Chapter 2 Flashcards
Molecular biology
1
Q
Carbon
A
- forms basis of organic life due to its ability to form large and complex molecules via covalent bonding
- can form 4 covalent bonds w/ other carbon atoms or atoms of other elements
2
Q
4 types of macromolecules
A
Carbon-based compounds found in living organisms
- lipids
- carbohydrates
- nucleic acids
- proteins
3
Q
Macromolecules
A
Organic compounds that living organisms are made of
- build living cells
- take part in numerous biochemical reactions
- made up of smaller monomers, form larger structures called polymers
4
Q
Carbohydrates
A
- contains carbon, hydrogen and oxygen atoms
- ratio of hydrogen to oxygen is 2:1
Function:
- source of energy
- also a short-term energy storage option
- important as a recognition molecule and as a structural component (part of RNA/DNA)
5
Q
Lipids
A
- non-polar, hydrophobic molecule that come in a variety of forms
- are a major component of cell membranes (phospholipids and cholesterol)
- contains carbon, hydrogen and oxygen atoms
- phospholipids also contain phosphorus
Function:
- a long-term energy storage
- as a signalling molecule (steroids)
6
Q
Nucleic acids
A
- contains carbon, hydrogen, nitrogen and oxygen atoms
- genetic material of all cells and determines the. inherited features of an organism
- consist of nucleotides, arranged in long chains
7
Q
Proteins
A
- contains carbon, hydrogen, nitrogen and oxygen atoms (some may contain sulphur)
- consist of amino acids, arranged in long chains
Functions: - major regulatory molecules involved in catalysis (all enzymes are proteins)
- may also function as structural molecules or play a role in cellular signalling (transduction pathways)
8
Q
Common carbohydrates and their functions
A
- Alpha-D glucose- used in production of ATP in cells
- Beta-D glucose- used to build cell walls in plants
- Starch- used as long-term storage in plants
- Ribose- used as a component of DNA and RNA
9
Q
Common lipids and their functions
A
- Triglycerides- used as long-term storage in adipose tissue in animals
- Steroids- used as chemical messengers in the body, have a distinctive ring shape
- Phospholipids- major component of plasma membranes
10
Q
Common proteins and their functions
A
- Structural proteins- proteins eg. keratin and collagen form structural framework of many parts of the body
- Enzymes- metabolic proteins that speed up chemical reactions in the body
- Polypeptides- a sequence of AA that may make up a protein, or a series of polypeptides can also make up a protein
11
Q
Common nucleic acids and their functions
A
- DNA- used to store genetic information
2. RNA- used to create proteins at ribosomes using information stored in DNA
12
Q
Monomers
A
Small recurring subunits that make up complex macromolecules
- monomeric subunits join together to form larger polymers
NB/ lipids don’t contain recurring monomers, but, certain types may be composed of distinct subunits
13
Q
Functional groups of monomers
A
Amino acid:
- functional group -COOH (carboxyl group)
- functional group -NH2 (amine group)
Fatty acid:
- functional group -COOH attached to a long hydrocarbon chain
Sugar:
- when hydrogen: oxygen ratio is 2:1
- ribose = 5 carbons
- glucose = 6 carbons
14
Q
Metabolism
A
web of all enzymatic reactions in a cell or organism
Metabolism = anabolism + catabolism
15
Q
Anabolism
A
synthesis of complex molecules from simpler molecules, requires input of energy
- includes formation of macromolecules from monomers by condensation reactions
16
Q
Catabolism
A
breakdown of complex molecules into simpler molecules- energy is released
- eg. hydrolysis of macromolecules into monomers
- eg. glycolysis, breakdown of fats to release energy
17
Q
Hydrolysis reaction
A
breaking of chemical bonds by addition of water molecules
18
Q
Condensation reaction
A
Reaction in which 2 smaller organic molecules combine to form a larger molecule w/ accompanied formation of water or some other simple molecule
19
Q
Urea
A
- organic compound; formula- CO(NH2)2
- used by human body to excrete nitrogen as urea is non-toxic and highly soluble
- also widely used as a nitrogen fertiliser- this has led to its artificial synthesis on a large scale
20
Q
Artificial synthesis of urea
A
- it was artificially synthesised accidentally by Wohler
- he demonstrated that a by-product of life could be artificially synthesised in a lab
- his experiment was the first to show that synthesis of an organic compound from 2 inorganic molecules was achievable
- later, he provided evidence that contradicted the theory of vitalism
21
Q
Theory of vitalism
A
Organic compounds could only be synthesised by living organisms as they possessed an ‘element’ that non-living things didn’t have
- element has been referred to as divine principle
- hence, artificial synthesis of urea from inorganic chemicals in lab helped to falsify it
22
Q
Water
A
- consists of 2 hydrogen atoms and 1 oxygen atom
- O is more electronegative than H atoms; O has greater pull on electron cloud between the atoms
- hence, O acquires slightly negative charge, leaving each H atom w/ slightly +ve charge
23
Q
Water molecules
A
- polar due to their partial +ve and -ve charges
- allows formation of hydrogen bonds between water molecules
- partial +ve H atoms of one molecule are attracted to partial -ve O atoms of other water molecules
24
Q
Hydrophilic compounds
A
Polarity of water molecules allows them to attract other polar/charged compounds and form hydrogen bonds w/ them
- this will cause polar compounds to dissolve in water
- such compounds are hydrophilic
eg. sugars and salts
25
Hydrophobic compounds
Non-polar substances have no attraction to water molecules, instead they repel each other
26
Properties of water
1. Cohesion
2. Adhesion
3. Thermal properties
4. Solvent
27
Cohesion
Tendency of water molecules to stick to each other due to hydrogen bonding between them
- each molecule can potentially form 4 H bonds w/ other water molecules in a tetrahedral arrangement
- although hydrogen bonds are weak, presence of a large no. hydrogen bonds in water gives cohesive forces great strength- responsible for high surface tension of water
28
Adhesion
Interaction that water molecules have w/ other molecules
- why water molecules stick to other polar compounds by forming hydrogen bonds
- responsible for capillary action
29
Capillary action
Movement of water molecules, and all thing dissolved in it, within thin spaces without relying on gravity
30
Latent heat of vaporisation
Energy needed to break hydrogen bonds between water molecules- removes energy from the surroundings
- hydrogen bonds are stronger than other intermolecular forces, hence, water has a high latent heat of vaporisation and fusion
- a lot of energy is needed to change its temp. and to melt/ evaporate it- makes water a great coolant
- hence, water plays an essential role in temp. regulation of living organisms
31
Water as a solvent
- water is one of the best known solvents
- can dissolve ionic as well as many polar compounds
- all reactions in cells occur in liquid medium- are dependent on water to dissolve reactants for reactions to proceed
32
Water's cohesive properties and benefit to living organisms
- allows water to be pulled up from roots to leaves of plants
- allows insects to walk/float on surface of water to catch their prey
33
Water's adhesive properties and benefit to living organisms
- capillary action generated by adhesive forces assists pumping action of heart to help blood move through blood vessels
- adhesion of water molecules to cellulose cell wall of xylem cells- helps water move against gravity from roots to leaves
34
Water's thermal properties and benefit to living organisms
- evaporation of sweat from body surfaces involves heat loss- brings about a cooling effect
- evaporation of water from leaves during transpiration has a cooling effect on plants
35
Water's solvent properties and benefit to living organisms
- water dissolves mineral ions in soil + transports it along xylem vessels from roots to all parts of plant
- water in blood plasma dissolves a range of solutes and gases- allows blood to transport nutrients and gases around the body
36
Sweat as a coolant
- sweat evaporates from body surfaces
- a large amount of heat is lost
- energy is used to break hydrogen bonds to convert water from liquid to vapour state
- makes water a great coolant
37
Glucose in water and blood
- a polar molecule
- is soluble in water and blood
- blood glucose conc. needs to be strictly maintained between certain levels because of its effect on osmotic potential
38
Amino acids in water and blood
- form zwitterions (molecules that have both +ve and -ve charge) in water
- generally soluble in water
- extent of solubility in water varies depending on size and nature of R group
- polar AA are easily transported in blood = hydrophilic
- non-polar AA may be transported in blood but in lower conc.
39
Fats in blood and water
- non-polar
- generally insoluble in water
- transported in lipoproteins
40
Lipoproteins
A single layer of phospholipids w/ proteins embedded among molecules surrounding fat
41
Cholesterol in blood and water
- required for synthesis of many biologically important molecules
- is a component of membranes
- requires help of transport lipoproteins to be transported in blood- hydrophobic
42
Oxygen in blood and water
- non-polar
- due to its small size it's soluble in water to a limited extent
- why oxygen transported in blood is bound to protein haemoglobin in humans
43
Sodium chloride in blood and water
- transported in blood as Na+ and Cl- ions
44
Water vs. methane
Water:
- consists of 2 hydrogen atoms attached to 1 oxygen atom
- polar molecule (why it has cohesive, adhesive, thermal and solvent properties)
- polarity is caused by small +ve charge on hydrogen atoms, small -ve charge on oxygen atom and hydrogen bonding between the 2 molecules
- excellent solvent
- extensive hydrogen bonding
Methane:
- 1 carbon atom bonded to 4 hydrogen atoms
- non-polar molecule
- not a solvent
- no hydrogen bonding
Both:
- covalent compounds
- both small in size
- similar molecular mass
- v. different properties
45
Hydrogen bonding in water makes it:
- most appropriate medium for reactions to take place in
- a very good coolant
- a very stable habitat
- a very good solvent
46
Carbohydrates
Composed of: carbon, hydrogen and oxygen
- ratio of hydrogen: oxygen is always 2:1 (same as water molecules)
General formula: Cx(H2O)y
- classified as monosaccharides, disaccharides or polysaccharides
- form the most important source of energy in the body
47
Lipids
Composed of: carbon, hydrogen and oxygen
- arranged in combinations of fatty acids and glycerol
- important role in supply and storage of energy
48
Triglycerides
Formed in a condensation reactions, w/ 3 fatty acids and 1 glycerol
49
Monosaccharides
Simplest type of carbohydrates
| - act as monomers to make larger complex carbohydrate molecules
50
Disaccharide
2 monosaccharide monomers are linked together by a condensation reaction which forms a glycosidic bond producing a disaccharide
51
Polysaccharide
Several monomer units linked together form a polysaccharide
52
Condensation reaction
Refers to reaction where 2 smaller organic molecules combine to form a larger molecule and a molecule of water or some other simple molecule
53
Important properties of glucose
1. Has 2 isomers:
D-glucose and L-glucose (mirror images of each other)
2. L-glucose can't be used by cells
3. D-glucose is biologically active
- exists in 2 forms (alpha and beta)
3. Alpha-D-glucose and Beta-D-glucose differ only in direction that -H and -OH groups point on carbon 1
54
Hydrolysis
When water is added and used to break up a polymer, a disaccharide or a dipeptide into smaller monomers
55
Carbohydrates and their monomers
- sucrose
- maltose
- lactose
- starch
- glycogen
- cellulose
```
1. Disaccharide
Sucrose: Alpha-D-glucose and fructose
Maltose: Alpha-D-glucose (2 units)
Lactose: Beta-D-glucose and galactose
2. Polysaccharide
Starch: Alpha-D-glucose
Glycogen: Alpha-D-glucose
Cellulose: Beta-D- glucose
```
56
Properties of starch
1. Made of alpha-glucose units, linked by 1,4 glycosidic bonds, causes molecule to form a helical shape
2. Two forms of starch
- amylose contains 1,4 glycosidic bonds and forms linear helices
- amylopectin also contains some 1,6 glycosidic bonds, causes branching
3. Glycogen has same structure as amylopectin involving both 1,4 and 1,6 glycosidic bonds
57
Properties of cellulose
1. Made of straight chains of Beta-D-glucose subunits, held together by Beta 1,4 glycosidic bonds, w/ -OH groups forming hydrogen bonds between them
2. Hydrogen bonding between chains in cellulose causes formation of strong straight fibres
58
Monosaccharides and its examples
Plants: Fructose
- a sugar found in fruits and honey
Animals: Glucose
- used as a source of energy- used in glycolysis step
Other examples: ribose and galactose
59
Disaccharides and its examples
Plants:
1. Maltose (glucose + glucose)
- found in grains (produced from hydrolysis of starch during germination process)
2. Sucrose (glucose + fructose)
- found in sugar cane and sugar beets
Animals: Lactose (glucose + galactose)
- found in mammalian milk
60
Polysaccharides and its examples
Plants:
1. Cellulose
- molecule w/ high tensile strength
- makes it a useful structural component of plant cell walls, it resists expansion of cell (preventing bursting) following water absorption
2. Natural starches form energy stores in plants
Animals:
1. Glycogen
- storage form of carbohydrate
- found in liver and muscles
61
Utilisation of starch in industry
1. Amylopectin- gives starch its characteristic stickiness
- useful in food, paper and chemical industries
- used to make paste, glue or as a lubricant
2. Amylopectin makes up 80% of starch content in potatoes
- genetically modified potato, predominantly produces amylopectin starches (useful for adhesive making) has been produced and approved for cultivation
3. Separation of 2 starch components is v. costly for processing industry
- results in large quantity of wastewater
- use of a genetically modified potato that produces mainly amylopectin is justified
62
Fatty acids
- carboxylic acids, have a -COOH group attached to a hydrocarbon chain
- come in 3 basic forms: saturated, monounsaturated and polyunsaturated
63
Saturated fatty acid
Has no double bonds between any of the carbon atoms that make up the hydrocarbon chain
64
Unsaturated fatty acid
Monounsaturated:
- Has a single double bond
Polyunsaturated:
- 2 or more double bonds in its hydrocarbon chain
Unsaturated fatty acids can be either cis or trans isomers
- depends on position of 2 hydrogen atoms around carbon-carbon double bond
65
Key features of cis-isomers
- commonly occur in nature
- 2 hydrogen atoms are attached to same side of 2 carbon atoms
- double bond causes fatty acid to bend
- because of bend, close packing isn't possible
- lipids/triglycerides formed from cis fatty acids have lower MP (liquid at room temp.)
66
Key features of trans-isomers
- produced when polyunsaturated fatty acids from plants are 'partially hydrogenated' chemically
- makes plant fatty acids more solid- improves shelf life
- hydrogen atoms are on opposite side of 2 carbon atoms
- no bend in fatty acid chain
- allow close packing of fatty acid chain (straight chains)
- lipids made from trans fatty acids tend to have higher MP and are generally solid at room temp.
67
Formation of triglycerides and phospholipid
Triglycerides
- formed by condensation reactions between one glycerol and 3 fatty acids, creates an ester bond
Phospholipid:
- if 1 fatty acid in a triglyceride is replaced by a phosphate group
- major component of membranes
68
Why are lipids better for energy storage than carbohydrates?
1. Higher energy content
- 1g of lipid gives twice amount of energy as 1g of glycogen
- each g of glycogen is usually associated w/ 2g of water, while lipids are stored in pure form
2. Can act as thermal insulators
Using lipids as a long-term storage molecule = animals have a lighter body mass, essential for their body mass
69
Glycogen
Carbohydrate used for energy storage in animals
- it's stored in liver and muscles, can be easily broken down to glucose ( form in which it can be rapidly transported around the body for use in cellular respiration)
- energy stored in glycogen is more accessible than energy stored in fat
70
Key properties of lipids
1. Energy content
- more energy per g than carbohydrates or proteins
2. Density
- less dense than water; oil floats on water
3. Solubility
- non-polar
- so, will dissolve other non-polar compounds, but doesn't affect movement of water
4. Insulation
- excellent heat insulator
71
Lipids and health
- high energy content of lipids may contribute to obesity if eaten in excess
- being overweight or obese is bad for health, increases risk of:
- type 2 diabetes
- coronary heart disease (CHD)
- certain types of cancer
72
Bad fats
1. Trans fats
- formed by hydrogenation of vegetable oils by adding hydrogen to unsaturated fats under pressure
- increases spreadability of veg oil + extends shelf life
2. Saturated fatty acids
- occur naturally in many foods
- majority come form animal sources eg. meat and dairy
73
Impacts of bad fats on health
Trans fats and sat fats contribute to formation of atherosclerotic plaques in arteries- leads to heart attack
- supported by evidence obtained from patients who died from CHD
- shows that high conc. of trans fats are present in fatty deposits in diseased arteries
74
Body mass index
A measure of body fat based on height and weight
High BMI = indicator of high body fatness
- doesn't provide a diagnosis of body fatness or health of an individual
75
Equation for BMI
BMI = W/ H^2
```
W= weight in kg
H= height in m
```
76
Polypeptides
A sequence of amino acids linked together by peptide bonds
- these peptide bonds between each AA are result of a condensation reaction
- also called proteins
Basic unit: amino acid
- a carbon-based compound w/ a carboxyl group (-COOH) and an amine group (-NH2)
Initially, 2 amino acids bind to form a dipeptide
- the carboxyl group and amine group provide OH and H for formation of a water molecule
20^n different types of polypeptides can be formed
n= no. of AA per polypeptide
77
Genes
- coding sections of a genome (DNA)
- normally codes for one polypeptide, each polypeptide has one function
- order of amino acids is controlled by the gene
78
mRNA
Genes are found in nucleus
- polypeptides are synthesised in cytoplasm
- mRNA is first made (contains specific instructions)
- this carries instructions for amino acid sequence to ribosome (found in cytoplasm)
79
Polypeptide chain no. and name of protein
1 PP chain = lysosome
2 PP chains = insulin
3 PP chains = collagen
4 PP chains = haemoglobin
80
Polypeptides
- many amino acids linked together
- order of AA determines shape and function of protein
- 20 AA differ by their R groups- determines types of bonds and interactions w/ other molecules they can make
- this, defines how polypeptide chain or chains fold up in protein
- directly affects its 3D structure- conformation
81
Conformation
A change in order of AA can cause changes in a protein's conformation
- results in a change in shape or loss of function
- gene mutations can cause these changes in order of amino acids
- even a single AA can upset conformation and functioning of a protein
82
Primary structure
Sequence of amino acids
| - defines all aspects of structure and function of a protein
83
Secondary structure
Involves folding of chains on themselves to form pleated sheets or helixes
84
Tertiary structure
When polypeptide folds and coils to form a complex 3-D shape
85
Quaternary structure
Only occurs in proteins made of 2 or more polypeptide chains
- refers to way multiple subunits are held together in a multi-subunit complex
eg. haemoglobin
- has 2 alpha and 2 beta chains
- forms a functional group that can transport oxygen
86
Genome
The complete and unique DNA content that each organism has
87
Proteome
The unique set of proteins that are coded by their genome
88
Proteome analysis
- new tool in medical research and cancer treatment
- to treat certain cancers, proteome of a patient's cancer cell is analysed to determine if a particular chemotherapy will be successful
89
Two forms of proteins
Globular
| Fibrous
90
Globular proteins
- spherical
- play active roles in cell's metabolism
- consist of complex polypeptide chains that can be linked to other chains to form large complex proteins
- usually soluble in water - their hydrophobic R groups are folded into core of molecule, away from surrounding water molecules
eg/ haemoglobin- has 2 alpha and 2 beta chains
91
Fibrous proteins
- like a fibre, long and thread-like
- made of long polypeptide chains where hydrophobic R groups are exposed making molecule insoluble
- found in structural parts of organisms eg. tendons
92
Examples and functions of globular proteins
1. Rubisco
- an enzyme involved in fixation of CO2 in chloroplasts
2. Insulin
- hormone produced by beta cells of pancreas
- involved in glucose uptake from blood
3. Immunoglobulins
- large Y-shaped proteins, also called antibodies
- involved in fighting infections by specifically recognising and binding to antigen molecules
4. Rhodopsin
- protein linked to pigment found on membrane of rod cells of retina
- allows v. low light intensities to be detected
93
Fibrous proteins examples and functions
1. Collagen
- structural protein
- found in muscles, tendons and ligaments, where it gives tensile strength
- also occurs in skin, prevents tearing and in bones, prevents fracturing
2. Spider silk
- produced by spiders for their webs
- can be extended, very resistant to breaking
94
Two ways to dentaure proteins
1. Exposing protein to higher temperatures
2. Changing the pH of the surrounding solution
NB/ Because proteins have an optimum temperature and pH at which they function best
- any deviation from these values influences functionality of the proteins
95
Temperature and proteins
- proteins lose their conformation, interaction between certain AA will be changed
- quaternary and tertiary structures are irreversibly changed
- results in denatured proteins losing their form and function
NB/ peptide bonds holding adjacent AA don't break during denaturation process
96
pH and proteins
- strong alkaline or acidic solutions can break bonds between non-adjacent AA or between PP chains of quaternary proteins
- protein denatures and loses functionality
97
Enzymes
Biological catalysts- are globular proteins that can speed up a biochemical reaction
- Large polypeptides w/ a tertiary or quaternary conformation
98
Active site
Region of an enzyme to which substrates bind and where reactions are catalysed
- result of folding of polypeptide chains
- resulting 3D shape that's formed by PP chain forms active site- where substrate interacts with the enzyme
99
Enzyme-substrate specificity
One enzyme can only catalyse one type of reaction
- Interaction between substrate and active site of enzyme is highly specific
- only one type of substrate fits into the active site
100
Substrates to products
Reaction that converts substrate into products takes place in active site of enzyme
101
Induced fit
Substrate enters active site, it triggers a change in 3D shape of enzymes that allows a tighter fit- induced fit
- possible due to the flexibility of the protein molecules that make up the enzyme
- when enzyme and substrate fit together tightly, enzyme induces weakening of bonds within molecules of substrate, reducing activation energy needed for reaction
- when enzyme-catalysed reaction is completed, products are released from enzyme
102
How do enzymes work?
Enzymes can speed up a reaction by lowering activation energy of that reaction
103
Activation energy
Minimum energy that reacting particles should possess for a reaction to occur
104
Catalytic reaction
When an enzyme converts substance into products
105
Enzyme catalysis
- involves molecular motion and collision of substrates w/ active site
- motion of atoms and molecules is random and depends on temp.
- catalysis of reaction is only possible if substrate and active site happen to be correctly aligned when they collide to allow binding to take place
106
Exothermic reaction
A reaction where product formation is associated w/ release of energy, usually in form of heat
107
Endothermic reaction
A reaction where product formation is associated w/ absorption of energy, usually in form of heat
108
Temperature and rate of activity of enzymes
- each enzyme has an optimum temp. that depends on type of enzyme and where it's found
Temp. is low:
- enzymes have low KE- are inactive
- hardly any collisions between enzymes and substrate molecules are possible
Temp. is high:
- enzymes start to denature
- causes a drop in enzyme activity
109
Substrate concentration and rate of activity of enzymes
Substrate conc. increases:
- rate of enzymatic conversion will increase to a certain point
- if all active sites of enzymes are occupied by a substrate, then increasing substrate conc. will have no further effect
- once Vmax is reached, substrates have to wait for enzyme active sites to be available before they can bind
Vmax = max. rate possible
110
pH and rate of activity of enzymes
- enzymes are made of AA
- they tend to donate or accept H+ ions when pH drops below or increases above optimum point
- this affect their tertiary and quaternary structure, causes a change in conformation of active site
- overall effect = drop in activity of enzyme
111
Denaturation
An irreversible change to a protein meaning it can no longer function
- enzymes are proteins and can be denatured
- can be caused by extreme pH values, heat and presence of heavy metals
- destroys tertiary or quaternary conformation of a protein
- when temp. is high enough or pH is extreme, secondary structure of a protein can be destroyed
A protein loses its conformation w/ denaturation
- beta sheets and alpha helices lose their form
- the protein reverts to a primary conformation
- there is no longer a functional active site
112
Immobilisation of enzymes
- used by attaching them to a material (immobilisation) so movement is restricted
- if enzymes aren't immobilised, they are often present in final product, this restricts conc. that can be used to process food for human consumption to avoid adverse effects
- but, use of immobilised enzymes permits higher conc. of enzymes to be used- allows a faster rate of reaction
- immobilisation of enzymes allows immediate separation of enzymes from reaction mixture
- allows them to be recycled, reducing production costs
Benefit:
- they are more stable
- less likely to degrade due to fluctuations in pH and temperature
113
Industrial sectors using immobilised enzymes
- detergent industry (manufacture of biological washing powders and liquids)
- food industry (production of lactose-free milk
- pharmaceutical industry (antibody production)
114
Advantages of producing lactose-free products
- no ill effects after consumption
- quicker fermentation eg. in yoghurt production as bacteria ferment glucose and galactose more readily than lactose
- sweeter tasting milk (glucose and galactose are sweeter tasting than lactose)
115
Production of lactose-free products
1. Add enzyme lactase to milk
- lactase breaks down lactose into its constituent monomers, glucose and galactose
- this leaves enzyme in the end product
- presence of lactase can cause other problems, so it's better to remove it from the end liquid
2. Lactase can be immobilised in alginate beads, while milk is allowed to flow past
- no lactase ends up in final dairy product, making it better for consumption
116
Nucleotides
Basic structures of DNA and RNA
117
DNA vs RNA
Similarities:
- both made of nucleotides
- composed of 3 parts: pentose sugar (5 carbon atoms), a phosphate group and a base
118
Classifying bases
Classified based on no. of rings present in their structure
119
Purines
Bases that have 2 rings in their structure
- pyrimidines contain only one ring
- Thymine, cytosine and uracil are pyrimidines
- adenine and guanine are purines
120
Strands
- nucleotide units link together through a phosphodiester bond to form a single strand, a polynucleotide
- phosphodiester bond is always formed between phosphate group attached to the 5-C of one sugar and hydroxyl group attached to 3-C of another sugar
121
Differences between a DNA and RNA molecule
DNA:
- contains sugar deoxyribose
- bases involved are adenine, thymine, guanine and cytosine
- is a double stranded molecule
RNA:
- contains sugar ribose
- bases involved are adenine, uracil, guanine and cytosine
- is a single stranded molecule
122
Key points about DNA:
- genetic material of living organisms
- DNA parents pass on to offsprings is exactly the same in structure- powerful evidence for theory of evolution
- Guanine always pairs w/ cytosine
- adenine always pairs w/ thymine
123
Two strands
- held together by hydrogen bonds between G and C (3 H bonds) and between A and T (2 H bonds)
- are antiparallel to each other
- one strand runs from 5-C to 3-C, and opposite strand runs from 3-C to 5-C
3-C and 5-C refer to exposed carbon (on the sugar) at the ends of the DNA chains
124
Complementary base pairing
G always pairs w/ C
A always pairs w/ T
DNA always forms an alpha helix and the 2 strands are antiparallel
125
Model to elucidate the DNA structure
Crick and Watson built on the pre-existing knowledge on chemistry of DNA to determine its actual structure
- used info from DNA X-ray diffraction patterns produced by Franklin and Wilkins
- then, deduced that the DNA molecule must have a regular double helix structure
- integrated, Chargaff's base ratio- finding showed that A is always = to T and C is always = to G in DNA molecule to work out complementary base pairing
126
S-phase
- DNA is replicated to. make identical copies
| - each daughter cell is a perfect copy of the parent cell
127
Genes
- are made of DNA
- contain coding information for. proteins
Eukaryotes: genetic information is contained in the nucleus
Prokaryotes: genetic information is contained in the cytoplasm
128
How do cells make proteins from DNA?
1. Transcription: copying the DNA by synthesising mRNA from DNA base sequences
2. Translation: interpreting genetic code to synthesise polypeptide chains on ribosomes
129
Cell division
- when a cell divides, 2 daughter cells are formed
| - daughter cells are identical copies of parent cells
130
Tumourigenesis
If copying process goes wrong, a tumour can result
| - mutations in DNA or errors when DNA is copied can cause this
131
Replication
- process of copying DNA
- occurs during S phase of cell cycle
- in most cases, replication results in identical copes of DNA in daughter cells
132
Structure of DNA
DNA is normally supercoiled by being tightly wound around histones to from nucleosomes
133
Steps of replication
1. Unwind the DNA coils tightly wound around histones to form nucleosomes- makes strands accessible to enzymes
2. Enzyme helicase unwinds double helix and separates the 2 DNA strands by breaking hydrogen bases between the bases
3. Once strands are separated and bases exposed, DNA polymerase can start making new strands of DNA using two 'old parent' strands as templates
134
Key points in DNA replication
- 2 DNA strands of double helix are anti-parallel to each other
- DNA polymerase proceeds in opposite directions during replication
- on one strand it moves in same direction as replication fork (immediately behind helicase)
- it moves in reverse direction on the other strand
- DNA replication always occurs in 5-C to 3-C direction
It is semi-conservative
- each daughter molecule formed contains one original strand from parent molecule and one newly synthesised strand
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Transcription
- coding information is copied/transcribed into mRNA
- DNA functions as a template, single-stranded mRNA molecule that is made follows complementary base pairing rules of DNA
- in an mRNA molecule, whenever there's an A in the DNA template, a U will appear in newly formed mRNA
- complementary base pairing is an extra control mechanism of transcription- ensures that mRNA formed is a true copy of the DNA
- in transcription, section of DNA that contains required gene is unwound and separated
- so, RNA polymerase can access DNA bases
- RNA polymerase then transcribes a sequence of DNA bases into mRNA
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Gene
a section of DNA on a chromosome that codes for a particular protein
- each chromosome contains many genes, but only a few are expressed at any given time
- these are the only ones that are transcribed
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RNA polymerase
responsible for:
- separating DNA strands of double helix
- joining ribonucleotides together by phosphodiester bonds to form an mRNA strand
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Sense strand
DNA strand that isn't transcribed
- has the same sequence of bases as mRNA molecule
- except thymine is replaced by uracil
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Antisense strand
- the transcribed strand
| - is complementary to the mRNA molecule
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Translation
synthesis of polypeptides by ribosomes
- once gene has been transcribed into mRNA
- mRNA molecule forms the template for protein synthesis
- hence, on leaving the nucleus, mRNA binds to one or several ribosomes and allows translation to begin
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Organic compound
a compound that contains carbon and is found in living things
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Monomers of carbohydrates
Carbohydrates are composed of monomers called monosaccharides
- monosaccharides are the building blocks of disaccharides
- most monosaccharides form ring structures and can exist in different 3D configurations
eg. ribose and glucose
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Subunits of lipids
- lipids exist as many different classes that vary in structure
- don't contain a common recurring monomer
- but, several types of lipids contain fatty acid chains as part of their overall structure
Fatty acids= long chains of carbohydrates that may be saturated or unsaturated (contain double bonds or don't contain double bonds)
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Monomers of proteins
- composed of monomers called amino acids; they join together to form polypeptide chains
- each AA consists of a central carbon connected to an amine group (NH2) and an opposing carboxyl group (COOH)
- a variable group (R) gives different AA different properties
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Monomers of nucleic acids
- composed of monomers called nucleotides, join together to from polynucleotide chains
- each nucleotide has 3 components: a pentose sugar, a phosphate group and a nitrogenous base
- type of sugar and composition of bases differs between DNA and RNA
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Structure of polysaccharides
- structure of complex carbohydrates may vary depending on composition of monomeric subunits
- polysaccharides may differ according to type of monosaccharide they possess and the way the subunits bond together
- glucose monomers can be combined to form a variety of different polymers eg. glycogen, cellulose and starch
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Steps of cellular respiration
1. Glycolysis- glucose is broken down to pyruvate in the cytoplasm
2. Link reaction- pyruvate is converted into acetyl- CoA and enters the mitochondrion
3. Acetyl-CoA enters the Krebs cycle, generating FADH2 and NADH + H+
4. The FADH2 and NADH + H+ are oxidised in the electron transport chain and ATP is produced
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Cellular respiration
gradual and controlled release of energy by breaking down organic compounds to produce ATP (Adenosine TriPhosphate)
- involves enzymes that control the process to ensure that energy is produced when it's required
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The 3 main process of cellular respiration
1. Glycolysis
2. Krebs cycle
3. Electron transport chain
All generate energy in the form of ATP
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Location of cellular respiration
Glycolysis- takes place in the cytoplasm
Krebs cycle- occurs in the mitochondria, in the matrix
Electron transport chain- located on the inner membrane of the mitochondrial envelope in the mitochondria
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What is ATP?
ATP = Adenosine TriPhosphate
- fuel's most of the body's energy needs
- ATP from cell respiration is immediately available as a source of energy in the cell
- energy is produced when ATP is hydrolysed
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Anaerobic cell respiration
- when respiration takes place without oxygen
| - occurs only in the cell cytoplasm as it involves only glycolysis
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ATP during exercise
- we breathe air during strenuous exercise, our muscle cells use up all the available oxygen
- they need ATP to continue the exercise
- without oxygen, the muscles cells start to respire anaerobically
- produce a small amount of ATP, allows power of muscle contractions to be maximised
- during anaerobic respiration, animals produce lactate- causes soreness in muscles after strenuous exercise
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Key properties of anaerobic respiration
- takes place in the cytoplasm
- takes place without the presence of oxygen
- generates a smaller amount of ATP (only 2 ATP) than aerobic respiration
- in yeast, it produces ethanol (alcohol) and CO2
- in animal muscle cells, it produces lactate
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Aerobic cell respiration
- when oxygen is present, aerobic respiration can yield far more ATP than under anaerobic conditions
- because all the energy contained in a glucose molecule can be harvested and converted into ATP
- this increased ATP production is because all 4 steps of cellular respiration are completed
- reason for this increased yield is that 6-glucose is systematically and gradually broken down to 6 CO2 molecules
- each step yields potential energy, can be converted into ATP in ETC
NB/
- requires oxygen
- gives a large yield of ATP from oxidation to glucose
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Equation for aerobic cell respiration
Glucose + oxygen --> carbon dioxide + water + energy (ATP)
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Respirometer
a simple apparatus that can measure the rate of respiration
- cellular respiration uses oxygen and produces carbon dioxide and water
- we can measure the consumption of oxygen as an indication of the respiration rate
- it can give us a good idea of the respiration rate of germinating seeds, a resting animal or a moving animal- allows us to compare different species
- can measure the influence of temperature on respiration
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How is a respirometer used?
Tube A- organism to be. tested is positioned and tap is closed
- organism starts respiring, consuming O2 and producing CO2 and H2O
- alkali solution at the bottom of Tube A will absorb the CO2
Tube B- control where no O2 is used or CO2 is produced as no living organism is present
NB/ the capillary connecting the two tubes is a manometetr
Reduction of O2 in Tube A will reduce the pressure in Tube A- will move coloured liquid in the manometer in the direction of Tube A
- provides an indirect measurement of the oxygen consumed, allowing rate of oxygen to be calculated
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Photosynthesis
the reaction of carbon dioxide and water using energy from light to produce carbohydrates and oxygen in cells
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Chloroplasts
- tiny organelles in plant or algae cels where photons are captured
- look green because chlorophyll a and chlorophyll b, the pigments that capture the photons, reflect green light and absorb most of the other wavelengths in the visible light spectrum
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How is colour of leaves determined?
Colour of leaves of any plant is determined by colour of light from the visible spectrum that is reflected
- chlorophyll absorbs red and blue light most effectively and reflects green light more than other colours
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Action spectrum
shows efficiency of photosynthesis or rate of photosynthesis achieved over the various wavelengths of light from the visible spectrum
- a good indicator of which wavelengths are most efficient in photosynthesis
- some wavelengths cause a higher photosynthetic rate than others
- shows different rates of photosynthesis that occur at different wavelengths of visible light
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Absorption spectrum
shows which wavelength of visible light is absorbed by a particular photosynthetic pigment eg. chlorophyll a or b
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Graph of absorption and action spectrum for photosynthesis
- the x-axis is labelled light wavelength/ frequency and y-axis is labelled rate of photosynthesis
- the curve increases, decreases and then increases again to decrease again
- one peak is approx. at 425nm/blue region
- second peak is approx. at 670 nm/red region
- first peak is higher than the second peak
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Photolysis of water
splitting of water by light
- energy in photons is used to split water molecules
- generates hydrogen ions, electrons and oxygen
2 H2O + photons --> 4e- + 4H+ +O2
electrons are used to generate ATP through cyclic or non-cyclic phosphorylation
- both ATP and hydrogen ions are used in later stages of photosynthesis
- oxygen is a waste product that diffuses out of the plant
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Two stages of photosynthesis
1. Light-dependent reaction
- requires light and occurs on the thylakoids of chloroplasts
2. Light-independent reaction
- has no light requirement
- takes place in the stroma of chloroplasts
NB/ both require energy, usually as ATP
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Calvin cycle
name for the light-independent reactions; a cycle of chemical reactions where CO2 is the starting material for the production of carbohydrates
- Calvin cycle is comparable to the Krebs cycle in mitochondria
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Limiting factor
a factor that restricts the rate of reaction when present in low amount
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Limiting factor and photosynthesis
- as process of photosynthesis is catalysed by enzymes, it works best at an optimum temperature
- as light, water and CO2 are required for photosynthesis to occur, these will also influence the rate at which the process can take place
- water is a limiting factors but only under extreme conditions- if water becomes so scarce that the plant is likely to die, photosynthesis will stop
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The 3 factors that can limit rate of photosyntheis
Light
Carbon dioxide
Temperature
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Light as a limiting factor in photosynthesis
- light intensity is a. limiting factor
- at night, when there's v. little light, rate of photosynthesis slows down
- when sun comes down, rate of photosynthesis increases, but only up to a certain point
- beyond this point, chemical reactions of photosynthesis can't go any faster- any further increase in light intensity doesn't increase the rate
- rate is expressed as the uptake of CO2
- another method to measure rate of photosynthesis would be to measure production of oxygen
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Carbon dioxide as a limiting factor in photosynthesis
- a raw material in the production of carbohydrates, takes place in Calvin cycle
- once all the active sites of enzymes in this cyclic process are occupied w/ a substrate, any further increases in CO2 conc. won't increase the rate
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Limiting factor vs. maximum potential
Limiting factor: as far as an increase in a. particular factor causes an increase in rate of photosynthesis, factor is limiting
Maximum potential: once rate remains constant, indicates that some other factor is limiting or the plant has reached its maximum potential
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Temperature as a limiting factor in photosynthesis
- optimum temp. of photosynthesis differs enormously for plants
- when temp. increases beyond the optimum level, enzymes start to denature, hence rate of photosynthesis decreases
- when all enzymes are denatured, photosynthesis stops
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Relationship between temperature, light intensity and carbon dioxide concentration in photosynthesis
- at optimum temp., rate of photosynthesis is. limited by light intensity and CO2 conc.
- at v. high light intensity and optimum temp., increasing CO2 will further increase rate of photosynthesis but only up to a certain point
- then rate of photosynthesis will reach a plateau
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Changes to Earth's atmosphere
- changes in oxygen content of Earth's atmosphere, oceans and rock deposition can be attributed to photosynthesis
- cyanobacteria were the earliest photosynthetic organisms, took hundred millions of years before other organisms, arrived
- it took a long time before the contribution of cyanobacteria to atmospheric conc. became apparent
- initially, oxygen released from photosynthesis may have been used in oxidation of other minerals, eg. iron, and ended up in sediments and rocks
- 2000 million years ago, eukaryotes appeared
- from then on, algae and other organisms living in the ocean have increased oxygen conc. in the water
- once oceans and deposits were saturated, Earth's atmospheric oxygen started to build up
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Chromatography
a technique used to separate mixtures of substances based on movement of different substances on a piece of paper by capillary action
- makes use of a mobile phase and a stationary phase for separation process
- in paper chromatography, paper is the stationary phase while solvent used to develop chromatogram is mobile phase
- pigments are commonly separated using a mixture of propanone and petroleum ether
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Leaf pigments
- contains several different pigments, eg. chlorophylls, beta carotene and xanthophyll, can be separated using paper chromatography
- pigment is first extracted from the leaves by using a suitable solvent that dissolves mot plant pigments
- a sample of extract is then placed on chromatography paper and transferred to a containers w/ chromatography solvent
- pigments move at different rates on stationary phase, so they separate out to form a chromatogram
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Retention factor
the ratio of distance moved by a pigment to the distance moved by the solvent is a constant
Rf = distance travelled by sample/ distance travelled by solvent
NB/ by comparing Rf value to known Rf values of plant pigments, the pigments present in the plant extract can be deduced
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Thin layer chromatography
- uses the same principle as paper chromatography
- the stationary phase is usually silica gel, aluminium oxide or cellulose instead of paper
Advantage:
- gives a better result as well-defined and well-separated spots are obtained
