Module 2 - Maintaining Life Flashcards
How many amino acids are there?
20 amino acids
What is a codon?
Nucleotide triplet that codes an amino acid
What is a reading frame?
Reading frame = a way determining how the triplets are divided into consecutive, non-overlapping codons
-starts at the beginning of a codon (can be anywhere on RNA/DNA)
Concept of Frameshift Mutations
Frameshift Mutation occurs when the reading frame changes (due to addition/removal of nucleotides) leading to nonfunctional proteins or terminates protein synthesis
Start and Stop Codons
Start = AUG (methinione)
Stop = UAA, UAG or UGA
Genetic code degeneracy
Genetic code is degenerate meaning several codons can code for one amino acids
A cellular mechanism that reduces negative impacts of mutations
DNA Transcription
- occurs in the nucleus, transcribing DNA into RNA
- reason for transcribing long-lasting DNA into short-term RNA = protecting genetic code, DNA is too large, copies indicate more proteins
Initiation:
RNA polymerase binds to promoter sequence on the initiation site on DNA strand (anti-sense, 5’-3’)
RNA polymerase starts to unwind DNA helix
(in bacterial transcription: sigma factor is used to guide RNA polymerase where to bind. Sigma factor binds to a recognisable sequence that is always present before transcription site)
Elongation:
RNA polymerase runs along DNA strand bringing free nucleotides complimentary to the anti-sense strand (replica of sense strand)
Termination:
RNA polymerase reaches termination site and RNA polymerase + made RNA is released
Sigma factor positions
TTGACG = -35 region TATAAT = -10 region
DNA Translation
Initiation:
small subunit attaches to RNA then large subunit forming initiation complex
tRNA binds to start codon on P site of ribsome
Elongation:
Codon recognition by tRNA, next tRNA with anticodon attaches to next codon at A site
Peptide bond forms between two amino acids
Ribosome moves along RNA strand and tRNA at P site is released at E site
tRNA at A site gets shifted to P site
Termination:
ribosome reaches end codon
Release factor = anticodon (stop codon) binds in A site causing tRNA and the protein made in P site to break off and ribosomal units dissociates
What is tRNA
-transportational RNA
small folded RNA that have amino acid attachment site (CCA) and anticodon on opposite side (complimentary to codon)
What is ribsome
- rRNA
- consists of large and small subunit that dissociate when not active and reassociates during translation
Splicing of RNA from transcription to mRNA
Pre-mRNA contains all genetic information but introns must be spliced out
Only EXONS are kept (coding for proteins)
Caps are added to the start of mRNA to protect
5’ cap
Poly-A tail - adds a lot of A bases (~200) buffer to protect and protein can be recognized as mRNA to migrate from nucleus to cytosol
How does splicing occur?
Spliceosome = protein that brings together two exons together, cutting out the intron (must be very specific/precise)
Spliceosome is made up of RNA molecules called snRNAs and proteins
Promoter sections (eukaryotes, replacement of sigma factor)
Eukaryotes have transcription factors
- 1 promoter site per gene
- RNA polymerase II binds to transcription factors
What is electrical energy?
Energy from separation of charges
-different electrical gradients across cell membranes help drive the movement of ions
What is chemical energy?
Energy stored in chemical bonds
-energy stored in covalent bonds and released when broken by hydrolysis reaction
What is light energy?
Energy in a form of electromagnetic radiation stored as photons
-captured by pigments found in eye/chlorophyll photosynthesis
What is mechanical energy?
Energy of motion
-produced in muscle movement
What is heat energy?
Energy transference due to temperature change
- energy in the form of heat
- can be released in biochemical reactions, altering body temperatures
Definition of Metabolism
sum of all the chemical reactions occurring in a biological system at a given time
What is Gibb’s Free Energy (G)?
amount of energy available to work/use
Equation:
ΔG = ΔG (products) - ΔG (reactants)
If ΔG is greater than 0 = free energy is required for reaction (endothermic/endergonic)
If ΔG is less than 0 (negative) = free energy is released from reaction (exothermic/exergonic)
Catabolic reactions
break down of complex, large molecules into smaller, simple molecules (usually releases energy)
e.g. hydrolysis of maltose into glucose
Entropy INCREASES
Anabolic reactions
build up of smaller molecules to form larger, complex molecules (usually requires energy)
e.g. condensation/synthesis of sucrose from glucose + fructose
Entropy DECREASES
Laws of Thermodynamics
- No energy can be destroyed or created. Total amount of energy before a transformation is the same after.
- Total entropy in a closed environment always increases (NEVER decreases). After transformation in a closed environment, energy available to do work is always less than before.
Enzyme process
substrate binds to active site –> enzyme-substrate complex –> products
Enzymes rely on orientation, causing structure change due to physical straining or application of charges on products
ATP as energy
Consists of ribose, 3 phosphate groups and adenine
Bond between phosphate and oxygen (phosphate group) is relative unstable. Bond breakage of P-O is used for energy (very low activation energy)
ATP + H2O –> ADP + Pi + free energy
To synthesize ATP requires phosphorylation of ADP (requires energy)
Oxidation reactions
lost of electrons
Reducing agent = loses electrons
compounds that are more oxidised give off less energy
Reduction reactions
gain of electrons
Oxidising agent = gains electrons
Principles of oxidising glucose
- complex chemical transformations occur in a series of separate reactions
- each reaction is catalysed by a specific enzyme
- many metabolic pathways are similar in all organisms
- in eukaryotes, metabolic pathways are compartmentalised in specific organelles
- key enzymes can be activated or inhibited to control rate of reactions
ΔG of glucose oxidation = -686 kJ/mol
Oxidation in Glycolysis
1 molecule of glucose –> fructose 1,6-biphosphate –> 2 molecules of glyceraldehyde 3-phosphate
- requires 2 ATP
glucose is partially oxidised into pyruvate in the cytosol
products = 2 ATP and 2 NADH (10 metabolic reactions)
Pyruvate is further oxidised into acetyl CoA for citric acid cycle (krebs cycle)
products: NADH and CO2
Oxidation in Citric Acid Cycle (krebs cycle)
Acetyl CoA gets oxidised to form citrate (6C compound)
Definition of Chemiosmosis
converts electrical energy of proton concentration gradient to chemical energy in ATP
Oxidative Phosphorylation
ATP is synthesized by re-oxidation of electron carriers in the presence of oxygen
Occurs in Electron Transport Chain and Chemiosmosis
ETC:
electrons from NADH and FADH2 pass through a chain of membrane-associated proteins creating a proton gradient across the inner mitochondrial membrane
Proton motive force = potential energy created by the proton gradient
Chemiosmosis:
Electrons flow back across the membrane (down the concentration gradient) through channel ATP synthase
Overall products produced from aerobic respiration
36 ATP 10 NADH 2 FADH2 6 CO2 6 H2O
Redox reactions in Photosynthesis
12 H2O → 24H+ + 24e– + 6 O2
Oxidation of water (light reaction)
6 CO2 + 24 H+ + 24e– → C6H12O6 + 6 H2O
Reduction of carbon dioxide (light-independent reaction)
Light Dependent Reaction (photosynthesis)
-occurs in thylakoid lumen membrane (chloroplast)
- starts at photosystem II (P680) where light is absorbd by accessory pigments (chlorophyll a and b), causing electrons to be excited from ground state
- electrons get passed down ETC through primary electron acceptors (PQ - plastoquinone then PC - plastocyanin then ferredoxin)
- PQ passes excited electrons to PC through cytochrome reaching photosystem I (P700) + pumping in protons
- light excites electron once again and ferredoxin transports it to NADP reductase to form NADPH
1 ATP is produced at PQ and PC
Pumped in protons + made protons (from oxidation of water) is used at ATP synthase for Calvin cycle
Light-Independent Reaction (calvin cycle)
First stage: Carbon fixation
-RuBisCo fixes carbon dioxide onto ribulose 1,5-biphosphate (RuBP) forming a 6C compound (3-phosphoglycerate)
Second stage: Reduction
- 3-phosphoglycerate is reduced to glycerate-3-phosphate (G3P)
- G3P is reduced into two molecules of triose phosphate (using the reduced NADPH and ATP from light-dependent)
- 1 molecule of TP is put aside for production of glucose
- other molecule of TP is regenerated by accepting CO2 (using 3 ATP) to form RuBP (5C compound)
1 cycle involves 3 molecules of RuBP and 3 molecules of CO2 forming 6 molecules of 3-phosphoglycerate
Gluceogenesis
Formation of glucose from triose phosphate
Cyclic Phosphoryation
Occurs in light-dependent reaction when there is a lack of NADPH
- electron is passed to NADP reductase but returns to Photosystem I through ferredoxin
- allows protons to be pumped in = more ATP
Linkage of calvin cycle and krebs cycle (citric acid cycle)
Joined together by glycolysis and gluceogenesis
Examples of Catabolic Interconventions
-hydrolysis of polysaccharides into glucose (glycolysis)
-lipids are broken down into:
glycerol –> DHAP –> glycolysis
fatty acids - acetyl CoA –> krebs cycle
-proteins are hydrolysed into amino acids (glycolysis or krebs cycle)
Examples of Anabolic Interconventions
- Gluconeogenesis forms glucose from krebs cycle and glycolysis intermediates
- Acetyl CoA can be used to form fatty acids
Regulation of Metabolic Pathways
Negative feedback:
excessive produce of a product inhibits enzyme that catalyses its production (end-product inhibition)
Positive feedback: final product (compound) catalyses an enzyme to produce more of a specific compound
Glucose balance in humans
- glucose catabolism releases energy required by heart beat (cardiac cells) and releases through blood stream
- muscle produces lactate, liver can convert it into pyrvuate which is used in respiration (krebs cycle)
Disturbance of Glucose Transport
Insulin - beta cells of pancreatic islets
Glucagon - alpha cells of pancreatic islets
If glucose is required by the body, insulin is produced to take in glucose from food (converts glucose into glycogen)
Insulin receptor can be malfunctioned (type 2 diabetes)
OR
Insulin production can be malfunctioned (type 1 diabetes)
This leads to glucose unable to be used by cells in body + elevated levels in blood
Regulation through signals
Signals can affect cell’s function (e.g. rate of metabolic pathway)
Signal cascade = response to a signal spreads amongst cells
Signal Pathways
Signal transduction pathways include a signal, receptor and range of responses
(signal transduction pathway = set of chemical reactions that occur when receptor binds to signal)
- not all cells can respond to a signal (lacks receptors)
- signal can be chemical (glucose or damaging salt) or physical stimulus (light or temperature)
-cell must have specific receptor to detect the signal (may require enzymes or transcription factors)
Types of Receptors
Intracellular receptors = located inside the cell (interacts with both chemical and physical signals)
Membrane receptors = large or polar ligands (e.g. insulin) binding to cell receptors
(ligand = substance that forms a complex with a biomolecule)
3 types of membrane receptors:
Ion channel receptors - allows ions to leave or enter cell (e.g. acetylcholine receptor)
Protein kinase receptor - catalyses phosphorlation of itself or of another protein (e.g. insulin receptor phosphorylates itself + other proteins to begin converting/transport of glucose)
G Protein-linked receptor - signal binds to a G protein, activating an effector protein
Chemical signal types
Autocrine = signals affecting the cells that released them
Juxtacrine = signals affecting adjacent cells
Paracrine = signals affecting nearby cells
Hormones = signals affecting distant cells, travels to destination (usually by circulatory system)
