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Topic 2: Molecular Biology Pt.2 - Coggle Diagram
Topic 2: Molecular Biology Pt.2
Catalysis
An enzyme is a globular protein which speeds up the rate of chemical equation b lowering the activation energy, they are not consumed by the reaction and can be re-used
The molecule the enzyme reacts with is called the
substrate
, which binds to a complementary region on the enzyme's surface called the
active site
.
Specificity
Lock and key model:
Enzyme and substrate complement each other precisely in terms of both their shape and chemical properties
The active site and the substrate will share specificity.
Induced fit model:
active site is not rigid fit for the substrate and changes its conformation to better accommodate the substrate
This stresses the substrate bonds and induces catalysis
Enzyme kinetics
The rate of enzyme catalysis can be increased by increasing the frequency of enzyme-substrate collisions
The rate of enzyme catalysis is decreased by denaturation
Industrial enzymes
Immobilized enzymes are often used in industrial practices
They are fixed to a static surface to prevent enzyme loss
This improves separation of product and purity of yield
One application for immobilised enzymes is the production of lactose-free milk and associated dairy products
Lactase (enzyme) digests lactose into glucose/galactose
Lactase is fixed to an inert surface
Milk is passed over this surface to become lactose free
There are several benefits associated with lactose-free milk:
Provides a source of diary for lactose-intolerant people
Increases sweetness of milk (Less need for sweeteners)
-Reduces crystallization and production times for cheese
Factors affecting enzyme activity
Temperature:
-Increases enzyme activity (more kinetic energy = more collisions)
-Enzyme activity peaks at an optimal temperature
Higher temperature decrease activity (causes denaturation)
pH -
Enzyme activity is highest at optimal pH range
Activity decreases outside of this range (due to denaturation)
Substrate concentration:
Increases enzyme activity (more particles = more collisions)
At a certain point, activity plateaus (saturation of active site)
Nucleic acids
The monomer of a nucleic acid is called a nucleotide
Each nucleotide consists of 3 basic components:
A pentose sugar
A phosphate group
a nitrogenous base
Nitrogenous bases
Each nucleotide possesses 1 of the 5 different nitrogenous bases:
Adenine
Guanine
Cytosine
Thymine
Uracil
Bases may either be purines (A,G) or pyrimidines (C,T,U)
T is present in DNA, whereas U is present in RNA
Polynucleotide formation
Nucleotides are linked together into a single strand via condensation reactions (between 5'-phosphate and a 3'-hydroxyl group of adjacent nucleotides)
This polynucleotide arrangement results in the formation of a sugar-phosphate backbone that is covalently linked together by phosphodiester bonds
DNA structure:
2 complementary strands line up in opposite directions (anti-parallel) with the bases facing inwards and connected by hydrogen bonds (G - C and A - T)
The double stranded molecule then twists in order to adopt a more stable energy configuration - a double helix
RNA structure:
The polynucleotide chain remains single stranded, but may fold upon itself to form double stranded motifs
DNA vs RNA
DNA and RNA are both polymers of nucleotides, however they differ in a few key structural aspects
DNA:
Sugar is deoxyribose
Has thymine (T) along with A,C and G
Is double stranded and forms a double helix
RNA:
Sugar is ribose
Has uracil (U) alng with A,C and G
Is single stranded
Watson and Crick
The structure of DNA was elucidated by Watson and Crick in 1953
Using data from previous scientific experiments they developed a DNA model that demonstrated:
A double helix structure composed of anti parallel DNA strands
Internally facing bases with complementary pairing (A-T and G-C)
Semi-conservative
DNA replication is semi-conservative - 1 strand is from an original template molecule and one strand is newly synthesised, this occurs because each base will only pair with it's complementary partner and then ensures the sequence is conserved
DNA replication
Helicase:
Unwinds and seperated the double stranded DNA
Breaks the hydrogen bonds between the base pairs
DNA polymerase III:
Free nucleotides line up opposite complementary partners
DNA pol III covalently joins the dree nucleotides together
Melselson-stahl experiment
The meselson-stahl experiment supported the theory that DNA replication occured via a semi-conservative process
They incorporated radioactive nitrogen isotopes into DNA:
Templates were prepared with heavier 15N
New sequences were replicated with lighter 14N
The DNA was then seperated via centrifugation in order to determine it's composition of radioisotopes:
1st division: DNA had 15N and 14N
2nd division: DNA is mixed or has 14N only
Polymerase chain reaction
The polymerase chain reaction (PCR) is an artificial method of DNA replication that is used to rapidly copy sequences
PCR occurs in a thermal cycler over 3 repeating steps:
Denaturation: DNA heated in order to seperate strands
Annealing: Primers attach to ends of a target sequence
Elongation: A heat-tolerant polymerase copies strands
A standard reaction of 30 cycles would generate more than a billion copies of the target DNA sequence
Transcription
Transcription is the synthesis of an RNA sequence from a DNA template, occurs within the nucleus of a cell
Transcription is mediated by the enzyme RNA polymerase, which:
Seperates the DNA strands (breaks the H bonds between base pairs)
Covalently joins free complementary RNA nucleotides together
After transcription, the RNA is released to the cytoplasm for translation and the DNA remains within the nucleus and reforms a double helix
Types of RNA
3 main types of RNA may be produced:
mRNA - Transcript used to make protein
tRNA - Transfers amino acid to ribosome
rRNA - Catalytic component of ribosome
Genetic code
The genetic code is the set of rules by which information encoded in mRNA sequences is converted into a polypeptide sequence
Codons - triplets of bases which correspond to a particular amino acid
The order of the codons determines the amino acid sequence for a protein
A coding sequence always begins with a START codon (AUG)
-A coding sequence is terminated with a STOP codon
The genetic code has 2 key features:
Universality - All organisms use the same genetic code
Degeneracy - Multiple codons may code for the same amino acid
Translation
Translation is the process of polypeptide synthesis by the ribosome:
Messenger RNA (mRNA) is transported to the ribosome
A ribosome reads an mRNA sequence in base triplets called codons
Each codon codes for a specific amino acid (as oer the genetic code)
Amino acids are transported to ribosomes by transfer RNA (tRNA)
-Each tRNA aligns opposite a codon via a complementary anticodon
The ribosome moves along the mRNA sequence (5' - 3') and joins amino acids together with peptide bonds (condensation reaction)
The synthesis of a polypeptide is intiated at a start codon and is completed when the ribosome reaches a stop codon
Gene - Protein
A gene is a sequence of DNA which encodes a polypeptide sequence
1 gene = 1 polypeptide (proteins may have multiple polypeptides)
There are exceptions to this fundamental relationship:
Genes may be alternatively spliced (1 gene = many polypeptides)
Genes encoding tRNA or rRNA are transcribed but not translated
Genes may be mutated to alter the original polypeptide product
Cell respiration
Cell respiration is the controlled release of energy from organic compounds to produce ATP
The main organic compounds used are carbohydrates but lipids or proteins can also be used
Different organic compounds will have distinct breakdown pathways and so ave varied ATP yields
ATP
ATP (adenosine triphosphate) is a molecule that functions as an immediate source of energy when hydrolysed (to form ADP)
Gylcolysis
Cell respiration begins with the break down of glucose via a process called glycolysis, occurs in the cytosol
Glucose is broken down into pyruvate (x2)
There is a small ATP yield (net gain = 2 atp)
Requires the reduction of NAD+ (to form NADH)
Anaerobic vs aerobic respiration
Pyruvate from glycolysis will follow one of the 2 pathways:
Anaerobic respiration:
Occurs in the cytosol and does not require oxygen
Results in a small energy yield (2 ATP from glycolysis)
Forms lactic acid (animals) or ethanol and CO² (plants/yeast)
Also known as fermentation and is reversible
Aerobic respiration:
Occurs in the mitochondria and requires oxygen
Results in a large energy yield (36 ATP per glucose)
Forms carbon dioxide and water
Use hydrogen carriers to make ATP (oxidative phosphorylation)
Fermentation
Fermentation is a reversible anaerobic process that allows ATP production to continue in the absence of oxygen
Fermentation restores NAD+ stocks (needed in glycolysis) to ensure a continued production of ATP (by glycolysis)
Fermentation in animals produces lactic acid, and is used to maximise muscle contractions when oxygen is limited, this reaction can be reversed when oxygen is restored
Fermentation in plants and yeast produce ethanol and CO² gas which can be used in baking, also for production of alcohol, yogurts and cheese
Respirometry
A respirometry determines an organism's respiration rate by measuring either carbon dioxide production or oxygen uptake, commonly used for invertebrates or germinating seeds
A simple respirometry may involve the use of a manometer:
An organism is sealed in a container with a CO² absorbant
Oxygen uptake creates a pressure change which displaces the fluid in the manometer allowing for quantitation
Photosynethesis
Photosynthesis involves the use of light energy to synthesise organic compounds from inorganic molecules
6CO² + H²O ---Light----Chlorophyll-----C6H12O6 + 60² + 6H²0
Light spectrum
Visible light has a range of wavelengths (400-700 nm)
Violet has the shortest wavelength and red has the longest
Light absorption
Pigments are required for the conversion of light energy into chemical energy in photosynthetic organisms
Chlorophyll is the main photosynthetic pigment, although other accessory pigments also exist, chlorophyll absorbs red light and blue light most effectively and reflects green light more than other colours
Stages of photosynthesis
Light dependent reactions - light energy is converted into chemical energy:
Light is absorbed by chlorophyll to produce ATP
-The photolysis of water forms oxygen and hydrogen
Light independent reactions - carbon compounds are made from the chemical energy:
ATP and hydrogen are fixed with carbon dioxide
-This results in the formation of organic molecules
Chromatography
Pigments can be seperated by chromotography:
Pigments are dissolved in fluid
The fluid is passed through a static material
Pigments are seperated according to size
A retardation force (RF value) is calculated by distance of pigment/ distance of solvent
Limiting factors
When a process depends on more than one condition, the rate will be limited by the factor nearest its minimum value
Limiting factors in photosynthesis include:
Temperature
-Light intensity
Carbon dioxide concentration