Lecture 1 Flashcards
What are the main functions of the plasma membrane?
- Acts as a selective barrier
- Contains ion channels and transporters
- Active transport and facilitated diffusion
What are the functions of the nucleus
- Location of gene replication
- Location of transcription
- Holds all genetic information (Euchromatin and Heterochromatin)
What are the main functions of mitochondria?
- Oxidative phosphorylation for ATP synthesis
- Involved in cell signalling and the cell cycle
What are the main functions of the golgi?
- Modifies, packages and secretes proteins
- Involved in lysosome formation and the secretory pathway
What is the main function of lysosomes?
- Contains hydrolytic enzymes to degrade proteins and other large molecules
- Used in immune defences to degrade pathogens
Describe rough endoplasmic reticulum and state its function
Interconnected network of flattened membrane enclosed sacs.
Studded with ribosomes on its outer surface which is the location of late-phase protein synthesis.
Involved in transport of proteins to golgi
What is the function of Smooth Endoplasmic Reticulum and how does it differ from Rough Endoplasmic Reticulum?
- Does not contain ribosomes on its outer membrane.
- Involved in lipid and carbohydrate metabolism as well as detoxification and transport of proteins to golgi.
What is the function of ribosomes?
- Location of protein synthesis
What is meant by the macromolar structure of a protein?
It’s primary, secondary, tertiary (and sometime quaternary) structure
When do hydrogen bonds occur and why?
- When a H atom is bound to a highly electronegative atom such as O, N or F.
- Electronegative atom decentralises the electron cloud, pulling it towards itself. This creates partial charges (dipoles) on the atoms
When do zwitter ions arise in proteins and how? What benefit does this have to the protein?
- When to R groups are in close proximity and one has COOH and the other NH2.
- The H of the carboxyl group transfers to the amine group (COO- and NH3)
- Increases stability of the protein
Describe a peptide bond
- Carboxyl group of one a’a is linked to the amino group of the next via a condensation reaction
- The bonds around the peptide bond are in trans formation
What is a hydrophobic interaction and at what level of macromolar structure are they found?
- When two hydrophobic R groups are in close proximity they interact and repel water. Adds to the stability and function of a protein.
- Found in the tertiary structure of a protein
What are van der waals and how are they formed?
- Weak interactions between atoms which aid stability
- Formed as the electrons in an electron cloud are constantly mobile. This creates partial charges on the atoms in the compound (d+/d-). When two atoms with partial charge are in close proximity they attract/repel each other.
How do hydrogen bonds affect solubility of proteins?
-Atoms with a high potential to form hydrogen bonds will be highly soluble
Are polar molecules soluble or insoluble and why?
Polar molecules contain electronegative atoms, giving the compound the ability to produce hydrogen bonds and thus are soluble
Are non-polar molecules soluble or insoluble? Can they contain electronegative atoms?
Non-polar molecules are insoluble as they do not have the ability to form hydrogen bonds. They may contain electronegative atoms, however it is not in a high enough proportion to make the entire molecule soluble
Are molecules which contain both polar and non-polar regions soluble or insoluble?
Soluble - they form micelles with hydrophobic, non-polar regions on the inside and the hydrophillic polar regions on the outside
What is pH?
-Measure of the acidity/basicity of an aqueous solution
What is pK?
- A measure of how likely a molecule is to accept or donate a proton
In terms of pH and pK, when is a molecule likely to be protonated/deprotonated?
- If pHpK then the molecule will be deprotonated
What is a buffer?
An aqueous solution with a highly stable pH
What are buffers made from?
An acid/base with its conjugate
What are the non-polar hydrophobic amino acids?
Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Phenylalanine, Tryptophan.
What amino acids are polar, uncharged?
Serine, Threonine, Asparigine, Glutamine, Tyrosine, Cysteine
Which amino acids are Polar and charged?
Lysine, Arginine, Histidine, Aspartate, Glutamate
What is an isoelectric point?
The point at which a protein has no overall charge
Will the isoelectric point of an acidic protein by high or low and why?
- Low
- Acidic proteins contain many negatively charged amino acids
Will the isoelectric point of a basic protein be high or low and why?
- High
- Basic proteins have many positively charged amino acids
What is primary protein structure?
- The linear sequence of amino acids
What is secondary protein structure? List two types
- The local spatial arrangement of the polypeptide back bone
- Doesn’t involve R groups
- a-helix and b-strand
Describe the features of an a-helix
- Right handed helix
- 3.6 a’a/ complete turn
- 0.54nm pitch (vertical distance in one turn)
- Stabilised by H bonds
Describe a b-strand
- Has an extendeed conformation due to the R groups being on alternate sides
- multiple multidirectional strands held together through H bonds form B-pleated sheets
Which bonds are involved in tertiary structures of proteins?
- Disulphide Bonds
- Hydrophobic interactions
- Ionic bonds
- Salt bridge
What is a quaternary protein structure?
Two or more polypeptides non-covalently and covalently linked
Eg, Hb, ribosomes
How does heat denature proteins?
Increases Vibrational Energy
How does pH denature proteins?
- Alters ionisation states of a’a which breaks bonds
How do detergents/solvents denature proteins?
- Disrupt hydrophobic interactions
- Change oxidation states
What would cause the formation of amyloid fibres?
- Misfolding of proteins resulting in an insoluble long fibrous structure
Describe globular proteins
- Contain several secondary structures
- Compact
Describe fibrous proteins
- single type of secondary structure - usually B strand
- involved in support, eg collagen
