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Flashcards in Biological Molecules Deck (187):
1

Hydrolysis

Breaking a bond using water

2

Covalent bond

A pair of electrons shared between two electrons

3

Hydrogen bond

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

4

Carbohydrates elements, monomer, polymer

CHO
Monosaccharides (glucose)
Polysaccharides (starch)

5

Protein elements monomer polymer

CHONS
Amino acids
Polypeptides and proteins

6

Nucleic acid element monomer polymer

CHONP
Nucleotides
DNA and RNA

7

Properties of water

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

8

Use of water being liquid

Provides habitats for living things in rivers, lakes and seas

9

Use of water being dense

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

10

Cohesion and surface tension use

Allows insects like pond-skaters can walk on water

11

High specific heat capacity

Provides aquatic organisms need a stable environment in which to live

12

Heat latent heat of vaporisation

Allows sweating to cool animals

13

Reactant

Extremely important for digestion and synthesis of large biological molecules

14

Carbohydrates

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

15

Monosaccharides

Simplest carbohydrates

16

Disaccharides

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

17

Condensation

Reaction removal of water

18

How do you draw a glucose?

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

19

How do you draw haemglobin

Alpha beta
Beta Alpha
( all are glucose)

20

Collegan

Three twists

21

How do you draw cellulose?

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

22

How to draw glycogen?

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

23

How to draw starch?

Circle circle circle
Hexagon= circle

24

Name six functions of proteins?

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

25

What is special about myoglobin?

It allows the body to have own blood supply like haemoglobin

26

Name a protein messenger?

Adrenaline

27

What makes up proteins?

Amino acids

28

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

A specific sequence

29

What do different amino acids have?

Different properties

30

What do the different properties of amino acids cause?

A different effect on the proteins effect

31

How many different amino acids with different R groups?

20 different amino acids

32

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

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

33

Name the protein structure levels

Primary
Secondary
Tertiary
Quaternary

34

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

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

35

Secondary bond and description

hydrogen bond
Alpha helix beta pleated sheets

36

Tertiary bond and description

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

37

Quaternary bonds and description

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

38

What structure do gobular have?

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

39

Fibrous proteins

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

40

Give some examples of gobular proteins

Haemoglobin, insulin, pepsin (named enzyme)

41

Fibrous protein examples

Collegan
Keratin
Elastin

42

Primary structure of gobular proteins

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

43

Fibrous proteins primary structure

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

44

Solubility of gobular proteins

Soluble in water

45

Solubility of fibrous proteins

Insoluble in water

46

Gobular protein typical functions

Carrying oxygen hormone

47

Fibrous proteins

Structural proteins

48

What is carbohydrates

Glucose
Monosaccharide
Made of oxygen hydrogen and carbon

49

Glucose

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

50

Features of monosaccahides

Soluble in water
Sweet tasting
Form crystals

51

Role of monosaccahides in living organisms

To release energy through process of respiration
Used to make storage molecules starch (plates)

52

Compare between monosaccahides and polysaccharides

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

53

Are glucose and glycogen monosaccahides or polysaccharides

Glucose -monosaccahides
Glycogen polysaccharides

54

Getting glucose

Gluconeogenesis

55

Reducing glucose

Glycogenolysis

56

Polysaccharides what's its role in living organisms?

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)

57

How does polysaccharides carry out their role?

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

58

ATP is

The universal energy molecule

59

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

Enzymes that can specifically break down the glucose molecule

60

What type of glucose do animal and plants break down?

Alpha glucose only

61

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

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

62

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

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

63

Features of amylose

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

64

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

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

65

Glycogen features

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

66

Cellulose

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

67

Amylose and glucose both are:

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

68

Calcium symbol and charge

Ca2+

69

Functions of calcium in the body

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

70

Sodium symbol and charge

Na+

71

Functions of sodium

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

72

Potassium symbol and charge

K+

73

Potassium functions

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

74

Hydrogen symbol and charge

H+

75

Hydrogen functions

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

76

Ammonium symbol and charge

NH4 +

77

Ammonium functions

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

78

Nitrate symbol and charge

NO3 -1

79

Nitrate functions

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

80

Hydrogencarbonate symbol and charge

HCO3 -1

81

Hydrogencarbonate functions

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

82

Chloride symbol and charge

Cl-

83

Chloride functions

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

Phosphate functions

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

85

Phosphate symbol and charge

PO4 3-

86

Hydroxide charge and symbol

OH-

87

Hydroxide functions

Involved in regulation of blood pH.

88

How to test for starch

Add iodine solution (in potassium iodide) to sample

89

If starch is present what will happen

Colour change of yellow-brown to blue-black

90

What causes this colour change?

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

91

Reducing sugars what are they?

All monosaccahides, some polysaccharides

92

Why are they known as reducing sugars?

They can reduce or give electrons to other molecules

93

How do you do Benedict's test?

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

How would you do reducing sugars last step more efficient?

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

95

How would you test non-reducing sugars?

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

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

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

97

How do you test for proteins?

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

What happens if protein present?

Purple layer forms

99

What happens if no protein is present?

Solution will stay blue

100

Why do you need to look carefully?

Because colours are pale

101

How do you test for lipids?

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

102

What shows a positive result for the emulsion test?

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

103

What shows a negative result for the emulsion test?

Solution will stay clear

104

How much of ions are required in humans and plants?

Some in large amounts (macronutrients/main elements)
Some in small amounts (micronutrients/ trace nutrients)

105

Who can display deficiency symptoms?

Plants and humans

106

How can humans and plants show deficiency sighs?

If they don't consume enough of a particular ion

107

Give some examples of deficiency symptoms

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

108

What does Benedict's reagent detect the presence of?

Reducing sugars

109

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

Amount of precipitate increases
Amount of copper (II) ions remain in solution decrease

110

How can we quantify concentration of sugar in original sample?

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

111

How does a colorimeter work?

Shining a light through a sample

112

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

A centrifuge

113

What is Benedict's solution in this example?

Supernatant

114

How can we use a colorimeter?

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

115

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

Small vial
Made of glass/ plastic

116

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

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

117

What are often used for greater accuracy?

Colour filters

118

What would using a red filter in this example do?

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

119

What is percentage transmission?

How much passes through

120

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

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

121

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

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

122

What usually happens between readings?

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

123

What does using a colorimeter give us?

A semi-quantitative test for sugar
Can compare how much sugar contained in different samples

124

What do you need to do to find exact amounts?

Create a calibration curve

125

How do we create a calibration curve?

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

What does plotting a graph provide?

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

127

How do biosensors work?

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

128

What applications do biosensors have?

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

129

Fibrous proteins are like:

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

130

Gobular proteins are like:

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

Functions of collagen?

Artery walls
Tendons
Bones
Cartilage and connective tissue

132

Why is collagen helpful in artery walls?

Prevents artery bursting under high pressure from blood pumped by heart

133

Why do tendons have collagen?

Connect muscles to bone allowing them to pull on bone

134

How are bones made from collagen?

Reinforced with calcium phosphate

135

What is keratin rich in?

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

136

Where is keratin found?

Finger nails
Hair
Claws
Hoofs
Horns
Scales
Fur
Feathers

137

What does keratin provide?

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

138

What makes the structure of elastin strong and extensible?

Cross-linking and coiling

139

What does the structure of elastin cause it to be?

Strong and extensible

140

Where is elastin found?

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

141

What is skin like with elastin?

Can stretch around bones and muscles
Without it skin wouldn't go back to normal after being pinched

142

Where else does elastin work in the body?

Lungs- allows to inflate and deflate
Bladder- helps expand to hold urine

143

How is elastin like collagen?

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

144

What's haemoglobin made up of?

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

Chain of haemoglobin?

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

Function of haemoglobin?

Carry oxygen from lungs go tissues

147

What happens in lungs that allows this to happen

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

148

Insulin made of

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

What makes insulin soluble in water?

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

Pepsin is?

Enzyme digests protein in stomach

151

What's pepsin made of

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

152

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

Four -basic
43- acidic

153

What does this help explain?

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

What's the tertiary structure held together by?

Hydrogen bonds and two disulfide bridge

155

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

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

156

How can scientists predict protein shapes?

Using computer modelling techniques

157

Why can scientists do this?

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

158

How are these probabilities derived?

Already known protein molecular structures

159

What makes this so exciting?

Usually tertiary structure of protein molecules contributes directly to bioactive function

160

What are the two broad approaches?

Ab initio protein modelling
Comparative protein modelling

161

Ab initio protein modelling

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

Comparative protein modelling

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

163

What is the aim of chromatography?

To separate a mixture into constituents

164

What are the two components?

Stationary phase
Mobile phase

165

What is the stationary phase?

Either chromatography paper or thin-lined chromatography plate

166

What is the TLC plate usually coated in?

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

167

Mobile phase is what?

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

168

Things to remember?

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

What happens as solvent travels up the paper/plate?

Components of solution mixture travels with it.

170

What happens by the time the solvent reaches the top?

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

171

What can you use to identify pigments?

Relative distance
Rf value

172

How to calculate the Rf value

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

173

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

Each pigment's Rf value

174

How can you identify a certain pigment?

Rf value of this pigment

175

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

Ultra violet light
Ninhydrin
Iodine

176

How is uv light a solution?

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

How is ninhydrin a solution?

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

178

How is iodine a solution?

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

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

Solubility in solvent and polarity
In paper chromatography may also depend on size

180

How does this happen?

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

How can it be difficult to tell between two molecules?

Same speed
If this happens different solvent or change pH

182

What is thin-layer chromatography used for?

To monitor progress of reactions because works relatively quickly.

183

What is it also used for?

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

184

Function of amylase?

Storage

185

Function of cellulose?

Plant structure

186

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

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

187

Bond holds sucrose together is?

Glycosidic