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Biochemistry by Mind Map: Biochemistry
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Increased gass/lung contact

Lower CO2, Lower H2CO3, Lower H+ + HCO3-, Alkidosis, Vasoconstriction, Hb affinity for O2 increases, Lower O2


pH = -Log[H+]

[H+] = 10^-pH

[H+] = ([HA]Ka)/[A-]

[H+][OH-]=10^-14 M

Weak acid, Ka = [H+][A-] / [HA], Ka low = weak acid, pKa = -log(Ka), pKa+pKb=14, pH=pKa + log([A-]/[HA]), [A-] = X, [HA] = Concentration-X


Blood clotting

Vitamin K, Function, Add carboxylic acid group to a glutamate amino acid residue, form a gamma-carboxyglutamate (Gla) residue, Usage, VKOR reduces to vit K hydroquinone, K hydroquinone oxidised, Allows carboxylation of Glu to Gla, By gamma-glutamyl carboxylase, Also vit-K dependens carboxylase, Only happens if oxidation to vit K epoxide works, Linked reaction, Vitamin K epoxide is then reconverted to vitamin K by VKOR, Reduction and subsequent reoxidation of vitamin K coupled with carboxylation of Glu is called the vitamin K cycle

Enzyme function

Features, Protein/RNA catalysts, Specificity, Regulation, Enzyme expression, Enhancers, Inhibitors, Catalytic power, Lower activation energy

Additional components, Cofactors, Coenzymes, If tightly bound, = Prosthetic group, Group bound = holoenzyme, Group unbound = apoenzyme

Calculations, v = d[A]/dt = K[A], A+B > P+Q, v= dA/dt = dB / dt = dP /dt = dQ / dt, v = k[A][B], ES <k1 / k-1 > E+S, (k-1)[ES]<>(k1)[E][S], Ks=[ES]/[E][S] = (k-1)/(k1), E+S <k1/k-1> ES >k2> E+P, Km = (K1+K2)/(K-1), v =

Substrate binding, H bond, Ionic, Vd Waals

Inhibitors, Effects, Km, Vmax, Reversible, Competitive, Same binding site as substrate, Km up, Noncompetitive, Pure, IE and E binding to S are same, Km same, Vmax down, Mixed, IE-S binding altered, Close to binding site, Conformational change, Interact with E and ES, Uncompetitive, I binds ES only, Km up, Vmax down, Irreversible, Suicide substrate, Permanent binding (covalent)


Glycogenolysis, Glycogen(n residues) + Pi <> glycogen(n-1 residues) + glucose-1-phosphate, 1. Glycogen phosphatase phosphorilates a-1-4, Until 4 residues before a-1-6 branch, Glygogen debranching puts 3 onto another branch, α[1→6] glucosidase hydrolises last glucose off, Only case of non G1P, Hexokinate converts it to G1P, 2. G1P to G6P, by phosphoglucomutase

Glycogenesis, 1. Glucose to G6P, Glucokinase, Hexokinase, 2. G6P to G1P, Phosphoglucomutase, glucose-1,6-bisphosphate`intermediate, 3. G1P to UDP-Glucose, Uridyl Transferase, aka UDP-glucose pyrophosphorylase, Pyrophosphate formed, Hydrolyses to 2 Pi, Pyrophosphatase, 4. Chain assembly, Glycogen synthase, Start on old chain, Or glycogenin (primer), Process, Binds to UDPG, Oxonium ion forms, Add to 4 hydroxyl group, 5. Branching, amylo-α(1:4)→α(1:6)transglycosylase, End of chain onto earlier part

Protein structure


Primary, Aminoacid sequence, Aminoacids, Only L configuration in bio, 20 aminoacids in human code, Amino group, -NH2, Acid group, -COOH, Peptide bond, -C(=O)NH-

Secondary, Alpha helix, Right hand coiled, Backbone NH H links to C=O, 4 residues earlier, 3.6 resudues per turn, Beta sheet, Lateral connection, At least 2-3 bonds per line, Configurations, Parallel, Anti-parallel, No covalent bonds

Tertiary, 3D structure, Non-specific hydrophoibic interactions, Salt bridges, H bonds, Disulfide bonds, Tight packing of side chains

Quarternaru, Multi tertiary units, Same noncovalent bonds as tertiary, Multiple polypeptides, Multimere, Di/trimer etc


Prions, Transmissable confirmational changes, PrP, PrP(c) is ok, Membrane, a-Helical, Cell adhesion & communication, PrP(sc) is not ok, Mutated, Higher proportion of beta sheets, Clogs up cell, Death

Specific proteins


Hemoglobin saturation curve, CO2 decreases O2 affinity, BPG lowers O2 affinity, First O2 molecule binds, heme Fe ion is drawn into the porphyrin ring plane, Confirmational change to subunits, Enhance O2 affinity, H+ promotes dissociation, Deoxyhemoglobin, Higher H+ affinity, Some CO2 transported directly, O NH-COO, Fetal blood has lower BPG affinity, Hogher O2 affinity

Structure, 2 a-units, 2 b-units, Each unit has heme group with Fe

Trouble, Sicle cell disease, Advangates, Protection against malaria, Characteristics, Hemoglobin mutation, b-Globulin chain mutation, Glutamic acid is replaced, Hydrophobic valine, Confirmational change, @Low oxygen, Non-covalent polymerisation


Behavior, Binds 1 O2, Traditional Michaelis-menten graph, Oxygen storage in muscle


Structure, Connective tissue

Prolyl hydroxylase, Needs vit C to function, Cofactor to keep Fe++ in reduced state, Involved in collagen synthesis


Linked glucose units

Starch, a-1-4 Glycocidic bonds

Cellulose, b-1-4 Glycocidic bonds

Glycogen, a-1-4 linkages, a-1-6 linksge branches

Dextrans, a-1-6 linkages, a1-3 branches

Linked Agarobiose units

Agarose, 1-4 bonds

= D-galactose + 3,6-anhydro-L-galactopyranose

Linked N-Acetylglucosamine

Chitin, b-1-4 linkage, Structure similar to cellulose

a and b bonds


Gene expression

Transcription, Phases, Pre-initiation, Initiation, Promoter clearence, Elongation, Gyrase introduces negative super coils, Reduce strain, Topoisomerase to remove negative coilks after bubble, Termination, Rho factor (enzyme), Termination site (sequence), Steps, DNA to mRNA, Recognition of promoter (TATAAT), Sigma factor, RNA-polymerase binds, Helicase enzymes make transcription bubble, RNA polymerase runs, 3'UTR poly-A tail and a 5'UTR cap

Translation, Initiation, 30S ribosome complex binds, IF3-30S-IF1, IF-2 delivers tRNA-fMet into P site, GDP bound, 50S subunit binds, GTP hydrolysed, IF-2 dissociated, Results in 70S subunit, Elongation, Complex shit, will add if bored, Termination, Stop codon found, RF-/RF2 +RF-3:GTP binds to A site, Confirmational jumbo, Dissociation


Can cleave own backbone, 2' hydroxyl oxygen attacks the phosphodiester bond

Uracil, Replaces thymine in RNA, Uracil methylation results in Thymine, Deaminated cytosine is uracil, Uracil DNA glycosilate fixes

Evolved before DNA

Types, Mainstream, mRNA, tRNA, rRNA, ncRNA, Lesser known, miRNA, siRNA, piRNA, snRNA, snoRNA, dsRNA


PCR, Step 1, Isolate target sequence, Heat to 95 celcius, Cool to 70, Step 2, Add 1000 fold excess primer, Step 3, (Taq) DNA polymerase, Heat resistant, dTTP, dATP, dGTP, dCTP, Step 4, Heat to 95, Cool to 70, Step 5, Repeat 4

Forensic PCR

DNA profiling, VNTRs, variable number tandem repeats, STR, particularly short tandem repeats



1 fatty acid tails, COO attached to glycerol, On 1 and 2


Phosphate group, G-OP(=O)(O-)-O-topgroup, On 3

Top group of sorts, Often choline

Membrane transport

Passive diffusion

Active transport

Transporter proteins, Primary, Pump, ATP, Secondary, Uniport, Cotransport, Symport, Antiport, Gradient