2A- Amino acids and proteins Flashcards
Give the general structure of an amino acid
i. All 20 amino acids in the body are α-amino acids, which means the amino group is attached to the α-carbon (the 1 next to the carboxylate group) ii. The α-carbon also has a H and a side chain (-R). The side chain makes each amino acid different.
At physiological pH, what charge does the amino and carboxylic group have?
Amino has + Carboxylic has -
What is the pKa of the primary carboxylic group of an AA?
~2
What is the pKa of the primary amino group of an AA?
~9.5
Name the 3 amino acids which are postively charged
Arg, His, Lys
What are the 2 amino acids which are negatively charged?
Asp, Glu
What are the 4 amino acids that are polar uncharged?
Ser, Thr, Asn, Gln
What are the 3 “special” amino acids?
Cys (has an SH) Gly (just an H) Pro (has a N ring)
What are the 8 hydrophobic amino acids?
Ala Val Ile Met Phe Tyr Trp
Name the 5 true nonpolar amino acids
Ala Ile Leu Pro Val
Name the 3 aromatic amino acids
Phe Tyr Trp
Name the 2 acidic amino acids
Glu
Asp
Name the 3 basic amino acids
His
Arg
Lys
Name the 3 alcoholic amino acids
Tyr, Ser, Thr
Name the 4 amide amino acids
Arg Lys Asn Glu
What is glycosylation and what is it’s function?
Oligosaccharides (small carbohydrate chains) are bound to proteins by N or O linkages N-linked oligo’s are on cell surface proteins, where they protects the cell from proteolysis or an immune attack O-linked oligo’s is a common way of attacking ologo;s to the Ser or Thr OH groups in secreted proteins.
What is fatty acylation and it’s function?
Fatty acids are often attached to plasma membrane proteins or to intracellular vesicles.
What is phosphorylation of amino acids and its function?
Phosphorylation is adding a PO4 group to an end of an AA. It introduces a large, bulky, negatively charged group thatt can alter the acitivity of the protein
What is ribosylation and its function?
ADP-ribosylation is the trasnfer of an ADP-ribose from the NAD+ to an Arg, Glu, or Cys residue on a target protein in the membrane This regulates the activity of the proteins
What is carboxylation modification of amino acids and what is its function?
It is the addition of -COO to the AA its important for attachment by binding a blood clot to the surface of a vessel in certain blood-clotting proteins.
What is a peptide bond and its characteristics?
It’s the bond between the carboxylic acid of 1 AA and the amino group of another AA This process has water as a byproduct
What are the chemical forces that govern protein structure?
The peptide bond forms the backbone of the protein structure the side chains extend outwards and interact with the backbone or sidechains of other proteins (or the same protein) This forms hydrophobic regions, electrostatic bonds, H bonds, or disulfide bonds.
What is the primary structure?
The peptide backbone of the protein showing the molecules involved with the sidechains and everything
What are secondary structures?
Regions within polypeptide chains that form recurring, localized structures. Forms either a alpha-helix or a beta-sheet
What are alpha-helixes?
2o structure Formed by strong H-bonds between each carbonyl O atom and the amide H of an AA located 4 resudies down the chain. Proline can’t form a-helixes because it has a weird cyclic structure that doesnt promote H-bonding.
What are beta-sheets?
2o structure H-bonding between peptide backbones while maintaining the allowed torsion angles. Usually occurs between regions of separate strands alligned parallel to each other running in opposite direction (usually).
What are tertiary structures?
it’s the folding pattern of the 2o structural elements into 3D conformation it creates specific and flexible binding sites for ligands
What are quatenary structures?
It refers to the association of subunits
What occurs during protein folding?
the primary structure of a protein dictates the way that it folds into its tertiary structure, which is a stable conformation. chaperons act as templates to overcome kinetetic barrier to reach a stable conformation prion proteins cause neurodegerative diseases by acting as a template for misfolding. Heat, acid and other agents misfold proteins.
What are some protein denaturation processes through nonenzymatic modification?
It can be either nonenzymatic glycosylation or oxidation such modifications leads to a loss of fxn and denaturation of the protein, sometimes into a form that cannot be degraded in the cell
What does changes in pH do to protein folding?
at low pH, ionic bonds and H-bonds formed by carboxylate groups would be disrupted At a high pH, hydrogen and ionic bonds formed by basic amino acids would be disrupted. This commonly occurs by stomach acid when we eat food.
What are prions and how do they work?
Prion proteins act as a template to misfold other cellular prion proteins that cannot be degraded. Our normal prion protein, PrP(c), gets misfolded into our brain into a form called PrP(sc). The (sc) has 3 more beta sheets even though it has the same AA sequence. Ex: CJD/mad cow, Kuru
What are the structural differences between myoglobin and hemoglobin?
Both are very similiar, however: -Myoglobin is a globular protein with 1 O2 binding site -Hemoglobin is a tetramer somposed of 2 different subtypes (alpha and beta)
How does the oxygenation saturation curve compare between myoglobin and hemoglobin?
Myoglobin has a much smaller P50 than Hb. This means they are 50% saturated with O2 at a much lower partial pressure of O2.
What are 3 things that will shift the O2-binding curve of Hb to the left?
Basically, it’s increasing the affinity to O2 at a lower partial pressure of O2.
The P50 will decrease.
Decrease CO2
Decrease 2,3-BPG
Increase pH
What are 3 things that would cause a larger P50 for Hb and O2?
Basically, things that will cause a decrease in association of Hb and O2. The Hb will need a higher partial pressure of O2 to become saturated, thus shifting the P50 to the right of graph. Increase in CO2 (competitive for binding spot) Increase 2,3-BPG (competitive for binding spot) Decrease in pH (Bohr effect)
How does CO2 get transported in the blood?
Label 1-6
1 and 4 = pH
2 and 5 = CO2
3 and 6 = 2,3-BPG
What are the differences between adult and fetal Hb?
Fetal have a different type of subunit which has a higher affinity for O2, thus making the P50 for fetal Hb lower than adult Hb
