Topic 3: Proteins Flashcards
What are proteins?
Functional unit of the cell
Information for function and structure is encoded
How are proteins polymers of amino acids?
Twenty different amino acids are used in protein synthesis
Each protein contains these amino acids in varying proportions
All amino acids have the same basic structure but are distinguished by their side-chains (R-group)
Different amino acids are classified according to their R groups (non-polar, polar uncharged, polar charged acidic (-), polar charged basic (+))
The alpha carbon is asymmetric meaning there are two stereoisomeric forms called D- and L-amino acids
Only L-isomers exist in proteins (in nature)
What is the process of evaluating hydrophobicity?
Water is a polar molecule because it contains a covalent bond where the electrons are shared unequally resulting in a dipole on the atoms
Water is the solvent of life
Oxygen is highly electronegative (high affinity for electrons)
Oxygen and hydrogen have permanent dipoles
What is cysteine?
Can form disulphide bonds (type of covalent bonds) between interacting cysteines
What is tyrosine?
Can be post-translationally modified by phosphorylation (as can Thr and Ser)
How do peptide bonds polymerize proteins?
Chain of amino acids has an intrinsic directionality with the N terminus translated first
Peptide bonds are formed in translation (covalent linkage between a.a.)
In a polymer of L-amino acids the side chains alternate in either side of the protein backbone
Peptide bonds has partial double bond character, therefore peptide is planar (no relation which restricts number of theoretical shapes)
What are primary structures?
Primary structure dictates folding
Folding dictates function
Bonds stabilize the different levels of protein structure
What are secondary structures?
H bonding between a.a. backbones (determined by primary sequence)
Proteins fold spontaneously into lowest energy conformation
Shape maximizes favourable interactions between R groups
What are tertiary structures?
Disulphide bridges, H bonds, van der Waals interaction, hydrophobic interactions and ionic interactions
Forces that drive folding: hydrophilic interactions of non-polar R groups
Forces that stabilize folding: R group interactions
What is the relationship between folding and function?
Folding is driven by hydrophobic associations
Non polar amino acids do not form stable associations with water, therefore it is more favourable for them to aggregate
Non-polar amino acids aggregate in the middle of a folded protein
What was the Ribonuclease Denaturation/Renaturation Experiment?
Used ribonuclease enzyme and denatured it with urea (disrupts stabilizing interaction) = loss of enzymatic activity
Washed out urea to permit refolding = regained enzymatic activity
Showed: primary structures are sufficient to allow proper folding and function
What is sickle-cell anemia?
Shows the importance of primary sequence to folding
Single base pair mutation causes hemoglobin to crystallize in the red blood cells and cause the shape of the cell to sickle
This can impede flow through the capillaries as well as limit oxygen carrying capacity
Caused by a single amino acid change: Glu (-) —> Val (np) in hemoglobin
How is folding spontaneous?
Most protein folding is spontaneous, cotranslational, and sequential
Most proteins cannot be unfolded easily and refolded
How do proteins contain multiple functional domains?
Different regions of secondary structure can form different functional regions, or domains, within the protein
Domains: modules of tertiary structure, unique folded and functional regions of a single protein
What factors affect folding pattern and protein function?
pH: affects stability of ionic bonds
temperature: breaks all bonds
urea: disrupts ionic associations
beta mercaptoethanol: disrupts signal sequence
organic solvents: disrupt hydrophobic association
