CHAPTER 3 - BIOLOGICAL MOLECULES Flashcards
1
Q
What 6 elements are the most abundant in biological molecules?
A
Carbon
Hydrogen
Oxygen
Nitrogen
Phosphorus
Sulfur
2
Q
Which other elements have important roles in biochemistry
A
Sodium
Potassium
Calcium
3
Q
explain how atoms join together to form molecules
A
atoms form bonds by sharing pairs of electrons
according to the bonding rules
4
Q
explain the difference between cations and anions
A
cations are ions that have lost one or more electrons
Has a net positive charge
anions are ions that have gained one more electrons
Has a net negative charge (1)
5
Q
explain why cells are visible under a light microscope but electron microscopes are needed to see chromosomes
A
cells are larger than ribosomes
electron microscopes have a higher resolution
molecules are smaller that the resolution limit of light and molecules are larger than the resolution limit of electron beam
6
Q
What are the chemical elements that make up Lipids
A
C, H and O
7
Q
What are the chemical elements that make up Carbohydrates
A
C, H, O (usually in the ratio Cx(H2O)x )
8
Q
What are the chemical elements that make up proteins
A
C, H, O, N, S
9
Q
What are the chemical elements that make up Nucleic acids
A
C, H, O, N, P
10
Q
What type of ion are Calcium ions, what is its chemical formula and what are they necessary for?
A
Cation
Ca 2+
Nerve impuse transmission
Muscle Contraction
11
Q
What type of ion are Sodium ions, what is its chemical formula and what are they necessary for?
A
Cations
Na +
Nerve impulse transmission
Kidney function
Regulates water potential
12
Q
What type of ion are Potassium ions, what is its chemical formula and what are they necessary for?
A
Cation
K+
Nerve impulse transmission
Stomatal Opening
13
Q
What type of ion are Hydrogen ions, what is its chemical formula and what are they necessary for?
A
Cation
H+
Catalysis of reactions
pH Determination
14
Q
What type of ion are Ammonium ions, what is its chemical formula and what are they necessary for?
A
Cation
NH4 +
Production of nitrate ions by bacteria
15
Q
What charge are Cations?
A
Positive (it is positive if you iron a cat)
16
Q
What charge are on Anions?
A
Negative
17
Q
What type of ion are nitrate ions, what is its chemical formula and what are they necessary for?
A
Anion
NO3 -
Nitrogen supply to plant for amino acid and protein formation
18
Q
What type of ion are Hydrogen Carbonate ions, what is its chemical formula and what are they necessary for?
A
Anion
HCO3 -
Maintenance of blood pH
19
Q
What type of ion are Chloride ions, what is its chemical formula and what are they necessary for?
A
Anion
Cl-
Balance positive charge of sodium and potassium ions in cells
20
Q
What type of ion are Phosphate ions, what is its chemical formula and what are they necessary for?
A
Anion
PO4 3-
Cell membrane formation
nucleic acid and ATP formation
Bone formation
21
Q
What type of ion are Hydroxide ions, what is its chemical formula and what are they necessary for?
A
Anion
OH -
Catalysis of reactions
pH determination
22
Q
What is a covalent bond?
A
A chemical bond formed when two or atoms share electrons.
23
Q
What is ionic bonding?
A
Transfer of electrons. this forms positive and negative ions.
The oppositely charged ions are electrostatically attracted
24
Q
state the ‘bonding rules’
A
carbon atoms form 4 bonds
nitrogen atoms form 3 bonds
oxygen atoms form 2 bonds
hydrogen atoms form 1 bond
25
explain why life is often referred as 'carbon-based'
carbon forms the backbone of most biological molecules as it can form 4 bonds
26
What are polymers?
long chain molecules made up by linking multiple individual molecules called monomers in a repeating pattern
27
what is an inorganic ion
An ion that doesn't contain carbon
28
Example of a Biological molecule that exists asa Polymer
Carbohydrates - monomers are sugars (saccharides)
Proteins - monomers are amino acids
29
what are the roles of water
solvent
transport medium
coolant
habitat
30
what is a polar molecule?
a molecule with an uneven distribution of charge
e.g. Water
Region of negative charge = oxygen
region of positive charge = hydrogen
31
explain how hydrogen bonds form
Oxygen and hydrogen share electrons unequally when they bond.
Oxygen is more negative
Hydrogen, has a smaller share/is more positive
The more negative oxygen atom is attracted to the more positive hydrogen atom
32
Explain why water is a polar molecule
Water is a molecule with an unequal distribution of charge,
the Oxygen side is (-) and the hydrogen side is (+) due to the sharing of electrons in the covalent bond
33
What are Intermolecular forces
forces of attraction between molecules
34
What are intramolecular forces
bonding forces that hold the atoms of a molecule together
35
What is a hydrolysis reaction
addition of water to break bonds
36
what is a condensation reaction
water is produced
bonds are made
37
What is Cohesion
Attraction between molecules of the same substance
38
What is an adhesive
a substance that unites or bonds surfaces together.
this is where water molecules are attracted to other materials like other polar molecules or charged ions
39
How strong are hydrogen bonds?
weak
which break and reform between constantly moving water molecules
but the intra-molecular forces are very strong
40
explain why water a liquid at room temperature? (or have a unusually high boiling point)?
it can form hydrogen bonds between individual molecules
hydrogen bonds absorb a lot of energy
so water has a high specific heat capacity, taking lao too energy to break hydrogen bonds
so it doesn't experience a rapid temperature change
41
explain why water having a high specific heat capacity is important for the survival of organisms
the temperature of water is likely to be more stable than it Is on land
as it takes a lot of energy to increase the temperature.
this makes a good habitat METABOLIC reactions can occur in the same rate and GASES remain SOLUBLE
42
Define specific heat capacity
the energy needed to raise the temperature of 1 gram a substance by one degree Celsius
43
explain why hydrogen bonds have a high latent heat of evaporation
takes a lot of energy to break hydrogen bonds between water molecules
so a lot of energy is used to break these bonds for water to evaporate
44
explain how high later heat of evaporation of water is important for the survival of organisms
used as a cooling technique
for instance mammals can sweat
this is because it takes energy from mammals to break hydrogen bonds that hold water molecules together
in order for water to evaporate
cooling down organisms
45
explain why the cohesive retry of water is important for the survival or organisms
its good for the transportation fo substances
water being cohesive helps create a flow
eg in plant stems In the transpiration stream
46
Explain why ice floats in reference to the properties of water
hydrogen bonds fix the positions of the polar molecules slightly further apart than in liquid state
producing a giant, rigid but open structure
so water becomes less dense
47
what causes a 'skin' of surface tension
The water molecules are more strongly cohesive to each other than they are to air
48
explain why a pond skater can 'walk' on water
the water molecules are more strongly cohesive to each other
than they are to air
resulting in a 'skin' of surface tension
that is strong enough to supports the pond skater (and other small insects)
49
explain how water acts as a POLAR solvent
water is polar
biological molecules such as amnio acids are also polar molecules
and charged ions
both attract to water
molecules in forces of attraction
the molecules then breakdown and are able to dissolve
surrounded by water molecules
50
explain why water makes up most cytosol (cytoplasm) of most prokaryotic and Eukaryotes
water is a liquid
water allows the movement of substrates and enzymes
necessary for reactions to take place
water is a substrate for some reaction
water is a polar solvent and most biological molecules are polar solvents and charged ions both dissolve in the water for a chemical reaction to take place
51
explain why water makes a good transportation medium
cohesion between water molecules (molecules stick together)
and adhesion between water molecules and other polar molecules
result in water exhibiting a capillary action
so water can rise up a narrow tube against the force of gravity
52
explain why xylem can draw up water
water has cohesive properties
this means it moves as one mass as the molecules are attracted to each other
so when water is drawn up the molecules don't separate
and adhesion between water molecules and other polar molecules
result in water exhibiting a capillary action
so water can rise up a narrow tube against the force of gravity
53
What is capillary action?
the attraction of the surface of a liquid to the surface of a solid
54
explain why water acts as a coolant during chemical reactions in prokaryotic and Eukarytic cells
due to the large amounts of energy required to overcome hydrogen bonding
maintaining constant temperatures in cellular environments is really important as enzymes are only active in narrow temperature ranges
55
What is a coolant?
helping to buffer temperature changes during chemical reactions
56
explain why water can provide a constant environment for aquatic organisms
it does not change temperature easily
Floating ice can insulate water belowwhat
57
What are the different properties of water
- thermal stability
- forms a liquid
- Higher density than ice
- surface tension
- cohesion
- solvent
- metabolic
- transparency
- high specific heat capacity
- high specific latent heat of vaporisation
58
What is the benefit of thermal stability of water to an organism
Stable enviroment for aquatic organisms
59
What is the benefit to an organism of water as a liquid
Transport medium in animals and plants
60
What is the benefit to an organism of the low density of ice
Ice floats on water and insulates the water below
61
What is the benefit to an organism of the surface tension of water
Small animals can move across the surface of the water
62
What so teh benefit to an organism of water being cohesive
Water molecules form a strong water column that moves up the xylem of plants
63
What is the benefit to an organism of water being transparent
Water allows light to move through it so aquatic plants can photosynthesise
64
What is the benefit to an organism of water being metabolic
Water is used to break bonds in hydrolysis and make bonds in condensation reactions
65
Suggest with reasons which properties of water make it such an important component of blood
Liquid so transport medium
Polar solvent
Biological molecules are polar
Ions are charged
Coolant so resistant to temp change
66
Water forms the basis of the storma in chloroplasts and the matrix in mitochondria.
Describe which properties of water make it such an important component of these particular organelles
Water as a POLAR solvent
Biological molecules that are polar and charged ions would dissolves
Water is a liquid
Allows movement of substance AND enzymes
Necessary for reaction to take place
Water is a sub star ate fro some reactions
67
How is water important for aquatic life
Water provides stable environment due to high specific heat capacity
It is a liquid between 0 and 100 degrees so it can be used as a transport medium in a aquatic plants and animals
Ice has a lower density than water so it floats on top of the water insulating the water below
Water is transparent so it allows light through to reach aquatic plants form phtotsynthesis
68
How does the structure of water contribute to its function as a transport medium
Water is a polar solvent (1)
liquid
Cohesion between water molecules and solute due to hydrogen bonds forming (1)
Adhesive between water molecules and wall / xylem/ blood vessel due to hydrogen bonds forming
69
explain how water is used as a coolant in maulticellular organisms
Water has a high latent heat of vaporisation
Water evaporates from surfaces taking heat with it
For example sweating /panting
70
What is the difference between specific heat capacity and latent heat capacity
Specific heat capacity is a measure of how much energy is needed to warm up a substance
Specific latent heat capacity is a measure of how much energy is needed to convert a substance from one stage to another - energy needed in breaking bonds that hold molecules together
71
explain why ice floating is essential for aquatic organisms
insulating layer on top of water
water below doesn't freeze
fish don't freeze and can still move around
72
explain why elephants spray themselves with water to cool down
water evaporates on the surface of elephant body
hydrogen bonds that hold water molecules together
need a lot energy to be broken from elephant
this cools surface of elephant body
73
What are Carbohydrates?
Molecules that only contain elements C, H, O
74
What does Carbohydrate mean and what ration are the elements in?
Hydrated carbon
Ratio Cx(H2O)y
75
Other names for carbohydrates?
Sugar or saccharides
76
Example of a monosaccharide
Glucose, Fructose and ribose
77
What is formed when 2 monosaccharides are joined together
Disaccharides
78
Example of Disaccharides
Lactose and Sucrose
79
What forms when a chain of monosaccharides join together?
Polysaccharide
80
Example of Polysaccharide
Glycogen, Cellulose, Starch
81
Formula for glucose
C6 H12 O6
82
What type of monosaccharide is glucose?
Hexose monosaccharide
83
What direction are carbons numbered on glucose?
Clockwise, Starting from Far Right
84
What are there 2 structural variations in Glucose?
Alpha and beta
85
What is the difference between the two glucose structures (alpha and beta)
The OH (hydroxyl) group on Carbon 1 is flipped
86
Properties of glucose
Polar
Soluble in water
can form H bonds
87
Where is dissolved glucose found in the cell
Cytosol
88
What is formed when 2 glucose molecules are next to each other
They react
Forms maltose and Water
89
What is the covalent bond formed in the condensation reaction of 2 glucose molecules?
Glycosidic
90
Sources of Monosaccharides
Fructose - Fruit
Galactose - Milk/Milk Products
91
Sweetness of monosaccharides
Fructose
Glucose
Galactose
92
Where are ribose sugars present?
RNA nucleotides
DNA nucleotides
Other Biological molecules
93
What type of Sugar is ribose
Pentose
94
What is formed when many Glucose molecules are formed?
Starch
95
Name one of the polysaccharides in starch
Amylose
96
What shape does Amylose form?
helix, stabilised by Hydrogen bonds
97
Why is amylose's structure suited to its function
More compact - more can be stored
Compact - Less Soluble
98
Why is amylopectin branched?
it has both 1,4 and 1,6 glycosidic bonds
99
What is the equivalent of starch in animals and fungi?
Glycogen
100
What is one advantage of Glycogen?
Forms more branches (than eg amylopectin) so it is more compact and needs less space for storage
101
Advantages of branching
Compact
Easy to add to (eg more glucose molecules to free ends)
Speeds up releasing of molecules
Insoluble
102
What is starch (in plants) and Glycogen (in animals and fungi) needed for?
Respiration
103
What type of reaction is undergone to release glucose from starch/glycogen
Hydrolysis - catalysed by enzymes
104
What is cellulose comprised of?
beta-glucose molecules
Alternately turned upside down
105
Cellulose make what bonds forming what?
Hydrogen bonds
Microfibrils
106
What do many microfibrils combine to create?
Macrofibrils
107
What do many macrofibrils join together to create?
Cellulose fibres
108
What quality of cellulose fibres make a good cell wall?
Insoluble
109
Explain how the structure of cellulose is related to its function
Cellulose makes cell walls strong
Can resist turgor pressure
Bonds difficult to break;
Resists action of enzymes/hydrolysis
110
Explain why beta glucose, when polymerised, leads to the production of cellulose instead of starch
In beta glucose the hydroxyl group at carbon 1 is above the ring
so alternate glucose molecules must rotate 180 degrees
so the hydroxyl groups on carbon 1 and carbon 4 are close enough to react.
Condensation reaction forming a glycosidic bond.
The rotation of molecules produces a straight chain molecules- cellulose.
111
How do reducing sugars act?
Donate electrons or reduce another molecule/chemical
112
What is the chemical test for a reducing?
Benedicts reagent
113
How is the Test for carbohydrates carried out?
Place sample in boiling tube (if solid, grind up or blend in water)
Add equal volume of Benedict's reagent
Heat mixture in water bath for 5 minutes
114
What will happen if a reducing sugar is precent?
Reducing sugars will react with the copper ions in the copper sulphate (Benedict's reagent)
Results in addition of electrons to blue Cu2+ ions and turns them to red Cu+ ions
115
What is Benedict's Reagent also known as?
Copper (II) Sulfate
Cu(SO4)
116
What are the positive tests for carbohydrate
(None - Blue)
Low conc - Green
Medium conc - Orange/yellow
High conc - Red
117
Test for non-reducing sugars
Negative result for Benedict's
Boil with dilute HCl
Positive result for Benedict's as the sugar has been hydrolysed
118
Acronym for Tests
CB SI PB LE
Carbohydrates - Benedict
Starch - Iodine
Proteins - Biuret
Lipids - emulsion
119
What is the iodine test method?
Add a few drops of potassium iodide solution to sample
If solution changes from yellow/brown to purple/black, starch is present
120
Name another method that can be used to test the presence of reducing sugars and one advantage
Reagent Strips
Shows concentration of the sugar
121
How is colorimetry of Benedict's test conducted?
Filter placed in colorimeter
Colorimeter calibrated using distilled water
Benedicts test performed on range of known concentrations of glucose
resulting solutions filtered to remove the precipitate
% transmission of each of the solutions measured
Calibration curve plotted
122
Example of a non-reducing sugar
Sucrose
123
Example of a reducing sugar
Glucose
124
What do biosensors do?
They use biological components to determine the presence and concentration of molecules such as glucose
125
what are the Components of a biosensor
Molecular recognition - A protein or single strand of DNA is immobilised to a surface eg. a glucose test strip, which will bind to the molecule under investigation
Transduction - Cause a change in a transducer. A transducer detects changes, eg pH, and produces a response, eg release of a dye or electric current
Display - This then produces a visible, qualitative or quantitative signal such as a particular colour on a test strip or reading on machine
126
Describe the feature of enzymes essential to their role as components in a biosensor
enzymes have active site
active site is specific to a molecule
127
Why does Benedicts reagent turn red when warmed with a reducing sugar?
Reducing sugars react with copper ions in Benedict’s reagent
resulting in the addition of electrons to blue Cu2+ ions
Reducing them to brick red Cu+ ions
128
Explain why an iodine test is used in experiments to show that plants require light for photosynthesis
Iodine test produces a purple/black colour indicating the presence of starch
Starch is a product of photosynthesis
The test shows that starch is produced when light is available to the plant
but not when the plant is kept in the dark
129
Suggest how reagent strips might be useful in the management of the medial condition diabetes, where a person's blood sugar level can become too high
Reagent strips are quantitative
They can be used to estimate the concentration
of glucose in the blood.
They are simple to use and interpret
130
What is the difference between a fat and an oil?
Fats are lipids that are solid at room temp
Oils are lipids that are liquid at room temp
131
Why are Lipids non-polar?
The electrons in the outer orbitals are more evenly distributed than in polar molecules
No positive or negative areas within molecule
Not soluble in water
132
Why are Lipids macromolecules?
Large and Complex
Built from monomers
133
How is a triglyceride formed?
Combining a glycerol (alcohol) with 3 fatty acids (Carboxylic acids with hydrocarbon chain attached)
134
How do Glycerol and Fatty acids react?
Glycerol is a triol
each OH group on alcohol reacts with OH of each COOH on fatty acid
Forms 3 ester bonds (esterification) and 3 water molecules
135
What is needed to reverse the triglyceride formation reaction
Water
Hydrolysis reaction
Forms glycerol and 3 fatty acids
136
What is the difference between saturated vs unsaturated fatty acids
Saturated chains have no double bonds present between carbon atoms - maximum amount of Hydrogens
Unsaturated chains have double bonds present, can be called mono- or polyunsaturated
137
What are Phospholipids?
Modified triglycerides that contain Phosphorus as well as C,H,O
One of the fatty acid chains on a triglyceride is replaced by a phosphate group
138
What charge are on Phosphate ions and what property does this give them?
negative (3-)
contains extra electrons
Soluble in water
139
What are the charges on a phospholipid
Hydrophilic, polar, charged (phosphate) Head
Hydrophobic, non-polar, uncharged (fatty acid) tails
140
What occurs when a phospholipid is in the presence of water?
Hydrophilic phosphate head will stick head on water
Hydrophobic Fatty acid tails stick out of water
Forms layer on top of water
141
What are Phospholipids also called?
Surface active agents or surfactants
142
What arrangement of phospholipids are present in membranes
Bilayer
143
What are sterols also known as?
Steroid Alcohols
144
What is an example of a sterol?
Cholesterol
145
What are sterols based on?
4 carbon ring structure with OH group at one end
Has hydrophilic and Phobic sides (OH is phillic, rest of molecule is phobic)
146
Where is cholesterol manufactured in the body?
Liver and Intestines
147
What role does cholesterol play in membranes
Adds stability and regulates fluidity
148
What are the roles of lipids?
membrane formation (creation of hydrophobic barriers)
Hormone Production
Electrical Insulation for impulse transmission
Waterproofing (eg birds feathers, plant leaves)
149
What role do lipids play under the skin and around vital organs?
Thermal Insulation to reduce heat loss (eg penguins)
Cushioning to protect vital organs (eg heart and kidneys)
Buoyancy for aquatic animals (eg whales)
150
How can lipids be identified?
Emulsion Test
151
Describe the method for the emulsion test?
Mix sample with ethanol
Add water and Shake
If a white emulsion forms as a top layer, lipid is present
152
Explain how hardening vegetable oils produces solid fats
hydrogenation
removes double bonds in fatty acids
closer packing of molecules
153
Explain why it is considered more healthy to have a low overall fat content as well as a low saturated fat content in a spread
unsaturated and saturated fat have high energy content
excess energy intake leads to obesity
154
Using your knowledge of the structure of fatty acids describe why oils are liquid and fats are solid at room temperature
Oils are unsaturated
unsaturated fatty acids contain double bonds
molecules cannot pack closely
Fats are usually saturated so fatty acids have no double bonds
155
Describe the formation and the hydrolysis of an ester bond
Hydroxyl group from glycerol
Hydroxyl group from fatty acid
Condensation reaction (forms ester bond)
Hydrolysis is reverse of the process above
156
Some bacteria are extremophiles meaning they live in extreme environments that are very high acidic or have very high temperatures. The phospholipids present in other bacteria or eukaryotic cells would be broken down in such extreme conditions. Extremophiles have membranes composed of modified phospholipids.
A) identify which of the phospholipids in the diagram is present in the cell membrane of extremophiles (pg58)
B) outline the similarities and differences between the two types of phospholipid
C) Suggest why the phospholipids oil the membranes of extremophiles can withstand extremes of temperature and pH
A) A
B) Both have phosphate group attached to glycerol
Both have fatty acid (tail)
Cross links between fatty acid tails in A
Ester bond not present (on A)
C) Cross links stabilise the membrane
157
Read the following statements
Lipids are not soluble in water
Lipids and ethanol are soluble in water
Water is more soluble than lipids in ethanol
use the information to explain how the emulsion test for lipids woks
procedure for emulsion test statement 2, sample / lipid, dissolved in ethanol
water is mixed with ethanol (and lipid) solution
statement 3, idea that water displaces lipid from ethanol forming suspension
statement 1, (suspension forms because) lipids not soluble in water
158
What are peptides?
Polymers made up of amino acid molecules
159
What is a protein
One or more polypeptides arranged as a complex macromolecule
160
What elements are proteins made from?
C, H, O, N
161
What is the structure of an amino acid?
Amine group (-NH2)
Carboxylic acid group (-COOH)
Central Carbon w/ a hydrogen and an R (variable group) attached
162
How is a peptide bond formed?
H on NH2 and OH in COOH group of 2 amino acids form water
Nitrogen then bonds to the carbon
163
Structural formula for Amino Acid and a dipeptide
NH2 CHR COOH
NH2 CHR CONH CHR COOH
164
What type of reaction forms a dipeptide?
Condensation
165
What is the name given to many amino acids joined together?
polypeptide
166
What is the enzyme which catalyses the reaction for peptide bond formation and where is it found?
Peptidyl Transferase
Ribosomes - sites of protein synthesis
167
What happens when Various R groups interact with each other?
Leads to long chains of amino acids (polypeptides) folding into complex precise 3D shapes (proteins)
168
What method is used to separate individual components of a mixture?
Thin Layer Chromatography
169
What are the 2 phases in chromatography?
Mobile phase (Organic Solvent)
Stationary Phase (Silica Gel)
170
How are amino acids separated in TLC?
Solubility in mobile phase
If they are more soluble, they will be higher up the plate
if they are less soluble, they will be lower down the plate
171
Describe the method for TLC
Draw line 2cm up from the bottom of the plate using pencil
Mark point(s) (equally spaced if multiple)
Spot Amino acid solution onto base line using capillary tube, let dry, then spot again
Place plate into a closed jar of solvent, no more than 1 cm deep
Leave plate until solvent has reached 2cm from top, mark solvent front with pencil
Spray plate with Ninhydrin in fume cupboard, Mark each spot with pencil
Analyse results
172
Suggest why gloves were worn by the student and the plate was only handled by the edges (TLC)
Prevent contaminating stationary phase
Biological material on skin
173
A mixture of solvents (such as hexane, water, acetic acid and butanol) is usually used as the mobile phase when separating an unknown mixture of amino acids. Suggest Why (TLC)
testing unknown compounds
not known whether substance is polar or non-polar
Different solvents will dissolve both polar and non-polar compounds
174
Explain why the solvent was no more than 1 cm deep (TLC)
so the concentrated spots were not covered
175
Suggest why the jar was sealed (TLC)
Air inside jar is saturated with solvent
prevents evaporation of solvents
176
What is Primary structure of a protein?
The sequence in which he amino acids are joined together
Directed by information in DNA
Particular amino acids in the sequence will fold to give its shape
177
What bonds are involved in primary protein structure?
Peptide bonds only
178
What is the secondary structure of a protein
Alpha Helix or Beta pleated sheet
Hydrogen bonds form, coiling it into shape
179
What bonds are in secondary structure of a protein?
Peptide and Hydrogen
(R groups are not involved in this stage)
180
What determines if a secondary protein is an alpha helix or a beta pleated sheet?
Hydrogen bonds that form due to the sequence of amino acids
181
What is Tertiary protein structure
Folding of a protein into its final shape, often including sections of secondary structure
Interaction of R groups
182
What bonds are in tertiary protein structure
Hydrophobic and Hydrophilic interactions (R-groups)
Hydrogen Bonds
Ionic bonds (R-groups)
Disulphide bridges (R-groups)
Peptide Bonds
183
What is quaternary protein structure?
The association of 2 or more individual proteins called subunits
Same interactions in tertiary structure, but are between proteins rather than within a molecule
184
Can protein sub units be different?
Protein subunits can be identical or different
Enzymes often consist of 2 identical subunits
Hormones can consist of 2 different subunits eg insulin
185
Name an example of a quaternary structured protein
Haemoglobin
Found in Blood
Two sets of 2 identical sub units (2 alpha chains, 2 beta chains)
186
What determines if the protein is hydrophobic or hydrophilic, and the way it folds?
R-Groups
187
What enzyme is used to catalyse the breakdown of peptides?
Proteases
188
What test is used to identify proteins?
Biuret test
189
Describe the procedure of a biuret test
Add 10% Sodium Hydroxide solution to equal volume of liquid sample
Then add 1% Copper sulphate solution dropwise until blue
Mix Solution and leave to stand for 5 minutes
If violet coloured, proteins are present
190
State the colour you would expect to see on addition of the copper sulfate solution if protein is present in the sample?
Purple
191
State the colour you would expect to see if the sample contains amino acids instead of proteins
No peptide bonds present as no protein
Test is negative
Solution remains blue
As Copper sulfate solution is blue
192
Suggest why the Biuret test is not used quantitatively
Biuret test identifies peptide bonds
Degree of colour change dependent on number of peptide bonds
Different proteins have different numbers of peptide bonds
Different degrees of colour change could indicate different proteins not different quantities of protein
193
Describe the formation of a peptide bond
Condensation reaction
between amine group of one amino acid
and carboxylic acid group of another
forming a water molecule.
194
Describe how hydrogen bonds form within the secondary structure of proteins
Oxygen is relatively negative and hydrogen (attached to nitrogen) is relatively positive
Oxygen and hydrogen are attracted to each other, forming bonds
195
Alpha Keratin, a protein found in sheep's will, is primarily composed of alpha helices. Explain why alpha keratin has a more regular structure than the quaternary protein haemoglobin
Secondary structures are simple repeating structures
haemoglobin, has multiple tertiary structures
tertiary structure is formed from complex folding of secondary structure
196
Compare and contrast the role of R-group interactions in the formation of the tertiary and quaternary proteins
R groups on amino acids interact
tertiary structure – interactions within a protein molecule
determines shape of molecule
quaternary structure – interactions between protein molecules
holds molecules together
Both involve the same interactions
i.e., hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic and hydrophilic interactions
197
What are the two main groups of proteins?
Fibrous and Globular
198
Describe Globular Proteins and their properties
Tertiary proteins
Water soluble
Compact
Roughly Spherical
199
Example of a Globular protein
Insulin
200
What does insulin do?
Regulates blood glucose
201
Where are hormones transported?
Bloodstream
202
How do hormones effect a target cell?
Hormones fit into specific receptors on cell-surface membranes therefore needing precise shapes
203
What are conjugated proteins?
Globular proteins containing a non-protein prosthetic group
204
What types of prosthetic groups are there
Lipids
Carbohydrates
Lipoproteins
Glycoproteins
Metal ions eg Iron ions
205
Example of a conjugated protein?
Haemoglobin, contains harm group (iron ions) bound reversibly to each sub unit
Catalase, contains 4 haem groups
206
What does catalase do?
Speeds up breakdown of harmful Hydrogen Peroxide into water and oxygen, due to its Iron II ions
207
What are fibrous proteins
Long, insoluble molecules
high proportion of amino acids are hydrophobic
High repetition, organised structures
208
Examples of Fibrous protein
Keratin, Elastin, Collagen
209
What is Keratin, where is it found and what properties does it have?
A fibrous protein
Present in hair, skin and nails
Large proportion of sulfur containing amino acids, so they have lots of disulphide bridges
Strong, inflexible and insoluble
210
What is elastin, where is it found and what properties does It have?
Elastin is a fibrous protein found in elastic fibres
Present in blood vessel walls and alveoli of the lungs
Gives flexibility
Quaternary protein Made from stretchy molecules called tropoelastin
211
What is Collagen, where is it found and what properties does it have?
Fibrous protein
Connective tissue found in the skin, tendons, ligaments and the nervous system
made up of 3 polypeptides wound together in a long, rope-like structure
gives strength and flexibility
212
Suggest what property the arrangement of collagen fibres into large bundles gives to tendons
strength or non-elastic
213
As we age, the collagen in our skin starts to break down. This leads to the loss of Full of wrinkles. Many beauty products are available that contain collagen in the form of creams and capsules. Using your knowledge of the structure of collagen, suggest why these products are unlikely to have any beneficial effect in reducing or preventing wrinkles.
large molecule so unlikely to enter skin
has a complex structure,
Individual components arranged in hierarchical structure,
New molecules would not incorporate into existing collagen
214
What is the order for increasing bond strength out of these three bonds, weakest-strongest,
ionic bonds, disulphide bonds, hydrogen bonds?
Hydrogen bonds
Ionic bonds
Disulfide bridges
215
Explain the difference between a simple protein and a conjugated protein
Conjugated proteins contain a non-protein group
called a prosthetic group
simple proteins do not
216
Describe the differences in properties and functions of insulin, a hormone, and keratin, present in nails and hair
Insulin globular protein
soluble (1)
specific shape (1)
binds to receptor (1);
chemical messenger
Keratin fibrous protein
strong
structural function (e.g. hair, nails)
217
Describe why global proteins are soluble in water but fibrous proteins are not
Globular proteins hydrophobic R groups, in the centre (of the molecule) not in contact with water
hydrophilic R groups, on the outside (of the molecule) / in contact with water
Hydrophobic R groups are repelled by water / hydrophilic R groups are attracted to water
fibrous proteins have R groups on the outside of the molecule
218
Myoglobin is an oxygen carrying molecule found primarily in muscle tissue. It is formed from a single polypeptide chain which is folded to form eight alpha helices. This chain is further folded around a central prosthetic group which binds reversibly with oxygen. The hydrophobic R groups of the amino acids are positioned towards the centre of the molecule.
Discuss the similarities and differences in the structures of haemoglobin and myoglobin.
similarities
globular (protein)
alpha helices
prosthetic group
hydrophobic R groups positioned towards the centre (of the molecule)
differences
single polypeptide not four
polypeptides / myoglobin tertiary not quaternary
no beta chains
219
What are nucleic acids?
Large molecules discovered in the nucleus of cells
220
What are the two types of nucleic acid?
DNA and RNA
221
What elements comprise nucleic acids and nucleotides?
C, H, O, N, P
222
What are the 3 components to a nucleotide monomer?
Pentose sugar (ribose)
Phosphate group -PO4 2-
Nitrogenous base
223
What are phosphodiester bonds bonding
Phosphate at Fifth carbon pentose (ribose) sugar (5') of one nucleotide bonds covalently to the OH group at carbon 3 (3') of the next sugar
224
What are phosphodiester bonds also known as?
Sugar Phosphate backbone
225
What does DNA stand for and what is the difference from RNA (not asking bases)
Deoxyribonucleic acid
One fewer oxygen atom on the ribose sugar
226
What 2 type of bases are there?
Pyrimidines (smaller) - C, T
Purines Bigger - A, G
GorillAs are BIGGER than CaTs (Egypt worshiped cats so CT are pyrimidines)
227
What are the complementary base pairs in DNA?
Adenine - Thymine (2 Hydrogen Bonds)
Guanine - Cytosine (3 Hydrogen Bonds)
228
What structure does a DNA molecule form? (2 strands)
Double Helix
229
How is a double Helix held together?
Hydrogen bonds
230
How are the two DNA strands orientated?
Antiparallel
3'-5' one chain
5'-3' opposite chain
231
Why does complementary base paring help DNA structure?
maintains constant distance/ chain width between backbones
Equal Volumes of CG and equal volumes of AT
232
function of DNA
stores genetic information that controls protein synthesis
233
function of RNA
polynucleotide molecules that synthesise proteins from copying and transferring instructions in DNA
234
What base is different in RNA?
Thymine is replaced by Uracil (bonds to adenine)
235
Why is mRNA necessary to life?
DNA is to big to fit through nuclear pores
mRNA molecule transcribes information and leaves nucleus through pores
Much shorter than the whole chromosome
Travels to ribosomes
236
What reaction creates phosphodiester bonds
Condensation
237
What happens to RNA after protein synthesis?
Degrades in the cytoplasm
Phosphodiester bonds are hydrolysed
Nucleotides are released and reused
238
Describe the method used to extract DNA from plant material?
Grind sample in mortar and pestle - breaks down cell walls
Mix sample with detergent - breaks down cell membrane, releasing cell contents into solution
Add salt - Breaks the hydrogen bonds between the DNA and water molecules
Add Protease - Breaks down proteins associated with DNA in the Nuclei
Add a layer of Ethanol on top of the sample - Alcohol causes the DNA to precipitate
The DNA will be seen as white strands forming between the layer of sample of alcohol
Can be picked up by spooling onto a glass rod
239
The temperature should be kept low throughout this DNA extraction procedure. Suggest why.
Reduce activity of enzymes
Reduce breakdown of DNA
240
Explain why detergent breaks down cell membranes
Disrupts membrane structure
Phospholipids form suspension in aqueous solution
241
Describe the differences between DNA and RNA nucleotides
DNA nucleotide – deoxyribose sugar, thymine base
RNA nucleotide – ribose sugar, uracil base
242
Explain the base pairing rule
A pyrimidine base always pairs with a purine base
Adenine and thymine/uracil always hydrogen bond together
Cytosine and guanine always hydrogen bond together
243
Explain how the structure of DNA is ideally suited to its role
Polymer so contains a lot of information
Base sequence is used as a code
Double stranded so molecule is stable
Double stranded so accurate replication
244
How does DNA replicate
Semi-conservatively
245
Describe the process of Semi-conservative replication
Double helix unwinds into two strands, Hydrogen bonds between bases broken, Catalysed by DNA Helicase
Free nucleotides will pair with exposed bases of separated strands
Hydrogen bonds will form between them
New Nucleotides will join to their adjacent molecules with phosphodiester bonds, Catalysed by DNA Polymerase
2 molecules of DNA created - 4 strands, Each molecule consisting of 1 old strand and 1 new strand
246
What enzymes are involved in DNA replication?
DNA Helicase
DNA Polymerase
DNA Ligase
247
What direction does DNA polymerase move
Travels in direction 3' to 5' (known as leading strand)
248
DNA polymerase has to replicate both of the strands, in opposite directions. Which side is continuously replicated and what side is discontinuously replicated?
Continuous: 3' to 5' (direction of movement of DNA polymerase)
Discontinuous: 5' to 3' (opposite to movement of DNA polymerase)
249
What is Discontinuous Replication
Where the DNA polymerase has to go back after it has finished the Continuous strand
Adds DNA in sections (Okazaki fragments) then joined together, catalysed by DNA Ligase
Lagging strand
250
Describe the difference between Continuous and Discontinuous replication
Continuous replication – DNA polymerase binds to the end of a strand, free DNA nucleotides added without any breaks;
discontinuous replication – DNA polymerase cannot bind to the end of a strand, free DNA nucleotides added in sections, sections then joined.
251
Using your knowledge of enzymes, explain why DNA polymerase does not catalyse the joining of Okazaki fragments into a single strand but a different enzyme (DNA Ligase) is used
Enzymes are (substrate) specific
DNA polymerase catalyses the joining of nucleotides
Nucleotides have a different shape to Okazaki fragments
252
What occurs as a result of a replication error
Mutation
253
What is the Genetic code?
DNA code for sequences of Amino acids, that make up proteins that are the foundation to different physical and biochemical characteristics of living things
254
What is a codon
A sequence of 3 bases, each codon codes for an amino acid
255
What is a gene
A section of DNA that contains the complete sequence of bases to code for an entire protein
256
What is Degenerate code
Many amino acids can be coded for by more than one codon
many codon options for most amino acids
(not necessary) eg. Argentine can be coded CGG, CGA, CGC, CGT, AGA, AGG,
257
Explain why DNA replication is described as semi-conservative
Semi-conservative means ‘half the same’
When DNA replicates the double helix unwinds
into two separate strands
Free nucleotides pair with their complementary bases
Two new molecules of DNA are produced
Each with one old strand and one new strand
258
Explain what is meant by the triplet code
The triplet code is a particular sequence of three bases
That codes for a specific amino acid
259
Enzymes are cellular proteins that catalyse reactions, they have active sites in which specific substrates fit precisely. Suggest how a genetic mutation may result in an enzyme becoming non-functional.
mutation in the DNA changes the triplet code
meaning different amino acids are incorporated into the protein/enzyme
that the DNA codes for. If such a change affects the precise structure of the active site
a substrate may not be able to bind
260
The sequence of bases in specific sections of DNA and the sequences of amino acids in specific proteins are both used to compare how closely related different species are. The fewer differences in the sequences, the more closely related species. Explain why there are likely to be more differences, overall, between base sequences of DNA than between amino acid sequences of proteins.
The triplet code of DNA is degenerative
there are 64 different triplets/codons but only 20 amino acids
therefore an amino acid can be coded for by more than one codon
so more opportunity for differences in DNA sequence than amino acid sequence
261
What are the two stages of Protein synthesis
Transcription and Translation
262
Where is DNA contained in a Eukaryotic Cell
Nucleus (inside nuclear envelope)
263
Where does protein synthesis occur?
Ribosomes in cytoplasm
264
Why can't DNA molecules leave the nucleus
too large to fit through the nuclear pore
265
What does Transcription produce
Shorter molecules of RNA
266
Which strand acts as the template strand?
Antisense (sense strand is desired code)
267
Describe the process of Transcription
Section of DNA that contains gene for protein is unzipped, H bonds break, catalysed by DNA Helicase
Sense strand is 5' to 3' codes for protein
Antisense strand is 3' to 5' and is template, doesn't code for a protein
Free RNA nucleotides will base pair with exposed antisense strand
Phosphodiester bonds form between RNA nucleotides, catalysed by RNA Polymerase
When Transcription stops, a molecule of Messenger RNA (mRNA) is formed
Same base sequence as sense strand (U instead of T)
mRNA Detaches and leaves through the Nuclear pore to go to ribosome in cytoplasm
Double helix reforms
268
Describe Translation
mRNA binds to specific site on small subunit of ribosome, large subunit clamps on top
Transfer RNA (tRNA) contains complementary anticodons folded in a way so they are on end of molecule
tRNA anticodons bind to complementary codons, amino acid is created and primary structure is coded by the mRNA
Amino acids are added one at a time to form a polypeptide chain
Ribosomes catalyse assembly of protein (peptide transferase in rRNA component of ribosome)
Once completed, Polypeptide is released, and folds into secondary and tertiary structure and sent to the Golgi for further modification
Many ribosomes can join onto the mRNA molecule to synthesise protein, one after the other
269
Describe the roles of mRNA, tRNA and rRNA in protein synthesis
mRNA –
copies gene from DNA
takes copy to ribosome
tRNA –
brings amino acid to ribosome
rRNA –
formation of ribosome
270
An enzyme forms part of the structure of a ribosome. Suggest the role of this enzyme
catalyse the formation of bond between two amino acids
Peptide bond
Peptidyl Transferase
271
rRNA also forms part of the structure of a ribosome. Suggest why RNA needs to be present in a ribosome
bind to tRNA
complementary base pairing
272
Ribosomes are either free floating within the cytoplasm or bound to endoplasmic reticulum. Suggest a reason for the different ribosomal sites
Free floating ribosomes produce proteins for use in cell
RER bound ribosomes produce proteins for export from the cell
273
Post transcriptional modification of mRNA is carried out before it can leave the nucleus. This involves capping each end to protect the mRNA from degradation in the cytoplasm and the removal of Introns. Introns are non-coding sections of DNA and have no role in the formation of proteins.
1) Explain why unnecessary base sequences must be removed before protein synthesis begins
2) suggest an advantage of being able to edit mRNA
3) Suggest a reason for the presence of Introns within Genes
1) role of protein dependent on structure
shape / 3D structure, dependent on primary structure / sequence of amino acids
base triplets / codons, on mRNA, code for amino acids
introns would code for, unnecessary amino acids / stop signal
codons could cause frameshift
2) different proteins produced from one gene
3)originally functional gene
could be mutated mutated
base sequence/s changed
no longer code for (useful) amino acid
274
What processes do cells require energy for
Synthesis (eg proteins)
Transport (eg ions across membranes via active transport)
Movement (eg protein fibres that cause muscle contraction)
275
What is the universal energy currency?
ATP
276
What is an ATP molecule comprised of
3 Phosphate groups
Ribose sugar
Adenine base
277
How does ATP release energy?
Small amount of energy is required to break the bond holding the last Phosphate group
Releases large amount of energy
Forms ADP + Pi + Energy
278
Why is ATP not a good long-term energy store
Phosphate groups are too unstable
279
How is ATP created?
Cellular respiration of Fats and Carbohydrates (better long term energy stores)
280
How is ATP recycled?
Reattaching a Phosphate group group to an ADP molecule (Phosphorylation)
281
Why do cells not store large amounts of ATP
Unstable
Good source of immediate energy
282
Properties of ATP
Small - Can move easily in, out and within cells
Water soluble - energy requiring processes happen in aqueous environments
Contains Bonds between phosphates for immediate energy that is large enough for cellular reactions but not so large that energy Is wasted
Easily regenerated - can be recharged with energy (the addition of a phosphate)
283
Describe the structure of ATP
sugar/ribose sugar
joined to a base/adenine
Three phosphates
284
Describe why ATP is called the universal energy currency
Present in all cells (1)
It is present in all organisms
It releases energy in, small/ manageable quantities
285
People and other animals store excess energy in the form of fat. Explain why fat is stored, not ATP
fat is long term energy store
Fat is stable molecule and ATP is unstable molecule
fat has other uses
e.g., insulation
286
Outline how energy is transferred with reference to bond formation and cleavage
Bond formation releases energy
bond uses energy
287
Discuss the validity of the statement: ATP is the universal energy currency
ATP provides energy for, reactions / processes
ATP is present in all living organisms
idea that there is no other equivalent molecule
therefore statement is valid
