VL 1 (Petra Wendler) Flashcards
Amino acids
Name the aminoacid ground structure
Amino acids
What does chiral means?
Chiral: refers to molecules that have mirror-image versions that cannot be superimposed. These mirror-image forms are called enantiomers and have different chemical and often biological properties. Chirality is important in drug development and has implications in various chemical and biological processes.
Contagan
In Proteins aa are mostly L-Isomere
Amino acids
Explain Zwitterionic properties of amino acids
Amino acids have:
1. amino group (-NH₂), which can donate a proton (H⁺) and become positively charged
2. carboxyl group (-COOH), which can accept a proton and become negatively charged.
When an amino acid is near physiological pH, it can donate a proton from the amino group to the carboxyl group.
This results in the formation of a zwitterion, which has a neutral overall charge but contains both positive and negative charges.
Amino acids
Which amino acids have an hydrophobic, aliphatic side chain?
- Glycin (Gly,G)
- Alanine (Ala,A)
- Valine (Val, V)
- Leucine (Leu, L)
- Isoleucine (Ile, I)
- Methionine (met,M)
- Proline (Pro, P)
Amino acids
Which amino acids have an hydrophobic, aromatic side chain?
- Phenylalanine (Phe, F)
- Tryptophane (Trp, W)
Amino acids
Which amino acids have an polar, neutral side chain?
- Serine (Ser,S)
- Threonine (Thr, T)
- Tyrosine (Tyr, Y) also aromatic
- Asparagine (Asn, N)
- Glutamine (Gln, Q)
- Cystein (Cys,C) contains sulfur
Amino acids
Which amino acids absorb UV light?
aromatic amino acids
Amino acids
Which amino acids have negatively charged side chains?
- Aspartate (Asp,D)
- Glutamate (Glu,E)
Side chains have a negative charge at physiological pH
Amino acids
Which amino acids have positively charged side chains?
- Lysine (Lys, L)
- Arginine (Arg, R)
- Histidine (His, H) conatins Imidazolring
- Side chains have a positive charge at physiological pH
Amino acids
What is a His-Tag?
- A molecular tag added to recombinant proteins for simplifying their purification and detection.
- Typically consists of 6-10 histidine residues.
- Allows easy purification via immobilized metal affinity chromatography (IMAC).
- Facilitates detection and quantification using specific antibodies.
Amino acids
Which amino acids have readily ionizable side chains?
- Aspartate (Asp, D)
- Glutamate (Glutamate, E)
- Histidin (His, H)
- Cystein (Cys, C)
- Tyrosine (Tyr, Y)
- Lysine (Lys, K)
- Arginine (Arg, R)
Amino acids
How are amino acids linked? Explain how this bond works
Amino acids are linked by peptide bonds.
Amino acids
How can you calculate the molecular weight of an Protien?
- A polypeptide bond has directionality and is often called polarity.
- The amino terminal end marks the beginning of the polypeptide chain.
- The polypeptide has a main chain (backbone) and a variable part with distinctive amino acid side chains.
- Proteins typically consist of 50 to 2000 amino acids
- The average molecular weight of an amino acid is approximately 110 g/mol. This can also be expressed in Daltons (Da).
Proteins are build from a repertoir of 20 aa
Protein structure
Alpha Helix (secondary structure)
- esentially all alpha helices in proteins are right handed (Thumb rule)
- Hydrogen bonds between
C=O and NH
(next hydrogene bond: i and i+4 ) - Side chains on β carbon
have destabilising effect - Prolin breaks helix
- Distance between 1 Ribbon (1 Windung) is 5.4 A (3.6 aa)
Protein structure
Beta sheet (secondary structure)
- formed by adjacent beta-strands
- Polypeptide in beta-strand is fully extended
- hyrogen bonds link strands in beta-sheets
- parallel: N – C and N–C (above each other)
- anti-parallel: C –N and N – C (above each other)
Protein structures
Tertiary Structure
(How do water-soluble Proteins fold)
- Water-soluble proteins fold into compact structures with nonpolar cores
- Spatial arrangement of amino acids
- aa 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
of charged and polar amino acids -
Membrane proteinshave the reverse
distribution of hydrophilic and
hydrophobic amino acids (they oftne have a waterfilled hydrophobis channel)
Protein structures
Motifs and domains (tertiary structure)
- motifs: (supersecondary structures) are combinations of secondary structure that are found in many proteins
- domain : Some proteins have 2 or more motifs, called domain
Protein structure
Quaternary Structure
- Many proteins are composed of multiple polypeptide chains (subunits).
- Quaternary structure can be as simple as two identical polypeptide
chains or as complex as dozens of different polypeptide chains
e.g: Heamoglobin, Ribosome, Polymerse, almost all Enzymes
Protein Life cycle
What is the Life cycle of a Protein?
- DNA –> RNA
- RNA –> Polypeptide
- Polypetide –> Mature (active) protein
active helper:
1. RNA-Polymerase, Spliceosome
2. Ribosome
3. Protein folding, Protein targeting & secretion, Cofactor incorporation, Posttranslational modifications
Protein Life cycle
Protein folding
- Levinthal´sche Paradoxon: Proteins dont fold by trying all possible conformations
- Proteins fold sponatnousley
- Native and refolded protein have identical properties
- Folding information is coded in sequence
- Nucleation- condensation model: progressive stabilisation of folding intermediates
Protein Life cycle
What are chaperons?
Chaperons help Proteins to fold correctly, prevent missfolding and maintain their stability and functionallity
Fuctions:
- assist protein folding
- protein aggregation
- heat shock response (Hsp70/40)
- protein homeostasis
Protein Life cycle
Protein targeting
compartmentalisation creates transport proteins
- transport across membrane
- transport between compartments
Principal components:
- signal sequence necessary for targeting
- organelle specific receptors or soluble targeting factors
- Protein conduction channel formed by integral mebmbrane protein
- Driving force for translocation
- molecuar chaperons
Protein degradation
- In aqueous solution, peptide bond cleavage is exergonic.
- Proteases generally are not ATP dependent
The catalytic mechanism, in all protease classes, is based on
* transfer of protons
* nucleophilic attack on the carbonyl-C atom of the peptide substrate.
* covalent intermediate or not, depending on the protease class
