Week 1 - Amino acids and Proteins Flashcards
Functions of lysosomes
- Cellular digestion: intracellular, contain hydrolytic enzymes
- Degrade certain macromolecules
- Phagocytose particulate matter
Functions of Golgi complex
- Export of proteins
2. Packages and modifies macromolecules synthesised on the surface of RER
Functions of mitochondria
- ATP synthesis
2. Generate heat in brown fat instead of ATP
Functions of nucleus/nucleolus
- RNA synthesis
- DNA synthesis and repair
- RNA processing and ribosome assembly (nucleolus)
Functions of plasma membrane:
- Cell morphology and movement
- Transport of ions and small molecules
- Selective structural barrier
Functions of cytoplasm
- Metabolism of carbohydrates, amino acids and nucleotides
2. Fatty acid synthesis
Name the bonds important for macromolecular structure.
- Hydrogen bonds: between neutral groups/ between peptide bonds
- Ionic interactions: attraction/repulsion
- Hydrophobic interactions
- Van der Waals interactions: any 2 atoms in close proximity
Explain the differences between hydrophobic and hydrophilic molecules in water.
Hydrophilic molecules from hydrogen bonds and dissolve.
Hydrophobic molecules cannot form hydrogen bonds and are insoluble.
Explain the concept of pH.
pH is the concentration of protons in aqueous solution.
pH= -log(H+)
Explain the concept of pK.
pH = pKa + log[A-]/[HA]
The larger the Ka, the stronger the acid.
Buffers
A buffer is a solution that resists change in pH following the addition of an acid or base.
A buffer can be created by mixing a weak acid with its conjugate base.
Maximum buffering capacity: pH = pKa
If [HA] = [A-], pH = pKa
List all non-polar amino acids.
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Methionine
- Proline (non-polar aliphatic)
- Phenylalanine, Tryptophan (non-polar aromatic)
List all polar uncharged amino acids.
- Serine
- Threonine
- Asparagine
- Glutamine
- Tyrosine
- Cysteine
List all polar, positively charged amino acids.
- Lysine
- Arginine
- Histidine
List all polar, negatively charged amino acids.
- Aspartate
2. Glutamate
How is the charge on an amino acid affected by pH?
If pH of the solution group will be protonated.
If pH of the solution > pK value –> group will be deprotonated.
List the key features of a peptide bond.
- Partial double-bond character (shorter than a single bond)
- Rigid and planar –> prevents free rotation around the bond between the carbonyl carbon and the nitrogen of the peptide bond.
- Almost always a trans bond: mostly because of steric interference of R groups when in cis position
Motifs
Folding patterns containing 1 or more elements of secondary structure
Types of motifs
- B-alpha-beta loop
2. Beta-barrel
Domains
-Part of a polypeptide chain that fold into a distinct shape
-Often has a specific functional role
Example: calcium binding domains of troponin C
Factors that can cause denaturation
- Heat: increased vibrational energy
- pH: alters ionization states of amino acids; changes ionic and hydrogen bonds
- Detergents and organic solvents: disrupt hydrophobic interactions
Amyloid fibres
-Misfolded, insoluble form of a normally soluble protein
-Highly ordered with a high degree of beta sheet
-Core beta sheet forms before the rest of the protein
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How many amino acids are there in one turn of an alpha-helix?
3.6
How many base pairs are there in one turn of a DNA double helix?
10
