Chapter 2: Biological Molecules Flashcards

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1
Q

How do saturated and unsaturated lipids vary in structure

A

Sat have C-C only single bonds

Unsat have double bonds

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2
Q

What are 3 types of unsaturated lipids in terms of no. of double bonds

A

Mono unsat
Di unsat
Poly unsat

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3
Q

Which states are sat and Unsat lipids at room temp, and what are their originsm

A

Sat - solid, animals

Unsat - liquid, plants

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4
Q

Why are unsat lipids liquid at room temp

A

Double bonds make them melt more easily because the double bond causes gaps in the tail

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5
Q

What is the formula for formation of an Ester?

A

(carboxylic) acid+ alcohol —> ester + water

Recall structural formulae equation

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6
Q

How is a triglyceride molecule formed (process and raw materials)

A

Glycerol+ 3 Fatty acids with hydrocarbon tails
—> By-product water and Triglyceride molecule

—> = Condensation

Recall structural formulae equation

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7
Q

How is a phospholipid formed

A

When one of the 3 fatty acids in triglyceride is replaced by a phosphate group

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8
Q

What is a dipole

A

Unequal distribution of charge

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9
Q

Where do dipoles essential occur

A

Molecules containing -OH, -CO & -NH groups

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10
Q

What is a hydrogen bond (eg in water)

A

In water negatively charged oxygen of one molecule is attracted to positively charged hydrogen of ANOTHER molecule, the attraction between the 2 is the H bond

Note: the attraction between 2 atoms WITHIN the SAME molecule is the covalent bond

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11
Q

What are polar molecules

A

Having dipoles

HYDROPHILIC

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12
Q

Why are non polar molecules insoluble

A

They not have dipoles (uncharged) to attract dipoles of water molecules
HYDROPHOBIC

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13
Q

What is the specialty of H bonds?

A

Individually weak, but collectively very strong

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14
Q

Which lipids are sol and which are insol

And why

A

Sol-phospholipid(hydrophilic) : charged phosphate attracts partially +ve hydrogen

Insol-triglyceride(hydrophobic) : no charged groups

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15
Q

Tests (2) for lipids:

A
  • 1cm3 unknown + 1cm3 of alcohol/organic solvent (ethene) —> sample dissolved if lipid is present
  • 1cm3 of unknown + 1cm3 of water —> sample will not dissolve if lipid is present(emulsion)
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16
Q

Confirmatory test for lipids:

A

1cm3 unknown + 1cm3 organic solvent —> lipid will dissolve

Transfer to testtube with water. Milky white ppt formed, lipid is confirmed

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17
Q

Why are lipids significant energy reserves

A

They are richer in carbon-hydrogen bonds than carbs, which when broken supply hydrogen yo make nadh and fadh2.
A given mass of lipids yields more energy on oxidation than same mass of carb (high caloric value)

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18
Q

How are lipids insulators

A

Below the dermis of skin, and around the kidneys it prevents heat loss

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19
Q

Lipids can be blubber. What is this

A

In sea mammals, insulated and provides buoyancy (float)

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20
Q

How are lipids metabolic sources of water

A

When oxidised in respiration they are converted to CO2 and H2O. It is important for survival in dry habitats

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21
Q

General formula of carbohydrates :

A

Cx (H2O) y

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22
Q

Carbohydrates aka

A

Hydrates of carbon

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23
Q

Elements in carbs:

A

C
H
O

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24
Q

What 3 types of carbs

A

Monosaccharides (1 sugar unit)
Disaccharides
Polysaccharides

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25
Q

Examples of
Monosaccharides
Disaccharides
Polysaccharides

A

Mono - glucose, fructose, galactose
Di- maltose, sucrose, lactose
Poly- starch, glycogen, cellulose

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26
Q

General properties of monosaccharides :

A
  • 1 sugar unit
  • sweet in taste
  • easily soluble in water
  • general formula : (CH2O) n
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27
Q

Types of monosaccharides based on n (name, n, formula, eg)

A

Trioses n=3 C3H603 glyceraldehyde 3 phosphate

Tetroses n=4 C4H8O4 trythulose

Pentoses n=5 C5H10O5 ribose and deoxyribose

Hexoses n=6 C6H12O6 glucose, galactose, fructose

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28
Q

Linear structure of glucose

A

Recall structure (aldehyde/ketone and carbonyl groups, 6 carbons)

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29
Q

How is ring structure of glucose formed from linear

A

Long chain of carbon atoms is enough to close up on itself to form stable ring

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30
Q

Recall the ring structure of glucose

A

lol k

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31
Q

Structural difference between α and β glucose?

A

α- anomeric carbon (C1) has H bonds at top and OH at bottom

β- C1 has H bonds at bottom, and OH at top

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32
Q

Recall exact structures of α & β glucose

A

kkkayy

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33
Q

Where is anomeric carbon derived from

A

Carbon of ketone/aldehyde functional group of the open chain form of carbohydrate

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34
Q

What is anomerization

A

Process of interconversion of one anomer to another

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35
Q

3 roles of monosaccharides

A

2f acts as building block (glucose: starch glycogen, cellulose)

Nucleic acid (RNA & DNA, each have basic functional unit ie nucleotide, which is made of PO3-, nitrogenous base- A, G, T, C, U, pentosugar)

Many C-H bonds broken to release energy which is transferred to help make ATP

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36
Q

What are sucrose, lactose, maltose made of?

A
Sucrose= glucose + fructose ( transport form in plants, sold sugar) 
Lactose= glucose + galactose (milk sugar) 
Maltose= glucose + glucose (malt sugar)
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37
Q

Difference between reducing and non reducing sugars?

A

Red- free anomeric carbon (c1)

Non red- free anomeric (c1) carbon absent

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38
Q

Examples of red and non red sugars

A

Red- maltose, lactose

Nonred- sucrose

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39
Q

Bonds involved in monosaccharides and in disaccharide maltose and process. Also recall structural formulation of maltose

A

α glucose + α glucose —> α1,4 glycosidic bond (C-O-C) by condensation

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40
Q

Bonds involved in monosaccharides and in disaccharide sucrose and process. Also recall structural formulation

A

α glucose + β fructose —> β1,2 glycosidic linkage by condensation

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41
Q

State the test for reducing sugars and the mechanism

A

1cm3 of sugar+ 1cm3 of benedicts (CuSO4) reagent (excess to react all sugar) —> brick red ppt (confirms)

Reducing sugar+ Cu(II) blue —> brick red ppt(Cu+) + oxidised sugar
Cu2+ reduced to Cu+ by reducing sugar

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42
Q

Steps for testing for a non reducing sugar:

A

1) Convert it to reducing sugars
2cm3 of non red sugar + 1cm3 HCl —mix and heat 2min, break glycosidic bond—> α glucose + β fructose

2) Neutralise HCl
Add 1ml of NAOH OR NAHCO3 until fizzing stops (benedicts works best under alkaline condition)

3) Perform benedicts.
To above + 2ml benedicts –heat–cool–> brick red ppt (confirms presence of non red sugar). If no color change still no sugar

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42
Q

Why use excess benedicts ?

A

Ensure all reducing sugar has reacted

This helps in calculating exact concentration of sugar in solution using a colorometer

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43
Q

How does color of ppt change for benedicts with concentration of sugar

A

Intensity

Blue, green, yellow orange red, brick red

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44
Q

Outline how benedicts test can be used to estimate concentration of a reducing sugar

A

Add benedicts. Heat in water bath. Will turn gradually from green, yellow, orange, red as insol Cu(i) oxide forms a ppt.
Use color standards made by comparing color against colors obtained with reducing sugar tests of known concentrations.
Or use colorimeter to measure more precisely (graph of conc plotted against colorimeter reading)

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45
Q

Why are they called reducing sugars?

A

Can carry out reduction, by themselves getting oxidised in the process. (lose electrons, to make other reactant ion less positively charged)

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46
Q

How can a benedicts test tell you if both reducing and non reducing sugars are present

A

Ppt obtained in non reducing test will be heavier than benedicts normal test

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47
Q

What are Polysaccharides

A

Made up of more than 2 sugar units

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48
Q

What is starch

A

A Polysaccharide, storage form in glucose in plants, in chloroplasts.

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49
Q

What is starch made up of

A

Amylose and amylopectin

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50
Q

Structure of Amylose

A

Polymer of α glucose

α 1,4 glycosidic bond

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51
Q

Structure of amylopectin

A

Polymer of α glucose
α 1,4 and α 1,6 glycosidic bonds
Branched

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52
Q

Structure of glycogen :

A

Polymer of α glucose
α 1,4 and α 1,6 glycosidic bond
More branching than in amylopectin

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53
Q

Function of glycogen

A

Storage form of glucose in animals. Stored in muscle and liver cells

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54
Q

Why can glucose not be stored as such in cells

A

It is very reactive and will affect cell chemistry badly.
It will dissolve the cytoplasm and make it too concentrated that will further sensitively affect osmotic properties of the cell

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55
Q

Why is glucose stored as glycogen

A

It is inert (unreactive)
Needs less space
Insoluble doesn’t affect osmotic properties of cell

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56
Q

Most abundant organic molecule in plant ?

A

Cellulose

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57
Q

Structure of cellulose:

A

Polymer of β glucose with β 1,4 glycosidic bond

In the β isomer the -OH group on C1 is above ring. In order to form a glycosidic bond with C4 where -OH group is below ring, one glucose must be upside down (180°) relative to the successive one

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58
Q

How do cellulose fibres provide strength to cell wall

A
  • Adjacent cellulose molecules are held by hydrogen bonds between +H and -O
  • Individual H bonds are weak, collectively strong
  • Many cellulose form microfibrils, many of these form fibres
  • Cell wall has several fibres running in different directions to provide strength
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59
Q

How do cellulose molecules form fibres?

A

60-70 molecules are tightly cross linked to form bundles called microfibrils. These are held together in bundles called fibres by hydrogen bonding

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60
Q

Why are cellulose fibres so strong

A

Arrangement of β glucose molecules in such a way that hydrogen bonds existing between the large no. of -OH groups collectively provide huge strength

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61
Q

Enzymes are which organic molecule

A

Proteins

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62
Q

Proteins are components of _ and function as _

A

Cell membrane

Receptors and signallers

63
Q

Examples of protein hormones

A

Insulin

Glucagon

64
Q

Size of mirofibril

A

10nm diameter

65
Q

Size of cellulose fibre

A

50nm

66
Q

Which oxygen carrying pigments are proteins

A

Haemoglobin in RBC

Myoglobin in muscle cell

67
Q

What other component of blood apart of haemoglobin and Myoglobin is protein

A

Antibodies

68
Q

Collagen is made of _ and adds _ to animal _

A

Protein
Strength
Tissues

69
Q

What do hair nails and layers of skin contain

A

Protein keratin

70
Q

Which proteins are responsible for muscle contraction

A

Actin

Myosin

71
Q

Casein in milk and ovalbumin in egg white are _ proteins

A

Storagwb

72
Q

Functional unit of protein

A

Amino acid

73
Q

How many essential and non essential amino acids and define

A

E- 9 body can’t make, rely on external source

Non E- 11 body can make

74
Q

General structure of amino acid:

Recall structure

A

Amine group -NH2
Alkyl group -R (CH3 methyl, C2H5 ethyl, C3H7 propyl)
C-H
Carboxylic acid -COOH

75
Q

What makes the 20 amino acids different

A

The R group

76
Q

How do 2 amino acids link

A

Loss of water molecule by condensation to form peptide bond and hence a dipeptide molecule

77
Q

What’s a peptide bonds structure

A

C=O
|
N-H

78
Q

How is condensation done between amino acids

A

One loses -OH from COOH while other loses H from NH2

This leaves carbon of first amino acid to bond with Nitrogen of second

79
Q

Types of protein based on no of amino acids

A

Dipeptide -2
Tripeptide- 3
Polypeptide- many

80
Q

Which organelles help in protein synthesis

A

Ribosomes join amino acids

81
Q

Where in digestive system is protein digestion done

A

Stomach (acidic pH, enzyme pepsin)

and small intestine

82
Q

What is primary structure of proteins

A

Linear sequence of amino acids in a polypeptide chain

83
Q

What are 2 ends of Polypeptide chain called

A

NH2 terminal

COOH terminal

84
Q

What is secondary structure

A

Regular coding folding of amino acid chain

85
Q

What is secondary coding

A

α helix

Due to hydrogen bonding between oxygen of CO on one amino acid and NH of an amino acid four places ahead

86
Q

What is folding secondary structure

A

β pleated sheet
NH group in backbone of one fully extended strand establishes hydrogen bond with C=O group in backbone of adjacent fully extended strand

87
Q

2 orientations of adjacent Polypeptide chains

Recall diagrams

A

1) same direction OR parallel

2) opp direction OR antiparallel

88
Q

How can hydrogen bonds in β pleated sheets be broken even though are strong enough

A

High temp

pH changes

89
Q

What is tertiary structure

A

3d coiling of already folded SINGLE chain of amino acids, of both α helix and β sheet

90
Q

Which 2 enzymes have tertiary structure and what’s their function

A

Hyzozyme - in tears, hydrolyses bacteria by breaking peptidoglycan chain in cell wall to lyse/burst the cell

Myoglobin - 02 carting pigment in muscle

91
Q

Test for proteins

A

1cm3 of sample + 1cm3 biuret reagent (CUSO4 in KOH/NaOH alkaline medium) —> Purple color (not blue) confirms presence of protein

92
Q

What extra reagent can be added to biuret to avoid ppt formation

A

CUSO4 mixed with KOH or NaOH by adding sodium potassium tartrate or sodium citrate

93
Q

Mechanism of biuret test

A

Cu + N - copper of biuret forms complex with N of peptide bond to result in purple color

94
Q

Structure of Myoglobin

A

α helix linked by polypeptide chains. Haem group attached contained Fe2+ and porphyrin ring

95
Q

Which 4 bonds stabilise tertiary and quarternery structure

A

Hydrogen
Covalent (disulfide)
Ionic
Weak hydrophobic interactions

96
Q

Where do H bonds form

A

Between strongly polar groups

NH, CO, OH

97
Q

Howis H bond represented

A
98
Q

Where do disulfide bonds form

A

Between cysteine molecules (an amino acid)

99
Q

How can disulfide bonds be broken

A

By reducing agents

100
Q

Recall diagram of disulfide reaction

A

2S-H (sulphydryl group) (-2H oxidation) –> S-S disulfide bond

101
Q

Wher3 in proteins are ionic bonds formed

A

Ionised Amine (NH3+) and ionised carboxylic acid (COO-)

102
Q

How can ionic bonds be broken

A

pH changes

103
Q

Where do weak hydrophobic interactions occur, and how do they stay together though weak

A

Between non polar R groups

Repelled by watery environment around them

104
Q

What is the order of strength of bonds

A

covalent(disulfide)>ionic>hydrogen>hydrophobic interaction

105
Q

What is quarternery structure

A

3d arrangement of 2 or more Polypeptides, or of a Polypeptide and a non protein component

106
Q

Structure of haemoglobin

A

2 α globin Polypeptide chains
2 β globin Polypeptide chains
Each chain has a heam group, which is non protein or prosthetic group
Each haem has an Fe atom to bind with a molecule of O2

107
Q

Each iron atom can _ bind with _ oxygen atoms

A

Reversibly

8

108
Q

Where are oxy and deoxy haemoglobin found and what are their colors

A

Oxy -lung, red

Deoxy -tissue, purple

109
Q

What maintain the shape and solubility of haemoglobin

A

Shape - interactions between hydrophobic R groups inside the molecule
Sol - onward pointing hydrophilic R groups on surface of molecule

110
Q

What is sickle cell anaemia

A

A genetic disorder
Happens at position 6 of amino acid of β polypeptide chain
At 6, glutamic acid (hydrophilic) is replaced with valine (hydrophobic) responsible for sickle shape RBC

111
Q

What is cooperative binding

A

1) each haemoglobin molecule can bind to 4O2
2) haemoglobin exhibits cooperative binding. As O2 binds to iron of any one polypeptide subunit increases the rate (affinity) of other subunits TI bind with O2 in a sequential manner
3) increased affinity is caused by a confirmational change or a structural change in haemoglobin-each of subunits

112
Q

3 differences between globular and fibrous protein

A

G- ball shaped or globular F- long strand or fibre
G- soluble because hydrophobic amino acids towards centre and hydrophilic to peripheral
F- insol, mostly hydrophobic amino acids
G- takes part in metabolic reaction
F- takes part to maintain structural parts ie tendon ligaments

113
Q

Examples of globular and fibrous protein

A

G - enzyme (lysosome), haemoglobin, myoglobin

F - structural protein like collagen, keratin

114
Q

What are the 2 types of metabolic reaction

A

Annabolic - making

Catabolic - breaking

115
Q

What is nature of collagen

A

Insoluble fibrous protein

116
Q

Locations of collagen

A
Skin
Tendons 
Cartilage
Bones
Teeth 
Blood vessel walls
117
Q

Structure of collagen

A
  • 3 polypeptide chains, wound around each other in shape of triple helix.
  • The 3 strands are held together by hydrogen bonds and some covalent.

•Every 3rd amino acid is glycine, smallest amino acid. It is found on insides of strands and it’s small size allows the 3 strands to lie close together and form a tight coil. Other amino acids too large

  • Many of these triple helices lie side by side, linked by covalent cross links between side chains of amino acids near ends of polypeptides to form fibrils.
  • The ends of parallel molecules are out of step/staggered preventing a weak spot running across the fibril and hence making collagen stronger

•Many fibrils lie alongside eachother forming strong bundles called fibres

118
Q

5 differences between triple helix and α helix

A

1) T has 3 chains, α has 1
2) T has glycine every 3rd position, α amino acids are linked by peptide bonds to form coils
3) T has H and covalent bonds to stabilise structure, α has H bonds to stabilise the structure between CO and NH of amino acid 4 placed ahead
4) Collagen is in skin etc, α is secondary structure
5) T has 3 amino acids per turn, α has 3.6 amino acid residues

119
Q

Dipole in water molecule

A

Small Δ- on oxygen atom

Small Δ+ on hydrogen atoms

120
Q

What makes water molecules difficult to separate

A

Hydrogen bonding

121
Q

Why is it difficult to convert water from l to g

A

A lot of energy needed to break hydrogen bonds

122
Q

Why is hydrogen disulfide gas at normal air temperature

A

Lacks hydrogen bonds

123
Q

Examples of systems using water as a transport medium

A
Blood circulation 
Lymph 
Digestive system 
Excretory 
Xyle/phloem
124
Q

What is specific heat capacity

A

Amount of heat energy needed by a given mass of a substance- 1kg to raise it’s temperature by 1°C

125
Q

The higher the _ the higher the energy needed TI raise _

A
Kinetic energy (due to molecule speed)
Temperature
126
Q

Why do large water bodies not change temp as easily as air

A

More mass

Hence more energy needed to raise temp even by a bit

127
Q

Role of water in photosynthesis

A

Reagent

128
Q

Photosynthesis equation

A

sunlight
6CO2+6H2O—————-> 6CO2+C6H1206
chlorophyll

129
Q

Water has a role in _ opp of condensation

A

Hydrolysis

130
Q

What is cohesion

A

Ability of water molecules to stick to each other because of hydrogen bonds

131
Q

What is surface tension

A

Property of water to attain minimum surface area by keeping water molecules close together by Hydrogen bonds

132
Q

How do organisms exploit surface of water as habitat

A

High cohesion and surface tension of water due to hydrogen bonds

133
Q

What in plants uses cohesion and surface tension of water to it’s advantage

A

Tranpirational pull of water through xylem

134
Q

Test for starch

A

1cm3 of sample+Iodine (I2) dissolved in potassium iodide —-> blue black color, because (recall structure) I2 fits into middle hole of starchs helical coil

135
Q

What is a macromolecule

A

Large biological molecule (no repeat unit)

Eg protein, polysaccharide

136
Q

What is a monomer

A

Simple molecule, uses to basic building block for polymer synthesis, many monomers are joined ie by condensation reactions

Eg monosaccharides, nucleotides

137
Q

What’s a polymer

A

Giant molecule made from many similar repeating subunits/functional groups joined together, which are smaller and simpler ie monomers

Eg polysaccharides, nucleic acids

138
Q

What makes water a good solvent

A

Dipoles

139
Q

What happens when NACL dissolves in water

A

Na+ and Cl- separate and spread between water molecules

Na+ is attracted to -ve charge of O, and Cl- TI +ve charge of H

140
Q

Where and how do dipoles occur

A

Molecules with OH, CO, NH groups

Hydrogen bonds form between the partially oppositepy charged parts

141
Q

Molecules with dipoles are said to be

A

Polar

142
Q

Why are polar molecules called so?

A

Have dipoles
Attracted to water molecules as they also have dipoles
Hydrophilic, sol in water

143
Q

Molecules without dipoles are

A

Non polar

144
Q

Non polar molecules are _ in water they are _

A

Insoluble

Hydrophobic

145
Q

What is latent heat of vaporization

A

Measure of heat energy needed to vaporise a liquid to gas/vapor

146
Q

Why does water have high latent heat of vaporization

A

High specific heat capacity

Hydrogen bonding makes molecules stick to eachother

147
Q

How does high latent heat of vaporization of water help animals and plants (organismally)

A

When water evaporates it absorbs a lot of heat from it’s surrounding
Animal- sweat evaporates from skin ie cooling effect
Plant- transpiration from leaves

148
Q

Why is it less likely for water bodies to freeze

A

Water should change from liquid to solid right
So in this case it must lose a lot of energy, that’s why it’s hard to freeze
Hence advantage to aquatic animals

149
Q

What is the peculiarity of ice and what’s the reason behind it

A

In solid form, ice is less dense and doesn’t sink when submerged
Reason: crystalline structure of ice

150
Q

Which direction does water freeze

A

Top to bottom

151
Q

When water cools what happens? What happens further to become ice?

A

Temp decreases
Density increases
Because molecules lose kinetic energy and get closer below 4°C.

This trend is reversed when water approaches freezing point 0°C, when water forms a lattice and stretches by forming elastic hydrogen bonds.
Density decreases lower than at 4°C and ice floats

152
Q

How does the water below ice stay as water? How is this good?

A

Layer of ice acts as an insulator, slowing down heat loss from water beneath which remains at 4°C and liquid

This allows organisms to live even when air temps are below freezing point

153
Q

What makes water circulate nutrients

A

Changes in density of water with temperature cause currents which circulate nutrients in oceans

154
Q

7 properties of water:

A
  • Solvent
  • Tranport medium
  • High specific heat capacity
  • High latent heat of vaporization
  • Density (freezing point)
  • Reagent
  • High cohesion and surface tension
155
Q

Location of glycogen

A

Live and muscle cells