain polymer of a-glucose, joined by 1,4 glycosidic bonds. - Amylopectin is more complex, also made out of a-glucose units joined in 1,4 glycosidic bonds but also contains 1,6 bonds that form the occasional branches. These branches form more accessible points for amylase to break it down. Amylose coils up and together with the amylopectin, makes a compact, water insoluble storage molecule.

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47
Q

Explain how the structure of glycogen makes it a good storage molecule.

A

-Insoluble: no effect on water potential -Metabolically inactive -Compact- lots of energy stored in small space -a-glucose: 1,4 glycosidic bonds with 1,6 bonds forming branches- lots of ends to add more glucose

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48
Q

Where is starch found?

A

Starch is a storage polysaccharide found in animal cells with High metabolic rates - Forms dense granules and the highly branched structure creates more accessible ends for enzymes to hydrolyse It into a-glucose for respiration

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49
Q

Describe the structure of cellulose.

A

Cellulose is made of successive b-glucose units linked at 180c to each other in a long and straight molecule. 60-70 of these molecules are cross-linked by hydrogen bonds forming microfibrils which are grouped in bundles/fibres.

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50
Q

Where is cellulose found and what characteristic make it suitable for this role?

A

Cellulose is a structural polysaccharide found in the cell wall of plant cells. It is extremely strong with high tensile strength due to its many cross-links between molecules, it is therefore able to withstand the high pressures generated in osmosis.

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51
Q

glucose + glucose

A

maltose

52
Q

glucose + fructose

A
  • sucrose –> non-reducing sugar
53
Q

glucose + galactose

A

lactose

54
Q

Glycogenolysis

A

the breakdown of glycogen to glucose

55
Q

What is the difference between the isomers alpha and beta glucose?

A

In alpha glucose, the carbon 1 hydroxyl points below the plane of the ring and in beta glucose the carbon 1 hydroxyl points above the plane of the ring.

56
Q

Name a hexose monosaccharide?

A

Glucose

57
Q

Name a pentose monosaccharide?

A

Ribose

58
Q

What is the difference between glycogen and amylopectin?

A

Glycogen has more branches extending from the chain (more 1-6 glycosidic bonds) and shorter 1-4 glycosidic bonds.

59
Q

How are starch, glycogen and cellulose stored?

A

Starch- chloroplasts and starch grains in plants, glycogen- granules in the cytoplasm of animal cells, cellulose- cell wall of plants.

60
Q

In which solvents are lipids soluble?

A

Non-polar solvents

61
Q

State some functions of lipids.

A

Source/storage of energy, membrane component, insulation, waterproofing, bile acids and hormones.

62
Q

What do triglycerides consist of and how are they formed?

A
  • 3 fatty acids joined to a glycerol molecule by ester bonds - formed in a condensation reaction between the carboxylic acid of the fatty acid and the hydroxyl group of glycerol.
63
Q

Describe the components of triglycerides.

A

Glycerol- alcohol with three hydroxyl groups. Fatty acids- long hydrocarbon chain and a terminal carboxylic acid group, the degree of saturation (C=C bond presence) of the chain influences the properties of the lipid.

64
Q

What state is a saturated lipid at room temp.?

A

Lack of double bonds (saturated carbon atoms) strengthens the Intermolecular forces between the lipid molecules - Makes the structure rigid and therefore solid

65
Q

What state is a mono/poly-unsaturated lipid at room temp.?

A

The double bonds create a kink in the fatty acid chain, weakening the intermolecular forces, making the structure fluid and therefore liquid.

66
Q

Why are lipids good energy reserves?

A
  • High energy density and are osmotically inactive - In respiration, they produce more ATP than glucose (RQL= 0.7, RQG=1) –> due to the large number of hydrogen bonds to be broken in respiration.
67
Q

Why are lipids good for animals in habitats with less water?

A

They are highly reduced so produce a lot of metabolic water in respiration.

68
Q

Why are lipids good storage molecules for energy?

A

They are insoluble so they do not effect the balance of cells.

69
Q

How are phospholipids different to trigylcerides?

A
  • Phospholipids have only two fatty acids bonded to the glycerol - phosphate group covalently bonded to the third hydroxyl group of the glycerol –> This creates a hydrophilic and hydrophobic region.
70
Q

What is the difference between being hydrophobic and hydrophilic?

A

Hydrophilic- attracted to water due to its charge Hydrophobic- repelled by water due to a lack of charge/being non-polar

71
Q

Ester bond

A

Covalent bond formed by a condensation reaction between the OH group of a carboxylic acid and the H group of an alcohol.

72
Q

Give two examples of the use of lipids for insulation.

A

Mechanical- around major organs/ glands Electrical- myelin sheath in nerve cells.

73
Q

Describe the features of cholesterol.

A
  • Has a hydrophilic and hydrophobic region, allowing them to fit between phospholipids of cell membranes –> gives membranes mechanical stability and regulates membrane fluidity - Hydrophobic region prevents leakage of ions through membranes.
74
Q

Which two functions of lipids rely on cholesterol?

A

Steroid hormones and bile acids.

75
Q

Name the general functions of proteins.

A

Structure, Immunoglobulins, Enzymes, Hormones and neurotransmitters

76
Q

Describe the use of proteins structurally.

A

membranes use proteins protein-lined channels in the transport of ions and Polar molecules across the membrane - Carrier proteins are Involved in active transport and facilitated diffusion across the membrane - Muscles contain actin and myosin which form fibres which move to contract the muscle - Collagen gives strength, and flexibility to specific body structures.

77
Q

Describe the use of proteins as immunoglobulins.

A

Antibodies are proteins, made in the lymphocytes and involved in the body’s defence against disease.

78
Q

How many amino acids acids can proteins be made from?

A

20

79
Q

What is the basic structure of amino acids?

A

Amino acids contains a carbon atom bonded to an amino (NH2) group, a carboxylic acid (-COOH) group, a hydrogen and an R group (variable: e.g hydrogen, basic, acidic, hydrophobic).

80
Q

Why is the possession of both an acidic and basic group useful in an amino acid?

A

Amino acids can act as buffers, with the ability of accepting H+ when it is in excess and can donate H+ to excess hydroxyl (-OH) ions producing water.

81
Q

What is used to make amino acids in plants?

A

Photosynthate and nitrate/ammonium.

82
Q

What is a peptide bond and how is it formed?

A
  • Peptide bonds are the C-N covalent bonds joining amino acids together - They are formed in condensation reactions when the hydroxyl from the carboxylic acid group and the hydrogen from the amino group are removed, producing water.
83
Q

How are peptide bonds broken?

A
  • Hydrolysis breaks peptide bonds with the addition of water, as the C-N bond is broken - Hydrogen bonds to the amine group and the hydroxyl forms a bond with the carboxylic acid group. Hydrolysis is involved in digestion of proteins using enzymes.
84
Q

What does the ‘Primary structure’ of a protein mean?

A

The sequence of amino acids, determined by the base sequences in DNA.

85
Q

What is the secondary structure of proteins?

A

The curling/folding of polypeptide chains into a-helices and b-pleated sheets (looser due to the formation of hydrogen bonds)

86
Q

Why are hydrogen bonds formed within polypeptide chains, allowing for a folded shape?

A
  • The oxygen of a C=O of one amino acid is slightly negatively charged - The hydrogen of an N-H of another amino acid is slightly positively charged –> so many weak hydrogen bonds are formed stabilising the secondary structure.
87
Q

What is a disadvantage of the hydrogen bonds in the secondary structure?

A

hydrogen bonds- weak, easily broken- High temperatures and pH changes. -Affect the specific shape and function of a protein- denature

88
Q

Describe what the tertiary structure of proteins involves.

A

The tertiary structure overall specific 3D shape of a protein determined by interactions and properties of the R groups. Interactions between R groups include: disulphide bonds, ionic bonds, hydrogen bonds, and hydrophobic/philic interactions.

89
Q

Describe disulphide bonds in proteins.

A

Disulphide bonds are strong covalent bonds formed between the R groups of two cysteine molecules.

90
Q

Describe ionic bonds in proteins.

A
  • Formed between R groups that have charge - Between amine and carboxylic acid groups - Broken easily by pH changes
91
Q

Describe hydrogen bonds in proteins (TQS)?

A

Hydrogen bonds form between amino acids with strongly polar R groups. The bonds are individually weak, collectively strong.

92
Q

Describe hydrophobic/philic interactions.

A

Hydrophobic parts of the R groups clusters in the centre of the polypeptide to avoid the solution it is suspended in. The hydrophilic parts are found at the edge of the polypeptide to be close to water.

93
Q

What does ‘Quaternary structure’ mean in regards to proteins?

A

-Specific shape of a protein determined by multiple polypeptide chains or prosthetic groups -It is also held together by the interactions of the R groups

94
Q

What is a conjugated protein?

A

Protein that functions with a non-protein element, e.g a prosthetic group.

95
Q

What does it mean for a protein to be globular?

A

a protein that is spherical in its specific shape for its specific function as enzymes or hormones and for transport - It is also soluble in water for its metabolic roles.

96
Q

Describe how the structure of haemoglobin contributes to its function.

A
  • Haemoglobin is globular and made from 4 polypeptide chains (2x a and 2x b) and 4 haem (prosthetic) groups - Held by bonds between the R groups - Soluble in water due to the position of hydrophobic/philic groups - The prosthetic haem groups contain Fe2+
97
Q

Describe the structure and function of the globular protein insulin.

A

Insulin- produced in pancreas - Formed of one a-helix and one b-pleated sheet - joined by disulphide links - hydrophilic groups on the outside so can dissolve in water - Has the specific shape to bind to the receptors on cells to lowers blood glucose

98
Q

What are fibrous proteins?

A

Long, strong and insoluble proteins which have structural roles. Formed by long polypeptide chains in a repeating sequence of amino acids, The chains form fibres which are strong. The amino acids tend to have non-polar R groups so are insoluble in water.

99
Q

Describe the structure and function of collagen.

A

Function: - Structural fibrous protein that provides mechanical strength - The skin, tendons- good tensile strength, cartilage, bone and blood vessels (withstand the pressure in artery walls) Structure: - Made from 3 polypeptide chains wound around each other making a triple helix - Triple helices line up parallel to each other and are held together by hydrogen bonds - There are also covalent cross links between a carboxyl group and the amino group - A stagger between ends of molecules- strengthens the protein.

100
Q

Describe the structure and function of two other fibrous proteins.
keratin
elastin

A

**Keratin:
* rich in cysteine
* lots of disulphide bridges and Hydrogen bonds - very strong
* found in areas typically exposed to forces/mechanical damage: nails, hair, claws, fur, feathers
* provides mechanical protection via an impermeable barrier to infection
* waterproof to prevent entry of water-borne pollutants.

** Elastin: -**
* cross-linking and coiling structure is strong and extensible
* found where stretch is needed: skin, lungs- inflation/deflation, blood vessels- maintain structure with pressure

101
Q

What is the difference between cations and anions?

A

Cations have a positive charge and anions have a negative charge.

102
Q

What is the charge of the cation Calcium?

A

Ca2+

103
Q

What is the charge of the cation Sodium?

A

Na+

104
Q

What is the charge of the cation Potassium?

A

K+

105
Q

What is the charge of the cation Hydrogen?

A

H+

106
Q

What is the charge of the cation Ammonium?

A

NH4+

107
Q

What is the charge of the anion nitrate?

A

NO3-

108
Q

What is the charge of the anion Hydrogencarbonate?

A

HCO3-

109
Q

What is the difference between qualitative and quantitative testing?

A

Qualitative requires categorical data described with words, quantitative requires numerical data.

110
Q

What is the test for carbohydrates?

A

Iodine solution

111
Q

What is the positive result of a test for carbohydrates?

A

Qualitative test- from yellow-brown to blue-black. This is because the iodine ion I3- slips into the amylose helix.

112
Q

What is the test for lipids?

A

Emulsion test- mixing sample with ethanol, filtering and pouring into water.

113
Q

What is the positive result of a test for lipids?

A

Cloudy-white emulsion due to the presence of emulsified lipid droplets.

114
Q

What is the test for proteins?

A

Biuret test

115
Q

What is the positive result of a Biuret test?

A

Colour change from light blue to lilac as a complex between the nitrogen in the peptide chain and Cu2+ ions in Biuret solution is formed.

116
Q

What is the test for reducing sugars?

A

Heating with Benedict’s solution at 80c for 3 minutes.

117
Q

What is the positive result of a reducing sugars test?

A
  • Colour change from blue to green/yellow/orange-red - Due to the Cu2+ in the Benedict’s solution being reduced to Cu+ - Forming an orange-red copper oxide precipitate - Benedict’s solution in excess, intensity of red proprtional to conc of red. sugar
118
Q

What is the difference between a reducing and a non-reducing sugar, how does this affect testing for them?

A

Reducing: All monosaccharides and few disaccharides can be reduced, are able to give electrons –> can be a reducing agent for Cu2+ in Benedict’s solution –> Test: Benedict’s solution Non-reducing sugars: Can’t be reduced, no free carboxyl group –> Cannot be a reducing agent in Benedict’s solution –> Glycosidic bonds must be hydrolysed with hydrochloric acid before testing –> Neutralise with sodium hydrocarbonate –> Test again with Benedict’s solution

119
Q

What is the test for non-reducing sugars?

A

Breaking the glycosidic bonds in the polysaccharide that prevent it from reducing 1.Test for reducing sugars to check 2. Boil with hydrochloric acid to hydrolyse bonds 3. Cool and use sodium hydrocarbonate to neutralise 4. Test for reducing sugars again. (can extract precipitate by filtration)

120
Q

Describe the semi-quantitative test for reducing sugars that uses the mass of precipitate.

A

Testing using Benedict’s solution and then filtering to measure mass of precipitate. Can be calibrated using known solutions and a calibration curve.

121
Q

Describe the semi-quantitative test for reducing sugars that uses colourimetry.

A

Using a centrifruge to separate precipitate from the solution, then placing in a cuvette into a colourimeter. This is where light will be shone through and the transmission/ absorbance will be measured. If there is a lot of unreacted copper sulfate the transmission will be low and If there is little unreacted copper sulfate, transmission will be high.

122
Q

Describe how an accurate result can be achieved using colourimetry.

A

A calibration curve can be created by plotting known solutions on a curve of % transmission/absorbance against concentration. Therefore, unknown sample concentrations can be found along the curve using %.

123
Q

Explain how another method of quantitative testing works.

A

Using biosensors- where a chemical variable is converted into an electrical signal.

124
Q

Describe and explain why collagen is a fibrous protein.

A

Long chain of amino acids -little/no tertiary structure -Insoluble -Structural function- strength

125
Q

Explain why collagen is such a strong molecule.

A

Polypeptides overlap due to staggered ends, no weak point -many hydrogen bonds -more covalent bonds/crosslinks

126
Q

Outline the method of chromatography that will separate the main amino acids in collagen.

A

To hydrolyse protein (break peptide bonds): -Place sample on TLC (stat. phase), chromat. paper (pencil line) -Dry and repeat -Place paper in solvent (below pencil line) -Spray with ninhydrin to see amino acids

127
Q

Describe and explain how the structure and properties of different carbohydrates and lipid molecules suit them to their role as storage molecules in plants and animals. (6)

A

Carbohydrates: - Polymers of glucose -> glucose can be used in respiration to release energy - Large molecules, insoluble -> doesn’t affect water potential of cell -1-4 glycosidic bonds -> easy to make and break - Coiled/compact -> doesn’t take up much space in cell - Branched (glycogen), or less branched (amylose/amylopectin) -> more/less rapid release of monomers Lipids: - more C-C bonds than C-H bonds - energy-rich, more energy per molecules -> more energy stored in less space - Insoluble -> don’t affect water potential - fatty acids, long carbon chains -> can be broken down to release two carbon/acetyl groups, enter Krebs cycle

BIO A LEVEL (17 decks)

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