Major Amino Acids + MCAT Biochem: Amino Acids + Proteins

  • Native fold: normal fold in 3D configuration of the protein

  • Residue: normally refers to the R group

  • Electrostatic interactions: temporary interactions when the charges aren’t equally distributed

  • Primary structure: actual order for knowing the amino acids

    • Held together by peptide bonds (amide linkage), which is the only type of bonds that make up the primary structure

      • Peptide bond can have resonance but is planar and rigid

    • Amide = carbonyl with amine group directly adjacent

    • Rotation can happen around the amide nitrogen (phi) or the carbonyl carbon (psi)

      • Some might not happen due to steric crowding, while some might be favored due to favorable H-bonding interactions

      • Chart this is using a Ramachandran plot

  • Secondary structures: alpha helix and B-pleated sheets form the backbone

    • Made up of only hydrogen bonding

    • Beta-pleated sheets can be parallel or antiparallel

      • Antiparallel: parallel but order is going in opposite directions, like strands of DNA

    • Alpha helix: bond between the first and the fourth amino acids per turn

      • Length is 5.4 A (A = Angstrom)

      • Predominantly a right-handed turn

      • Parts that go through the hydrogen bonding: H, O, N

    • Beta-pleated sheets = when multiple Beta interactions occur, leading to sheets forming

      • They can be going in the same direction or opposite directions (antiparallel)

      • B-turns = 180 degree turn accomplished over four acids

        • Proline and Glycine are more likely to be present in forming B-pleated sheet

    • CD analysis: analyzing when the 2D structures will turn

    • Alanine and Leucine do normally create alpha helices

    • Proline forms a ring structure

    • Glycine is very flexible since it is just a hydrogen

      • Gly and Pro have difficulties forming the alpha helix

    • Carbonyl has negative while amide has positive dipole moment

      • Dipole moment = measurement of separation between electric charges

      • Electronegativity determines the dipole moment

  • Tertiary structure: involve R group interaction, like disulfide bonds

    • Aromatic R groups are all also nonpolar in addition to the nonpolar chains

    • Fibrous proteins: more linear proteins in 3D struc:ture

      • Example includes collagen, which is made up of glycine and proline

      • Normally formed when alpha helices combine to make one big twist

    • Disulfide bridge: only forms when you have two cysteines bonded together

    • Alpha-ketoglutarate: reacts with ascorbate, making it lose a H

    • Histidine and lysine covalent bonding is important for collagen

    • Silk Fibroin: antiparallel structure, with Ala and Gly structure

      • Has really high tensile strength

    • Motif: fold in a protein

    • Some amino acids tend to have more disorder

      • Lys, arg, Pro

  • Quaternary structure: only structure found only some proteins, which is that there are interactions between multiple polypeptides

  • Protein interacting with DNA: histones, chromatin

  • All proteins have at least 3 structures: primary, secondary, and tertiary

  • X-ray crystallography: helps to determine shape of a protein

  • NMR: collecting signals for hydrogens based on ppm and what compounds they bond to

  • Proteostasis: synthesis, assembly, degradation of proteins in vivo

  • Denaturation: breakdown of a protein, normally due to breakdown of bonds like disulfide bridges

    • Ribonuclease denatures around urea and mercaptoethanol, and spontaneously reform after those two compounds are removed

    • Some instances can lead to permanent denaturation, like a nuclear reaction or starvation of oxygen

  • Chaperones are functional enzymes that help to assist the proper folding of a protein

    • Alzheimer’s has found a relationship with some instances of misfolding chaperone proteins

  • KNOW THAT PROLINE FAVORS PARTICULAR CONFIGURATION (I THINK IT TRANS?)

Chapter 5:

  • Induced fit: ligand moves to help the substrate fit better

    • All ligand fitting is like this, not like a lock and key

  • Binding site: area where the protein binds to the ligand

    • Normally has reversible binding

      • Binding to protein: Ka

      • Ligand dissociating from enzyme: Kd

    • Fraction of bound sites depends on free ligand concentration and Kd

      • Kd = 0.5/ 1.0 on concentration of occupied ligand sites

        • Is also inverse of Ka

  • The Kd is reached very quickly for hemoglobin, which is how it can exhibit cooperativity, as the first oxygen binding is difficult, but gets easier over time

    • The antibody-antigen has a really low Kd since they are very specific to their particular antigen that they fight

  • Lock-and-key model: thought that the enzyme and ligand were pre-formed so that they automatically fit

  • Polarity is found through partial charge that are being shared between compounds, while ionic charge is determined by full charges that a compound loses charge (transfer of charge)

  • Globin are binding proteins, but proteins can’t bind oxygen well

    • Some transition metals are able to bind to oxygen relatively well, like Iron

  • Myoglobin:

    • Oxygen can bind to the Fe2+

  • Carbon monoxide is normally made in a combustion reaction, so when carbon is burned in the presence of oxygen gas and heat

    • Only overcome CO by increasing in the concentration of O2 so that it can be produced over CO

  • (positive) Cooperativity: binding affinity of a particular compound increases as more molecules bond to it

    • Negative cooperativity: as more molecules bond to it, it becomes less likely that something will bind to the compound

      • Like any sort of inhibitor

  • Hill equation: mathematical measurement for affinity between two compounds

  • Allosteric protein: binding to one site affects binding to another site on same protein

  • Hemoglobin:

    • T= tense state

      • Where oxygen is not bound

    • R= relaxed state

      • Where oxygen is bound

    • O2 binding triggers T –> R conformation

  • The higher the pH, the lower the dissociation constant

  • Bohr effect: difference between the acidity of the pH….

  • 2,3-bipshopho glycerate regulates oxygen binding

    • Product found in glycolysis

    • Modulates interaction between oxygen and glucose

    • BPG changes hemoglobin from T to R state so it can increase oxygen saturation rate

  • Sickle cell anemia

    • Glu6 → Val in the Beta chain of Hb

    • Ends up sickling the cell

  • Cell immune system

    • T cells can attack and kill their own infected cells

  • Fluid immune system

    • T

  • Macrophages are eaters in cells and they can eat bacteria

  • Antigens stimulate production of antibodies

    • Antibodies: proteins made because of antibodies

  • Immunoglobulin G

    • Has two heavy and two light chains

      • Light: one constant and one variable domain

      • Heavy: three constant and one variable domain

    • Variable chains make up the antigen part of the cell

  • Antigen binding causes induced fit

  • Troponin is on the actin filament and acts like a binding site

  • Glucose and glycogen can be stored in the cell

    • Like in glycolysis

  • Exam:

    • 2 essay questions

      • First one about R group

        • Draw all R groups and state proper name of the amino acid

        • Need to memorize the R groups, not having a typed out response

      • Second will be posted soon

    • 40 MCQ

      • If not on powerpoints, then it won’t be on the test

  • Print out Pre-Lab

  • Electronic devices allowed but not during the lab

  • No eating or drinking during the lab