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Biochemistry by Mind Map: Biochemistry

1. Protein structure

1.1. Levels

1.1.1. Primary Aminoacid sequence Aminoacids

1.1.2. Secondary Alpha helix Right hand coiled Backbone NH H links to C=O 3.6 resudues per turn Beta sheet Lateral connection At least 2-3 bonds per line Configurations No covalent bonds

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

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

1.2. Problems

1.2.1. Prions Transmissable confirmational changes PrP PrP(c) is ok PrP(sc) is not ok

2. Specific proteins

2.1. Hemoglobin

2.1.1. 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 H+ promotes dissociation Deoxyhemoglobin Higher H+ affinity Some CO2 transported directly Fetal blood has lower BPG affinity Hogher O2 affinity

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

2.1.3. Trouble Sicle cell disease Advangates Characteristics

2.2. Myoglobin

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

2.3. Collagen

2.3.1. Structure Connective tissue

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

3. Genetics

3.1. Gene expression

3.1.1. Transcription Phases Pre-initiation Initiation Promoter clearence Elongation Termination Steps DNA to mRNA Recognition of promoter (TATAAT) RNA-polymerase binds Helicase enzymes make transcription bubble RNA polymerase runs 3'UTR poly-A tail and a 5'UTR cap

3.1.2. Translation Initiation 30S ribosome complex binds IF-2 delivers tRNA-fMet into P site 50S subunit binds Elongation Complex shit, will add if bored Termination Stop codon found RF-/RF2 +RF-3:GTP binds to A site Confirmational jumbo Dissociation

3.2. RNA

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

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

3.2.3. Evolved before DNA

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

3.3. DNA

3.3.1. 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 dTTP, dATP, dGTP, dCTP Step 4 Heat to 95 Cool to 70 Step 5 Repeat 4

3.4. Forensic PCR

3.4.1. DNA profiling VNTRs variable number tandem repeats STR particularly short tandem repeats

4. Phospholipids

4.1. Structure

4.1.1. 1 fatty acid tails COO attached to glycerol On 1 and 2

4.1.2. Glycerol

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

4.1.4. Top group of sorts Often choline

5. Membrane transport

5.1. Passive diffusion

5.2. Active transport

5.2.1. Transporter proteins Primary Pump ATP Secondary Uniport Cotransport Gradient

6. pH

6.1. Hyperventilation

6.1.1. Increased gass/lung contact

6.1.2. Lower CO2 Lower H2CO3 Lower H+ + HCO3- Hb affinity for O2 increases Lower O2

6.2. Formulas

6.2.1. pH = -Log[H+]

6.2.2. [H+] = 10^-pH

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

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

6.2.5. Weak acid Ka = [H+][A-] / [HA] Ka low = weak acid pKa = -log(Ka)

7. Processes

7.1. Blood clotting

7.1.1. Vitamin K Function Add carboxylic acid group to a glutamate amino acid residue Usage Reduction and subsequent reoxidation of vitamin K coupled with carboxylation of Glu is called the vitamin K cycle

7.2. Enzyme function

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

7.2.2. Additional components Cofactors Coenzymes If tightly bound

7.2.3. Calculations v = d[A]/dt = K[A] A+B > P+Q v= dA/dt = dB / dt = dP /dt = dQ / dt 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 =

7.2.4. Substrate binding H bond Ionic Vd Waals

7.2.5. Inhibitors Effects Km Vmax Reversible Competitive Noncompetitive Uncompetitive Irreversible Suicide substrate

7.3. Glycogen

7.3.1. Glycogenolysis Glycogen(n residues) + Pi <> glycogen(n-1 residues) + glucose-1-phosphate 1. Glycogen phosphatase phosphorilates a-1-4 2. G1P to G6P

7.3.2. Glycogenesis 1. Glucose to G6P Glucokinase Hexokinase 2. G6P to G1P Phosphoglucomutase 3. G1P to UDP-Glucose Uridyl Transferase Pyrophosphate formed 4. Chain assembly Glycogen synthase 5. Branching amylo-α(1:4)→α(1:6)transglycosylase

8. Polysaccharides

8.1. Linked glucose units

8.1.1. Starch a-1-4 Glycocidic bonds

8.1.2. Cellulose b-1-4 Glycocidic bonds

8.1.3. Glycogen a-1-4 linkages a-1-6 linksge branches

8.1.4. Dextrans a-1-6 linkages a1-3 branches

8.2. Linked Agarobiose units

8.2.1. Agarose 1-4 bonds

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

8.3. Linked N-Acetylglucosamine

8.3.1. Chitin b-1-4 linkage Structure similar to cellulose

8.4. a and b bonds