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200 Cards in this Set
- Front
- Back
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Cytosol, highly concentrated solution containing... |
Enzymes and the RNA molecules that encode them Amino acids amd nucleotides from which the macromolecules are assembled Hundreds of metabolites, intermediates in biosynthetix and degradative pathways Coenzymes, compounds essential for enzyme-catalyzed reactions Inorganic ions Ribosomes, small particles composed of protein and RNA; the sight of protein synthesis |
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Eukaryotes vs Prokaryotes |
Eukaryotes - have nuclear envelopes Prokaryotes - lack nuclear envelopes (eg bacteria) |
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Endomembrane System |
Segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reactions can occur Make use of exocytosis and endocytosis |
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Exocytosis vs Endocytosis |
Transports out of and into cells respectively, involving membrane fusion and fision |
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Fision vs Fusion |
Fision - splitting Fusion - joining |
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Proteins |
Large polymers of amino acids which function as enzymes, receptors, transporters or structural elements |
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Polysaccharides |
Polymers of simple sugar, such as glucose, which serve as energy-yielding fuel stores Extracellular structural elements with specific binding sites for particular proteins |
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Lipids |
Structural components of membranes Energy rich fuel store Pigments Intracellular signals |
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Stereoisomers and Enantiomers |
Stereoisomers - molecules with the same chemical bond but different configuration Enantiomers - mirror image stereoisomers |
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Ribosomes |
Protein synthesis |
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Cytoskeleton |
Gives cell shape and enables molecular transport within the cell |
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Lysosomes |
Degredation of excessive or old organelles and destroys intracellular pathogens |
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Golgi Complex |
Transporting, modifying and packing proteins and lipids into vesicles for delivery to targetes destinations |
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Rough and Smooth ER |
Rough - synthesis and export of proteins Smooth - synthesis of hormones and lipids |
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Nucleus |
Storage and replication of genetic material |
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Peroxisomes |
Degradation of fatty acids |
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Mitochondria |
Cellular respiration and energy production |
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Plasma Membrane |
Regulates transport of substances in and our of the cell |
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Endogenous vs Exogenous |
Endogenous - inside the cell organism Exogenous - outside the cell or organism |
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Covalent and Ionic Bonds |
Covalent - sharing of electrons Ionic - complete transfer of electrons, generally between a metal and a non-metal |
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Polar and Non-polar Bonds |
Polar - bonds with a net charge Non - bonds without net charge. Eg C-H or bonding to same element |
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Hydrogen Bonds |
Provide cohesive forces that make water liquid at room temperature Give water a higher melting and boiling point |
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Enthalpy |
Heat absorbed or released in a reaction |
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Entropy |
Randomness in system |
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Gibbs free energy = |
Free energy = Change enthalpy - (temp. x change in entropy) Change in free energy = -Gas constant x temperature x ln Keq |
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Clathrates |
Crystalline compounds of nonpolar solutes and water |
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Micelles |
Stable structures of amphipathic (compounds that contain polar regions of molecules together) compounds in water |
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Hydrophobic Interactions |
Forces that hold nonpolar regions of molecules together Result from thermodynamic stability by minimising number of ordered water molecules required to surround hydrophobic portion |
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van der Waals Interactions |
Interactions between two uncharged atoms, random variations in electron positions may create transient electric dipole, inducing an opposite dipole in the nearby atom |
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Colligative Properties |
Influenced by solutes Include vapour pressure, boiling point, melting point and osmotic pressure |
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Bond Energy |
Energy required to break one mole of bonds |
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First Law of Thermodynamics |
In any physical or chemical change, the total amount of energy in the universe remains constant, although the form of energy may change |
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Endergonic vs exergonic |
Endergonic - thermodynamically unfavourable, energy requiring Exergonic - releases energy |
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Anabolism vs Metabolism |
Anabolism - requires input of energy Metabolism - generates energy |
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Protein Structures |
Primary - amino acid and residue sequence Secondary - d-helix and Beta Sheet Tertiary - fold-pathway backbone Quartery - association of monomer proteins with one another |
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Semiconservative Replication |
Each DNA strand serves as a template for the synthesis of a new strand, producing two new DNA molecules, each one with new and old strand |
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Replication Forks |
Parent DNA unwound so seperated strands can be replicated quickly |
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Leading and Lagging Strand |
Leading - synthesis occurs in the same direction as the replication fork 5'-3' Lagging - synthesis occurs in 3'-5' and us synthesised into pieces called Okazaki Fragments |
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Nucleases and DNases |
Nucleases - enzymes that degrade DNA or RNA rather than synthesise it DNases - enzymes that degrade DNA only |
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Exonucleases and Endonucleases |
Exonucleases - degrade nucleic acids from one end of the molecule (5' or 3'). Can proofread from 3' end Endonucleases - degrade at specific internal sites in a molecule, reducing it to smaller fragments |
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DNA Polymerase 1 |
Single-polypeptide from E. Coli cells Removes primer from 5' end of Okazaki Fragment, replacing it With DNA nucleotides |
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Primer |
Strand complementary to template with a free 3' hydroxyl group to which a nucleotide can be added Can be made from DNA or RNA but is always singlestranded RNA - made by primase for DNA replication DNA - made in DNA synthesis machine for PCR |
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DNA Polymerase 3 |
From e. Coli Synthesises nucleotide continuously as both strands from 5'-3' |
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Topoisomerase |
Relieves accumulated winding strain generated during the unwinding of the helix |
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Helicases |
Enzymes that move along the DNA and seperate strands using chemical energy from ATP |
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Primases |
RNA synthesised by enzymes that act as a template for Okozaki Fragments |
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DNA ligases |
Seal DNA cuts, bond 3' end of one Okazaki Fragment to the 5' end of another |
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Primesome |
DnaB helicase and DnaG primase constitute a functional unit within the replication complex |
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Replisome |
Responsible for coordinated DNA synthesis at a replucation fork |
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DNA Structure |
Nitrogen-containing base, phosphate, and a deoxyribose sugar DNA backbone composed of alternating sugar and phosphate units |
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OriC |
Origin of replication, bacteria contain one, eukaryotes contain multiple |
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DnaA |
Protein that activates initiation of DNA replication in bacteria |
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DnaB |
Helicase that unwinds DNA template to allow replication |
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DnaC |
Loading factor for DnaB helicase |
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PCR Primer Rules |
Optimal length between 18-28 bases GC content should be between 50-60% Melting temperature should be between 50-70°C where Tm = 4(G + C) + 2(A + T) GC clamp should be present at the 3' end of primer, however no runs of threes near the end |
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Promoters |
Double stranded DNA, where RNA binds to promoter to produce RNA. |
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Transcription vs Translation |
Transcription - DNA -> RNA, requires DNA-dependent RNA polymerase, which uses DNA as a template for transcription to make a complementary RNA strand Translation - RNA -> protein, requires ribosome, mRNA and tRNA, where ribosomes are complexes of rRNA molecules and proteins that act as enzymes to catalyse |
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Reverse Transcription |
RNA -> DNA, requires RNA-dependent DNA polymerase, an enzyme used to generate complementary DNA (cDNA) from RNA template in a process termed reverse transcription |
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Mutations |
Frame Shift - insertion or deletion of one base, altering sequence of triplets Point - single base is altered Nonsense - results in premature stop codon Missense Mutation - point mutation which causes change in amino acid expression |
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RNA Polymerase |
In eukaryotes, with transcription factors, synthesised new strands 5'-3' direction by incorporaring ribonucleotides in the toung polynucleotide chain |
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Alcohol Hemiacetal Reactions |
Basis for the formation of glycosidic bonds OH of one monomer condenses with intramolecular hemiacetal of another monomer with elimination of water Hydrolysis is the reverse reaction |
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Disaccharides |
Consist of two monosaccharide units linked by a glycosidoc bond between anomeric carbon of one and an OH group One product of a glycosisic bond formation |
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Sucrose |
Disaccharide where both anomeric carbons have been used in the glycosidic bond |
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Amylose |
Key component of starch, major carbohydrate storage polymer in plants Amylopectin is the other major component |
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Glycogen and Starch |
Major carbohydrate storage in animals Starch for plants |
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Carbohydrates |
Have the capacity to bond to one another in multiple different configurations Generates structural and functional diversity, through glycosidic linkage being either a or B anomeric, different hydroxyl C positions of adjacent monosaccharide and branching capacity of oligosaccharide chains Carbohydrate structure depends on proteins that can distinguish different structure Can be covalently linked to protein to form glycoprotein or lipid to form glycolipid |
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Polysaccharides |
Subunits, length and linkages are highly Subunits of sugar polymers can be homo or hetero polysaccharides Length not defined by template, rather presence and activity of enzymes |
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Glycoconjugates (eg glycoprotein or glycophingolipids) |
Protein or lipid covalently linked to a sugar Sugar exhibits great diversity of oligosaccharide configuration based on glycoid linkages beong alpha or beta anomers Give rise to high number of glyco topologies that contruct sugar code Glycans displayed on molecules and act as police or postcodes |
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Glycosylation |
Occurs in lumen of ER and Golghydrophilic sugars alter polarity and solubility of attached proteins, altering protein structure
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Sugar Code |
Read by dedicated proteins called lectin Mediates cell-cell interactions Recruits protein partners to a location |
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D-isomers and L-isomers |
D-isomers - Carbohydrate isomers that have the same configuration at the chiral centre that is most distant from the carbonyl carbon oberserved in D-glyceraldehyde L-isomers - oberserved on L glyceraldehyde instead |
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Pyranoses and Furanoses |
Pyranoses - monosaccharides with six atoms in the ring Furanoses - five atoms in the ring |
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Extracellular Matrix |
ECM - gellike matrix composed of heteropolysaccharides and fibrous proteins including collagens, fibronectins and elastins |
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Saturated vs Unsaturated |
Saturated - only single bonds Unsaturated - at least one double bond |
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Crystalisation of D-fructose |
Occurs through oxygen within hydroxyl group(nucleophile) bending to carbon in carbonyl group(electrophile) to form a hemiketal(fructofuranose) |
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Glycosidic Bond |
Reaction to hemiacetals and hemiketals with another molecule containing alcohol group, resulting in formation of a full acetal or ketal |
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Lactose |
Natural disaccharide in milk Two B-D-glucose joined by Bl-4 glycosidic bond |
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Sucrose |
Most common disaccharide Linkage at glucose Cl and B linkage at fructose C2 |
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Trehalose |
Bactera, fungi, plant, invertebrate source of energy, can be used as a sweetener Two a-D-glucose joined by al-l glycosidic bond |
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Chitin |
Linear polymer of N-acetylglucosamine residues linked by Bl-4 glycosidic bonds |
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Lectins |
Protein that binds to carbohydrates with high specificity and affinity |
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Proteoglycans |
Major component if ECM, locayed on cell surface Consists of glycosaminoglycans covalenty joined to membrane or secreted protein |
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Partial Hydrogenation |
Converts many cis carbon-carbon double bonds to single bonds, increasing melting temperature |
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Glycerophospholipids |
Membrane lipids with two fatty acids attached by ester linkage to 1st and 2nd glycerol, and a phosphodester linkage to polar group 3rd carbon |
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Sphingolipids |
One polar head, two non polar tails Maid of ceramide |
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Sphingomyelins |
Contain phosphocholine or phosphoetanolamine Predominantly present in myelin in neurons |
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Gangliosides |
Complex sphingolipids that have oligosaccharides as polar groups and one or more residues of sidic acid at termini |
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Sterols |
Steroid nucleus consisting of four fused rings and is rigid Cholesterol is the main sterol in animals |
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Membrane Rafts |
Proteins anchored to membrane by two long-chain fatty acids within glycosphingolipids Glycosylphosphatidylinositol(GPI)-anchored proteins attached to polar head group within glycosphingolipids |
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Cavedin |
Integral membrane protein with two globular domains linked by hairpin-like hydrophobic domain, anchoring protein to membrane Forms dimers with cholesterol-rich regions which behave as membrane rafts |
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Cholesterol |
Decreases membrane fluidity at high temperatures and increases at low temperatures |
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C-terminus |
Where new amino acid residues are added |
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N-terminus |
First residue due to ATG start codon |
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Peptide Bond |
Inflexible and planar Similar length bond as double bond |
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Ramchandran Plot |
Dark regions highly energetic, white has very little energy |
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B-Sheet |
Made of B-strands bonded by hydrogen bonds |
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Antiparallel |
Straighter bonds alternate long and short |
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Water Dissociation |
Creates hydrogen (H+) and hydroxide (OH-) ions Hydrogen ion associates with water to create a hydronium (H3O+) ion H2O + H2O <-> H3O+ + OH- |
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Acids vs Bases |
Acids - can donate a proton or accept an electron pair Bases - can accept a proton or donate an electron pair |
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Buffer Solution |
Weak acid and conjugate base |
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Ka, pKa and pH |
Ka = [A-][H+] / [HA] Strong Acids - High Ka Weak Acids - Low Ka pKa = -log Ka Strong Acids - Low pKa Weak Acids - High pKa pH = pKa + log [A-] / [AH] |
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Amino Acid |
Building block of proteins and peptides All have amino(NH3+) group, carboxyl(COO-) group, and a hydrogen atom attached to alpha-carbon |
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Isoelectric Point |
pH at which amino acid has no net charge |
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Polarity and Charge |
Non-Polar - mostly or compleyely made of C and H atoms Polar - contains uncharged NH2, OH or SH atoms + Charge - contains charged amino group - Charge - contains charged carboxyl group
Aromatic - contaons benzenering structure |
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Disulfide Bonds |
Covalent bonds derived from thiol groups Cysteine amino acid can form these bonds |
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Isoelectric Focussing |
Matrix contains pH gradient through which protein moves until pH equals the isoelectric point |
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Antiparallel Beta Sheets |
Side chains located on different sides of the sheet Doesnt alternate side chains above and below |
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Tertiary Structure |
Overall 3D structure of atoms |
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Quaternary Structure |
Only proteins with multiple side chains Describes protein chain coming together to form a mult-subunit complex |
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Fibrous Proteins |
Polypeptide chains arranged in long strands Insoluble in water due to high concentration of hydrophobic amino acids Usually have single type of secondary structure Provide strength and flexibility |
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Collagen |
Fibrous proteins found in connective tissue Most abundant protein in mammals Unique secondary structure, collagen triple helix, consists of three polypeptide chains |
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Globular Proteins |
Polypeptide chains folded into spherical globular shape Mainly soluble in water and contain several types of secondary structure Vast majority of enzymes and regulatory proteins Quaternary structure present with only one protein chain |
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Myoglobin |
Manomeric globular protein in muscles Single polypeptide chain Tertiary structure of 8 alpha helicies separated by loop regions |
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Proteostasis |
Collectuon of processes responsible for maintaining structure and function Includea protein synthesis, folding, refolding, trafficking, and degradation |
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Denaturation |
Protein loses 3D shape due to loss of secondary, tertiary and quaternary structure Caused by heat, pH, or chemicals like alcohol |
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Misfolded Proteins |
Aggregste and form toxic species Marked for degredation in proteasone by atrachment of ubiquitin Undergo assisted refolding with help of molecular chaperones |
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Anfinsen's Paradigm |
Native structure of protein encoded in primary structure Globular proteins denatured by extreme environmental conditions able to spontaneously return to native fold when conditions return to normal |
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Protein Folding Entropy |
Protein entropy decreases, surrounding water solvent entropy increases |
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Levinthal Paradox |
Protein folding not a random trial and error process Local formations of hydrogen and salt bridges drive folding Amino acids within protein chain unable to access entire conformational space resulting in faster protein folding than expected Weak interactions limit conformational space Assumes each residue acts independently of each other |
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Unfolded State |
High confirmational entropy and high free energy Available conformational space rapidly reduced by hydrophobic collapse and local formation of secondary structure |
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Molecular Chaperones |
Specialised protein which helps protein folding Requires ATP Doesn't promote folding, rather prevents aggregation through binding exposed hydrophobic regions |
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Hsp 70 |
Heat shock protein family which promoted ATP hydrolysis Synthesis increased by stress of high temperatures Assist unfolded or partially folded proteins into native conformation Requires 1 ATP Can eject ADP and bound protein with helo from NEF |
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GroEL/GroES |
Large chaperone complex in ecoli Requires single ring co-chaperones GroES and 7 ATP molecules to function GroES binds GroEL in presence of ATP to allow chaperon to bind misfolded or unfolded protein |
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Partially Folded |
Prone to formong toxic aggregates such as soluble oligomers and fibrilliar amyloid deposits |
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Prion Protein (PrP) |
Causative agent of prion disease (eg mad cow disease) , a failure of chaperones to rescue misfolded proteins |
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Unfolded Protein Response |
Activates transcription regulators to increase concentrations of molecular chaperons in ER and/or decrease rate of protein synthesis |
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Alzheimer's Disease |
Accumulation of extracellular amyloid deposition by neurons, forming amyloid plaques, causing neural death Amyloid-B protein produced by cleavage of amyloid-B precursore protein Amyloid-B misfolding causes accumulation of protein, formong amyloid aggregates, which deposit in the brain |
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Parkinson's Disease |
Misfolding protein is alpha-synuclein which aggregates into filamentous masses called Lewy bodies Accumulation of Lewy bodies causes progressive neurdegeneration |
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Huntington's Disease |
Huntington protein is misfolded amd aggregated into fibrillar aggregates Frameshift mutation causes long polyglutamine |
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Protein Catalysts |
Subject to denaturation, contributes to pH and temperature optimisation Active Site: definied AAs in site, defines selectivity towards substrate, can contribute to reaction mechanism (AAs define structure and function) |
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Pro-protein vs Apo-protein |
Pro - Non-functional precursor activated by proteolysis Apo - without bound cofactor/coenzyme (prosthetic group) - with bound cofactor/coenzyme (holoenzyme) |
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Vmax |
Maximal reaction rate that can be achieved by a fixed amount of enzyme with a large excess of substrate (dependent on amount of enzyme) |
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Km (Michaelis Constant) |
Concentration of substrate at which half Vmax is reached Indicates affinity the enzyme has for the substrate |
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Kcat |
Number of substrate molecules that can be converted to product by one enzyme molecule in 1 second Gives indication of effectiveness of enzymes as a catalyst |
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Ka and Kd |
Ka - association Kd - dissociation Ka = 1 / Kd The lower the dissociatiom constant, the tighter the bond |
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Rate of Reaction Equation |
Rate of Reaction (k) = [Boltzmann Constant(k) x Temperature(T) / Planck's Constant] x e ^ -ΔG / RT |
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Cofactors |
Inorganic ions such as Fe2+ or Zn2+ |
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Enzyme-Substrate Complex |
Stabilised by weak interactions Limitation to mobility increases probability of collision between enzyme and substrate |
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Ka and Kd when E + S <--> ES |
Ka = [ES]eq / [E]eq [S]eq Kd = [E]eq [S]eq / [ES]eq |
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Acidic Amino Acids vs Basic Amino Acids |
AAA - in COOH form (unchanged) at low pH and COO- form (-1 charge) at high pH pH = pKa + log [A-] / [HA] BAA - in NH3+ form (+1 charge) at low pH and NH2 form (unchanged) at high pH pH = pKa + log [B] / [BH+] |
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Chromatography |
Negative bonds in cation exchange resin binds positively charged proteins Positvive bonds in aniom exchange resin binds negatively charged proteins |
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Enzyme Limited Mobility |
Helps enzymes collide with substrate Colocalisation of enzymes and their hydrophobic substrates in membranes allows 2D vs 3D scanning Colocalisation of sequential enzymes in a pathway increaaes metabolic flux Processivity - many enzumes that act on DNA or RNA have a clamo thag holds them to the template and prevents rapid dissociation |
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Protein Function determined by... |
Interactions with other molecules |
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Fraction of Binding Sites Occupied |
= [PL] / [PL] + [P] = ΔA / ΔAbsmax Asumption - if [P] << [L], concentration of binding sites is much lower than concentration of ligand, meaning [L]free ~ [L]total and either can be used |
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Scatchard Analysis |
Ka = [PL] / [P][L] = k / (k - 1) = 1 / k |
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Nucleophiles and Electrophiles |
Nucleophiles - functional groups able to donate or share electrons Electrophiles - functional groups that seek electrons Interaction between the two forms a covalent bond (sharing) |
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Source and Sink |
Source - negatively charged Sink - positively charged |
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Lock and Key Model |
Substrate fitted into enzyme perfectly |
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Induced Fit Model |
Substrate triggers conformational change in enzyme that brings substrate closer to transition state |
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Conformation Selection / Stabilisation Model |
Multiple natural enzyme conformations exist in the absence of the transition state Binding of substrate to one shifts distribution of conformers to that form |
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Free Energy |
Whether a reaction is possible, not probability of reation occurring |
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Kinetic Stability |
Reaction so slow it can not be observed A reaction can be spontaneous and kinetically stable |
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Kinetics vs Thermodynamics |
Kinetics - rates Thermodynamics - possibility |
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Transition State |
High Energy State May require removal or water from environment or physical distortion to achieve |
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Desolvation |
Removing solvent (water) from the environment increases chance of the reaction occurring Water interferes with biochemical reactions by providing competing for interest side chain interactions Non polar environments created by enzymes through hydrophobic amino acids increases chance of reaction Active sites of enzymes generally deep inside protein where solvent is limited. Binding of substratr causes conformationak change and forces water out |
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Acid-Base Catalysis |
Any mechanism involving transfer of a proton Enzymes can use both conjugate acids and bases concurrently |
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Covalent/Nucleophilix Catalysis |
Nucleophilic side chain attscks electrophil centre in substrate to form covalent intermediate, which is attacked by a low molecular weight nucleophile to generate product |
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Electrostatic Catalysis |
Charhed grouo on enzyme stabilises transition state, or an intermediate close to transition state carries opposite charge |
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Electrophilic Catalysis |
Positive charge serves as an electron sink and axtswas a catalytic electrophile Often involves metal ions as cofactor |
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Enzymes Activation Energy |
Enzymes lower activation energy by binding to substrate and product Entropy of substrates generally reduced when bound by enzyme Entropy also reduced due to reduction in randomness in substrate movement |
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Competitive Inhibitor |
Reversible Ligand resembles substrate and interacts with enzymes, blocking its use On Lineweaver Burk Plot, lines cross-over on y-axis |
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Uncompetitve Inhibition |
Reversible Inhibitor binds to ES complex, not competing with substrate On Lineweaver Burk Plot, lines cross-over on x-axis |
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Noncompetitive Inhibition |
Reversible Can bind to ES complex or substrate On Lineweaver Burk Plot, lines don't cross-over |
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Irreversible Inhibition |
Permanently bloxk or destory enzyme ability to catalyse reaction, usually by binding covalently to enzyme, but can also turn the inhibitor over |
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Hexokinase |
Hexokinase - Catalyses first step in glycolysis, breakdown on glucose as an energy store dor the cell Hexokinase 1 and 2 - in muscle cells, low km enzymes, can break down glucose for energy even when it is in short supply Hexokinase 4 - respond directly to change in blood, depending on what is needed |
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Enzyme Regulation |
Extracellular signals Transcription of specific gene(s) mRNA degradation mRNA translation on ribosome Protein degradation (ubiquitin proteosomes) Enzyme sequestered in subcellular organelle Enzyme binds substrate or ligand Enzyme undergoes (de)phosphorylation Enzyme combines with regulatory protein |
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Phosphofructokinase (PFK) |
Key regulatory enzyme in glycolysis Regulated by multiple allosteric effectors and is both inhibited and activated |
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ATP |
Limited fixed pool (like NADH) Ratio indicates energy available Metabolic regulator |
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Glycolytic Pathway |
First steps in breaking down glucose Creates NADH Consumes and creates ATP |
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Flux and Pools |
Flux - amount of flow along a pathway, determined by input, output and activity of enzymes Pool - amoint of molecules, filled and emptied by pathways, sometimes fixed |
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Prepatory and Payoff Phase |
Prepatory Phase - use of energy Payoff Phase - everything occurs twice |
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Pyruvate |
Pyruvate to lactic acid (lactate) if oxygen is absent or unavailable Pyruvate to ethanol in yeast if oxygen is not present |
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Lactate Dehydrogenase (LDH) |
Tetrameric enzyme catalyses inter-conversion of pyruvate and tactate Regenerates NAD+ in anaerobic glycolysis |
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Citric Acid Cycle |
Can play a role in catabolic or anabolic, making ot amphabolic, but only catabolic is needed for this course |
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Citric Acid Cycle Input |
2-carbon acetyl group from Acetyl-CoA Acetyl group and 4-carbon oxaloacetate from citrate is used in the first step of glycolysis |
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Citric Acid Cycle Step 2 |
Reactions catalysed by citrate synthase, isocitate dehydrogenase and a ketoglutarate dehydrogenase complex, essentially irreversible, ensuring cycke turns in one direction only |
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Citric Acid Cycle Step 3 |
Reactions catalysed by isocotrate dehydrogenase and alpha-ketoglutarate complex both produce CO2 net loss 2 carbons, balancing 2-carbon input from Acetyl-CoA (not the same carbons) |
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Citric Acid Cycle Step 4 |
Reactionw catalysed by isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex, and malate dehydrogenase produce NADH |
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Citric Acid Cycle Step 5 |
Reaction catalysed by succinate dehydrogenase which harvests electrons in the form of FADH2 |
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Citric Acid Cycle Final Step |
Reaction catalysed by succinyl-CoA synthase, includes substrate-level phosphorylation, producing GTP to be donated to third phosohatr grouo for ADP to form ATP |
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Electron Transport Chain Complex 1 |
Deals with NADG by taking away electrons, leaving NAD, moving up the chain and causing hydrophobic ubiquinol to dispense and float around membrane Each electron moves up the chain, knocking the one in front further on up, causing structural change through proton pump |
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Electron Transport Chain Complex 2 |
Enzyme FADH2 from CAC performs same concept as complex one (knocking up) without proton pump |
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Electron Transport Chain Complex 3 |
Ubiquinol causes Cyclic C to go to complex 4 Receives two electrons but Cyclic C only requires 1, the other electron forming a semiquinome (two of which will make a ubiquinol) |
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Electron Transport Chain Complex 4 |
Oxygen converted to water, requires 4 electrons |
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Plasmid Components |
Plasmid Backbone Multiple Cloning Site Antibiotic Resistance |
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RNA-Dependent RNA Polymerase |
Replicates RNA from RNA template |
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RNA-Dependent DNA Polymerase |
DNA from RNA template |
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DNA-Dependent DNA Polymerase |
Replicates DNA from DNA template 5' - 3' Only (lagging strand in its 5' - 3' which is leading strands 3' - 5') |
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DNA-Dependent RNA Polymerase |
Makes RNA from DNA template |
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ATP Hydrolysis Example |
ATP breaking bond releases more energy than it took to break the bind Hydrolysis favourable as ATP is highly unstable ATP helps reaction cross activation energy threshold Phosphate from ATP hydrolysis added to glucose to form glucose-P, which binds with fructose to form sucrose |
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α helicies and β sheets common |
Maximum use of weak interactions, including hydrogen bonds, ionic bonds and van der Waals interactions |
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Initial Reaction Rate |
(Kcat / Km) x [E][S] |
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Lipid Melting Favtore Determinates |
Hydrocarbon Length Unsaturation Charge Headgroup Species |
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Lipid Fluid Mosaoc Determinates |
Length of fatty acid side chains Low hydrocarbon sidechains Cytoskeletal proteins Saturation in fatty acid chains in lipids (double bond kinks affect stacking) |
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Opposite of Glycolysis |
Gluconeogenesis |
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Malate-Asparate Shuttle |
Reduces dihydroxyacetone phosphate |
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TCA infinitability |
Due to anaplerotic reactions, which require no oxygen and convert glucose to lactate |
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Chemiosmosis |
Movement of electrons or protons couples to ATP synthesis Emergy in protein gradient from NADH and FADH2 |
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Acetyl CoA |
Produces 3 ADP per mole |
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Gel Electrophoresis |
From negative to positive |
