Biochemie

at physiological pH

at physiological pH

• Histidin can accept or donate protons at physiological pH

• polypeptide bond has directionality (polarity)

• amino terminal = beginning of polypeptide chain

• polypeptide consists of repeating part = backbone + variable part = amino acids

• essentially all alpha helices in proteins are right handed

• hydrogen bonds between C=O and NH in i and i+4

• side chains on beta carbon have destabilising effect

• Prolin breaks the helix

• beta sheets are formed by adjacent beta-strands

• polypeptide in beta-strand is fully extended

• hydrogen bonds link strands in beta-sheet

• spatal arrengement of amino acids

• amino acids that are far apart in primary structure can be neighbours

• globular proteins are very compact

• interior of globular proteins consists mainly of hydrophobic amino acids

• exterior of globular proteins consists charged and poalr amino acids

• membrane proteins have the reverse distribution of hydrophilic and hydrophobic amino acids

• motifs (secondary structures) are combinations of secondary structures that are found in many proteins

• some proteins have two or more identical or similar compact structures called domains

• many proteins are composed of multiple polypeptide chains (subunits)

• Quarternary structure can be as simple as two identical polypeptide chains or ascomplex as dozen of different polypeptide chains

• proteins dont fold by trying all possible conformations

• real folding time is 1s

• proteins fold spontaneously

• native and refolded protein have identical properties

• folding information is coded in sequence

• nucleation-condenstation model: progressive stabilisation of folding intermediates

• some proteins need help folding

  -> generally requires ATP

• signal sequences are necessary and sufficient for protein targeting

• organelle specific receptors or soluble targeting factors

• Protein conducting channels formed by integral membrane proteins

• driving force for ranslation

• molecular chaperons

• peptide bond cleavage is exergonic

• proteases are not ATP dependent

• catalytic mechanism:

  • transfer of protons

  • nucleophilic attack on the carbonyl-C atom of the peptide substrate

  • covalent intermediate or not (depends on class)

• digestion, Production of acetyl-CoA, complete oxidation of acetyl-group to CO2

• Phototrophic organisms: get energy from sunlight

• Chemotrophic organisms: get energy through oxidation of nutrients

• energy carrier: ATP, NADH, NADPH, FADH2

• deltaG kleiner 0 -> exergonic

• deltaG größer 0 -> endergonic

• deltG=0+

• ATP/ADP

  • high posphorylation potential of ATP is achieved by

    • resonance stabilization

    • electrostatic repulsion of the 4 negative charges at ATP

    • stabilisation through hydration of ADP and Pi

    • gain in entropy

• carriers are kinetically very stable

• exchange of activated groups is carried out by a small set of carrier molecules (economical and elegant)

• based on watersoluble vitamins

  • FADH, FMN -> Vitamin B (Riboflavin)

  • NADH, NADPH -> Vitamin B3 (Niacin)

  • Coenzym A -> B5 (Pantothenate)

• NAD+/NADH in catabolic processes

• NADP+/NADPH+ in anabilic processes

• ATP, NADH, CoA, FAD all contain an ADP

• open system equilibrium

• hexokinase, phosphofructokinase and pyruvate kinase

  • speed-determining steps

  • pacemaker reactions

• flow of intermediates is constant in steady state

• synthesis and degradation are in balance

• formation of glucose from non carbonhydrates via pyruvate to keep blood sugar levels constant

• relevant during hunger

• can not produce glucose from acetyl-co

• exergonic reactions are bypassed

• 3 cell compartments: cytosol, mitochondria, ER

• costs more energy than glycolysis

• Pyruvate needs to be further processed to generate NAD+ and maintain redox balance

• takes place in all cells

• supplies riboses for DNA and RNA

• delivers NADPH/H+

• NADH

  • used to produce ATP in the respiratory chain

  • is predominantly oxidized as needed in Glycolysis

• NADPH

  • for reductive biosynthesis

  • protects the erythrocyte membrane and liver cells from dell toxins

  • preferably present in the reduced form

• Acetyl-CoA

  • smallest common product of degradation of amino acids, fatty acids and carbohydrates

  • takes C2-molecules into Krebs cycle

  • produced in mitochondrium

• localised in the mitochondiral matrix

• catalysis the oxidative decarboxylation of pyruvate to acetyl CoA

• is a multi enzyme complex