Unit 2 - Molecular Biology
2.1 - Molecules to Metabolism
Living organisms control their composition by a complex web of chemical reaction.
Molecular biology explains processes in terms of chemical reactions
● It is a reductionist theory
● Thus emergent properties are lost
Carbon is the basis of life:
● All life is carbon based
○ It’s very stable
■ Has 4 electrons, thus needs 4 covalent bonds
○ Easy to add stuff on
■ Due to symmetric and opposite bond structure
Metabolic reactions:
Metabolism def: Any chemical reactions inside living organisms.
1. Anabolic reaction - the building up of stuff
● Process called condensation synthesis (also dehydration synthesis)
○ Links many monomers together (by chemical reaction)
○ Forms polymers
● Needs energy
● Produce water as a byproduct
2. Catabolic reaction - the breaking down of stuff
● Process called hydrolysis
○ Breaks bonds in polymers (by chemical reaction)
○ Forms monomers
● Release energy
● Needs water
Monomers / The building blocks of life:
● In carbohydrates
○ Monosaccharides (simple sugars)
○ Glycosidic bonds
● In lipids
○ Fatty acid
○ Glycerol
○ Ester bonds
● In protein
○ Amino acid
○ Peptide bonds
● In nucleic acid
○ Nucleotides
○ Phosphodiester bonds
Vitalism theory (disproven):
● States: all molecules produced by living things are special
○ Can only be produced inside living organisms
Disprove:
● Urea is found in urine (produced inside the body)
● Urea can be synthesized (outside the body)
2.2 - Water
Water is the medium of life.
Water molecules:
●
●
Water is polar*
○ A positive and negative end
○ Forms a dipole
Forms hydrogen bonds
○ Due to polarity
*most properties of water result from its polarity
Properties of water (due to hydrogen bonds):
Cohesion:
● Water molecules stick to one another
Adhesion:
● Water molecules stick to other polar molecules
Solvent properties:
● Dissolves polar molecules
● Necessary for chemical reactions of metabolism
Thermal properties:
● High specific heat capacity
○ Requires a lot of energy to heat up
○ A lot of energy is released when cools down
● High latent heat of vaporization
○ Hard to boil
○ A lot of energy needed to break hydrogen bound (in order to boil)
○ High boiling point
● High heat of fusion
○ Hard to freeze
○ Low freezing point
Application:
Sweating releases a lot of energy due to the high latent heat of vaporization of water
Methane to water comparison:
● Formula:
CH4 (methane)
● Liquid state: for 22℃
H2O (water)
for 100℃
Transport of molecules:
Water dissolves all polar (hydrophilic) molecules
Of Sodium chloride (ionic compounds):
● They ionize thus become polar
○ Polar molecules dissolve in water
Of Glucose and amino acids:
● Ussaly polar ─ thus dissolves in water
Of Oxygen:
● Non polar
● Small enough to partially dissolve in water
● The use of haemoglobin
○ A protein
○ Binds to oxygen in order to transport it in the bloodstream
Of Fats and cholesterol:
● Non polar, hydrophobic (do not dissolve)
● Carried in lipoprotein
○ Phospholipid single-layer
■ Similar to membranes but only half (a single layer)
■ Tails attract fats and cholesterol
○ No water inside
2.3 - Carbohydrates and Lipids
Compounds of carbon, hydrogen and oxygen are used to supply and store energy.
●
Both energy storage molecules
2.3a - Carbohydrates / Saccharides:
Types of molecules:
● Monomers/building blocks
○ Monosaccharides
■ No bonds, single saccharides
■ eg. glucose, fructose, galactose
● Polymers - by glycosidic bonds
○ Disaccharides
■ 1 bond, 2 saccharides
■ eg. sucrose, lactose, maltose
○ Polysaccharides
■ Many bonds and saccharides
■ eg. starch, glycogen, cellulose
Monosaccharides to draw:
Examples:
2.3b - Lipids:
●
All oils (plants) and fats (animals)
Types of molecules:
● Monomers/building blocks
○ Fatty acid
■ Saturated
● No double bonds
■ Unsaturated (pick 2)
A) Cis-unsaturated
● Naturally occuring
● Hydrogen (H) on same side (at double bond)
○ Thus creates a kink
B) Trans-unsaturated
● Synthesised (unnatural)
● Hydrogen (H) on opposing side (at double bond)
○ Thus straight molecule
1) Monounsaturated
● 1 double bond
● Adds rigidity
2) Polyunsaturated
● 2+ double bonds
● Most rigid
○ Glycerol
●
Polymers
○ Triglyceride (Glycerolx1 + Fatty acid x3)
■ Long-term energy
■ By ester bond
○ Phospholipids
■ Tails
● Fatty acids
● Non-polar
■ Heads
● Glycerol + Phosphate
● Polar
Body Mass Index (BMI):
𝐵𝑀𝐼 =
𝑚𝑎𝑠𝑠 (𝑖𝑛 𝐾𝑔)
2
ℎ𝑒𝑖𝑔ℎ𝑡 (𝑖𝑛 𝑚)
Normal is 18 to 25
2.4 - Proteins
Proteins have a wide range of functions in living organisms.
Types of molecules:
● Monomers/building blocks
○ Amino acid
■ 20 different types
● Some exceptions
■ Composed of
● Amino group
● Carboxyl group
● Central carbon (C)
● The R group
○ This is the source of variability
● Polymers
○ Polypeptides
■ Chain of amino acids
■ Linked by peptide bonds
● Synthesis in ribosomes
■ Always unbranched
■ Gets variability from:
● Type of amino acid (choice
between 20)
● Length of chain
Shape dictates function:
● Primary structure
○ Type of amino acid (20 options)
○ Length of polypeptide chain
● Secondary structure
○
●
●
Shape of chain
■ ⍺-helix
■ β-pleated sheet
○ Dictated by hydrogen bonds
Tertiary structure
○ Infolding of protein on itself
■ Hydrophobic interactions
● Like membranes
■ Hydrogen bonding
Quaternary structure
○ Multiple polypeptide chains
○ Creates functional protein
Denaturation:
● Negative change in shape/fold (3D
structure) of protein
○ Irreversible
○ Alter/halt function of protein
● Causes
○ High temperatures (not low)
○ Unnatural pH
Examples:
● Rubisco
○ Enzyme
■ Found in chloroplast
○ Fixes carbon in photosynthesis
● Insulin
○ Hormone
■ From Β-cells in the pancreas
■ Signals cells to absorb glucose
● Immunoglobulins
○ Antibodies
○ Signal immune cells to attack
● Collagen
○ Fibrous
○ Strength in tendons
● Spider silk
○ Fibrous
○ Strength and flexibility
Proteome:
● All the proteins produced by a cell, tissue or organism at a given time
● This is unique
○ DNA is unique
○ Environment is unique
2.5 - Enzymes
Enzymes control the metabolism of the cell.
Def: A protein functioning as a biological catalyst,
speeding up reaction rates by lowering activation energy.
How they work:
● Globular protein
● Active site
○ Site on surface where substrates
(reactants) bind
○ Shape of active site determines function
■ Like a lock and a key
● When substrate bind
○ Called enzyme-substrate complex
● Needs a collison
○ Enzyme and substrate(s)
○ Thus more heat, more collison
■ Kinetic molecular theory
● note: enzymes (like protein) can be denaturalized
Rate of reaction variables:
Substrate concentration:
pH level:
Temperature:
Enzyme concentration:
Immobilized enzymes:
● Enzymes can be immobilized
○ Attached to glass
○ Incorporated in gel
● Industrial advantages:
○ Easily removable from product
○ Easy reuse
○ Substrate can be exposed to more enzymes
■ Since enzyme location is fixed
■ Collisions can be artificial
■ Thus faster
○ Reduces cost of production.
Lactose free milk:
● Lactose is a disaccharide (sugar)
● Lactase is an enzyme
○ Used to digest (break down) lactose
■ Into glucose and galactose
○ Cultivated in Kluveromyces lactis (a fungus)
● Often used in food processing
Reasons for using lactase in food processing:
● Lactose allergies (lactose intolerance)
● Glucose and galactose are sweeter
○ Tastes better
○ Reduces the amount of sugar added
● Has a smoother texture
○ Better for ice cream
○ Glucose and galactose dissolve better
● Glucose and galactose ferment faster
○ Cheese and yogurt production is faster
2.6 - Structure of DNA and RNA
The structure of DNA allows efficient storage of genetic information.
Composition of Nucleotide (monomer unit):
● Sugar-phosphate backbone
○ Sugar/carbohydrate
■ Deoxyribose (in DNA)
■ Ribose (in RNA)
○ Phosphate group
■ Links sugars together
● Nitrogenous base
○ Purines (large molecules)
■ Adenine
■ Guanine
○ Pyrimidines (small molecules)
■ Cytosine
■ Thymine (in DNA)
■ Uracil (in RNA)
note: Nucleotides form polynucleotide chains connect via phosphodiester bond
RNA vs. DNA:
DNA (deoxyribonucleic acid)
-
Deoxyribose sugar
2 polynucleotide chains
Bases: A, Thymine, C, G
Double helix
RNA (ribonucleic acid)
-
Ribose sugar
1 polynucleotide chains
A, Uracil, C, G
No double helix
Complementary Base Pairing:
● DNA’s double helix is hydrogen bonded
T/U (2 bonds)
○ A
G (3 bonds)
○ C
● In antiparallel nature
○ One side is facing up (on the left)
○ Other side is facing down (on the right)
● Always 3’ to 5’ direction
↔️
↔️
Drawing DNA/RNA chains:
Remember:
● Phosphate
● Deoxyribose sugar
● Nitrogenous base
● Phosphodiester bond
● Hydrogen bond
● Nucleotide
● Sugar phosphate backbone
2.7 - DNA Replication, Transcription and Translation
Genetic information in DNA can be accurately copied and can be translated to make the
proteins needed by the cell.
2.7a - DNA Replication
Semi convervative model:
● Double helix separate
○ Each strand is a template (for the new DNA)
○ Thus half of each new strand comes from the original
● Nucleotides are pared using complementary base pairing
T/U (2 bonds)
○ A
G (3 bonds)
○ C
● 2 DNA’s are produced
○ Genetically identical
● DNA is:
○ A 4 letter alphabet
○ 3 letter long words (called codons/triplets)
■ 64 combinations (43=64)
■ Code for an amino acid
↔️
↔️
Evidence (Meselson & Stahl experiment):
Procedure:
● E-coli grown in 15N solution (instead of 14N)
○ Thus nitrogenous base of DNA is dense (15N)
● Moved to 14N solution
○ Thus newly created DNA is less dense (14N)
● After multiple generations, DNA is extracted and
density is measured
Results (density of DNA):
Gen. 0
○ All is dense
● Gen. 1
○ All is mid density
○ Conservative model disproved
■ If true, 2 lines would appear
● Gen. 2
○ ½ is mid density
○ ½ is low density
○ Dispersive model disproved
■ If true, only 1 line would appear
● Gen 3.
○ ¼ is mid density
○ ¾ is low density
●
DNA Replication procedure:
1. DNA helicase (enzyme)
● Unwinds DNA
● Breaks hydrogen bonds
2. DNA polymerase (enzymes)
● Adds nucleotides
○ Found in solution
○ Using base pairing rules
● Adds in a 5’ to 3’ direction only
○ Thus 1 strand is paired
backwards
Polymerase Chain Reaction (PCR):
● A method to rapidly increase DNA (cloning DNA)
○ Useful when the source of DNA is small
● High temperature replaces helicase
○ Unwinds & breaks hydrogen bonds
● TAQ polymerase replaces regular polymerase
○ Doesn’t denature at high temperatures
■ Found in hot springs (thus natural state)
note: Requires pre-made DNA primers & nucleotides
● Solution is cooled
○ Allows DNA to rebond and recoil
● This process is automated
● Produces sufficient DNA in 20 cycles (overnight)
2.7b - DNA Transcription & Translation (mRNA)
Transcription:
● mRNA is created using DNA as template
1. Initiation
● RNA polymerase (only enzyme used)
○ Binds to promoter region (start of gene)
○ Unwinds and breaks hydrogen bonds
2. Elongation
● One DNA strand is copied
○ Using anti-sense strand
(template strand)
3. Termination
● Terminator sequence is reached
○ Written into DNA
● RNA polymerase releases parts
Translation:
● Protein synthesis occurred using mRNA as template
1. Initiation
a. mRNA binds to small subunit (of ribosome)
b. First tRNA binds to start codon
● By complementary base pairing
c. Large subunit binds to ribosomal structure
● Ribosome has 3 parts
○ Small subunit
○ Large subunit
○ mRNA strand going through
2. Elongation
● 3 sections/steps in ribosome
○ A site
■ tRNA anticodon (with amino acid) binds
● According to complementary base pairing
○ P site
■ Amino acid separated from tRNA
■ attaches to polypeptide chain
○ E site
■ tRNA exists
3. Termination
● No tRNA for stop codon
● When nothing fits:
○ Polypeptide chain is released
○ Ribosome breaks up
■ Into 2 subunits
*note: need to indicate start codon when translating from table of amino acids
2.8 - Cell Respiration
Cell respiration supplies energy for the functions of life.
Photosynthesis and cell respiration:
● Complementary process
○ The products of one are the reactants of
the other
in chloroplast
● Photosynthesis
in mitochondria
● Cell respiration
➡️
➡️
Equation:
Adenosine triphosphate (ATP):
● ATP is cell energy
● When used (ATP ➝ ADP):
○ 3rd phosphate (P) is released
■ Bond is broken
■ Releases energy
○ Becomes ADP (2 phosphates)
■ Low energy molecule
● Goes to all parts of the cell
note: Cannot move between cells
● Uses of ATP:
○ Synthesizing polymers (eg. DNA, RNA, protein)
○ Active transport (membrane pumps)
○ Mouvement
○ Release of heat (waste product)
■ ATP can be used just to keep warm
Cell respiration:
The controlled release of energy (ATP) from organic compounds in cells.
● Organic compounds (glucose, fat, protein) are broken down
○ Make 38 ATP net (2 spent)
Anaerobic respiration (Glycolysis):
● Very fast production of ATP
● Without oxygen (O2)
● In cytoplasm
● Glucose (6 carbon molecule) is split in half
○ Becomes 2 pyruvate (3 carbon molecule)
○ Latter used in aerobic respiration (in mitochondria)
● 2 ATPs are made
●
If no O2 is available (intense exercise) anaerobic conditions:
○ Pyruvate stays in cytoplasm
■ Converted to waste product
■ Can be reconverted and be used aerobically
(once O2 is present)
● Explains shortness of breath after
exercise
■ Demand of O2 is oxygen debt
○ In humans
■ Pyruvate
Lactate (lactic acid)
○ In yeast
➡️
■
Pyruvate
➡️ Ethanol/CO
2
Aerobic respiration (krebs cycle + electron transport chain):
● Pyruvate is absorbed into mitochondria’s matrix (inner part)
● Goes through krebs cycle:
○ Broken down into CO2
○ Releases NADH2 and FADH2
● NADH2 and FADH2 go through electron transport chain (ETC):
○ NADH2 and FADH2 are oxidized/become NAD+ and FAD+
○ Energy released pumps H+ into cisternae (of mitochondria)
■ H+ goes back into matrix through ATP synthase
● Creates ATP (large amount)
○ H2O is a byproduct
●
Recap
○ Needs
■ Pyruvate (from glucose)
■ O2 as reactant
○ Creates
■ Lots of ATP
■ CO2 and H2O as waste product
Application of anaerobic respiration (in yeast):
● Bread making
○ Yeast consumes starches in flour (respires anaerobically)
○ Creates CO2
■ Makes bread rise
● Alcohol making
○ Yeast consumes sugars in fruit/grain (respires anaerobically)
○ Creates ethanol and CO2
■ Ethanol is the desired product
■ CO2 is kept (eg. beer & champagne) or escapes (eg. wine)
Cell respiration experiment:
Components of a respirometer:
1. Sealed glass tube (bell jar)
2. Alkali (soda-lime solution)
○ Absorbs CO2 produced
3. Capillary tube with fluid
● As organism respires, O2 is used
○ Volume decreases
○ Liquid is pulled up tube
●
■ This can be measured
All CO2 is absorbed
○ Does not affect volume
Animal use in experiments:
● If other methods are impossible
● If research is important
● No causing suffering
● No wild animals
● Use anesthetics/painkillers
2.9 - Photosynthesis
Photosynthesis uses the energy in sunlight to produce the chemical energy needed for life.
Early effects of photosynthesis:
● Started 3.5 billion years ago
● Oxygen (O2) levels
○ 0% at 3.5 billion years ago
○ 2% at 2.3 billion years ago
○ 20% 700 million (0.7 billion) years ago
● Evidence:
○ O2 and iron react in oceans
■ Forms iron oxide bands
■ Can be dated to measure O2 levels in the past
The process:
The process that plants, algae, and some bacteria use to produce all of the organic carbon
compounds they need.
●
●
Light energy splits H2O
○ Becomes O2 + H + e- (electrons/ions)
■ Hydrogen (H) is used to fix carbon (creating glucose)
note: This process (fixing carbon) requires energy from ATP
○ Called photolysis
Photosynthetic pigments absorb light ➝ create ATP (chemical energy)
○ Chlorophyll (green) is most common
■ Die first in the fall
○ Others are accessory pigments (fall colours)
Electromagnetic spectrum:
● 400nm - 525nm (blue)
○ Absorbed by chlorophyll
● 525nm - 625nm (green-yellow)
○ Not absorbed by chlorophyll
●
○ Absorbed by accessory pigments
625nm - 700nm (red)
○ Partly absorbed by chlorophyll
Chromatography:
● A technique used to separate mixtures
○ Chromatography paper is dipped in a solvent
○ Solvent moves up paper
■ Brings mixture with it
■ Separates mixture as it moves up
● Each pigment is represented by a Rf value
● 𝑅𝑓 =
𝑑𝑖𝑠𝑡𝑎𝑛𝑐𝑒 ∆ 𝑏𝑦 𝑝𝑖𝑔𝑚𝑒𝑛𝑡
𝑑𝑖𝑠𝑡𝑎𝑛𝑐𝑒 ∆ 𝑏𝑦 𝑠𝑜𝑙𝑣𝑒𝑛𝑡
Absorption vs. action:
Absorption spectrum (for chlorophyll):
Absorption spectrum (for all pigments):
Rate of photosynthesis variables (like enzyme concentration):
Light intensity:
CO2 levels:
Temperature:
Wavelength of light: