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A- Level Biology > C3- Biological molecules > Flashcards

C3- Biological molecules Flashcards

1
Q

What is hydrophilic?

A

A molecule which is attracted to water.

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2
Q

What is hydrophobic

A

A molecule that repels water.

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3
Q

Why is water a polar molecule

A

An unequal distribution of charge between the covalent bond. Electrons have stronger forces of attraction tot h oxygen atom.

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4
Q

What is a dipolar molecule

A

A molecule with 2 charged regions

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5
Q

What holds water molecules together

A

hydrogen bonds

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6
Q

6 properties of water

A
  1. Cohesion
  2. Adhesion
  3. solvent
  4. High surface tension
  5. ice is less dense than water
  6. transparent
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7
Q

What is water cohesion

A

How water molecules are attracted to other water molecules by hydrogen bonds, which allows water to be pulled as one continuous column.

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8
Q

What is water adhesion

A

Water molecules stick to the sides of walls of xylem due to forces of attraction, this aids the transpiration stream

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9
Q

How does water act as a solvent

A

Water dissociates ions and causes the ions to move to the either of the polar ends of the water molecule

then surrounds ions in solution

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10
Q

Is a soluble substance hydrophilic or hydrophobic

A

hydrophilic

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11
Q

Why do metabolic reactions take place in solvents

A

Substances dissolve in water and are free to move, this increases the chances of collisions and therefore reactions

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12
Q

Thermal properties of water

A

High latent heat of vaporisation, high heat capacity

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13
Q

Why does water have high heat capacity

A

Hydrogen bonding. It will absorb or loose a large amount of energy before its temperature changes. Temperature ‘buffer’

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13
Q

Why is waters density important

A

Ice floats, provides habitat and insulation

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14
Q

Why is waters constant temperature important

A

Maintains enzyme function, due to its narrow range of temperatures for optimum

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15
Q

Uses of waters high latent heat of vaporisation (2)

A

Sweating. Cooling effect as water evaporates from skin as energy is used up
Same effect but for transpiration

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16
Q

Water metabolite reactions (3)

A

Hydrolysis reactions- Large Molecules are broken down into smaller ones using water
Condensation reactions- water is produced when smaller molecules join together
Photosynthesis

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17
Q

Why is the fact that water is a solvent useful

A

Most biological reactions take place in a solution
Dissolved substances can be transported around the body

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18
Q

Hydroxyl Group

A

OH

Polar functional group
-> when added to a molecule it helps it mix with water

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19
Q

3 functions of carbohydrates

A

1- Energy source
-> Sugars

2- Energy store
-> Glycogen and starch

3- Structural
-> Cellulose, Chitin

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20
Q

Alpha glucose Vs Beta Glucose

A

Both are hexose monosaccharides

C1 OH and H Group are swapped around, OH down on alpha

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21
Q

What bond joins a disaccharide of alpha glucose

A

1,4 Glycocidic bond

Pointed downwards as OH groups were down`

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22
Q

Isomer

A

Same molecular formula but a different structural formula

E.g Alpha vs beta Glucose

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23
Q

Ribose Vs Deoxyribose

A

Both pentose Monosaccharides
-> 5C

C2OH Group on ribose looses oxygen on Deoxyribose

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24
Q

hydrolysis reaction

A

Large molecules broken down by addition of water

E.g Lactose is hydrolysed into glucose + Galactose

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25
Q

2 types of starch

A

Amylose
-> Unbranched

Amylopectin
-> Branched

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26
Q

Amylose (5)

A

Storage of glucose in plants

Alpha glucose monomers

1,4 Glycocidic bonds ONLY

Helical ( due to H bonds)

Not branched

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27
Q

Amylopectin (5)

A

More efficient store of glucose for plants

Alpha glucose monomers

1,4 AND 1,6 Glycocidic bonds

Helical

Quite branched
-> every 20 monomers

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28
Q

Glycogen (5)

A

Store of Glucose in Animals

Alpha glucose monomers

1,4 AND 1,6 Glycocidic Bonds

Helical

Very branched
-> Every 10 monomers

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29
Q

Explain how the structure of glycogen makes it a suitable storage molecule

A

highly Branched

Compact
-> Can store a lot of energy

Many terminal glucose molecules
-> Hydrolysed quickly

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30
Q

Glycogen is more branched than starch

What’s the significance of this for animals?

A

Animals are metabolically active
-> Need more energy

Glycogen stores more energy and releases it faster

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31
Q

Fatty acid general formula

A

RCOOH

R= variable number of N C O atoms

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32
Q

What type of reaction takes plac when glycerol reacts with a fatty acid

A

Condensation

3 H20 molecules produced

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33
Q

Type of reaction when a triglyceride is broken down in digestion

A

hydrolysis

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34
Q

Cellulose

structure
4

A

beta glucose monomers

Straight parallel unbranched chains

Hydrogen bonds crosslink chains

Every other beta glucose monomer is inverted

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35
Q

Which functional groups do H bonds form between parallel chains of cellullose

A

OH

Hydroxyl Group

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36
Q

Beta glucose monomers joined by ____ in cellulose

A

1,4 Glycosidic bonds

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37
Q

Structural feature that gives cellulose its high tensile strength

A

Cross linkages of hydrogen Bonds

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38
Q

Cellulose

Function

A

Structural polymer

Strength + rigidity

Inwards force to prevent bursting maintaining turgor

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39
Q

4 Cellulose properties

A

Insoluble

flexible

unreactive

high tensile strength

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40
Q

How is cellulose formed

3

A

Made of beta Glucose

1,4 glycosidic bonds

Formed by condensation polymerisation where every other beta glucose monomer inverts

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41
Q

Fats

5

A

Solid at RTP

Large macromolecules of C H O

Low mass for molecule size

Energy rich

insoluble

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42
Q

triglyceride

A

Glycerol + 3 fatty acids -> triglyceride

I—
I—
I—

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43
Q

Fatty acids

A

COOH - carboxyl group
–> carbocyclic acid

Saturated fatty acid general formula
Cn H2n+1 COOH

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44
Q

Esterification

A

Type of condensation reaction

Carboxyl group on fatty acid and hydroxyl group on glycerol

alcohol +acid -> ester + water

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45
Q

Ester bond

A

COO

o
 I o=c
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46
Q

Reducing sugars

A

All monosaccharides
some disaccharides

Can donate electrons
–> ability to reduce other molecules

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47
Q

Benedict’s reagent

A

Cu 2+ ions

Alkaline solution of Cu(II) sulfate

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48
Q

Reducing sugars Chemical test

method

A

1 place sample to be tested in a boiling tube, if not liquid then grind or blend in water

2 add equal volume benedict’s reagent

3 heat gently in >80c water bath for 5 minutes

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49
Q

benedict reagent

Result

A

Green to brick red
low to high level of reducing sugars

Cu 2+ ions reduced to red Cu + ions

More reducing sugars= more ions

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50
Q

Non reducing sugars chemical test

A

E.g. Sucrose

Acid hydrolysis
–> boil with dilute HCl

Sucrose hydrolysed to glucose and fructose
-both reducing sugars

Then use benedict’s Reagent

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51
Q

Saturated fatty acid chain

A

No double bonds present between carbon atoms

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52
Q

Unsaturated fatty acids

A

Double bonds between some of carbon atoms

causes molecules to kink
–> less dense at RTP
- cannot pack as closely together

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53
Q

Monounsaturated fatty acids

A

One double bond

More than one double bond
= polyunsaturated

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54
Q

Phospholipids

structure

A

Modified triglycerides
–> P C H O

PO4 3- ions

one fatty acid chain replaced with phosphate group

O
II

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55
Q

Phospholipid structure

A

Non polar tail - fatty acid
polar/charged head - phosphate

Tail= hydrophobic
head= hydrophilic

Surfactant- forms a layer on water surface

O
II

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56
Q

Phospholipid bilayer

A

Protect from water

Hydrophobic tails point inwards and hydrophilic heads point outwards in a ring

57
Q

sterols

A

steroid alcohols- type of lipid

OH group

4 carbon ring

Dual hydrophilic/phobic characteristics

58
Q

Cholesterol

A

Sterol - lipid

In cell membrane
–> between phospholipids and OH group

For stability of cell membrane

59
Q

Roles of lipids

6

A

Membrane formation

hormone production

electrical insulation- axons

thermal insulation

cushioning of organs

buoyancy

60
Q

Identification of lipids

test

A

Emulsion test.

Mix sample with ethanol

mix with water and shake

White emulsion formed = positive
Remains clear= negative

61
Q

Basic structure of an amino acid

A

H H O-H
N - C- C
H R =O

62
Q

Which elements are proteins made of

A

H N C O

S - cysteine only
–> Sulfur in R group

63
Q

Bond formed between two amino acids

and func groups

A

Peptide bond

Amine and carboxyl group

64
Q

Dipeptide

A

2 Amino acids bonded together

65
Q

R group on amino acids

A

On amino acid

Variable

Determines properties

66
Q

Polypeptides

Primary structure

A

Peptide bonds

Sequence in which amino acids are formed

Sequence influences how polypeptides form
–> determines function

67
Q

Polypeptides

Secondary Structure

A

Repeating structure of amino acids interact

–>not R groups

H bonds form in chain
- Coiled Alpha helix
- Beta pleated sheet

68
Q

Polypeptides

Quaternary structure

A

2 or more individual proteins called subunits

same interactions as tertiary except now between whole molecules and not within

subunits may be identical or different

69
Q

Tertiary structure

Hydrophilic and hydrophobic interactions

A

Protein folds based on whether the R group is hydrophilic or hydrophobic

70
Q

Breakdown of peptides

A

breaking peptide bonds is a hydrolysis reaction that is catalysed by proteases

71
Q

Polypeptides

Tertiary structure

A

Section of the secondary structure
–> interactions between R groups

1) Hydrophilic / hydrophobic interactions
2) H bonds ( weak)
3) Ionic bonds ( vulnerable to PH changes)
4) Disulphide bonds/ Bridges ( strong)

Final shape determines function
- specific 3D shape

72
Q

H Bonds

Heat

A

H Bonds are overcome

Causes 3D shape of protein to change
–> changing its function

‘denaturing’

73
Q

Polypeptide

Secondary structure
–> formation
(3)

A

H bonds

Form between amino acids in polypeptide chain

Causes regions of chain to twist into an alpha helix or fold into a beta pleated sheet

74
Q

Amino acid

Properties, 3

A

Soluble
- form polar ions in water

3 bases ( codon) codes for an amino acid

amphoteric
- Can donate or accept protons. Ph buffer

75
Q

Polypeptides

Primary structure

A

Sequence in which amino acids are formed

Peptide bonds

Sequence influences how polypeptides formed
–> determines function

76
Q

Polypeptides

Secondary structure

A

Repeating structure of amino acids interact
–> not R groups

H bonds form in chain
–> coiled alpha helix
beta pleated sheet

77
Q

Polypeptides

Quaternary Structure

A

2 or more individual proteins called subunits

Same interactions as tertiary
–> except now between molecules not within

Subunits may be identical or different

78
Q

Hydrophilic and hydrophobic interactions

A

Protein folds based on whether R group is hydrophilic or hydrophobic

79
Q

Breakdown of peptides

A

breaking peptide bonds is a hydrolysis reaction catalysed by proteases

80
Q

Polypeptides

Tertiary structure

A

Sections of secondary structure interact between R groups

1- hydrophilic/ hydrophobic interactions
2- H bonds ( weak)
3- Ionic Bonds ( vulnerable to Ph changes)
4- Disulphide bonds/ bridges ( strong)

Final shape determines function
–> specific 3D shape

81
Q

H bonds

Heat

A

H Bonds overcome

Caused 3D shape of protein to change

Denatured

82
Q

Polypeptide

secondary structure formation

A

H bonds

Form between amino acids in polypeptide chain

causes regions of the chain to twist into alpha helix or beta pleated sheet

83
Q

Amino Acids

Properties

A

Soluble- form polar ions in water

3 bases ( a codon) codes for amino acids

Amphoteric
–> can donate or accept protons
Ph buffer

84
Q

Globular proteins

SPADES

A

s- Compact and spherical
p- functional/ metabolic
a- irregular amino acid sequence
d- more sensitive to changes in pH or temperature
e- enzymes, haemoglobin, immunoglobins, insulin
s- ( generally soluble in water

85
Q

Conjugated proteins

A

Simple proteins with a non protein component within its structure called a prosthetic group

86
Q

Fibrous proteins

SPADES

A

s- long and narrow
p- structural
a- repetitive amino acid chain
d- less sensitive to pH or temperature changes
e- Collagen, Keratin, elastin
s- (generally) insoluble in water

cross linkages between 3 polypeptides chains

not folded- limited sec or tert structure

87
Q

SPADES

A

shape, purpose, acid sequence, durability, examples, solubility

Used to compare proteins

88
Q

Collagen

A

High proportion of glycine, so chains can lie close together

High tensile strength, but inelastic

Skin, tendons, ligaments

Structural component of skin

89
Q

Keratin

A

Fibrous protein

structural protein

High tensile strength, unreactive, insoluble

hair, skin, nails

90
Q

Elastin

A

Fibrous protein

allows stretch in vessels, accommodates blood pressure

Elastic, insoluble, unreactive

Walls of blood vessels, skin, alveoli

91
Q

Insulin

A

Globular protein

Soluble

Simple protein

Quaternary protein

Hormone to reduce blood sugar levels

92
Q

haemoglobin

A

Globular protein

Soluble

Conjugated- 4 Haem groups

Quaternary protein

Binds to oxygen on RBC

93
Q

Catalase

A

Globular protein

Soluble

Conjugated

Quaternary protein

Enzyme that decomposes hydrogen peroxide

94
Q

Constituents

Lipoproteins

Glycoproteins

A

Glycoprotein= Protein + carbohydrate

Lipoprotein= Protein + lipid

95
Q

Nucleotide

A

Phosphate group- po4 2-

Pentose sugar- 5 carbons

Organic base/ nitrogenous base

Water soluble due to phosphate group and OH group on pentose sugar

96
Q

Nucleic acids

A

Large polymers formed from monomers called nucleotides

97
Q

Pyrimidines

A

Single ring bases

Thymine
–> Uracil in RNA

Cytosine

98
Q

Purines

A

PURAG

Double ring structure

Adenine

Guanine

99
Q

DNA Chains

A

2 antiparallel strands of DNA

5’= Phosphate end on C5

3’= Sugar end on C3

100
Q

Elements in Nucleic acids

A

C H O N P

101
Q

Type of bond that joins individual nucleotides

A

Phosphodiester bond

102
Q

Risks for TLC practical

A

TLC= thin layer chromatography
–> used to separate non volatile mixtures

Solvent= irritant and flammable
- Used small volumes of solvent, ventilate room, gloves+ goggles

Ninhydrin 9 dye)= flammable
- Kept away from naked flames

103
Q

Rf value

A

Retention factor

Measured form the middle of the spot

Distance travelled by component/ distance travelled by the solvent

104
Q

TLC method

A

1 Cut paper, while wearing gloves, hang straight in jar

2- pour small Volume of solvent into the jar

3- Draw a pencil line with 2 points, dot on the amino acid using a cocktail stick then place paper in the jar for 20 minutes

4 remove when solvent front has reached 3/4 the way up the chromatogram

5- Spray chromatogram With ninhydrin to visualise spots and dry using a blow dryer

105
Q

Amino acid polarity

effect on solubility

A

Polar= soluble

non polar= insoluble

Strength of polarity determines how soluble an amino acid is

106
Q

What does how far an amino acid moves during TLC depend on ?

A

1 Solubility of amino acid in the solvent ( mobile phase)

2 How an amino acid interacts with the paper (stationary phase)

3 the Mr of the Amino acid

107
Q

DNA helicase

A

Catalyses reactions that break H bonds
between the complimentary base pairs

Causes a DNA molecule to unwind and the two strands to separate

108
Q

DNA polymerase

A

Catalyses the formation of phosphodiester bonds between nucleotides

Always assembles in 5’ to 3’ direction

109
Q

Semi conservative replication

A

Half the original DNA molecule is built into each new DNA molecule

One old, one new strand on each DNA molecule

110
Q

DNA

Sense strand

A

From 5’ to 3’

Contains sequence of bases that code for proteins to be synthesised

Coding strand

111
Q

DNA

Antisense strand

A

3’ to 5’

Contains complimentary copy of sense strand

Non coding for proteins

Template for MRNA

112
Q

Number of H bonds between bases

A

A=T
2 H bonds

C///G
3 H bonds

113
Q

DNA extraction

Why mix crushed fruit with detergent and salt

A

Detergent:
Degrades phospholipid bilayer, Hence releasing DNA

Salt:
Na+ ions shield PO4- ions that make DNA negatively charged, precipitating the DNA within the solution

114
Q

DNA extraction

Water bath?
Why cool the ethanol, and the mixture

A

Water bath at 60c
Denatures DNase, which would otherwise cut the DNA into fragments

Cooling ethanol-
Nucleic acids are insoluble in ethanol, so will precipitate into this layer

Cooling the mixture-
Slows the breakdown of DNA

115
Q

DNA extraction

Blend?

Protease?

A

Blend:
breaks down cellulose cell wall, permitting the release of DNA, only needed for plant cell walls

Protease:
Partially degrades proteins in preparation, Uncoils DNA removing histones

116
Q

Gene

A

Sequence of bases in DNA that codes for a sequence of amino acids in a polypeptide

117
Q

Genetic code

Triplet code

A

Each sequence of 3 bases on a DNA molecule is called a codon

This codes for a particular amino acid

This is a triplet code

118
Q

Genetic code

Degenerate code

A

Different combinations of bases (different codons) can code for the same amino acid

in nature : a mutation is less likely to have an effect

119
Q

Genetic code

Universal code

A

Genetic code is the same in all organisms

120
Q

Genetic code

Non overlapping

A

Each 3 bases can only ever be a part of one codon

121
Q

DNA transcription

Semi conservative replication process

A

Section of DNA containing the gene unwind and the two strands separate- this is catalysed by the enzyme DNA helicase

This exposes the nucleotides on Antisense strand which acts as a template for the synthesis of mRNA

Free RNA nucleotides form complimentary base pairs with the exposed DNA nucleotides

This is catalysed by RNA polymerase which catalyses the phosphodiester bonds being formed between RNA nucleotides

2 identical DNA molecules formed

122
Q

What do cells require energy for

A

synthesis
e.g. protein synthesis

transport

Movement
e.g. muscle contraction or spindle fibres

123
Q

ATP

function

A

Energy carrier in all living cells

Provides energy needed to drive metabolic processes

124
Q

How does ATP release energy

A

Energy is needed to break the weak bonds between phosphate groups

These bonds have a low activation energy so are broken easily

Large amounts of energy released when liberated phosphate undergoes other reactions

125
Q

ATP structure

A

3 phosphate groups on carbon 5

Ribose sugar

Adenine base on Carbon 1

126
Q

Hydrolysis of ATP

equation

A

Catalysed by ATP hydrolase

ATP + H2O –> Pi +ADP +energy

ATP= adenosine triphosphate

ADP= Adenosine diphosphate
–> two phosphate groups not 3

Pi= inorganic phosphate

127
Q

Rection form ADP to ATP

A

catalyses by ATP synthase

condensation reaction

Phosphorylation reaction

128
Q

Why is energy released so quickly form ATP

A

Single step reaction involving only on enzyme

Unlike respiration

129
Q

Properties of ATP

4

A

Small- moves easily into within and out of cells

Water soluble- energy requiring processes take place in aqueous environments

easily regenerated

releases energy in small quantities

130
Q

Biuret test

A

Blue black results

When added to starch

131
Q

Why add ethanol or propanone to a lipid in the first stage of lipid testing

A

to dissolve the lipid

132
Q

Non essential amino acids

A

can be synthesised from essential amino acids

133
Q

DNA translation

Protein synthesis

A

The mRNA binds to a ribosome, at its start codon on the small subunit

a tRNA molecule with an anticodon that is complementary to the first mRNA codon binds to the mRNA

The tRNA delivers the correct amino acid to the ribosome, as specified by mRNA codon

working along the mRNA in a 5’ to 3’ direction each codon is translated in this way and the amino acids are joined by peptide bonds, forming the polypeptide chain

the final polypeptide chain is modified and folded in the golgi apparatus

133
Q

DNA Transcription

Protein synthesis

A

The section of DNA containing the gene unwinds and the two DNA strands separate, catalysed by DNA helicase

This exposes nucleotides on the antisense strand which acts as a template for the synthesis of mRNA,

Free RNA nucleotides form complimentary base pairs with the exposed DNA nucleotides

adenine bonds with uracil not thymine on RNA strand

The mRNA nucleotides are joined by phosphodiester bonds in a reaction catalysed by RNA polymerase

Before the mRNA leaves the nucleus, introns are removed and exons are joined together- splicing

The newly formed mRNA detaches from DNA and leaves the nucleus

134
Q

Exons vs introns

A

Introns = non-coding and intervening (non-functional)

Exons are expressed sections of DNA

135
Q

Reason for the presence of introns

A

Originally functional genes

Mutated

Base sequence changed

No longer code for amino acids

136
Q

mRNA

tRNA

rRNA

A

mRNA= Messenger RNA, copies DNA from gene and transports to the ribosome

tRNA= brings amino acid to ribosome

rRNA= component of Ribosomes

137
Q

Anticodon

A

The anticodon is a sequence of 3 bases which are complementary to a codon (3 bases) on the mRNA molecule.

138
Q

Why use a stain for TLC

A

Ninhydrin

Visualise spots

A- Level Biology (7 decks)

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