Biological Molecules Flashcards
1
Q
Hydrolysis
A
Breaking a bond using water
2
Q
Covalent bond
A
A pair of electrons shared between two electrons
3
Q
Hydrogen bond
A
Weak interaction can occur whenever molecules contain slightly negatively charged atom bonded to a slightly positively charged hydrogen atom
4
Q
Carbohydrates elements, monomer, polymer
A
CHO Monosaccharides (glucose) Polysaccharides (starch)
5
Q
Protein elements monomer polymer
A
CHONS
Amino acids
Polypeptides and proteins
6
Q
Nucleic acid element monomer polymer
A
CHONP
Nucleotides
DNA and RNA
7
Q
Properties of water
A
Liquid Density Solvent Cohesion and surface tension High specific heat capacity High latent heat of vaporisation Reactant
8
Q
Use of water being liquid
A
Provides habitats for living things in rivers, lakes and seas
9
Q
Use of water being dense
A
Provides aquatic organisms with a stable environment in which to live through the winter
10
Q
Cohesion and surface tension use
A
Allows insects like pond-skaters can walk on water
11
Q
High specific heat capacity
A
Provides aquatic organisms need a stable environment in which to live
12
Q
Heat latent heat of vaporisation
A
Allows sweating to cool animals
13
Q
Reactant
A
Extremely important for digestion and synthesis of large biological molecules
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
15
Q
Monosaccharides
A
Simplest carbohydrates
16
Q
Disaccharides
A
Alpha glucose + alpha glucose-> maltose
Alpha glucose and fructose -> sucrose
Beta galactose + alpha glucose -> lactose
Beta glucose+ beta glucose-> cellobiose
17
Q
Condensation
A
Reaction removal of water
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
19
Q
How do you draw haemglobin
A
Alpha beta
Beta Alpha
( all are glucose)
20
Q
Collegan
A
Three twists
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
22
Q
How to draw glycogen?
A
Hexagons with O in centre of zig zag
Each needs flagpole
Put in v shape
23
Q
How to draw starch?
A
Circle circle circle
Hexagon= circle
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
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
