pH, Acids, Bases, Buffers, Protein Structure, and Folding Activity Flashcards
Are polypeptide bonds in a trans- or cis-configuration
They can be both but are usually found in the trans-configuration
What forces contribute to protein folding?
- Hydrogen bonding between neutral groups and between peptide bonds
- Ionic interactions (attraction and repulsion)
- Hydrophobic interactions
What amino acids have polar and uncharged R groups?
- Glutamine
- Cysteine
- Asparagine
- Threonine
- Serine
The uncharged R groups on these amino acids can participate in Hydrogen Bonding
What amino acid does di-sulfide bonds form between
Cystein
What amino acids have ionic interactions?
Which are positively charged and which are negatively charged?
Positively charged R groups:
- Histidine
- Arginine
- Lysine
Negatively charged R groups:
- Aspartate
- Glutamate
What amino acids form hydrophobic interactions?
Aromatic R Groups:
- Phenylalanine
- Tyrosine
- Tryptophan
Nonpolar, aliphatic R groups:
- Glycine
- Alanine
- Proline
- Valine
- Leucine
- Isoleucine
- Methionine
- Form hydrophobic interactions and tend to cluster together inside of proteins or interact with hydrophobic portions of ligands
Primary Structure
Linear sequence of amino acids
Secondary Structure
Alpha Helixes
Beta Sheets
Beta Turns
Result of hydrogen bonding between the amide hydrogens and carbonyl oxygens of the polypeptide backbone
Tertiary Structure
Overall three dimensional arrangement of a protein
Maximizes hydrogen bonding and ionic interactions. Clusters hydrophobic amino acids in the interior of the protein
Quaternary Structure
Three dimensional arrangement of subunits (multiple proteins) assembled together
What is an acidic and basic pH?
Acidic solutions: pH < 7
Basic solutions: pH > 7
Why is pH in the human body important?
- pH values of different body fluids are related to physiological function. Ex: Stomach acid pH 1.5, Ileum pH of 8.0, Blood has a normal pH of 7.35-7.45
- pH is important in medicine and drug absorption
- pH is important for enzyme function
- pH influences the binding of oxygen to hemoglobin
Strong acids and basis
Ionize completely in water
Weak acids and bases
Ionize only partially in water
What does a buffer consist of?
A weak acid and its conjugate base
Acidosis
- Blood pH less than 7.35
- Can be fatal if pH is less than 6.8
Alkalosis
- Blood pH greater than 7.45
- Can be fatal if pH is greater than 7.8
Plasma bicarbonate buffer system
Maintains pH of the blood around 7.4
CO2 CO2 + H20 H2CO3 H+ + HCO3-
CO2 produced by metabolsim (mainly TCA cycle) and eliminate through respiration
H2CO3 is carbonic acid
HCO3 - is bicaronate ion (conjugate base)
