Topic 2 - Molecular Biology Flashcards
(222 cards)
1
Q
properties of carbon compounds
A
- carbon forms covalent bonds with other atoms
- each carbon atom can form up to 4 covalent bonds (this is more than most other atoms)
- so carbon compounds can have complex structures
2
Q
types of carbon compounds
A
- carbohydrates
- lipids
- proteins
- nucleic acids
3
Q
carbohydrates
A
- made up of CHO
- ratio of H:O is 2:1 (hence the -hydrate)
4
Q
lipids
A
- made up of CHO
- insoluble in water
- contains less O than carbohydrates
5
Q
types of lipids
A
- steroids
- waxes
- fatty acids
- triglycerides
6
Q
triglycerides
A
- fats if solid at room temperature
- oils if liquid at room temperature
7
Q
proteins
A
- made up of 1 or more amino acid chains
- almost all the amino acids will contain CHON, but 2 of them also contain S
8
Q
nucleic acids
A
- chains of nucleotides
- contains CHONP
9
Q
types of nucleic acids
A
- DNA
- RNA
10
Q
ribose
A
- C5H10O5
- 5-membered ring with a side chain
- 4 carbon atoms are in the ring while 1 forms a side chain
- hydroxyl (OH) groups on carbon atoms 1, 2, 3, and 5 point up, down, down, up respectively
11
Q
glucose
A
- C6H10O6
- 6-membered ring with side chain
- 5 carbon atoms in the ring with 1 in the side chain
- in alpha glucose (most common), hydroxyl (OH) groups on carbon atoms 1, 2, 3, 4 point down, down, up, down respectively
- but in beta glucose, which is used in plants to make cellulose, the OH group on C atom 1 points up
12
Q
amino acids
A
the central C atom is bonded to:
- an amine group (hence the term ‘amino acid’)
- a carboxyl group (making the molecule an acid)
- a H atom
- the R group (variable part of amino acids)
13
Q
metabolism
A
- web of all enzyme-catalysed reactions in a cell/organism
- consists of pathways in which 1 type of molecule is transformed into another over a series of steps
- consists of over 1k reactions
14
Q
types of metabolism
A
- anabolism
- catabolism
15
Q
anabolism
A
- synthesis of complex molecules from simpler molecules
- requires energy (usually in ATP form)
16
Q
examples of anabolic reactions
A
- formation of macromolecules from monomers by condensation reactions
- protein synthesis using ribosomes
- DNA synthesis during replication
- photosynthesis
- synthesis of complex carbohydrates (e.g. starch, cellulose, glycogen)
17
Q
catabolism
A
- breakdown of complex molecules into simpler molecules
- releases energy and in some cases this energy is captured in the form of ATP
18
Q
examples of catabolic reactions
A
- digestion of food in the mouth/stomach/small intestine
- cell respiration in which glucose/lipids are oxidized to CO2 and water
- digestion of complex carbon compounds in dead organic matter by decomposers
19
Q
properties of water molecules
A
- formed by covalent bonds between an O atom and 2 H atoms
- the bonds between H and O involve unequal sharing of e-s (so it’s a polar covalent bond)
- H is partially positive while O is partially negative
- water molecules are v-shaped so the 2 H atoms form a pole while the one O atom forms an opposite pole
20
Q
hydrogen bonds
A
- attraction between a partially positive H atom and a partially negative atom when both are in polar covalent bonds with other atoms
- kinda like an affair :)
- it’s a weak intermolecular force but since there are so many water molecules per unit volume of water, there are a LOT of hydrogen bonds
21
Q
cohesion
A
binding together of 2 molecules of the same type
22
Q
adhesion
A
binding together of 2 molecules of different types
23
Q
significance of hydrogen bonds with regard to the properties of water
A
- cohesion: hydrogen bonds form between water molecules, causing them to stick to each other
- adhesion: hydrogen bonds can form between water molecules and other polar molecules
- high specific heat capacity/latent heat of vaporization/boiling point: hydrogen bonds restrict the motion of water molecules, so more energy (higher temp) is required to break those bonds
- solvent properties: water can form hydrogen bonds with other polar molecules, as its O pole is attracted to positive ions while its H pole is attracted to negative ions, causing them to dissolve
24
Q
applications of water’s cohesive properties
A
- useful for water transport in plants
- water is sucked through xylem vessels at low pressure
- this can only work if the water molecules aren’t separated by the suction forces
25
applications of water's adhesive properties
- in leaves, water keeps cell walls moist
- by adhering to cellulose molecules in cell walls
- if water evaporates and is lost from the leaf, adhesive forces will cause water to be drawn out from the nearest xylem vessel, thereby maintaining the walls' moisture
- so that the walls can continue to absorb CO2
26
applications of water's thermal properties
- as water has a high specific heat capacity, its temperature will remain relatively stable
- so it's a thermally stable habitat for aquatic life
- as water has a high latent heat of vaporization, it absorbs heat (energy)
- this makes it an effective coolant
- as water has a high boiling point, it is in liquid state for the majority of habitats on Earth
27
applications of water's solvent properties
cytoplasm is an example of a complex mixture of dissolved substances in which metabolic chemical reactions occur
28
hydrophilic
- substances that are chemically attracted to water
- they will dissolve in water
- they are polar
29
hydrophobic
- substances that dissolve in other solvents but not in water
- they are non-polar
- all lipids are hydrophobic
30
hydrophobic interactions
forces causing non-polar molecules to join together into groups in water
31
why do hydrophobic interactions occur?
- there is a slight attraction between non-polar molecules
- moreover, water molecules are more attracted to each other than to non-polar molecules
- so water can form more hydrogen bonds with each other
32
transporting sodium chloride in blood
- NaCl is an ionic compound
- so it's freely soluble in water
- it is carried by plasma in dissolved state
33
transporting amino acids in blood
- they are soluble in water
- but their solubility depends on the R group (some are hydrophilic, others are hydrophobic)
- to be carried in the blood plasma, they have to be soluble enough to dissolve
34
transporting glucose in blood
- glucose is polar
| - so it's freely soluble
35
transporting oxygen in blood
- oxygen is non-polar but due to its small size it can dissolve in water
- however, water will become saturated with oxygen even at low concentrations
- furthermore, the higher the temp of water, the lower the solubility of oxygen
- blood plasma at body temp cannot carry enough oxygen to facilitate aerobic respiration
- this problem is overcome by the presence of haemoglobin in red blood cells
- haemoglobin has binding sites for oxygen to increase the capacity of blood for oxygen transport
36
transporting fat molecules in blood
- fats are entirely nonpolar
- they are also larger than oxygen so they're insoluble in water
- so they're carried in blood using lipoprotein complexes
37
lipoprotein complex
- a group of molecules with a single phospholipid layer on the outside
- there are also proteins on the monolayer, hence the name
- they can store fats on the inside
38
transporting cholesterol in blood
- cholesterol molecules are largely hydrophobic
- so they are insoluble in water
- they are transported in lipoprotein complexes (like fats)
- but unlike fats, which are stored behind the monolayer, cholesterol molecules are positioned in the monolayer
39
monosaccharide
single sugar unit
40
examples of monosaccharides
- glucose
- fructose
- ribose
- galactose
41
disaccharide
two monosaccharides linked together
42
examples of disaccharides
- maltose
- sucrose
- lactose
43
polysaccharides
many monosaccharides linked together
44
examples of polysaccharides
- starch
| - glycogen
45
how do monosaccharides combine?
- through a condensation reaction
- involves a loss of OH from one molecule and H from another
- anabolic process (energy required)
46
structure of cellulose
- glucose's beta isomer forms a diagonal chain
- formed via condensation reactions
- each beta glucose molecule is oriented upwards/downwards in alternate fashion
- this is because the OH groups in C 1 and 4 on beta glucose points in opposite directions
- so for a condensation rxn to occur, each molecule has to be at 180 degrees to the previous one
- instead of being curved, cellulose forms a straight chain
- cellulose molecules are unbranched chains of beta glucose
- this allows them to form bundles of cellulose, with hydrogen bonds linking them together
47
cellulose microfibrils
- bundles formed from cellulose molecules
- high tensile strength
- its strength prevents the cell from bursting even at very high pressures due to osmosis
48
function of cellulose
used as the basis of plant cell walls
49
structure of starch
- made by linking alpha glucose molecules together
- formed via condensation reactions
- the OH groups in C 1 and 4 on alpha glucose points in the same direction
- so all molecules can be positioned similarly
- this causes starch to form a curved chain, not straight
50
forms of starch
- amylose
| - amylopectin
51
differences in structure between amylose and amylopectin
amylose: the glucose chain is unbranched and forms a helix
amylopectin: the chain is branched so it has a more globular shape
52
function of starch
- it's only made in plant cells
- starch is hydrophilic but too large to be soluble in water
- so they're useful for storing glucose
- a concentrated glucose solution would cause too much water to enter a cell via osmosis
- so starch can store glucose (i.e. energy) without endangering the cell
- there is no fixed size
- so it's easy to add/remove extra glucose molecules
- this can be done at any of the ends of a molecule (regardless of whether they have branches or not)
53
structure of glycogen
- similar to amylopectin starch but more branching occurs
| - so the molecule is more compact
54
function of glycogen
- made by animals and some fungi
- same function as starch in plants
- glycogen is hydrophilic but too large to be soluble in water
- so they're useful for storing glucose
- a concentrated glucose solution would cause too much water to enter a cell via osmosis
- so glycogen can store glucose (i.e. energy) without endangering the cell
- there is no fixed size
- so it's easy to add/remove extra glucose molecules
- this can be done at any of the ends of a molecule (regardless of whether they have branches or not)
55
lipids
- diverse group of carbon compounds
- all are insoluble in water
- fats are liquid at body temp but solid at room temp
- oils are liquid at both body temp and room temp
56
how are triglycerides formed?
- combining 3 fatty acids with 1 glycerol
- each of the fatty acids is linked to the glycerol via a condensation rxn
- they are linked via ester bonds
57
ester bond
- bond formed when an acid reacts with the OH group in an alcohol
- in triglycerides it's between -COOH (fatty acid) and -OH (glycerol)
58
function of triglyceride
- energy store
- energy from them can be released via aerobic cell respiration
- they are also used to insulate heat (e.g. in the blubber of Arctic aquatic mammals)
59
where are lipids stored?
- specialized cells called adipose tissue
| - they're located right below the skin and around some organs (e.g. kidneys)
60
lipids vs carbohydrates
- compared to carbohydrates, at the same mass lipids can release double the amount of energy in cell respiration
- fats form pure droplets in cells (no water) while carbohydrates are associated with water (each glycogen molecule is bonded to 2 water molecules)
- lipids are poor heat conductors so they can insulate heat
- lipids are liquid at body temp so they can act as shock absorbers
- this is why they are stored in subcutaneous adipose tissue near the skin, and around important organs
61
why is glycogen still stored if lipids are so efficient?
- lipids are more ideal for long-term storage
- but glycogen can be broken down to glucose and transported easily and rapidly
- fats can't be mobilized as rapidly
- also, glucose can be used in both aerobic and anaerobic respiration while fats can only be used in aerobic
- so they are efficient for short-term storage
- the liver stores 150 g of glycogen and some muscles store 2% glycogen by mass
62
BMI formula
BMI = mass (in kg) / height^2 (in metres)
the unit is kg m^-2
63
nomogram
type of chart used to calculate BMI
64
obesity
- due to excessive food intake and insufficient exercise
- this causes accumulation of fat in the adipose tissues
- obesity increases the risk of conditions (e.g. coronary heart disease)
- significantly reduces life expectancy
65
structure of fatty acids
- unbranched chain of C atoms
- with H atoms linked to them by single covalent bonds
- at one end of the chain there's an acidic part (carboxyl group, -COOH)
- there are usually 14-20 C atoms
66
saturated fatty acids
- C atoms are bonded to each other via single bonds
| - so it contains as much hydrogen as possible (thereby being 'saturated')
67
unsaturated fatty acids
- 1 or more double bonds between C atoms
- it doesn't contain as much H as its potential (thereby being 'unsaturated')
- fatty acids with only 1 double bond are called 'monounsaturated fatty acids'
- fatty acids with > 1 double bond are called 'polyunsaturated fatty acids'
68
types of unsaturated fatty acids
- cis-fatty acids
| - trans-fatty acids
69
cis-fatty acids
- AKA oils
- when hydrogen atoms are on the same side of the 2 C atoms that are double bonded, the molecule is called a cis-fatty acid
- there is a bend in the hydrocarbon chain at the double bond
- due to this, triglycerides containing cis fatty acids are not as good at packing together in regular arrays compared to saturated fatty acids
- so their melting points are lower
- they're liquid at room temp
70
trans-fatty acids
- when hydrogen atoms are on opposite sides of the 2 C atoms that are double bonded
- they don't have a bend in the hydrocarbon chain at the double bond
- higher melting point
- solid at room temp
- they're produced artificially in by partial hydrogenation of vegetable/fish oils
- this is done to produce solid fats for margarine and other processed foods
71
health risks of fats
- coronary heart disease: coronary arteries become partially blocked by fatty deposits
- this leads to blood clot formations and heart attacks
- a positive correlation between saturated fatty acid intake and CHD rates has been found
- but this doesn't prove the existence of a causation link
- the Maasai tribe in Kenya have a saturated fats-rich diet but CHD rates are exceedingly low among them
- furthermore, diets rich in olive oil (cis-monounsaturated fatty acids) are staples in Mediterranean countries but their populations have low CHD rates
- there's also a positive correlation between trans-fat intake and CHD rates
- a tentative causation link has been established
- because fatty deposits in the diseased arteries of CHD patients have been found to contain high concentrations of trans-fats
72
polypeptides
- amino acid chains
- made by linking amino acids together via condensation reactions
- this happens on ribosomes via translation
- polypeptides are the main components of proteins
- in many proteins, they are the only component
- some proteins contain only 1 polypeptide while other proteins contain 2+
73
production of polypeptides from amino acids
- condensation reaction between two amino acids
- an OH (from -COOH/carboxyl group) of one amino acid and a H (from -NH2/amine group) of another amino acid are removed to form H2O
- a peptide bond forms between the 2 amino acids
74
dipeptide
2 amino acids that are bonded together by a peptide bond
75
oligopeptides
chains that are made up of < 20 amino acids
76
similarities between amino acids in ribosomes
- C atom in the center
the C atom is bonded to:
- an amine group
- a carboxyl group
- a H atom
- an R (variable) group
77
polypeptide diversity
- and ribosomes link amino acids together one at a time
- amino acids can be linked together in any sequence
- the number of possible amino acid sequences can be calculated with dipeptides (i.e. 20^(number of amino acids))
- 20 coz most organisms make proteins using the same 20 amino acids
78
role of genes in polypeptide production
- the number of possible sequences is infinite
- but only a small percentage of those are produced by living organisms
- the information needed to code polypeptides are stored in the base sequence of a gene
- 3 bases of a gene is needed to code for 1 amino acid in a polypeptide (e.g. if a polypeptide needs 400 amino acids, the gene sequence will theoretically have 1200 bases)
- however, the gene sequence is always longer in reality (due to extra start/stop sequences in the beginning, end, and at certain points in the middle)
79
how many polypeptides are needed to synthesize a protein?
- some proteins are single polypeptides
| - others require more polypeptides to be linked together
80
lysozyme
- enzyme in secretions (e.g. in nasal mucus and tears)
| - kills some bacteria by digesting peptidoglycan in their cell walls
81
peptidoglycan
a component of bacterial cell walls
82
structure of integrin
- membrane protein with 2 polypeptides
- both polypeptides have a hydrophobic section (which is embedded in the membrane)
- so the 2 polypeptides can either be adjacent to each other or can unfold/move apart when they're working
83
function of integrin
- membrane protein
| - used to make connections between structures inside and outside a cell
84
structure of collagen
- 3 long polypeptides
- wounded together to form a rope-like molecule
- collectively, they have greater tensile strength together than they would have individually
- the winding allows a bit of stretching to occur
- this reduces the chance of the molecule breaking
85
function of collagen
- structural protein in tendons, ligaments, skin & blood vessel walls
- provides high tensile strength but limited stretching/flexibility
86
structure of hemoglobin
- 4 polypeptides
- with associated non-polypeptide structures
- collectively, these 4 polypeptides interact to transport oxygen more effectively than they would have separately
87
function of hemoglobin
- transport protein in RBCs
| - binds oxygen in the lungs and releases them in tissues with a reduced oxygen concentration
88
protein conformation
- 3-D structure of proteins
| - determined by the amino acid sequence of a protein as well as its constituent polypeptides
89
typical protein conformations
- most proteins are globular, with an intricate shape that often includes helical or sheet-like parts
- fibrous proteins like collagen are elongated, often with a repeated structure
90
protein conformation of globular proteins
- polypeptides gradually fold up while being made
| - this is stabilized by bonds between R groups that have been brought together by the folding
91
difference in protein conformation between globular membrane and non-membrane proteins
- in water-soluble globular proteins, hydrophilic R groups remain on the outside while the hydrophobic groups remain inside
- in globular membrane proteins, some hydrophobic R groups remain outside as they are attracted to the hydrophobic centre of the membrane
92
protein conformation of fibrous proteins
- amino acid sequence prevents folding up
| - this ensures that the amino acid chain will remain elongated
93
stability of protein conformation
- protein conformation is stabilized by bonds and interactions between R groups
- most of these bonds/interactions are weak and can be broken easily
94
denaturation
- change in the conformation of the protein
| - it's often permanent
95
denaturation of soluble proteins
- turns insoluble
- forms a precipitate
- due to the hydrophobic R groups in the centre becoming exposed to the water around as a result of change in conformation
96
causes of denaturation
- heat
| - extreme pH
97
how does heat cause denaturation?
- heat causes vibrations within the molecule
- this can break intermolecular bonds/interactions depending on the molecule's heat tolerance
- most proteins denature at around 40 degrees celsius
- but some can remain undenatured even at 80 degrees (e.g. proteins synthesized by microorganisms that live in volcanic springs)
98
how does extreme pH cause denaturation?
- when exposed to extreme pH, charges on R groups are changed
- this causes ionic bonds to break and new ones to form
- but not all proteins denature at extreme pH (e.g. stomach pepsin has an optimal pH of 1.5)
99
protein functions
- catalysis
- muscle contraction
- cytoskeletons
- tensile strengthening
- blood clotting
- transport of nutrients & gases
- cell adhesion
- membrane transport
- hormones
- receptors
- packing of DNA
- immunity
100
protein functions: catalysis
enzymes help catalyse specific chemical reactions
101
protein functions: muscle contraction
actin and myosin cause the muscle contractions used in:
- movement
- transport around the body
102
protein functions: cytoskeletons
- tubulin is the subunit of microtubules
- they give animal cells their shape
- they also pull on chromosomes during mitosis
103
protein functions: tensile strengthening
fibrous proteins give tensile strength needed in:
- skin
- tendons
- ligaments
- blood vessel walls
104
protein functions: blood clotting
- plasma proteins act as clotting factors
| - causes blood to turn from liquid to gel in wounds
105
protein functions: transport of nutrients and gases
proteins in blood help transport:
- oxygen
- CO2
- iron
- lipids
106
protein functions: cell adhesion
membrane proteins cause adjacent animal cells to stick to each other within tissues
107
protein functions: membrane transport
membrane proteins are used for:
- facilitated diffusion
- active transport
- electron transport (during cell respiration and photosynthesis)
108
protein functions: hormones
- some hormones are proteins (e.g. insulin, FSH, LH)
| - but hormones are chemically diverse, so not all are proteins
109
protein functions: receptors
- binding sites
| - taste/smell/light receptors
110
protein functions: packing of DNA
the protein histone helps condense chromosomes during mitosis
111
protein functions: immunity
- antibodies are proteins
| - this is the most diverse group of proteins
112
biotechnological uses for proteins
- enzymes for removing stains
- monoclonal antibodies for pregnancy tests
- insulin for treating diabetics
113
rubisco
- ribulose bisphosphate carboxylase
- catalyses the reaction fixing CO2 from the atmosphere
- provides the source of carbon from which all carbon compounds needed by living organisms can be produced
- present at high concentrations in leaves
114
immunoglobulin
- AKA antibodies
- sites at the tips of their arms bind to antigens on bacteria or other pathogens
- the other parts of the immunoglobulin cause a response, acting as a marker to phagocytes (which can then engulf the pathogen)
- each type of immunoglobulin has a different type of binding site
- this is the basis of specific immunity to disease
115
collagen
- rope-like proteins made of 3 polypeptides wound together
- a quarter of all proteins in the human body is collagen
- forms a mesh of fibres in skin and blood vessel walls that resist tearing
- bundles of parallel collagen molecules give ligaments and blood vessel walls their tensile strength
- also form parts of teeth and bones to help prevent cracks/fractures
116
insulin
- signals cells in the body to absorb glucose
- it is secreted by beta cells in the pancreas and is transported by blood
- its secretion is triggered by high glucose concentrations in the blood
- cells have a receptor specifically for insulin in their cell membrane to which insulin can reversibly bind to
117
rhodopsin
- membrane protein of rod cells in the retina
- one of the eye pigments that absorb light
- is made up of a light-sensitive retinal molecule (NOT amino acids) and surrounded by an opsin polypeptide
- retinal molecule changes shape when it absorbs a single photon of light
- opsin also changes as a result, leading to the rod cell sending a nerve impulse to the brain
- very sensitive; even low light intensities can be detected
118
spider silk
- dragline silk is stronger than steel and tougher than kevlar
- extensible and very resistant to breaking
- used to make the spokes of spiderwebs and lifelines spiders hang themselves by
- when first made, it contains regions where the polypeptide forms parallel arrays while other regions seem like disordered tangles
- but when the silk is stretched they all gradually extend
119
proteome
all of the proteins produced by a cell/tissue/organism
120
genome
all the genes of a cell/tissue/organism
121
how to determine a cell's proteome
- mixtures of proteins are extracted and separated via gel electrophoresis
- antibodies to the protein that are linked to a fluorescent marker can be used to identify the presence of a particular protein
- if the cell fluoresces, the protein is present
122
difference between proteomes and genomes
- genome is fixed while proteome is variable (as different cells in an organism make different proteins)
123
variation in proteomes
- there are strong similarities in the proteome of all individuals in a species but the proteome of each individual is unique
- this can be attributed to differences in activity and small differences in the amino acid sequence of proteins
- proteomes can also differ with age
124
enzyme
globular protein working as a catalyst
125
catalyst
substance that speeds up a chemical reaction without being altered
126
biological catalysts
- catalysts made up of living cells
| - they speed up biochemical reactions
127
substrate
substance that enzymes convert to products in enzyme-catalysed reactions
128
enzyme-substrate specificity
- a specific enzyme can only catalyse a specific biochemical reaction
- this is one way that enzymes differ from non-biological catalysts (e.g. metals used in catalytic converters of vehicles)
129
active site
- a special region on the surface of the enzyme where substrates bind to
- the shape and chemical properties of the active site and the substrate must match each other
- this allows the substrate to bind but not other substances
130
enzyme activity
catalysis of a reaction by an enzyme
131
stages of enzyme activity
1. Substrate binds to the active site of the enzyme (some enzymes have 2 substrates that bind to different parts of the active site)
2. Substrates bound to the active site will change into different chemical substances, which are the products of the reaction
3. The products then separate from the active site, leaving it vacant for substrates to bind again
132
collision
coming together of a substrate molecule and an active site
133
how do substrate-active site collisions occur?
- most reactions occur with substrates dissolved in water
- so particles are in continuous motion and can move separately
- so collisions occur due to random movements of both substrate and enzyme
- a successful collision occurs when the substrate and active site are correctly aligned to allow binding to occur
134
factors affecting enzyme activity
- temp
- pH
- substrate concentration
135
effect of temp on enzyme activity
- most enzyme-catalysed reactions occur in liquids
- when a liquid is heated, the particles in it are given more kinetic energy
- so they move faster
- the chance of a substrate molecule colliding with the active site of the enzyme is increased
- on the other hand, once heated to a certain point, enzymes will denature permanently
- so it will no longer be able to catalyse reactions
136
effect of pH on enzyme activity
- most enzymes have an optimum pH
- when the H ion concentration is too high/low (compared to the optimum), the enzyme may denature
- this causes permanent denaturation
137
effect of substrate concentration on enzyme activity
- enzymes can't catalyse reactions until the substrate binds to the active site
- if substrate concentration is increased, collisions will occur more frequently, thereby increasing enzyme activity
- but there is a limit to this
- an enzyme can only catalyse one reaction at a time
- so the increases in rate get smaller and smaller as substrate concentration rises (but it will never plateau)
138
denaturation of enzymes
- enzymes are proteins
- so their conformation can be irreversibly changed
- this process is called denaturation
- when it occurs, the active site is permanently altered so the substance can no longer bind
- in the event that it still binds, the reaction the enzyme is supposed to catalyse will not occur
- in many cases, denaturation causes enzymes dissolved in water to become insoluble and form a precipitate
139
designing enzyme experiments
1. Independent variable: factor to be investigated. Things to consider:
- how to vary this factor
- measurement unit to use
- what range is needed (including highest/lowest level and number of intermediate levels)
2. Dependent variable: what is measured to find out how fast the enzyme is catalysing the reaction. Things to consider:
- how to measure it (i.e. what meter to use)
- measurement unit to use
- how many trials are needed
3. Control variables: factors that could affect the dependent variable. Things to consider
- what all the controls should be
- how each can be kept constant
- what level they should be kept at (e.g. if temp, then what temp should be the constant?)
140
immobilized enzymes
- enzymes attached to another material
- to restrict movement of the enzyme
- they are commonly used in commercial chemical processes
e.g. trapping them in alginate gel or attaching them to a glass surface
141
advantages of enzyme immobilization
- enzyme can easily be separated from reaction products, preventing contamination
- it can be recycled, giving useful cost savings as many enzymes are expensive
- immobilization increases the stability of enzymes to changes in temp/pH and reduces their rate of degradation
- substrates can be exposed to higher enzyme concentrations than with dissolved enzymes (speeding up rxn rates)
142
nucleic acids
- very large molecules
| - constructed by linking together nucleotides to form a polymer
143
composition of nucleic acids
- pentose sugar (has 5 C atoms)
- phosphate group
- base containing nitrogen and has 1-2 rings of atoms
144
formation of nucleic acids
- covalent bonds form between the phosphate of one nucleotide and the pentose sugar of another
- creates a strong backbone for the molecule of alternating sugar and phosphate groups (with a base linked to each sugar)
- there are 4 different bases in both DNA and RNA so there are 4 nucleotides
- they can be linked together in any sequence
145
strand
nucleotide polymer in nucleic acids
146
differences between DNA and RNA
- the sugar in DNA is deoxyribose while the sugar in RNA is ribose (deoxyribose has 1 less O atom)
- DNA is double-stranded while RNA is single-stranded
- 1 of the 4 bases in DNA and RNA differ
147
types of DNA bases
- adenine
- cytosine
- guanine
- thymine
148
types of RNA bases
- adenine
- cytosine
- guanine
- uracil
149
structure of DNA
- each strand contains 1 chain of nucleotides linked by covalent bonds
- the 2 strands are antiparallel (run in opposite directions: 3' to 5' or 5' to 3')
- they're wound together in double helix formation
- the strands are held together by hydrogen bonds between the nitrogenous bases in a specific alignment (complementary base pairing)
- hydrogen bonds are weak, but in a DNA molecule there are a lot of them so they can successfully hold strands together at body temp
150
complementary base pairing
rule that one specific base will always pair with another to form a hydrogen bond
Adenine with Thymine
Cytosine with Guanine
151
semi-conservative replication of DNA
- when a cell divides, the 2 double helix strands separate
- each of those original strands serve as a template for the creation of a new strand
- new strands are formed by adding nucleotides and linking them together one by one
- the result is 2 DNA molecules: one is the original and one is newly synthesized
- the base sequence of the template strand determines the base sequence of the new strand
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helicase
- group of enzymes that unwind the double helix and separates the two strands by breaking their bonds
- they use energy from ATP to break hydrogen bonds between complementary bases
- coz double-stranded DNA can't be split into 2 strands while still helical
153
DNA polymerase
- links nucleotides together to form a new strand using the pre-existing strand as a template
- it assembles the new strand as a complementary base sequence to the template
154
DNA replication process
- free nucleotides are available in the area where DNA is being replicated
- only the nucleotide that is the complementary base pair of the template's nucleotide in that position can be added
- DNA polymerase will bring nucleotides into the position where hydrogen bonds can form, but if it's incompatible the nucleotide will break away again
- once a nucleotide with the correct base is brought in, hydrogen bonds will form between the 2 bases
- this is done by making a covalent bond between the phosphate group of the free nucleotide and the sugar of the template's nucleotide
- the sugar is the 3' terminal while the phosphate is the 5' terminal
- DNA polymerase will gradually move along the template strand, adding a complementary base sequence to form a new strand
155
polymerase chain reaction
- technique used to make many copies of a selected DNA sequence
- only a very small quantity of original strands are required
156
re-annealing
- upon being cooled in PCR, the DNA strands that have been separated can pair up again
- this is called re-annealing
157
primer
short sections of single-stranded DNA
158
Taq DNA Polymerase
- a variant of DNA polymerase
- taken from a bacterium found in hot springs
- so they're very heat-stable and can resist temperatures up to 95°C
- optimum temp is 72°C
159
polymerase chain reaction process
STAGE 1
- the DNA sample is loaded into a PCR machine
- the double-stranded DNA is separated into 2 single strands by exposure to 95°C for 15 seconds (thereby breaking the hydrogen bonds)
- they are then quickly cooled back to 54°C (which could allow re-annealing)
- however, there are a lot of primers present
- if primers bind rapidly to target sequences, they could prevent re-annealing
STAGE 2
- Taq DNA polymerase is used
- bc it can resist the brief 95°C heating
- it's used to attach the primers
- after being cooled to 54°C, the mixture is heated up to 72°C (optimum temp for this enzyme)
- at optimum temp, Taq DNA polymerase can add 1000 nucleotides per minute
- at this point 1 cycle is complete
- 1 cycle normally takes < 2 minutes
- up to 30 cycles are typical for this process and take < 1 hour
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transcription
- synthesis of mRNA that is copied from the DNA base sequences by RNA polymerase
- as RNA is single-stranded, transcription only occurs along 1 of the 2 DNA strands
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transcription process
1. RNA polymerase binds to a site on the DNA at the start of a gene sequence
2. RNA polymerase moves along the gene to separate DNA into single strands and pair up RNA nucleotides with complementary base pairing (as there's no thymine for RNA, uracil pairs with adenine)
3. RNA polymerase forms covalent bonds between RNA nucleotides
4. transcription stops at the end of the gene
5. the new RNA strand is released and the double helix reforms between the DNA parent strands
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product of transcription
- a RNA molecule
- has a base sequence complementary to the DNA template strand used
- should be identical with the other strand (with the exception of thymine)
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sense strand
the DNA strand with the same sequence as the new RNA strand in transcription
164
antisense strand
- the DNA strand used as the template
| - it has a complementary base sequence to the RNA and the sense strand
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translation
- the synthesis of a polypeptide
| - takes place on ribosomes
166
mRNA
- messenger RNA
- carries the codons specifying the amino acid sequence of the polypeptide to be synthesized
- it's the new RNA strand that was created in the transcription process
- its length is dependent on the number of amino acids in the polypeptide
- but the average length for mammals is 2000 nucleotide units
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types of RNA
- mRNA: messenger RNA
- tRNA: transfer RNA
- rRNA: ribosomal RNA
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tRNA
- transfer RNA
- involved in decoding the base sequence of mRNA into an amino acid sequence
- used during translation process
- each tRNA has a 3-base anticodon complementary to the mRNA codon for that particular amino acid
- they also carry the amino acid corresponding to that codon
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rRNA
- ribosomal RNA
| - part of the ribosome structure
170
codon
- a sequence of 3 bases on the mRNA
- each codon codes for a specific amino acid
- there are also start/stop codons used to denote the start/end of translation
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degenerate codons
codons that code for the same amino acid
172
role of ribosomes in translation
- acts as the binding site for mRNAs and tRNAS
- catalyses the assembly of the polypeptide
- has 2 subunits (1 big, 1 small)
- the small subunit is the binding site
- the large subunit is the site that makes peptide bonds between amino acids
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translation process
1. an mRNA binds to the small ribosome subunit
2. a molecule of tRNA binds to the ribosome (it must have a complementary anticodon to the first codon on the mRNA)
3. another tRNA binds to the next codon (again, it must be the complementary anticodon to the 2nd codon) -- a maximum of 2 tRNAs can be bound to the mRNA at the same time
4. the ribosome transfers the amino acid carried by the 1st tRNA to the 2nd tRNA by forming a peptide bond between the 2 amino acids, so the 2nd tRNA is carrying a dipeptide
5. the ribosome moves along the mRNA so that the 1st tRNA is released, moving the 2nd tRNA to the 1st position
6. another tRNA binds (again, a complementary anticodon to the 3rd codon)
7. the ribosome transfers the dipeptide on the 2nd tRNA to the 3rd RNA
8. stages 6-7 are repeated over and over until a stop codon is reached
9. at that point, the polypeptide is complete and is released
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synthetic production of insulin
- diabetes can be treated by injecting insulin into the blood
- porcine and bovine insulin (extracted from the pancreases of pigs and cattle respectively) are widely used, and shark insulin is used in Japan
- compared to human insulin, porcine insulin only has 1 difference in its amino acid sequence, bovine insulin has 3, and shark insulin has 17
- despite the differences, they can bind to human insulin receptors and have the same effects
- however, some diabetics are allergic to animal insulin
- now, human insulin is synthetically produced using genetically modified E. Coli bacteria
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how is the genetic modification of microorganisms possible?
- all organisms have the same genetic code
- this makes gene transfer between difference species a possibility
- in the production of insulin, the gene for production of human insulin has been transferred to microorganisms for mass production
- this way, the insulin produced will have exactly the same amino acid sequence as human insulin
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cell respiration
- one of the functions of life
- defined as the controlled release of energy from organic compounds (i.e. breaking down of organic compounds) to produce energy in the form of ATP
- carried out carefully using enzymes so that as much as possible of the energy released can be retained
177
ATP
adenosine trisphosphate
178
production of ATP
- is produced when a phosphate group is linked to ADP
- energy is required to carry out this reaction
- that energy comes from the breakdown of organic compounds
179
significance of ATP
- provides energy needed for various cellular activities
- can immediately provide energy when it's split into ADP and phosphate
- which can then be reconverted in ATP again via respiration
- it can't be transferred to different cells so all cells require a continuous supply
- when its energy is used, the energy is ultimately converted into heat
- heat is useful, but it can't be reused for cell activities and is eventually lost to the environment
- this is why a constant source of ATP is necessary for cell activities
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what sort of activities require ATP?
- synthesis of large molecules (e.g. DNA, RNA, proteins)
- active transport
- movement of things around the cell (e.g. movement of vesicles, or causing contractions in muscle cells)
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anaerobic respiration
- doesn't require oxygen
- in humans, glucose is broken down into lactate (dissolved form of lactic acid)
- in yeast/plants, glucose is broken down into ethanol and CO2
- only yields 2 ATP units but they can be produced quickly
- they produce products that are toxic in excess, so the products must be quickly removed from the cells that produce them or be produced in strictly limited quantities
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when is anaerobic respiration preferred?
- when a short but rapid burst of ATP is needed
- when oxygen supplies run out in respiring cells
- in oxygen-deficient environments (e.g. waterlogged soils)
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uses of anaerobic respiration in yeast
- baking
| - renewable energy source
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use of anaerobic respiration in yeast: baking
- yeast is used in the process of baking bread to create bubbles of gas
- this is to lighten the texture of the bread
- after kneading the dough, it's kept warm to encourage the respiration of yeast
- when yeast respires anaerobically, the CO2 produced can't escape from the dough and will form bubbles
- this causes the dough to rise
- ethanol is also produced but evaporates during baking
185
bioethanol
- ethanol produced by living organisms
- used as a renewable energy source
- commonly used as a fuel in vehicles, sometimes in pure state and sometimes mixed with gasoline (petrol)
186
uses of anaerobic respiration in yeast: renewable energy source
- sugar is converted into bioethanol by yeast in large fermenters via anaerobic respiration
- only sugars can be converted, so polysaccharides (e.g. starch, cellulose) are broken down into sugars
- their breakdown is catalysed by enzymes
- the produced ethanol is purified via distillation and water is removed from it to improve its combustion
187
why is there only a limited time for anaerobic respiration to be used in humans?
- lactate is toxic in high concentrations
- there's a limit the body can tolerate so this limits how much anaerobic respiration we can do
- lactate eventually has to be broken down using oxygen
- it can take several minutes for enough oxygen to be absorbed so as to fully break down lactate
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oxygen debt
demand for oxygen that builds up during a period of anaerobic respiration
189
aerobic respiration
- requires oxygen
- yields 30+ units of ATP (a lot more efficient compared to anaerobic)
- involves a series of chemical reactions
- produces carbon dioxide and water as byproducts
- in humans, half a litre is produced per day
- in eukaryotic cells, most aerobic respiration reactions occur in the mitochondrion
190
respirometer
device measuring respiration rate
191
typical components of a respirometer
- a sealed glass/plastic container to keep the organism in
- an alkali (e.g. KOH) to absorb CO2
- capillary tube containing fluid which is connected to the container
192
uses of respirometer
- to compare the respiration rates of different organisms
- to investigate the effect of temperature on respiration rate
- to compare the respiration rates of active and inactive organisms
193
what should theoretically be observed when using a respirometer
- if the respirometer is working correctly and the organisms carry out anaerobic cell respiration, the volume of air inside the respirometer will reduce and the fluid in the capillary tube will move towards the container with the organisms
- this is because O2 is used up while CO2 produced via cell respiration is absorbed by the alkali
194
methodology involved when using a respirometer
- the position of the fluid should be recorded several times
- if the rate of movement of the fluid is relatively even, the results are reliable
- but if the temperature is fluctuating, the results aren't reliable as an increase in air temperature will cause an increase in volume
- so the temperature should be controlled with a thermostatically-controlled water bath
195
ethics of animal use in respirometers
- is it acceptable to remove animals from their natural habitat? can they be safely returned to their habitat?
- will the animals suffer harm during the experiment?
- can the risk of damaging accidents be minimized?
- is the use of animals essential? is there any alternative method?
196
photosynthesis
- production of carbon compounds in cells using light energy
- this is an example of energy conversion
- light energy is converted to chemical energy in carbon compounds
197
accessory pigments
- light absorbing compounds
- found in photosynthetic organisms
- works in conjunction with chlorophyll a
- they are differently colored as they absorb different ranges of light
198
method used to separate photosynthetic pigments
- chloroplasts contain several types of chlorophyll as well as accessory pigments
- chromatography can be used to separate them
- paper chromatography can be used but thin layer chromatography is preferred
199
thin layer chromatography
- form of separation technique
- uses a plastic strip coated with a thin layer of porous material
- the solution to be separated is placed at one end of the strip
- a solvent is allowed to run up the strip to separate the different types of pigment
200
process of separating photosynthetic pigments
1. tear up a leaf and put them in a mortar
2. add a small amount of sand for grinding
3. add a small volume of propanone (acetate)
4. use the pestle to grind the leaf and dissolve the pigments, and if the propanone evaporates, add a little more
6. when the propanone has turned dark green, allow the solids to settle, then decant the propanone into a watch glass
7. use a hair drier to evaporate off all the propanone and water
8. when you have just a smear of dry pigments in the watch glass, add 3-4 drops of propanone and use a paintbrush to dissolve the pigments
9. use the paintbrush to transfer a small amount of the solution close to one end of the TLC strip (the solution should be very dark, so if it isn't dark enough, repeatedly add drops -- remember to let each drop dry before adding another drop)
10. slide the other end of the strip into the slot of a cork -- the slot should firmly hold the strip
11. Insert the cork & strip into a specimen tube -- make sure the strip doesn't quite touch the bottom of the tube -- and mark the outside of the tube just below the level of the spot on the TLC strip
12. take the strip and cork out of the tube, then pour a solvent in the specimen tube up to the mark
13. carefully lower the TLC strip & cork into the tube so that the tube is sealed -- the TLC strip should be just dipping into the solvent but the solvent must not touch the pigment spot
14. leave the tube completely alone for 5 minutes
15. when the solvent has nearly reached the top of the strip, remove it from the tube and separate it from the cork
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wavelengths of light
- light is made up of all wavelengths of electromagnetic radiation that our eyes can detect
- red has the longest wavelength while violet has the shortest
- visible light is used by plants in photosynthesis
- this is because they are more abundant than other forms of light at other wavelengths
202
pigments
- substances that absorb specific wavelengths of light
- so they appear colored to us
- pigments that can absorb all the colors emit no light, so they look black
- pigments are colored according to the wavelength they can't absorb, so the light is reflected instead of being absorbed
203
chlorophyll
- the main pigment used in photosynthesis
- effectively absorbs red and blue light
- but are far less effective at absorbing green light
- this is why plants look green
204
action spectrum
graph showing the rate of photosynthesis at each wavelength of light
205
absorption spectrum
graph showing the percentage of light absorbed at each wavelength by a pigment or group of pigments
206
drawing an action spectrum graph
```
x-axis = wavelength of light
y-axis = relative amount of photosynthesis (normally in %)
```
207
drawing an absorption spectrum graph
```
x-axis = wavelength of light
y-axis = % absorption
```
208
effect of photosynthesis on earth
- prokaryotes were the first photosynthetic organisms
- algae and plants began millions of years later
- this caused the increase of oxygen concentration in the atmosphere
- the increase began 2400 mya (mil years ago), pretty much 1100 mya after photosynthesis occured in prokaryotes
- by 2200 mya, it rose to 2% by volume in the atmosphere -- this is called the Great Oxidation Event
- at this point Earth experienced its first glaciation, likely due to a reduction in greenhouse effect
- the rise in oxygenation caused a decrease in CH4 concentrations, while photosynthesis caused a decrease in CO2 concentration; both are potent greenhouse gases
- increased oxygen concentrations in the oceans between 2400-2200 mya caused the oxidation of dissolved ion, causing it to precipitate on the sea bed
- a banded iron formation (distinctive rock formation) was produced, with layers of iron oxide alternating with other minerals
- they are the most important iron ores, which is why we now have an abundant supply of steel
- a significant rise in oxygen concentrations occurred around 750 mya ago, which corresponds to the evolution of many multicellular organisms
209
production of carbohydrates in photosynthesis
- plants convert CO2 and H2O into carbohydrates
CO2 + H2O --> carbohydrate + O2
- reactions involving the production of O2 are usually endothermic
- reactions involving combining smaller molecules to form larger ones are also usually endothermic
- so this reaction requires energy
- this energy is obtained by absorbing light
- so light energy is converted to chemical energy in the carbohydrates
210
limiting factors of photosynthesis
- temperature
- light intensity
- CO2 concentration
211
how to investigate the effect of CO2 on photosynthesis
- if the a stem of pondweed is placed upside-down in water and its end is cut, bubbles of gas can be seen escaping
- the gas is mostly O2, produced by photosynthesis
- so the rate of oxygen production can be measured by counting the bubbles
no CO2 condition:
- boil water
- let it cool, then repeatedly pour it from one beaker to another to oxygenate it
- put the pondweed in
```
CO2 condition(s):
add NaHCO3 in increments (at your own discretion) to increase CO2 concentration
```
212
stroma
- fluid in chloroplast
| - where light-independent photosynthesis reactions occur
213
glycolysis
- first step of all forms of cell respiration
| - assuming glucose is the organic molecule to be metabolized
214
process of glycolysis
- glucose enters a cell through the plasma membrane and floats in the cytoplasm
- an enzyme modifies the glucose slightly and a second enzyme modifies it more
- the 6-carbon glucose is cleaved into 2 molecules of 3-carbon pyruvates
- some of the energy released from bond-breaking is converted into ATP
- 2 ATP are needed to start the reaction and the product is 4 ATP
- thus net gain of 2 ATP
215
alcoholic fermentation
- type of anaerobic respiration used by yeast
- the 3-C pyruvate molecules obtained in glycolysis are converted to 2-C ethanol molecules
- so 1 C is lost, given off as CO2
- both ethanol and CO2 are waste products and are released
216
lactic acid fermentation
- type of anaerobic respiration
- used when there's not enough oxygen for aerobic pathway
- excess pyruvates are converted to lactic acid molecules (both are 3-C so no loss of carbon)
- when oxygen is available, the conversion of pyruvates to lactic acid is reversible
217
process of aerobic pathway
- the pyruvates enter a mitochondrion
- each pyruvate loses 1 CO2 molecule to become acetyl-CoA
- each acetyl-CoA molecule enters Kreb's cycle
218
kreb's cycle
- a series of reactions
- results in the same molecule that was used in the beginning
- ATP is generated both directly (during the cycle) and indirectly (in a later series of reactions involving oxygen)
219
Photosynthesis 1st stage
- light-dependent reactions
- photolysis of water occurs here
- useful products to the plants: ATP & hydrogen
- byproduct: oxygen
220
photolysis of water
- one of the stages in photosynthesis
- where molecules of water are split to release electrons needed in further stages
- photo: light; lysis: disintegration
- all the oxygen generated in photosynthesis comes as a byproduct of the photolysis of water
H2O --> 4e- + 4H+ + O2
221
Photosynthesis 2nd stage
- light-independent
- ATP and hydrogen are used to convert CO2 and H2O into useful organic molecules
- glucose is just one of the many possible products of photosynthesis
- typically this reaction is called fixation
222
fixation
- conversion of inorganic substance to organic
| - photosynthesis can be considered a series of reactions where CO2 and H2O are fixed into glucose with O2 as a byproduct
