Altklausur

1. A-Form: 11 bp per turn, grooves narrower and much deeper, helix rotation right handed

2. B-Form: 10 bp per turn, major & minor groove, helix rotation right handed

3. Z-Form: 12 bp per turn, helix rotation left handed, alternating pur-pyr config (purine changes to syn confirmation)

Components:

- telomerase reverse transcriptase (TERT)

- telomerase RNA (TER)

Function

- Telomerase adds G-rich sequence at end of telomeres (=chromosomes) → maintains chromosome integrity and prevents cellular aging

Ribonucleoprotein, reverse transcriptase (RNA is used as matrix, priming at the 3-OH-end of G & T rich telomerase strands)

Additionally:

- Telomerase is a ribonucleoprotein (RNP)

- Has a protein catalytic subunit (TERT)

- One or more associated proteins

- Telomeres facilitate end replication through the recruitment of an unusual DNA polymerase telomerase

- An integral RNA component that serves as a template for synthesis of telomeric repeats (termed hTR for human telomerase RNA)

Rho factor is an ATP dependent helicase

- Binds to C rich region of RNA transcript

- Moves along RNA chain to transcription site

- Termination depends on Rho´s ability to “catch up” to RNAP - RNAP slows down at end of gene

- Catalyses unwinding of RNA:DNA hybrid → RNAP dissociates

Helicase: breaks hydrogen bondings

Topoisomerase: removes supercoils

- Density regulated gene regulation (many bacteria needed on one spot)

- ↓ Autoinducer-concentration —> no gene expression

- ↑ Autoinducer-concentration —> gene expression

- Bacteria produce autoinducers that diffuse through the membrane

- Sensing of environmental signals results in transcriptional regulation

Compound classes:

- AHL

- PHRC (small oligopeptide)

- ComX (Pheromone) Quinolones, gram neg bacteria: - regulates virulence factors and biofilm formation

N-acyl-homoserine lactose, gram neg

- diffuse freely across cell membrane

- accumulate in environment as bacterial populations grow, allow cells to sense density and regulate gene expression

Autoinducing peptides, gram pos bac, short peptides

- ↓ Autoinducer-concentration —> no gene expression

- ↑ Autoinducer-concentration —> gene expression

- Bacteria produce autoinducers that diffuse through the membrane

Class I: copy and paste (Retrotransposons)

- Only eukaroytes

-Flanked with long terminal repeats

- Virus-like

- Transposition via RNA intermediate (reverse transcription) => does not contain inverted regions on ends!

- Replicate themselves

→ increase in number of copies, can lead to genome expansion

Class II: cut/copy and paste (DNA transposons)

-flanked with inverted repeats

- Bacteria and eukaryotes

- They excise themselves from one location to another without a copy → no increase in overall number

• Essential enzyme for both classes: Transposase

• Additional enzyme for Class II: Resolvase --> Resolves Cointegrate structure

• Modifications of Nucleotides, allows Wobble-base pairing → Less tRNA-variants needed.

• Optimise Decoding fidelity.

Two important functions of nucleotide modifications in tRNA are:

- They enhance the accuracy and efficiency of codon recognition during translation by fine-tuning how the tRNA pairs with mRNA, particularly through modifications in the anticodon loop (such as at the wobble position and position 37)

- They stabilize the overall tRNA structure and support proper folding, which promotes tRNA maturation and efficient aminoacylation by their corresponding synthetases, ensuring the tRNA can function correctly in protein synthesis.

These modifications are central to maintaining translational fidelity and the structural robustness of tRNA molecules.

30 S subunit: contains 16 ribosomal RNA (rRNA)

50 S subunit: contains 23 rRNA and 5 rRNA

→ S refers to Svedberg unit ??? (Eukaryotes: 40 S and 50 S)

The names 16S, 23S, and 5S refer to “Svedberg units” (S), which indicate each molecule’s sedimentation rate during ultracentrifugation—a rough measure influenced by size, shape, and mass. The Svedberg value is not strictly additive, so the complete ribosome is called 70S rather than the sum of its parts

- 5' cap (7-methylguanosine). Recruits ribosome.

- Poly-A tail promotes circularisation of mRNA --> Aids in recruitment of large subunit, eIF4E and reinitiation of ribosoms.

- Polycistronic mRNA (prokarya): Translation initiation can happen at several different shine-dalgarno sequences in the cell.

- Monocistronic (eukarya): Translation starts at only one position

Enzymatic activity: GTPase → hydrolyses GTP

Function of EF-G: Aids in the translocation of the tRNA in the A-Site to the P-Site, after the polypeptide has been transferred to it.

In which phase of translation does it play an additional role? Ribosome recycling → Translation termination

• An sp³ carbon atom forms four sigma bonds and has a tetrahedral geometry (bond angles of 109.5°).

• An sp² carbon atom forms three sigma bonds and one pi bond, with a trigonal planar geometry (bond angles of 120°).

• An sp carbon atom forms two sigma bonds and two pi bonds (linear geometry, bond angle 180°)

-Electron sharing → filling of orbitals to reach noble-gas state

- Electrons have a higher probability of residing in the proximity of the more electronegative atom, resulting in a partial charge.

electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities. Results in the transfer of an electron.

- Hydrogen-Bridge Bonds

- Pi-Effects

> pi-pi-interaction

> Cation/Anion-pi interaction

> Polar-pi interaction

- Van-der-vaals forces

> Dipole-Dipole

> Dipole-induced dipole

> London dispersion force

- Electrostatic Interactions

> Ion pairs

> Hydrogen bonding

> Halogen bonding

- Hydrophobic Interactions → Oil droplets in water.

- Halogen Bonding (Electrostatic attraction)

- Acid: Hydrogen donor

- Base: Hydrogen acceptor

• Strong acid/base fully dissociates in water

• weak acid/base shift H+/A- balance of water, they dont fully dissosciate,l.

• pH of 1M in water is 0 → -log10(1) = 0 - Strong acid conjugate is a weak base

• A buffer substance is typically a mixture of a weak acid and its conjugate base (or weak base and conjugate acid) that resists changes in pH when small amounts of acid or base are added by chemically binding the added H+ or OH−.

• The useful pH range of a buffer can be deduced from the pKa of its weak acid (or pkb of its weak base) and lies roughly within one pH unit above and below this value, where acid and conjugate base are present in comparable amounts.

• The capacity of a buffer is the amount of strong acid or base that can be added before the pH changes appreciably, and it increases with the total concentration of buffer components and is maximal when pH ≈ pKapKa.

cyclic compounds that have alternating double and single bonds in their ring structure

• Compounds chracterized by a divalent chemical unit consisting of a carbon (C) and an oxygen (O) atom connected by a double bond. → C=O

• Chemical properties:

  - Polar

  - Electrophilic

  - Reactive

• Reactivity: - Nucleophile reaction

• SN2 and SN1

• SN2 = One step: Addition of nucleophile → elimination of leaving group → Nucleophile “pushes” leaving group out (no intermediate product)

• SN1 = Two steps: Leaving group disassociates and takes “its” electron with it, ionizing the carbon atom → Intermediate Carbocation forms → Nucleophile binds to Carbocation

Leaving group: Weak bases and strong acids are good leaving groups - OH- bad

• Reactivity

  - SN2 : Strength of the nucleophile, steric hindrance, as well as the electronegativity of the leaving group

  - SN1 : Electronegativity of the leaving group and stability of the Carbocation.

  → Stability of the Carbocation depends on the availability of electron in the molecule, as well as possible isomiracation

- Resonance structures (Mesomerie in deutsch), are a way of describing delocalized electrons in the lewis model.

- Resonance stabilization describes the property of mesomeric systems to delocalized electrons, this allows the distribution of a charge over several atoms in the molecule, which stabalizes the Ion. Key-words: +M-Effect and +I-Effect

AS Functional groups:

- Amino Group (-NH2): Proton acceptor

- Carboxyl Group (-COOH): Proton Donator

Side chains Functional groups:

- Thiol (-SH): Reactive (Nucleophile), moderately polar, proton donator

- Sulfide (-S-): Reactive (Nucleophile), moderately polar

- Aromatic rings: Nonpolar, Hydrophobic, rigid & big structure, pi-pi-interactions

- Ring structures: Rigid and big

Side-chain properties:

- neutral-nonpolar: Glycin, Alanine, Valine, Isoleucine, Tryptophan, Phenylalanine, Proline, Methionine, Leucine

- neutral-polar: Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine

- acidic: aspartic acid, glutamic acid

- basic: lysine, arginine, histidine (Hurensohn → Basic)

Nucleotides in DNA

1. Adenine (A) - Nucleotide: Deoxyadenosine-5'-monophosphate (dAMP)

2. Cytosine (C) - Nucleotide: Deoxycytidine-5'-monophosphate (dCMP)

3. Guanine (G) - Nucleotide: Deoxyguanosine-5'-monophosphate (dGMP)

4. Thymine (T) - Nucleotide: Deoxythymidine-5'-monophosphate (dTMP)

Nucleotides in RNA

1. Adenine (A) - Nucleotide: Adenosine-5'-monophosphate (AMP)

2. Cytosine (C) - Nucleotide: Cytidine-5'-monophosphate (CMP)

3. Guanine (G) - Nucleotide: Guanosine-5'-monophosphate (GMP)

4. Uracil (U) - Nucleotide: Uridine-5'-monophosphate (UMP)

- Average structure of DNA: 10 bp per turn, major & minor groove, helix rotation right handed

- Stabalised by Hydrogen bonds in Base-pairing and pi-pi stacking interactions.

Sanger Sequencing:

• The classical chain-termination method requires a single-stranded DNA template, a DNA primer, a DNA polymerase, dNTPs, and modified ddNTPs, the latter of which terminate DNA strand elongation.

  → chain-terminating nucleotides lack a 3'-OH group required for the formation of a phosphodiester bond

• Sample is divided into four separate sequencing reactions, containing all four of the standard dNTP and only one of the modified ddNTPs. - After elongation, samples are separated by electrophoresis and analysed - Modern Sanger Sequencing usese capillary electrophoresis and a laser to detect the fluorescent ddNTPs.

- Fluorescence occurs when a molecule absorbs a photon of light, which excites an electron to a higher energy state. When the electron returns to its original state, it releases energy in the form of a photon i.e. it fluoresces

- The emission of light by an excited electron when it returns to its original energy state.

• The standard reduction potential is the likelihood that a species will be reduced

  → A measurement of a compounds affinity for electrons (the higher E 0 the higher the affinity)

• RedOx

  - The standard reduction potential helps determine whether a redox reaction will occur spontaneously.

  - The overall cell potential (E°_cell) is calculated by combining the standard reduction potentials of the two half-reactions. If E°_cell is positive, the reaction is spontaneous in the forward direction

• Side note: Electron transportation heavily rely on RedOx reactions (f.e. reduction of NAD+ or the oxidation of water at the WO

- For a reaction to be spontaneous, it should result in an overall increase in entropy.

- The Second Law leads to the concept of Gibbs free energy (G), which incorporates both the system’s enthalpy (ΔH) and entropy (ΔS) changes into a single value.

→ ΔG=ΔH−TΔS - If ΔG is negative (ΔG < 0), the reaction is spontaneous in the forward direction, as this corresponds to an increase in the total entropy of the universe.

- If ΔG is positive (ΔG > 0), the reaction is non-spontaneous in the forward direction and will either not proceed or will proceed spontaneously in the reverse direction.

- Primary: linear sequence of amino acids in a polypeptide chain. -

- Secondary: Local folding pattern → α-helix & β-pleated sheet, as well as turns and loops

- Tertiary: three-dimensional (3D) folding of a single polypeptide chain

- Quaternary: assembly of multiple polypeptide chains (subunits) into a larger, functional protein complex.

- covalent

- partial double bond due to resonance stabilization: delocalization of electrons between the carbonyl oxygen and the nitrogen atom, which makes the bond shorter and stronger

- Planar and rigid (partial double bond)

- Trans configuration (strong preference when folded): Minimizes steric hindrance between the side chains

- Stability: Peptide bonds are kinetically stable under physiological conditio

- α-helix: stabilized by hydrogen bonds between the carbonyl O of the amino acid in position “i” and the amide H of the amino acid in position “i+3” (in other word AA 1 interacts with AA 4)

- β-pleated sheet (Two configs: Parallel and antiparallel): Stabilization through Hydrogen bonds that form between the carbonyl oxygen of one strand and the amide hydrogen of an adjacent strand

- Turns and Loops: Stabilization by the formation of hydrogen bonds of opposing sides Side Note: Turns and Loops can stabilize the tertiary structure of the protein as they bring (sequentially) distant regions in closer contact.

regulation of a protein's activity through the binding of an effector molecule at a site distinct from the protein's active site.

• Phosphorylation: Addition of phosphate groups, often on serine, threonine, or tyrosine residues.

• Glycosylation: Attachment of carbohydrate moieties, which can affect protein folding and stability.

• Acetylation: Addition of acetyl groups, commonly on lysine residues, influencing gene expression and protein interactions.

• Methylation: Addition of methyl groups, typically on lysine or arginine residues, impacting protein function and interactions.

• Ubiquitination: Attachment of ubiquitin molecules that signal for protein degradation.

• Lipidation: Attachment of lipid groups that facilitate membrane association.

A coenzyme is a non-protein organic molecule

→ assists enzymes in catalyzing biochemical reactions Coenzymes often act as carriers for specific atoms or functional groups during enzymatic reactions Unlike enzymes, coenzymes are not permanently bound to the enzyme and can be reused multiple times.

examples: Coenzyme A, Biotin, Tetrahydrofolate, Pyridoxal Phosphate