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Biological Molecules Flashcards

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1
Q

Hydrolysis

A

Breaking a bond using water

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2
Q

Covalent bond

A

A pair of electrons shared between two electrons

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3
Q

Hydrogen bond

A

Weak interaction can occur whenever molecules contain slightly negatively charged atom bonded to a slightly positively charged hydrogen atom

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4
Q

Carbohydrates elements, monomer, polymer

A 
CHO
Monosaccharides (glucose)
Polysaccharides (starch)
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5
Q

Protein elements monomer polymer

A

CHONS
Amino acids
Polypeptides and proteins

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6
Q

Nucleic acid element monomer polymer

A

CHONP
Nucleotides
DNA and RNA

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7
Q

Properties of water

A 
Liquid
Density
Solvent 
Cohesion and surface tension
High specific heat capacity
High latent heat of vaporisation 
Reactant
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8
Q

Use of water being liquid

A

Provides habitats for living things in rivers, lakes and seas

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9
Q

Use of water being dense

A

Provides aquatic organisms with a stable environment in which to live through the winter

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10
Q

Cohesion and surface tension use

A

Allows insects like pond-skaters can walk on water

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11
Q

High specific heat capacity

A

Provides aquatic organisms need a stable environment in which to live

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12
Q

Heat latent heat of vaporisation

A

Allows sweating to cool animals

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13
Q

Reactant

A

Extremely important for digestion and synthesis of large biological molecules

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14
Q

Carbohydrates

A

Functional group- three fold, store of energy
Main groups are: monosaccharides, disaccharides and polysaccharides. Common monosaccharides and disaccharides all have names ending in ose

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15
Q

Monosaccharides

A

Simplest carbohydrates

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16
Q

Disaccharides

A

Alpha glucose + alpha glucose-> maltose
Alpha glucose and fructose -> sucrose
Beta galactose + alpha glucose -> lactose
Beta glucose+ beta glucose-> cellobiose

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17
Q

Condensation

A

Reaction removal of water

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18
Q

How do you draw a glucose?

A

1) draw hexagon
2) put oxygen in corner
3) put carbons around in hexagon
4) flag pole
5) tail has
When OH
H
It is beta glucose
When H
OH
It is an alpha glucose

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19
Q

How do you draw haemglobin

A

Alpha beta
Beta Alpha
( all are glucose)

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20
Q

Collegan

A

Three twists

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21
Q

How do you draw cellulose?

A

Draw key for hexagon= circle
One Zigzag from each circle
Have a OH flagpole top then bottom all way through
Do two rows

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22
Q

How to draw glycogen?

A

Hexagons with O in centre of zig zag
Each needs flagpole
Put in v shape

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23
Q

How to draw starch?

A

Circle circle circle

Hexagon= circle

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24
Q

Name six functions of proteins?

A 
Build cells 
Move muscles 
To fight bacteria and viruses 
Carry oxygen in blood 
Send chemical messages around the body 
Enzymes to speed up chemical reactions in body
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25
Q

What is special about myoglobin?

A

It allows the body to have own blood supply like haemoglobin

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26
Q

Name a protein messenger?

A

Adrenaline

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27
Q

What makes up proteins?

A

Amino acids

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28
Q

What must amino acids be bonded in to make a specific protein

A

A specific sequence

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29
Q

What do different amino acids have?

A

Different properties

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30
Q

What do the different properties of amino acids cause?

A

A different effect on the proteins effect

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31
Q

How many different amino acids with different R groups?

A

20 different amino acids

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32
Q

Give an example of how different properties of a amino can affect the protein?

A

If proteins contains a number of amino acids with hydrophobic R-groups then the final protein will have a specific shape

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33
Q

Name the protein structure levels

A

Primary
Secondary
Tertiary
Quaternary

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34
Q

What’s the bond and description of primary level of protein structure?

A

Bond is peptide
Sequence of o-o-o-o
Helix shape

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35
Q

Secondary bond and description

A

hydrogen bond

Alpha helix beta pleated sheets

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36
Q

Tertiary bond and description

A

Hydrophobic/hydrophilia , hydrogen bonds, disulphuric, van der waals
3D shape properties of aa

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37
Q

Quaternary bonds and description

A

Hydrophilia/ hydrophilia, hydrogen bonds, disulphuric, van der waals
Haemoglobin, four proteins two alpha two beta multiple protein polypeptides, collagen

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38
Q

What structure do gobular have?

A

Tend to roll up in compact ball shaped structure
Haemoglobin
Any hydrophobic R groups turned inwards towards centre of structure
Hydrophilic R-group tend to be on outside
Makes protein water soluble
Water molecules can easily cluster around them

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39
Q

Fibrous proteins

A

Form fibres
Most have regular repetitive sequences of amino acids usually insoluble in water
pH denatures ionic-tertiary, Avateraory temporary
Hydrogen bonds destroyed by heating

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40
Q

Give some examples of gobular proteins

A

Haemoglobin, insulin, pepsin (named enzyme)

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41
Q

Fibrous protein examples

A

Collegan
Keratin
Elastin

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42
Q

Primary structure of gobular proteins

A

Tend to roll up into compact globe or ball shaped structure
Hydrophobic R groups turned inwards towards centre of structure
Hydrophilia

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43
Q

Fibrous proteins primary structure

A

Form fibres
Most have repetitive sequences of amino acids
skin, tendons, Collegan injections
Every third amino acid in Collegan is

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44
Q

Solubility of gobular proteins

A

Soluble in water

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45
Q

Solubility of fibrous proteins

A

Insoluble in water

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46
Q

Gobular protein typical functions

A

Carrying oxygen hormone

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47
Q

Fibrous proteins

A

Structural proteins

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48
Q

What is carbohydrates

A

Glucose
Monosaccharide
Made of oxygen hydrogen and carbon

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49
Q

Glucose

A

Single sugar
Found in blood and in cells
Function source of energy made available from respiration source of raw material to make each other substances

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50
Q

Features of monosaccahides

A

Soluble in water
Sweet tasting
Form crystals

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51
Q

Role of monosaccahides in living organisms

A

To release energy through process of respiration

Used to make storage molecules starch (plates)

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52
Q

Compare between monosaccahides and polysaccharides

A

Similarities- hydrogen at top right, both have OH at bottom right, have six carbons, both carbohydrates
Differences- polysaccharides has two really big groups
Monosaccahides- pentagon ring

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53
Q

Are glucose and glycogen monosaccahides or polysaccharides

A

Glucose -monosaccahides

Glycogen polysaccharides

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54
Q

Getting glucose

A

Gluconeogenesis

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55
Q

Reducing glucose

A

Glycogenolysis

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56
Q

Polysaccharides what’s its role in living organisms?

A

Respiring substance
Alpha glucose broken down during respiration to make energy available
Used by cells to make new substances
Beta glucose to make cellulose
Alpha glucose to make glycogen and starch (amylose and amylopectin)

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57
Q

How does polysaccharides carry out their role?

A

Contains large number of bonds that can be broken to form simple molecules
Released energy used to make ATP through a series of enzyme controlled steps in the process of respiration

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58
Q

ATP is

A

The universal energy molecule

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59
Q

What must an organism have to be able to use glucose in respiration?

A

Enzymes that can specifically break down the glucose molecule

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60
Q

What type of glucose do animal and plants break down?

A

Alpha glucose only

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61
Q

Why can’t animals and plants break down beta glucose?

A

Because of its different arrangement of OH and H group at carbon 1

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62
Q

Why does the different arrangement of OH and H matter in breaking down glucose?

A

The different shape of the beta glucose molecule means that it doesn’t fit in the active sites of respirate tissues

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63
Q

Features of amylose

A

Many alpha glucose molecules
Via 1,4 glycodisic bond
Long chains can coil into spring-quite compact molecule
Not water soluble

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64
Q

What can iodine become in amylose and what is it the basis for?

A

Iodine molecules can become trapped in the coils of the spring causing the iodine to change colour
Basis of the starch test

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65
Q

Glycogen features

A

Many alpha molecules
Via a 1,4 glycosidic bonds for straight chains
Via a 1,6 glycosidic bonds for branches
Shorter chains than amylose
Highly branched so not as coiled as amylose
Not water soluble

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66
Q

Cellulose

A 
NOT me 
Many beta glucose molecules 
Straight chained molecules
Many H-bonds between the cellulose molecules go form bundles called microfibrils 
Not water soluble
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67
Q

Amylose and glucose both are:

A 
Alpha glucose storage molecules 
1-4 and 1-6 glucosidic 
If branched allows high density got storage 
Cross- linked
High strength 
Structure will complement the enzymes
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68
Q

Calcium symbol and charge

A

Ca2+

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69
Q

Functions of calcium in the body

A

Increases rigidity of bone, teeth and cartilage and is a component of the exoskeleton of crustaceans (crabs)
Activator for several enzymes such as lipase, ATPase and cholinesterase
Regulates permeability of cell membrane

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70
Q

Sodium symbol and charge

A

Na+

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71
Q

Functions of sodium

A

Contributes to nervous transmission and muscle contractions
Constituent of vacuole in plants which helps maintain turgidity
Affects absorption of carbohydrates in the intestine and water in the kidney

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72
Q

Potassium symbol and charge

A

K+

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73
Q

Potassium functions

A

Contributes to nervous transmission and muscle contractions
Involved in control of water levels in body fluid and maintenance of pH
Assists active transport of materials across the cell membrane

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74
Q

Hydrogen symbol and charge

A

H+

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75
Q

Hydrogen functions

A

Involved in photosynthesis and respiration
Involved in transport of oxygen and carbon dioxide in the blood
Involved in regulation of blood pH

76
Q

Ammonium symbol and charge

A

NH4 +

77
Q

Ammonium functions

A

Some hormones are made of proteins e.g. Insulin
A component of the nitrogen cycle
Essential part of nucleic acid

78
Q

Nitrate symbol and charge

A

NO3 -1

79
Q

Nitrate functions

A

A component of the nitrogen cycle
An essential component of nucleic acids
Component of amino acids, proteins, vitamins and chlorophyll

80
Q

Hydrogencarbonate symbol and charge

A

HCO3 -1

81
Q

Hydrogencarbonate functions

A

Involved in regulation of blood pH

Involved in transport of carbon dioxide into and out of the blood

82
Q

Chloride symbol and charge

A

Cl-

83
Q

Chloride functions

A

Used to produce hydrochloric acid in the stomach
Helps in production of urine in the kidney, and maintaining water balance
Involved in regulation of blood pH

84
Q

Phosphate functions

A

Component of phospholipids, ATP, nucleic acid and several important enzymes
Involved in regulation of blood pH
Helps root growth in plants

85
Q

Phosphate symbol and charge

A

PO4 3-

86
Q

Hydroxide charge and symbol

A

OH-

87
Q

Hydroxide functions

A

Involved in regulation of blood pH.

88
Q

How to test for starch

A

Add iodine solution (in potassium iodide) to sample

89
Q

If starch is present what will happen

A

Colour change of yellow-brown to blue-black

90
Q

What causes this colour change?

A

When dissolved in potassium iodide (I2) forms triiodide ion (I3. -) which slips into middke of amylose helix causes colour change

91
Q

Reducing sugars what are they?

A

All monosaccahides, some polysaccharides

92
Q

Why are they known as reducing sugars?

A

They can reduce or give electrons to other molecules

93
Q

How do you do Benedict’s test?

A

Add Benedict’s reagent (blue) to sample and heat it make sure solution doesn’t boil. If test’s positive will form coloured precipitate (solid particles supended in solution)
Colour of precipitate changes from: blue-> green-> yellow-> orange-> brick red
Higher the concentration of reducing sugar further the colour change goes use this to compare amount of reducing sugar in different solution

94
Q

How would you do reducing sugars last step more efficient?

A

More accurate way of doing this to filter solution and weigh precitate

95
Q

How would you test non-reducing sugars?

A

First break them down into monosaccahides
Do this by boiling test solution with dilute HCL and then neutralising it with sodium hydrogencarbonate then carry out Benedict’s test as reducing sugars

96
Q

What’s annoying about testing for non-reducing sugars?

A

If result positive sugar could have been reducing or non-reducing
To check you have to do reducing sugar test to

97
Q

How do you test for proteins?

A

Biuret test

1) test solution needs to be alkaline do add few drops of sodium hydroxide solution
2) then add some copper (II) sulfate solution

98
Q

What happens if protein present?

A

Purple layer forms

99
Q

What happens if no protein is present?

A

Solution will stay blue

100
Q

Why do you need to look carefully?

A

Because colours are pale

101
Q

How do you test for lipids?

A

Shake test substance with ethanol for about a minute then pour the solution in water.

102
Q

What shows a positive result for the emulsion test?

A

Solutions turn milky

The More lipid there is the more noticeable the milky colour will be

103
Q

What shows a negative result for the emulsion test?

A

Solution will stay clear

104
Q

How much of ions are required in humans and plants?

A

Some in large amounts (macronutrients/main elements)

Some in small amounts (micronutrients/ trace nutrients)

105
Q

Who can display deficiency symptoms?

A

Plants and humans

106
Q

How can humans and plants show deficiency sighs?

A

If they don’t consume enough of a particular ion

107
Q

Give some examples of deficiency symptoms

A

Humans and plants Deficiency of trace element cobalt causes anaemia
Deficiency of copper in plants causes young shoots to die back.

108
Q

What does Benedict’s reagent detect the presence of?

A

Reducing sugars

109
Q

What does Benedict’s test show if there are more reducing sugars?

A

Amount of precipitate increases

Amount of copper (II) ions remain in solution decrease

110
Q

How can we quantify concentration of sugar in original sample?

A

Assessing how
Amount of precipitate
Amount of copper (II) in solution vary
Colorimetry

111
Q

How does a colorimeter work?

A

Shining a light through a sample

112
Q

What would we use to separate the precipitate from the Benedict’s solution?

A

A centrifuge

113
Q

What is Benedict’s solution in this example?

A

Supernatant

114
Q

How can we use a colorimeter?

A

Using pipette take the supernatant
Place it in curvette
Which is placed into colorimeter

115
Q

What’s a curvette and what’s it made from?

A

Small vial

Made of glass/ plastic

116
Q

What should you ensure you don’t do with the curvette?

A

Leave a greasy fingerprint on the surface of the curvette as could affect transmission of light

117
Q

What are often used for greater accuracy?

A

Colour filters

118
Q

What would using a red filter in this example do?

A

Can shine red light through solution
Detect percentage transmission
Solution can reflect blue light but absorbs red light.

119
Q

What is percentage transmission?

A

How much passes through

120
Q

What happens to the percentage transmission and absorption of light if there’s a lot of unreacted copper sulfate?

A

Supernatant still quite blue
Absorption of red light is high
Percentage transmission is low

121
Q

What happens to the percentage transmission and absorption of light if there’s little unreacted copper sulfate?

A

Supernatant less blue
Absorption of red light is low
Percentage transmission is high.

122
Q

What usually happens between readings?

A

Device usually zeroed between each reading by placing appropriate blank sample to reset 100% transmission/ absorption
Blank would be water

123
Q

What does using a colorimeter give us?

A

A semi-quantitative test for sugar

Can compare how much sugar contained in different samples

124
Q

What do you need to do to find exact amounts?

A

Create a calibration curve

125
Q

How do we create a calibration curve?

A

Take series of known concentrations of reducing sugar
Using each sample carry out Benedict’s test
Use colorimeter to record light percentage transmission through each supernatant
Plot graph to show transmission of light against concentration of reducing sugars

126
Q

What does plotting a graph provide?

A

Calibration curve

Can use with other unknown samples to determine concentration of sugar in original sample

127
Q

How do biosensors work?

A

Take biological/chemical variable which can’t be easily measured and convert it to electrical signal

128
Q

What applications do biosensors have?

A

To detect
contaminants in water
Pathogens and toxins in food
Airborne bacteria (e.g. Counter-bioterrorism programmes)

129
Q

Fibrous proteins are like:

A

Repetitive sequences of amino acids
Usually insoluble in water
Able to form fibres
(structural function, Collagen, elastin, keratin)

130
Q

Gobular proteins are like:

A

Tend to roll up into almost spherical shape
Hydrophobics R groups turn inwards, hydrophilia groups on outside
Water soluble
Often specific shapes helps them take up specific roles -enzymes, hormones, haemoglobin

131
Q

Functions of collagen?

A

Artery walls
Tendons
Bones
Cartilage and connective tissue

132
Q

Why is collagen helpful in artery walls?

A

Prevents artery bursting under high pressure from blood pumped by heart

133
Q

Why do tendons have collagen?

A

Connect muscles to bone allowing them to pull on bone

134
Q

How are bones made from collagen?

A

Reinforced with calcium phosphate

135
Q

What is keratin rich in?

A

Cysteine so lots of disulfate bridges form between polypeptide chains alongside hydrogen bonding makes molecule strong

136
Q

Where is keratin found?

A 
Finger nails 
Hair 
Claws
Hoofs 
Horns 
Scales 
Fur 
Feathers
137
Q

What does keratin provide?

A

Mechanical structure
Impermeable barrier to infection
Waterproof prevents entry of water-borne pollutants

138
Q

What makes the structure of elastin strong and extensible?

A

Cross-linking and coiling

139
Q

What does the structure of elastin cause it to be?

A

Strong and extensible

140
Q

Where is elastin found?

A

Where there is a need for stretch/ adapt shape as part of life processes

141
Q

What is skin like with elastin?

A

Can stretch around bones and muscles

Without it skin wouldn’t go back to normal after being pinched

142
Q

Where else does elastin work in the body?

A

Lungs- allows to inflate and deflate

Bladder- helps expand to hold urine

143
Q

How is elastin like collagen?

A

Helps blood vessels stretch and recoil as blood pumped through them
Helping maintain pressure wave of blood as passes through

144
Q

What’s haemoglobin made up of?

A 
4 polypeptides 
Two alpha glucoses 
Two beta glucoses 
Has own tertiary structure 
When fitted together form 1 molecule
Interactions between polypeptides gives molecules specific shape
145
Q

Chain of haemoglobin?

A

One position outside chain space for haem group
Groups like prosthetic groups essential part without couldn’t function
Aren’t made of amino acids
Haem contains iron ion
Protein associated with conjugated protein

146
Q

Function of haemoglobin?

A

Carry oxygen from lungs go tissues

147
Q

What happens in lungs that allows this to happen

A

Oxygen molecule associates haemoglobin turns from purple red to red colour
Oxygen released by haemoglobin when reached tissues

148
Q

Insulin made of

A

2 polypeptide chains
A chain begins with section of alpha helix
B chain ends with section of beta pleat
Both chains fold into tertiary structure joined together by disulfide links

149
Q

What makes insulin soluble in water?

A

Amino acids with hydrophilia R groups on outside of molecule makes it soluble in water
Insulin binds to glycoprotein receptors on outside of muscle and fat cells increases uptake of glucose from blood increases consumption of glucose

150
Q

Pepsin is?

A

Enzyme digests protein in stomach

151
Q

What’s pepsin made of

A

Single polypeptide gushy of 327 amino acids folds into symmetrical tertiary structure

152
Q

How many amino acids with basic R group and acidic R group?

A

Four -basic

43- acidic

153
Q

What does this help explain?

A

Why it’s stable in acidic environment of stomach as there are few basic groups that accept H+ ions therefore can be little effect on enzymes structure

154
Q

What’s the tertiary structure held together by?

A

Hydrogen bonds and two disulfide bridge

155
Q

Give an example of how predicting the shape of a protein molecules from its primary structure is useful for biochemistry?

A

Predicting occurrence of biologically active binding sites in protein molecule can help identifying new medicines

156
Q

How can scientists predict protein shapes?

A

Using computer modelling techniques

157
Q

Why can scientists do this?

A

Techniques for prediction of secondary structure developed based upon probability of amino acids or sequence of amino acids in particular secondary structure

158
Q

How are these probabilities derived?

A

Already known protein molecular structures

159
Q

What makes this so exciting?

A

Usually tertiary structure of protein molecules contributes directly to bioactive function

160
Q

What are the two broad approaches?

A

Ab initio protein modelling

Comparative protein modelling

161
Q

Ab initio protein modelling

A

Model built based on physical and electrical properties of atoms in each amino acid in sequence
With this technique can have multiple solutions to same amino acid sequences and sometimes other methods need applying to reduce number of solutions

162
Q

Comparative protein modelling

A

Protein threading
Scans amino acids sequence against database of solved structures and produces set of possible models which would match sequence

163
Q

What is the aim of chromatography?

A

To separate a mixture into constituents

164
Q

What are the two components?

A

Stationary phase

Mobile phase

165
Q

What is the stationary phase?

A

Either chromatography paper or thin-lined chromatography plate

166
Q

What is the TLC plate usually coated in?

A

Either sheet of plastic with thin layer of silica gel
Aluminium hydroxide
(Either way have free OH group)

167
Q

Mobile phase is what?

A

Solvent
Can use alcohol or water
Flows through and across stationary phase

168
Q

Things to remember?

A

Wear eye protections draw line in pencil
Spot solution mixture onto pencil dot several times using capillary tubing
Wait for spot to dry to make smaller dot
Cover beaker with watch glass/watch plate
Let run until solvent reached just underneath top of paper. Then remove solvent and lay on tile to dry

169
Q

What happens as solvent travels up the paper/plate?

A

Components of solution mixture travels with it.

170
Q

What happens by the time the solvent reaches the top?

A

Some travelling slowly and some quickly so different positions on the plate

171
Q

What can you use to identify pigments?

A

Relative distance

Rf value

172
Q

How to calculate the Rf value

A

Rf= distance from pencil line to centre of spot of pigment/ distance from pencil line to solvent front.

173
Q

What will have the same value if you repeat the investigation?

A

Each pigment’s Rf value

174
Q

How can you identify a certain pigment?

A

Rf value of this pigment

175
Q

What are the three solutions to seeing colourless molecules finish using thin-layer chromatography?

A

Ultra violet light
Ninhydrin
Iodine

176
Q

How is uv light a solution?

A

Thin layer chromatography have chemical which fluoresce a under UV light. If you look at the plate under UV light most will glow except places where spots travelled to. Plates mask from UV light.

177
Q

How is ninhydrin a solution?

A

See amino acids allow plate to dry then spray with ninhydrin. Binds to amino acids which are then visible as brown/ purple spots

178
Q

How is iodine a solution?

A

Allow plate to dry
Place in enclosed container with few iodine crystals
Iodine firms gas the same binds to molecules in each of spots

179
Q

What does the speed of molecules along paper/ TLC plate depend on?

A

Solubility in solvent and polarity

In paper chromatography may also depend on size

180
Q

How does this happen?

A

Exposed -OH groups make surface of paper/plate very polar
Allow it to form hydrogen bonds with molecules along other dipole interactions
Highly polar solute will tend to stick to surface move more slowly
Non-polar solute travel very quickly

181
Q

How can it be difficult to tell between two molecules?

A

Same speed

If this happens different solvent or change pH

182
Q

What is thin-layer chromatography used for?

A

To monitor progress of reactions because works relatively quickly.

183
Q

What is it also used for?

A

Urine testing of athletes for illegal drugs
Analysing drugs for purity of components
Analysis of food to determine presence of contaminants

184
Q

Function of amylase?

A

Storage

185
Q

Function of cellulose?

A

Plant structure

186
Q

Why does pH falls during reaction and why did it stop?

A

Fatty acids formed which is acidic meaning the acid levels rise. Enzyme denatured due to low pH.

187
Q

Bond holds sucrose together is?

A

Glycosidic

Biology A Level (26 decks)

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