Topic 1A - Biological Molecules Flashcards
Introduction to Biological Molecules Carbohydrates Lipids Proteins Enzyme Action Factors Affecting Enzyme Activity Enzyme-Controlled Reactions
1
Q
Carbon atom structure
A
2,4
2
Q
what is organic chemistry
A
carbon, hydrogen and oxygen
3
Q
Biological molecules
A
A group of natural molecules created by and involved in the processes of living things.
4
Q
Atoms
A
The building blocks of chemistry, everything is made of atoms. Atoms come together to form molecules.
5
Q
Covalent Bonding
A
Bonds formed by the sharing of electrons between contributing atoms.
6
Q
Ionic Bonding
A
Bonds forms by the attraction between oppositely charged ions and the transfer of an electron from one to the positive to the negative.
7
Q
Intermolecular forces
A
The forces between molecules of a substance that arise due to polarity and regions of slight opposing charge.
8
Q
Hydrogen Bonding
A
The attraction between hydrogen and electronegative atoms in other molecules particularly common in water and involves an attraction between electronegative oxygen and electropositive hydrogen.
9
Q
Macromolecule
A
Large, often complex molecules formed of many component sub-units.
10
Q
Monomer
A
A smaller, simpler molecule that forms the subunit of macromolecules and polymers. They can be easily joined to create long chains.
11
Q
Polymer
A
The result of joining multiple monomers. A long chain-like molecule formed of many subunits.
12
Q
Polymerisation
A
A general term for the reaction by which polymers are formed and monomers are joined.
13
Q
Condensation Reaction
A
A specific form of polymerisation reaction where the joining of monomers releases a molecule of water.
14
Q
Hydrolysis
A
The reverse of condensation. The addition of water splits polymers back into the original monomers.
15
Q
Carbon Backbone
A
The long chain of carbon molecules that runs right through sugar.
16
Q
Monosaccharides
A
The simplest subunit of sugars, the ‘monomer’.
17
Q
Pentose Sugar
A
Monosaccharide containing five carbons.
18
Q
Hexose Sugar
A
Monosaccharide containing six carbons e.g. glucose.
19
Q
Isomerism
A
This is where two molecules may have the same general formula, but their molecular and structural formula is different. E.g. alpha and beta glucose.
20
Q
Isomer
A
A molecule with the same chemical formula but different arrangement of atoms, molecular formula.
21
Q
Glycosidic Bond
A
The bond that joins monosaccharides.
22
Q
Polysaccharide
A
The result of combining two or more monosaccharides to create a much more complex sugar (10+)
23
Q
Cellulose
A
Large polysaccharide found in cell walls. It is formed of long unbranched chains of cellulose (beta glucose) that maintain the cell wall’s structure.
24
Q
Cross-Links
A
Links between monosaccharides in certain polysaccharides.
25
Reducing Sugar
Sugar that is able to donate electrons to reduce or break down another substance, monosaccharides and some disaccharides (maltose and lactose).
26
Non-reducing Sugar
E.g. polysaccharides. Carbohydrate polymers that are must be broken down into monosaccharides before they can reduce another substance.
27
Benedict's Reagent
The blue reagent that is a test for sugars containing copper (II) sulphate, changes colour dependent on the concentration of reducing sugars.
28
How do you test for non-reducing sugar using Benedict's reagent?
Hydrolyse into monosaccharides by
add HCl acid,
heat in water bath
neutralise with sodium hydrocarbonate
test as normal
29
Iodine Test
The brown/orange reagent used to test for starch – will turn blue/black upon presence of starch.
30
Qualitative Test
Tells us if something is present.
31
Quantitative Test
Provides more detail than qualitative test, such as how much of a substance is present.
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Oligosaccharide
Chain of 3-10 monosaccharides
33
How do you number carbon bonds in a molecule?
Start at 3 on a clock and number consecutively clockwise
34
Maltose
Alpha glucose + Beta glucose.
35
Sucrose
Alpha glucose + fructose.
36
Lactose
Alpha glucose + galactose.
37
1,4 glycosidic bond
Glycosidic bond that joins C1 and C4 together with a shared oxygen (O).
38
What type of bond does maltose have?
1,4 glycosidic bond.
39
Monosaccharide general formula
(CH2O)n
40
Triose formula
C3H603
41
What type of monosaccharide is glyceraldehide?
Triose
42
Example of a tetrose?
Threose
43
What type of monosaccharide is ribose?
Pentose
43
What do you call a monosaccharide with the formula C5H10O5?
Pentose
44
What is a hexose with an example?
A monosaccharide with the formula C6H12O6,
Glucose
45
Name two hexose monosaccharides other than glucose
fructose
galactose
46
respiration reaction
glucose + O2 equals CO2 + H2O (+ ATP as a biproduct)
47
Why is glucose well adapted as an energy source?
small - easily transported via carrier proteins
soluble - easily transported
less reactive - breakdown must be catalysed so the rate of reaction is therefore more controlled
48
Two essential glucose isomers
alpha/beta glucose
49
How do alpha/beta isomers differ from each other?
the hydroxyl (-OH) groups are swapped on each side in format
alpha - same side
beta - opposite sides
50
What is the chemical formula of ribose?
pentose
C5H10O5
51
where is ribose found (two examples)?
RNA (ribonucleic acid) - used in transcription
ATP - main monomer (energy)
52
RNA
Ribonucleic acid
53
What polysaccharide is made up of a glucose chains?
Amylose
54
What type of chain is cellulose made up of?
B glucose
55
what type of bond in an a glucose chain forms the polysaccharide amylose?
1,4 glycosidic
56
what polysaccharide does a chain of B glucose monomers bonded with 1,4 and 1,6 glycosidic bonds form?
amylopectin
57
why is glycogen well adapted as an energy store?
compact - lots of energy in small area
insoluble - no risk of cytolysis because no effect on water potential
large - wont diffuse out until broken down
easily hydrolysed - broken down easily to then diffuse out to release energy
58
features of amylose
unbranched chain of a glucose
coiled structure
compact
59
features of amylopectin
branched a glucose
side branches allow enzymes to hydrolyse fast
60
what forms with a mix of amylose and amylopectin?
starch
61
features of cellulose
in a plant's cell walls
long unbranched B glucose chain
when bonded - straight cellulose chain
monomers linked by H bonds to from microfibils
provides structural support to cell
62
microfibils
strong fibres formed by H bonds joining monomers in cellulose
63
Triglyceride
A lipid that is formed from a glycerol molecule and three fatty acids.
64
Glycerol
Chemical substance with the structure CH2(OH)CH(OH)CH(OH)CH2(OH). Fatty acids can join at each of the OH groups to form lipids.
65
Fatty Acid
Monomer, smallest subunit of lipids. They consist of a long carbon chain and a COOH group.
66
Saturated
When a substance contains the maximum amount of hydrogen atoms for the length of the carbon chain present, meaning there are no double bonds C=C.
67
Unsaturated
A substance that contains at least one double bond C=C.
68
Polyunsaturated
A substance with more than one double bond C=C.
69
Monounsaturated
A substance with only one double bond C=C.
70
Hydrophobic
When a substance repels water.
71
Hydrophilic
When a substance actively seeks out water – it attracts it.
72
Emulsion test
Chemical test for lipids. Involves shaking a substance with ethanol and pouring into water. Lipids will show as a milky emulsion, the more obvious, the larger amount of lipid present.
73
what part of the hydrocarbon chain determines the type of lipid?
the end
74
how can the hydrocarbon be represented in a formula as short hand
R
75
are lipids polymers?
no
76
why are lipids not polymers?
there aren't any subunits for it to be broken down to - no repeating pattern
77
give an example of a macromolecule
triglyceride
78
what does non polar molecules mean
insoluble - the tails of lipids are hydrophobic
79
what is the structure of a triglyceride
one glycerol molecule
joined to three fatty acids
80
what is the structure of a phospholipid
one glycerol
one phosphate group
two fatty acids
81
how do phospholipids differ to triglycerides
phospholipids - glycerol , 2 fatty acid, phosphate group
triglyceride - glycerol, three fatty acids
82
what ics chemical formula for a carboxyl group
COOH
83
Ester bonding
triglyceride formed with condensation reaction (removal of water) joining glycerol and the three fatty acids
84
how many ester bonds does a triglyceride have?
3
85
how is a triglyceride broken down?
back into glycerol and fatty acids to release energy
86
what is a triglyceride well adapted to be
an energy store
87
how is a triglyceride well adapted to be a good energy store?
long tails - contain a lot of chemical energy (2x the energy/gram to that of carbohydrate stores)
insoluble - no effect on water potential so no risk of cytosis
88
explain how are triglycerides insoluble
the tails face inwards, shielding the molecule from the water with the glycerol head.
hydrophobic tails
89
are phospholipids hydrophobic or hydrophilic?
hydrophobic
90
name three functions of proteins and give examples
structural - muscles, tendons, bones
metabolic - enzymes
transport - haemoglobin, Hb
91
what is an amino acids structure
(C)(COOH)(NH2)(R)
central carbon bonded to a carboxyl group, an amino group and the variable group chain
92
what are the three ways an R group can vary
size
polarity
charge
93
explain how size can vary in an R group, with two examples
glycine - has just H as its R group
lysine - has a hydrocarbon chain followed by NH3
94
amino acids
The subunit of proteins/peptides. Composed of an amino group, carboxyl group and a unique R group that distinguish the twenty different amino acids.
95
amino group
The amino group is the -NH2 part of an amino acid.
96
dipeptide
Two amino acids bonded together.
97
polypetide
Two or more amino acids bonded together.
98
carboxyl group
The carboxyl group is the -COOH part of an amino acid and gives the amino acid its acidic quality.
99
R side chain
The R side chain is the name given to the part of the amino acid that is unique and differentiates it from others.
100
peptide bond
Peptide bonds form between amino acids in polypeptide chains.
101
hydrolysed protein
A protein that has been hydrolysed is one that has undergone hydrolysis.
been broken down into its amino acid subunits
102
α helix
A type of protein secondary structure where interactions between parts of a polypeptide chain cause it to twist.
103
Hydrogen bond
The intermolecular force that occurs between hydrogen and highly electronegative atoms like oxygen and nitrogen
104
Disulfide bridge
The double bond that forms between the sulphur atoms of two cysteine amino acids. These create extra strength within a protein’s tertiary and quaternary structures.
105
explain with examples how polarity can vary within R groups
can be neutral, negative or positive polarity
non polar = neutral, pos/neg = polar
eg alamine is non polar (CH3 end)
cysteine is polar (SH end) - it has neg and pos charge so neg is stronger than pos and will be neg polar
106
explain with examples how charge can vary within R groups
lysine (NH3+ end) has positive charge from the H+ ion it picked up
aspartic acid (CO2- end) has donated an H+ ion so is left negatively charged
107
Biuret test
test for proteins
add sodium hydroxide solution
add copper sulfate II solution
if protein - turn purple
if no protein - stays blue
colour change v subtle
108
for proteins with a single polypeptide chain, what is the final 3D structure?
tertiary structure
109
Primary structure
Amino acid sequence in polypeptide chain.
110
Secondary structure
The chain is not straight, H bonds form between amino acids, causing the chain to coil into an alpha helix or fold into a beta pleated sheet.
111
Tertiary structure
The coiled or folded chain can be made more complex in this way, with more H bonds forming between more parts of the chain. Disulphide bridges form between the sulphur atoms of cysteine molecules. Ionic bonds also form between positively and negatively charged parts of the chain. For proteins with a single polypeptide chain this is the final 3D structure.
112
Quaternary structure
For proteins consisting of multiple polypeptide chains bonded together. This structure indicates how these chains are assembled. For globular and fibrous proteins, this is the final 3D structure.
113
what is the final 3D structure of globular or fibrous proteins?
quaternary structure
114
what are some features of enzymes and why do they make them well adapted for their functions?
spherical - tightly folded chains
soluble - digestive (to aid metabolism) and easily broken down
115
what are four functions of proteins
enzymes
antibodies
structural proteins
transport proteins
116
antibodies features
work within the immune system
made of two short and two long chains bonded together
the sequences of amino acids can vary so they have variable regions to work within
117
features of transport (channel) proteins
found in cell membranes
contain both hydrophobic and hydrophilic amino acids causing them to fold to cause a channel
they transport molecules/ ions across membranes
118
some features of structural proteins
long chains
strong
lie parrallel with cross-links
119
examples of structural proteins
keratin, collagen
120
Catalyst
A substance that speeds up a chemical reaction without being used up itself.
121
Activation energy
The amount of initial energy needed for a reaction to progress to products.
122
Specificity
Specificity refers to the fact that the target molecule, or substrate for a given enzyme is specific.
123
Active site
The active site is the functional part of the enzyme protein that attaches to the substrate.
124
Enzyme-substrate complex
This is the temporary molecule formed when the enzyme and substrate bond.
125
Substrate
The substrate is molecule on which the enzyme is designed to work.
126
Intermediate
An intermediate is a molecule that exists temporarily during the course of a reaction, like an enzyme-substrate complex.
127
Lock and Key model
An earlier model of enzyme action that likened the enzyme to a lock and the substrate to a key. This model suggested the substrate fit the enzyme’s active site perfectly and then was broken down.
128
Induced fit model
A more modern approach to enzyme action that accounts for the flexible nature of an enzymes structure. This model suggests that the enzyme’s active site alters slightly to accommodate the substrate’s fit.
129
Denaturation
This occurs above a certain temperature, usually around 60°C or extreme pHs and causes the substructure of a protein to come apart and in the case of enzymes, it renders the active site ineffective.
130
Optimum
Optimum refers to the “best” scenario. Optimum pH is the pH at which the enzyme activity is highest. The same can be said for optimum temperature.
131
pH
pH is scale that measures the [H+] concentration of solutions. Derived from the calculation: pH = – log10 [H+ ]
132
Enzyme inhibition
This is where the presence of another substance directly or indirect impacts the effectiveness of an enzyme.
133
Competitive inhibitors
The inhibition of enzymes by inhibitor molecules binding to the active site and reducing those available for the actual substrate.
134
Non inhibitors
The inhibition of enzymes by inhibitor molecules that bind to an alternative site on the enzyme but deform it, changing the shape of the active site and preventing the substrate from binding.
135
what are the properties of an enzyme's structure?
v specific - only catalysing one reaction
eg maltase for maltose
only one substrate fitting each site, which is defined by the enzymes tertiary structure, which is defined by the primary chain structure
if the tertiary structure changes, the active site denatures and cant complete function.
136
what are two factors affecting enzyme activity
pH
temperature
137
what is the primary structure of an enzyme defined by and what does this mean
a gene, so genetic mutations will affect the tertiary structure
138
what do reactions do enzymes catalyse and at what levels - with examples
catalyse metabolic reactions at a cellular level (respiration) and in an organism as a whole (digestion)
139
give an example of how enzymes affect the structure and function of an organism
structure -the production of collagen
function - respiration/digestion
140
how do enzymes catalyse a reaction
they lower the activation energy which lowers the temperature at which a reaction needs to take place, which speeds up the rate of a reaction.
action can be intra or extracellular
141
how does temperature affect enzyme activity
higher temperature
higher kinetic energy
faster movement
more substrate enzyme collisions
also increased energy of collision and therefore chance of reaction
increased rate of reaction
142
what temperature do most enzymes denature
37'C + (some 60'C +)
143
why does a very high temperature denature enzymes
increased vibrations break bonds holding shape, active site changes, substrate doesn't fit, etc
144
how does pH affect enzyme activity
optimum pH for human enzymes - 7
except pepsin - 2 (in stomach)
above H+ and below OH- ions can interfere with ionic bonding holding the enzyme structure, which would then break down, change active site shape etc
145
how does enzyme concentration affect rate of reaction
more enzyme molecules
more collisions
more enzyme substrate complexes formed
increased rate of reaction
but if substrate limited then enzyme concentration will not affect rate once no of substrate = no of enzymes
- saturated
146
how does substrate concentration affect rate of reaction?
more substrates
more collisions
more complexes formed
increased rate until saturation
substrate conc will decrease over time and slow rate, so initial rate is the highest
147
what are the two types of enzyme inhibitor
competitive and non competitive
148
how do enzyme inhibitors work in general
they bind to the enzyme they inhibit and reduce rate of reaction
149
how do competitive inhibitors work and affect rate of reaction
similar shape to substrate they are inhibiting, they compete to bind to enzymes, blocking active site but produce no reaction
the level of inhibition is affected by the concentration of substrate vs inhibitor
if there is more inhibitors then reaction rate slows
if more substrate then rate increases
150
how do non competitive inhibitors work and affect rate of reaction
bind to enzyme away from active site, and force active site to change shape etc
not competing with substrate so changing the concentration of substrate wont affect the rate of reaction
decreases the rate of reaction by decreasing amount of enzyme active sites that substrates can bind to.
151
what are the two ways of measuring rate of enzyme controlled reaction
rate that product is produced
rate that the substrate is broken down
152
what enzyme catalyses the breakdown of hydrogen peroxide
catalase
153
what does hydrogen peroxide break down into
water and oxygen
154
outline a method to calculate the volume of oxygen produced in a catalase - hydrogen peroxide experiment (enzyme controlled reaction)
1- set up boiling tubes with same vol and concentration of hydrogen peroxide and buffer solution to control for pH changes
2 - set up apparatus as in diagram (or explain - upside down measuring cylinder in water bath - boiling tube, bung and delivery tube)
3 - add each boiling tube to different temp water baths, 10,20,30,40'C with a tube of catalase each
4 - wait 5 mins for enzyme to get up to temp
5 - add same vol and concentration of catalase to hydrogen peroxide solution and attach bung/delivery tube fast
6 - record volume of oxygen produced in 1 minute (stopwatch)
7 - repeat three times at each temp and
(7b - complete negative control at each temp with no catalase)
8 - calculate average rate by dividing average volume of oxygen by the time taken (1 min)
155
what enzyme breaks down starch
amylase
156
what does amylase break starch down into
maltose
157
explain how one might test to find the rate at which a substrate is broken down within an enzyme controlled reaction
1 - set up apparatus as shown (or explain - spotting tile, pipette, boiling tube)
2 - add drop of potassium iodide to each tile
3 - add drops of amylase/ starch solution to each tile and timed intervals
4 - record how long it takes for the tiles to stop turning blue/black - (indicating that the amylase has now broken down the starch)
5 - repeat with different concentrations of amylase - repeat three times at each concentration
158
how do you calculate the tangent of a curve on a rate of reaction line graph
draw tangent to curve at t=0 (time = 0)
position ruler equal distance from both sides of curve and draw line through 0 off the top of the graph
159
how do you calculate initial rate of reaction
the gradient of the tangent line drawn on the graph, is the initial rate of reaction.
gradient = change in y axis divided by change in x axis
