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TOPIC 2: BIOLOGICAL MOLECULES Flashcards

1
Q

2.2.1 WATER
What is the function of water?

A

a reactant in loads of importans chemical reactions
is a solvent, which means some substances dissolve in it
transpots substances
helps with temperature control because it has a high specific heat capacity and a high latent heat of evaporation

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2
Q

2.2.1 WATER
Explain the structure of water

A

a molecule of water is one atom of oxygen joined to two atoms of hydrogen 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 on the oxygen atom give it a slight negative charge
this makes a water polar molecue - it has a particial negative charge on one side and a particial positive charge on the other side

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3
Q

2.2.1 WATER
How is hydrogen bonding linked to water?

A

slightly negatively-charged oxygen atoms attract the slightly positively-charged hydrogen atoms of other water molecules
this attraction is called hydrogen bonding and it gives water some of itsuseful properties

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4
Q

2.2.1 WATER
How does the property high specific heat capacity link to water?

A
  • The specific heat capacity is defined as: the quantity of heat (J) absorbed per unit mass (kg) of material when its temperature increases 1K (or 1°C). Its units are J/(kg K) or J/(kg °C).
  • Water has a very high specific heat capacity due to the hydrogen bonds, as a great deal of energy is needed to break them.
  • This means water can absorb large amounts of energy before changing state so it’s temperature remains fairly stable (thermostable).
  • Doesn’t experience any rapid temperature changes, which is one of the properties that makes it a good habit
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5
Q

2.2.1 WATER
How does the property high latent heat of evaporation link to water?

A
  • The specific latent heat of a substance is the quantity of energy needed to change the state of 1kg of the substance without changing its temperature.
  • The latent heat of vaporization of water is very high as lots of energy is required to break the hydrogen bonds - they must be broken for water to evaporate.
  • Water vaporisation can be used for cooling down:
    When an organism sweats, the vaporised water molecules carry away lots of thermal energy from the body surface = cooling down.
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6
Q

2.2.1 WATER
How does the property very cohesive link to water?

A

cohesion - means that water ‘sticks’ to itself due to hydrogen bonding
water molecules are very cohesive because they’re popular
this helps water to flow, making it great for transporting substance
helps water to be transported up plant stems in the transpiration stream

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7
Q

2.2.1 WATER
How does the property lower density when solid link to water?

A

at lower temperatures water freezes - it turns from a liquid to a solid
water molecules are held further apart in ice than they are in liquid water because each water molecules form four hydrogen bonds to other water molecules, making a lattice shape
this makes ices less dence than liquid water - which makes ice float
useful for living organisms because in cold temperatures, ice forms an insulting layer on top of water - the water below doesn’t freeze
organisms that live in water, like fish, doesn’t freeze and can still move around

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8
Q

2.2.1 WATER
How does the property good solvent link to water?

A

Polar molecules & ions dissolve easily in water – they are described as hydrophilic.

The charges are attracted/ bind to the charged regions of water molecules

This enables them to be absorbed (by root hair cell/villi) & transported (in xylem/phloem or blood)

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9
Q

2.2.1 WATER
How does the property of taking part in many chemical reactions link to water?

A

water is a raw ingredient in photosynthesis
water is required for hydrolysis reaction

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10
Q

2.2.1 WATER
How does the property low viscosity ( flows freely ) link to water?

A

flowing freely due and resists deformation under stress less than other fluids due to weak intermolecular forces and molecular mobility

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11
Q

2.2.1 WATER
How does the property high surface tention link to water?

A
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12
Q

2.2.1 WATER
How does the property difficult to compress link to water?

A

water provides support in plants
molecules are close together

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13
Q

2.2.1 WATER
How does the property adhesion allows for capillarity link to water?

A

allows water to move against gravity up xylem vessles moleucles are attracted to surface

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14
Q

2.2.2 MACROMOLECULES AND POLYMERS
What is macromolecules?

A

are complex molecules with a relatively large molecular mass
can be made up of simialr or different molecules bonded together

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15
Q

2.2.2 MACROMOLECULES AND POLYMERS
What are polymers?

A

these are large complex molecules composed of long chains of monomers joined together
formed by condensation reactions

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16
Q

2.2.2 MACROMOLECULES AND POLYMERS
What are monomers

A

A small, simple molecule which is produced by hydrolysis of a polymer

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17
Q

2.2.2 MACROMOLECULES AND POLYMERS
What is hydrolysis and condensation reactions?

A

condensation - forms a bond between two molecules, producing a water molecule ( making a polymer )
hydrolysis - breaks a bond between two molecules by the addition of water ( creating monomers )

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18
Q

2.2.2 MACROMOLECULES AND POLYMERS
What are the properties of monosaccharides and disaccharide?

A

soluable in water
taste sweet
form crystals

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19
Q

2.2.2 MACROMOLECULES AND POLYMERS
What are three types of carbohyrdate of monsaccharides?

A

glucose
galactose
fructose

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20
Q

2.2.2 MACROMOLECULES AND POLYMERS
What are three types of carbohyrdate of disaccharides?

A

maltose
lactose
sucrose

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21
Q

2.2.2 MACROMOLECULES AND POLYMERS
What are three types of carbohyrdate of polysaccharides?

A

starch - plants
cellulose - plants
glycogen - animals, fungi

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22
Q

2.2.3 CARBOHYDRATES
What are carbohydrates made from?

A

made up of the same three chemicals - carbon (C), hydrogen (H) and oxygen (O)
the monomers that make up carbohydrates are called monosaccharides

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23
Q

2.2.3 CARBOHYDRATES
What is it called when the monomers make up the carbohydrates?

A

the monomers that make up carbohydrates are called monosaccharides

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24
Q

2.2.3 CARBOHYDRATES
How does the structure and properties of starch relate to their functions in living organisms?

A

energy storage molecule in plants - excess glucose from photosynthesis is stored as starch
insoluable in water so doesn’t interfere with osmotic potential of cells
contains lots of chemical bonds which release lots of energy when broken

contains of a mixture of two polysaccharides:
long, unbranched, coiled chains of alpha glucose - amylose
long, branched chains of alpha glucose - amylopectin

structure/function relationship : large - insoluable density packed, takes up little space, branches are easily hydrolysed - quickly releases energy

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25
2.2.3 CARBOHYDRATES How does the structure and properties of glycogen relate to their functions in living organisms?
energy storage molecule in animal and fungi - excess glucose from digestion is stroed as glycogen insoluable in water so doesn't interfere with osmotic potential of cells contains lots of chemical bonds which release lots of energy when broken some hydrogen bonds between sugar units in the chain contains long, highly branched chains of alpha glucose - 1,4 glycosidic with a 1,6 at branches similar to amylopectin, but many more side branches. this means its compact so more glucose molecules are readily available to meet increased respiratory demands of large, complex organisms structure/function relationship : large - insoluable, densely packed - takes up little space, even more branched which are easily hydolysed - quick relase of even more energy
26
2.2.3 CARBOHYDRATES How does the structure and properties of cellulose relate to their functions in living organisms?
important structural molecule in plants - plant cell walls insoluable in water so doesn't interfere with osmotic potential of cells consits of long, unbranched chains of beta glucose alternate molecules of beta glucose are inverted and bonded by 1,4 glycosidic bonds since they are inverted, the chains are straight hydrogen bonds occur between seperate chains of cellulose to form very strong fibres - microfibrils microfibrils are what cellulose is made of, and what gives plant cells thier great strength strucure/function relationship : straight chains with H - bonds = microfibrils = strong structural support
27
2.2.3 CARBOHYDRATES What is the structure of amylose?
unbranched chains are formed due to 1,4 glycosidic bonding only chains of alpha glucose has a helix shape hydrogen bonds between sugar units in the chain insoluable in water function is energy storage in plants
28
2.2.3 CARBOHYDRATES What is the structure of amylopectin?
branching occurs in amylopectin due to 1,6 glycosidic bonds as well as 1,4 glycosidic bonds alpha glucose chain some hydrogen bonds between sugar units in the chain insoluable in water function is energy storage in plants
29
2.2.4 LIPIDS What are lipids?
These are macromolecules all contains the chemical elements - carbon, hydrogen and oxygen
30
2.2.4 LIPIDS What are the functions of triglycerides?
AIDS buoyancy in aquatic mammals PROTECTION packaging around vital organs THERMAL INSULATION helps to reduce thermal energy loss by radiation source of WATER ( condensation reaction when storing fat ) aids ABSORPTION OF FAT - SOLUABLE VITAMINS ELECTRICAL INSULATION around neurons - helps to speed up conduction of action potentials they're a GOOD ENERGY STORAGE molecule due to their INSOLUABILITY and propensity ti cluster in small droplets/ micells ENERGY STORAGE in animals & plants due to long fatty acids - each bond is a potential source of chemical energy , they provide more energy than carbs due to the length of these chains - release ATP
31
2.2.4 LIPIDS What are triglycerides?
all triglycerides consits of one glycerol molecule and three fatty acid chains the fatty acids chains can be saturated or unsaturated contains ester bonds formed by condensation reactions = know as esterification triglycerides are formed by condensation reactions between a glycerol and 3 fatty acids
32
2.2.4 LIPIDS What is the structure of lipids in animals?
found in butter, lard and on meat are saturated don't contain any double bonds as each carbon is bonded to the maximum number of hydrogen as possible
33
2.2.4 LIPIDS What is the structure of lipids in plants?
found in oils, nuts and seeds are unsaturated these contain double bonds between some carbon atoms so there are fewer hydrogen atoms present
34
2.2.4 LIPIDS Explain the structure of saturated fatty acids?
every carbon atom is bonded to as many hydrogen atoms as possible no more can be added, hence 'saturated' ( with hydrogen ) contains carbon chain, with no ' kinks' trglycerides consisting of saturated fatty acids can pack togther to form solids fat as room temperature mainly found in animal fats from meat and dairy products carboxyl group (COOH) forms the acid
35
2.2.4 LIPIDS Explain the structure of unsaturated fatty acids?
not every carbon atoms is bonded to as many hydrogen atoms - hence 'unsaturated' double bondds introduce a definite 'kink' in the carbon atoms chain the more double bonds the more kinks there will be mainly found in vegetable oils, nuts and fish truglycerides consisting of 'kinked' unsaturated fatty acids do not pack together easily and form liquid oil as room temperature
36
2.2.4 LIPIDS What is the structure of phospholipids?
a phospholipids contains a glycerol bonded to two fatty acid chains and a phosphate group
37
2.2.4 LIPIDS What is the structure of cholesterol?
has a hydrocarbon ring structure attached to a hydrocarbon tail the rinf structure has a polar hydroxyl (OH) group attached to it
38
2.2.4 LIPIDS What is the function of phospholipids?
found in the cell membrane of all eukaryotes and prokaryotes they make up the phospholipid bilayer the centre of the bilayer is hydrophobic, so water-soluable substances can't easily pass through it - the membrane acts as a barrier to those substances can have a carbohydrate chains attached to form a glycolipid molecule which has an important role in cell signalling
39
2.2.4 LIPIDS What is the function of cholesterol?
helps to strenghten the cell membrane by interacting with the phospholipid bilayer has a small size and flatten shape - this allows cholesterol to fit in between the phospholipid molecules in the membrane they bind to the hydrophobic tails of the phospholipids, causing them to pack more closely together = this make the membranes less fluid and more rigid
40
2.2.5 PROTEINS What are proteins made from?
proteins are polymers the monomers of proteins are amino acids a dipeptide is formed when two amino acids join together a polypeptide is formed when more than two amino acids join together proteins are made up of one or more polypeptides
41
2.2.5 PROTEINS What is the general structure for amino acids?
a carboxyl group (COOH) an amino group (-NH2) attached to a carbon atom the difference between amnio acids is the variable group they contain
42
2.2.5 PROTEINS How are amino acids linked?
linked by peptide bonds to form dipeptides and polypeptides
43
2.2.5 PROTEINS What is the name of the reaction which releases a molecule of water?
condensation reaction
44
2.2.5 PROTEINS What is the name of the reaction which adds a molecule of water to break the peptide bond?
hydrolysis reaction
45
2.2.5 PROTEINS Explain the primary structure?
This is the sequence of amino acids in the polypeptide chain different proteins >> have different sequences of amino acids >> in their primary structure held together by the peptide bonds between two amino acids one amnio acids may change the structure of the whole protein the results of translation in protein synthesis
46
2.2.5 PROTEINS Explain the structure of the secondary protein
polypeptide chain doesn't remain flat and striaght hydrogen bonds from between the -NH and -CO groups of the amino acids in the chain This makes it automatically coil into an alpha helix or fold into a beta pleated sheet folding occurs due to hydrogen bonds between O (COOH) & H in (HN2) of different amino acids ( peptide bonds )
47
2.2.5 PROTEINS Explain the structure of the tertiary protein
3D structure lots of intermolecular interactions more folded and coiled further more bonds form between different parts of the polypeptide chain: - ionic bond - -ve charged R groups and +ve charged R groups have attraction - disulfide bond - 2 molecules of the amino acids cysteine come close together , the sulfur atom in one cysteine bonds to the sulfur in the other cysteine forming a disulfide bond - hydrophobic and hydrophilic intercations - (hydrophobic) water repelling R-groups are close together - tend to clump together ( hydrophilic )water attracting R-groups are likely to be pushed to the outside, which attracts how the protein fold up into its final strucure - hydrogen bonds - weak bonds form between slightly +ve charged hydrogen atoms in some R-groups and slightly -ve charged atoms in other R-groups on the polypeptide chain contains one polypeptide chain, peptide bonds between the amino acids
48
2.2.5 PROTEINS Explain the structure of the quaternary protein
some proteins are maded of several different polypeptide chains held together by bonds the quaternary structure tends to be determined by the tertiary structure of the individual polypeptide chains being bonded together quaternary structure is the proteins final 3D structure
49
2.2.5 PROTEINS What are the differences between fibrous and globular?
FIBROUS PROTEIN: - basic tertiary structure - long parallel polypeptide chains - cross linkages at intervals forming long fibres or sheets - usually insoluable - many have structural roles GLOBULAR PROTEIN: - have complex tertiary and sometimes quaternary structures - folded into spherical ( globular ) shape - usually soluable as hydrophobic side chains in centre of the structure - roles in metabolic reactions
50
2.2.5 PROTEINS Explain the the properties of fibrous protein
shape: long and narrow role : structural ( strenght and support ) soluability: insoluable in water sequence : repetitive amino acid sequence stability: less sensititve to changes in heat, pH etc. examples: collagen, myosin, fibrin, actin
51
2.2.5 PROTEINS Explain the the properties of globular protein
shape: rounded/spherical role : functional ( catalytic, transport, etc ) soluability: soluable in water sequence : irregular amino acid sequence stability: more sensititve to changes in heat, pH etc. examples: catalyse, haemoglobin, insulin etc
52
2.2.5 PROTEINS haemoglobin (globular)
what is its role? carries oxygen around the body in red blood cells why is it known as a conjugated protein? as its a protein with a non-protein group attached what is a prosthetic group? the non-protein part and each of the four polypeptide chains in haemoglobin has a prosthetic group called haem is it soluable? yes
53
2.2.5 PROTEINS insulin (globular)
what is its role? a hormone secreted by the pancrease and helps to regulate the blood glucose level to act as a chemical messenger >> signals liver & muscle cells to absorb more glucose form the blood to be dtored as glycogen >> decreases blood glucose levels is it soluable? yes what is it made of? it consists of two polypeptide chains what bonds are involved? disulfide bonds
54
2.2.5 PROTEINS amylase (globular)
what is its role? it is an enzyme that catalyses the breakdown of starch in the digestive system is it soluable? yes what is it made of? madde up of single chain of amino acid what level of protein structure is it? secondary struture which contains both & helix and beta pleated sheet
55
2.2.5 PROTEINS collagen (fibrous)
what is its role? provides sructural support to the extracellular space of connective tissue is it soluable? no what properties does it have? very strong molecule, inelastic but flexible what level of protein structure is it? quaternary - hydrogen bonds are presents between three polypeptide chains, forming tighty coiled triple helix molecules/fibrils
56
2.2.5 PROTEINS keratin (fibrous)
are all keratin molecules the same? no what's its role? protection helps form the tissues of the hair, nails and the outer layer of the skin can form a waterproof hard layer on skin surface what properties does it have? flexible hard and tough in nails is it soluable? no
57
2.2.5 PROTEINS elastin (fibrous)
what it's role? allows tisue in your body to stretch out and shrink back important role in connective tissue >> prevents blood vessles bursting under a slight increases in blood pressure also found in ligamnets and joint capsuales what properites does it have? elastic can be stretched to its orginal shape is it soluable? no
58
2.2.6 Inorganic ions What is the chemical symbol for the cation sodium and what is its role in biological processes?
formula : Na + charge : +1 role: rapid diffusion into an axon following stimulation (aids in communication along neurons)
59
2.2.6 Inorganic ions What is the chemical symbol for the cation ammonium and what is its role in biological processes?
formula : NH+ 4 charge : +1 role: substrate for nitrifying bacteria in the N cycle and in animals, it binds to carbon dioxide to make urea which is safely secreted
60
2.2.6 Inorganic ions What is the chemical symbol for the cation hydrogen and what is its role in biological processes?
formula : H + charge : +1 role: affects the pH of substances (more H+ ions than OH- ions on a solution creates an acid ). Also important for photsynthesis reactions that occur in the thylakoid membranes inside chloroplasts and respiration reactions that occur in the inner membrane of mitrochondria
61
2.2.6 Inorganic ions What is the chemical symbol for the cation calcium and what is its role in biological processes?
formula : Ca 2+ charge : +2 role: involved in the transmission of nerve impulses and the release of insulin from the pancrease acts as cofactor for many enzymes
62
2.2.6 Inorganic ions What is the chemical symbol for the cation potassium and what is its role in biological processes?
formula : K + charge : +1 role: important for regenerating nerve impulses for muscle contraction and for regulating fluid balance in the body activities essential enzymes needed for photosynthesis in plant cells
63
2.2.6 Inorganic ions What is the chemical symbol for the anion hydrogencarbonate and what is its role in biological processes?
formula : HCO - 3 charge : - 1 role: acts as a butter, which helpds to maintain the pH of the blood role in carbon dioxide transport around the body
64
2.2.6 Inorganic ions What is the chemical symbol for the anion chloride and what is its role in biological processes?
formula : CH - charge : - 1 role: helps to maintain the pH of the blood during gas exchange acts as a cofactor for the enzyme amylase also involved in the same nerve impulses involved in chloride shift
65
2.2.6 Inorganic ions What is the chemical symbol for the anion nitrate and what is its role in biological processes?
formula : NO - 3 charge : - 1 role: Substrate for denitrifying bacteria absorbed by root hair cells ( active transport ), maintains, water potential gradient & enables amino acid > growth
66
2.2.6 Inorganic ions What is the chemical symbol for the anion phosphate and what is its role in biological processes?
formula : PO4 3- charge : - 3 role: involved in photosynthsis and respiration needed for the synthesis of man biological molecules e.g. nucleotides, phospholipids, calcium phosphate
67
2.2.6 Inorganic ions What is the chemical symbol for the anion hydroxide and what is its role in biological processes?
formula : OH- charge : - 1 role: affects the pH of substances (more OH- ions than H + ions in a solution creates an alkali) more pH
68
2.2.7 Biochemical tests for Molecules What is a reducing sugar?
a reducing sugar is any sugar that is capable of acting as a reducing agent/ is oxidised (loses electrons)
69
2.2.7 Biochemical tests for Molecules What is the strucure for a reducing sugar?
in the ring structure, any sugar that has a C next to the O and an OH group ( for the chemist: a hemiacetal group ) can act as a reducing sugar therfore all monosaccharides are reducing sugars and some disaccharidea including lactose and maltose sucrose is a non-reducing sugar
70
2.2.7 Biochemical tests for Molecules How does the structure of water relate to reducing sugars?
in water, the ring of water sugar will open exposing, the aldehyde group which will be oxidised/ become the reducing agent
71
2.2.7 Biochemical tests for Molecules How does the structure of dissacharides link to reducing sugars?
in reducing sugars, dissacchrides such as maltose and lactose, one ring easily opens revealing the aldehyde group which gets oxidized sucrose does not
72
2.2.7 Biochemical tests for molecules What is a non-reducig sugar?
one which is not capable of acting as a reducing agent the carbons next to the O in both rings do not contain a OH group so cannot become a free aldehyde group ( the oxidizing agent ) when in solution
73
2.2.7 Biochemical tests for molecules How to test for Non-reducing sugars?
1) Carry out the Benedict test : negative result so no reducing sugar 2) Hydrolyse the unknown to split the sugar into monosaccharides: - Add hydrochloric acid - Heat in a water bath - Neutralise using hydrogen carbonate 3) Repeat Benedict’s test If it goes brick red this time there is non-reducing sugar present A negative results could mean the mystery sample contains a non-reducing sugar By the process of elimination we can determine if it contains a non-reducing sugar : we test it a second time after heating with acid to break the glycosidic bonds, and alkali to neutralise the acid If it turns red we know the solution contains a non-reducing sugar If it remains blue, the solution contains a different molecule
74
2.2.7 Biochemical test for molecules
With Benedict’s reagent, reducing sugars lose electrons to Cu2+ ions forming Cu+ ions This is seen as a colour change from blue to brick red The copper oxide is an insoluble precipitate and the sugar is oxidised forming carboxylate acid

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