Klausurfragen Biochemie

Hydrogen bonding between the Carbonyl group and the amino group

between N-H and C=O of i and i4 of Helix

1 + B

2 + D

3 + C

4 + A

1. Glucose -> Glucose-6-phosphate

   (Hexokinase)

1. Fructose-6-phosphate -> Fructose-1,6-bisphosphate

   (Phosphofructokinase)

1. Phosphoenolpyruvate -> Pyruvat

   (pyruvatkinase)

ATP

NAD+

Oxalacetate + H2O + Acetyl-CoA -> Citrate

• Isocitrate + NADH + H+ + CO2 -> alpha-Ketoglutarate

  (Isocitratdehydrogenase)

• alpha-Ketoglutarate + NADH + H+ + CO2 -> Succinyl-CoA

  (alpha-Ketoglutaratedehydrogenase complex)

• Citrate

• Isocitrate

• alpha-Ketoglutarate

• Succinyl-CoA

• Succinate

• Fumerate

• Malate

• Oxalacetate

The inhibitor binds only to the enzyme-substrate complex (ES) in what is essentially substrate-dependent inhibition.

• mix of competitve and uncompetitive inhibition

• inhibitor binds either enzyme or enzyme-substrate complex

• Ki and Ki’ are different

• influence on KM and Vmax

• example

  • alpha-amylase + starch -> maltose inhibitor: arcabose

  • succinate dehydrogenase + succinate -> fumarate

    inhibitor: malonate

• strong -> binds tightly to the enzyme

• Ki -> affinity of an inhibitor to its target

• strong= nm, moderate= micromolar, weak= millimolar

• Double-displacement (ping-pong) reactions are characterized by the formation of a substituted enzyme intermediate.

• two substrate mechanism

• parallel lines at increasing concentrations of the second substrate

• no ternary complex is formed

• competitive inhibitor is structurally similar to the substrate and can bind to the free enzyme → prevent the substrate from binding

• In competitive inhibition, Vmax of the enzyme is unchanged because the inhibition can be overcome by a sufficiently high concentration of substrate.

• However, KM in the presence of inhibitor, called KMapp, is increased.

• x-intercept: -Ki (Ki = dissociation constant of inhibitor)

• competitive

  • inhibitor binds to the free enzyme

  • Vmax no effect

  • KM is increased

• uncompetitive

  • inhibitor binds only Enzyme-Substrate complex

  • Vmax is decreased

  • KM is decreased

• linear mixed

  • inhibitor binds either enzyme or enzyme-substrate complex

  • Vmax is decreased

  • KM is increaased

• noncompetitve

  • inhibitor binds enzyme or enzyme-substrate complex

  • Vmax is decreased

  • KM no effect

catalysis often sensitive to pH changes (pKa)

• acid-base reaction governed by sidechains

• A Catalyst is a compound that takes part in a reaction by increasing the rate of the reaction without being consumed and without changing the chemical equilibrium of the reaction.

• The reaction is accelerated  by a reduction of the activation energy.

1. Acid base catalysis

2. electrostatic catalysis

3. metal ion catalysis

4. catalysis by approximation

5. covalent catalysis

serine 195 is one of 28 serine residues in chymotrypsin

• Serine is part of a catalytic triad that also includes Histidine and Aspartate

  • Histidine removes a proton from serine 195, generating a highly reactive alkoxide ion.

  • The alkoxide ion attacks the peptide bond of the substrate

  • Aspartate orients the histidine and renders it a better proton acceptor

  • The oxyanion hole, a region of the active site, stabilizes the tetrahedral reaction intermediate

Pyruvate can be converted to Alanine (via transamination) per transport into the liver

→ Alanine is converted into glucose in liver

→ generation of Glucose from Pyruvate

• Hyperammonemia = elevated levels of ammonia in the blood, common symptoms of liver failure

• Primary degradation product is Ammonia (NH3) –toxic!!!

• Solution: Conversion of toxic NH3 into non-toxic, soluble molecule: Urea

• Ammonia collected by glutamate is removed by glutamate-dehydrogenase

• (Arg) enhances conversion of ammonia to urea which is excreted then

Gout is a type of arthritis that occurs when urate crystals accumulate in the joints, often toes, leading to inflammation and pain

disrupts the production of deoxyribonucleotides needed for DNA synthesis

→ leads to a halt in cell division

Without a sufficient supply of deoxyribonucleotides, cells cannot efficiently repair damaged DNA

→ leads to the accumulation of genetic errors and eventual cell death/apoptosis

• Ribonucleotide reductase is important for catalyzing the conversion of ribonucleotides to deoxyribonucleotides

• Gemcitabine = nucleoside analog

• it reduces the hydroxygroup at the C-2 of the ribose of the nucleotides → suicide inhibitor

• → no replication

  → no repair → accumulation of damage

  → no DNA synthesis

  → cell apoptosis

• dihydrofolate reductase (DHFR) enzyme

• → thymidine (dTMP) de novo synthesis requires this enzyme

• It impairs the DNA and RNA replication, induces cell cycle arrest and eventually apoptosis

cell death, because they cannot synthesise thymine anymore to create more DNA

• reverse flow → electrons from PSI can be transferred back to cytochrome b6f by ferredoxin instead of NADP+

• Plastocyanine gets reduced and reoxidized by P700+

• ATP generation without NADPH formation

• takes place at high NADPH : NADP+ ratios

• no PSII, no O2 released

• oxygenic: chlorophyll a and b → PSI (P700) + PSII (P680)

• anoxygenic: bacteriochlorophyll a and b (P775 + P790)

• circular, substituted tetrapyrroles (porphyrins) → pigments

• oxygenic: H20, CO2, light (ADP → ATP)

• anoxygenic: H2S, CO2, light (ADP → ATP)

oxygenic:

• uses both photosystems

• linear electron transport

• electron donor: H2O

• pigments: chlorophyll

• byproducts: O2

• organism: plants, algae, cyanobacteria

anoxygenic:

• 1 PS used

• cyclic electron transport

• electron donor: H2S, H2, organic compounds

• pigments: bacteriochlorophyll

• byproducts: no O2

• organism: certain bacteria

PSI

• Core: Pair of homologous subunits PsaA and PsaB

• PS I catalyzes final stage of the light reactions

• chlorophyll special pair P700 at the center

• absorbs at 700 nm, initiating charge separation

PSII

• PSII core formed by D1 (gene: psbA) and D2 (gene: psbA) proteins (homologs of L + M of purple bacteria)

• Contains large number of additional subunits (e.g, chlorophyll bound proteins, increasing efficiency of light energy absorption)

2H2O + 2NADPH + 10H+ -> O2 + 2NADPH + 12H+

a)

• in presence of oxygen RuBisCO catalyzes oxygenation of RuBP

• formation of 3-Phosphoglyerate + Phosphoglycolate

b)

• Phosphogylcolate -> photorespiration

• no useful organic compound is produced

• release of CO2 without carbon fixation

• Cofactor: Mg2+ → CO2 (not substrate) reacts with a lysine side chain to form a carbonate

  → negative charge adduct → stabilized by cofactor Mg2+

Transketolase facilitates the exchange of functional groups between a ketose and an aldose, resulting in the formation of a new ketose and aldose with swapped residues

C7 and C3 → C5

For each CO2 molecule incorporated in a hexose, 3 ATP and 2 NADPH are required

6CO2 + 12NADPH + 12H+ + 18ATP -> C6H12O6 + 12NADP+ + 18ADP + 18Pi + 6H2O

• polar head has at least one phosphate group)

• Glycerol backbone

• 2 fatty acids (usually one saturated and one unsaturated) linked via ester bonds to glycerol backbone

• C-3 carbon has phosphoric acid group

1. Diffusion (Substances will diffuse down their concentration gradient (Entropy))

2. Osmosis (semipermeable membrane)

3. facilitated diffusion (transport proteins are helping molecules to cross membrane)

• Difference lies in their backbone

• Glycerophospholipids:

  • 3 carbon glycerol backbone

  • polar head with at least one phosphate group

  • backbone bonded to 2 fatty acids via ester linkages

• Sphingolipids:

  • Sphingosine backbone

  • backbone bonded to 1 fatty acid chain via amide linkage

    (organic aliphatic amino alcohol sphingosine)

mixture of different lipids and proteins, peripheral or integral

Saturated fatty acids

• No double bond → straight and more packed molecular structure

tight packing makes it more difficult for the molecules to move past each other, requiring a higher temperature to transition from a solid to a liquid state

• Quality of fatty acids: More unsaturated fatty acids → Kinks in the PM → Fatty acid residues can no longer be arranged in an optimal way → Less hydrophobic interactions => Structure is less stabilized → Less energy in form of temperature is needed → Lower melting temperature (membrane is more fluid)

• Number of double bonds: More double bonds → More kinks → Lower melting temperature (membrane is more fluid)

• Length of fatty acids: Shorter fatty acids → Less surface to hydrophobically interact and stabilize the structure → Lower melting temperature (membrane is more fluid)

• Cholesterol: Cholesterol has a complex role in modulating the fluidity and melting temperature of the lipid bilayer. It acts as a stabilizer, promoting membrane integrity and preventing excessive changes in fluidity across a range of temperatures. The precise effect of cholesterol on the melting temperature depends on the specific lipid composition and the environmental conditions of the membrane.

→ bitopic span the membrane only once

→ polytopic span the membrane multiple times

• Extrinsic = Peripheral (Associated with the membrane surface but are not embedded in the hydrophobic interior)

• Intrinsic = Integral (Embedded within the lipid bilayer)

  → Bitopic and polytopic belongs to the intrinsic membrane proteins

• lipid raft microdomains are enriched in sphingomyelin & cholesterol

• function as platforms for signal transduction as receptor signaling

• function as the site of budding of several enveloped viruses (including influenza)

• The virus uses these Lipid-Rafts to enrich there proteins in these small regions to make the assembly of there proteins more efficient

→ this leads to the formation of the envelope of the virus

• Sphingolipids (e.g., Sphingomyelin, Glycosphingolipids)

• Cholesterol

→ Higher order and tighter packing of lipids

• specific viruses bind as proteins which are at high concentration in lipid rafts

• matrix proteins cause the membrane deformation

• Cellular proteins involved in vesicle formation and membrane remodeling, such as ESCRT (endosomal sorting complexes required for transport) proteins, can contribute to membrane curvature during viral budding.

→ ESCRT-I and ESCRT-III as an example

giant unilamellar vesicles

• Large, 10-100 μm, can be observed via optical microscopy e.g. fluorescence microscopy

used for

• Protein-Lipid Interactions

  GUVs are used to investigate the interactions between proteins and lipid membranes.

• Fluorescence Microscopy and Imaging

• Drug Delivery Studies

• Molecular brightness is the intensity of the light emitted by one molecule

• It can be used for Quantitative Analysis, Detection of Molecular Interactions (like multimerization), Monitoring Environmental Changes, Studying Molecular Dynamics:

• Methode: N&B (number and brightness)

• To get information about molecule interactions, conformational changes, diffusion dynamics, binding kinetics

• Possible because fluctuations in the signal occur due to diffusion which is linked to many specific molecule properties (e.c. size, photostability)

Method: FCS (Fluorescence Correlation Spectroscopy)

w-3 fatty acid