Biochem 501
K
Lysine
M
Methionine
Titration curve of amino acids
pK1 -> pI -> pK2 (Amino+, Zwitterion, Carboxyl-)
Arpartate properties
(-) charge 2.77
Glutamate properties
(-) charge 3.22
Central dogma of biology
...
N
Asparagine
List all no polar amino acids
Gap V lim Glycine Alanine Proline Valine Leucine Isoleucine Methionine
S
Serine
Arginine properties
+ charge 10.76
Histidine properties
+ charge 7.59
Lysine properties
+ charge 9.74
5 Distinguishing Features of Living Organisms
-High degree of chemical complexity and microscopic organization -Systems for extracting, transforming, and using energy from the environment -Precise self-replication and self-assembly -Mechanisms for sensing and responding to alterations in surroundings -Defined functions for all components and regulated interactions between them. -A history of evolutionary change.
Diastereomer
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Draw a-D-Glucose
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Enantiomer
...
How are H bonds oriented?
...
Molecular Configuration
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Negative delta G?
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Polypeptide naming
...
Positive delta G?
...
Stereoisomer
...
H2O Bond Angle
104.5
How many H bonds per H2O in ice?
4
Oligopeptide
4-9 AAs bonded together
Uncommon Amino Acids
4-hydroxyproline 5-hydroxylysine 6-N-methyllysine y-Carboxyglutamate desmosine Selenocysteine ornithine citrulline
pKa of acetic acid
4.76
Polypeptide
A peptide containing 10 or more AAs
Beer's Law
Absorbance, A, is directly proportional to the concentration of the absorbing solute. A = EBC
A
Alanine
Nonpolar Aliphatic R Groups
Alanine Ala A Valine Val V Leucine Leu L Isoleucine Ile I Glycine Gly G Proline Pro P Methionine Met M
R
Arginine
Tyrosine Properties
Aromatic 5.66
Tryptophan Properties
Aromatic 5.89
Phenylalanine Properties
Aromatic. 5.48
Size-Exclusion Chromatography
Also called gel filtration. Separates proteins according to size. Large proteins emerge sooner than smaller ones!
Negatively Charged R Groups
Aspartate Asp D Glutamate Glu E
D
Aspartic Acid
Protein Hydrolysis
Breaking of peptide (amide) bonds to give smaller peptides & individual amino acids
Amphoteric
Can act as either an acid or a base.
The bacterium E. coli requires simple organic molecules for growth and energy - it is therefore a:
Chemoheterotroph
Glyoxysome
Contain digestive enzymes to free up food
C
Cysteine
Cytoplasm vs Cytosol
Cytoplasm means the inside of the cell; Cytosol is the liquid
E
Glutamic Acid Glu
Z
Glutamic Acid Glx
Q
Glutamine Gln
Free Energy
Delta G. Tells whether a reaction can happen spontaneously
Humans maintain a nearly constant level of hemoglobin by continually synthesizing and degrading it. This is an example of...
Dynamic steady state
Column Chromatography
Most powerful method for fractionating proteins Takes advantage of differences in protein charge, size, binding affinity and other properties.
G
Glycine
Enthalpy
H. Reflects the number and kinds of bonds.
Ion-Exchange Chromatography
Exploits differences in sign and magnitude of the net electric charge of proteins at a given pH. The column matrix is a synthetic polymer with cation exchangers and anion exchangers. Separatoin can be optimized by gradually changing the pH or salt concentration of the mobile phase to create a pH or salt gradient.
H
Histidine
Which is the only AA with pKa near neutral?
Histidine. It can be positively charged or uncharged at pH 7.0.
Oligomeric
If at least two chains are identical: the protein is said to be Oligomeric, and the identical units (one or more chains) are called Proteomers.
I
Isoleucine
L
Leucine
Proteins with chemicals that aren't AA's
Lipoproteins Glycoproteins Phosphoproteins Hemoproteins Flavoproteins Metalloproteins
Positively Charged R Groups
Lysine Lys K Histidine His H Arginine Arg R
Cytoskeleton
Made of Actin Filaments, microtubules, and intermediate filaments.
Types of residues
Methyl Phosphoryl Acetyl Adenylyl ADP-ribosyl
D, L system
Specifies the absolute configurations of amino acids. All amino acids are L-.
Gram Negative vs Positive membrane
Negative: Outer membrane, thin peptidoglycan layer Positive: No outer membrane, thicker peptidoglycan layer
Methionine
Nonpolar aliphatic 5.74
Glycine Properties
Nonpolar, Aliphatic. pI = 5.97
Alanine Properties
Nonpolar, Aliphatic. pI = 6.01
Leucine Properties
Nonpolar, aliphatic pI 5.98
Isoleucine
Nonpolar, aliphatic 6.02
Valine Properties
Nonpolar, aliphatic. pI = 5.97
Proline Properties
Nonpolar, aliphatic. pI = 6.48
P1A: In a bacterial cell, the DNA is in the...
Nucleoid
F
Phenylalanine
Aromatic R Groups
Phenylalanine Phe F Tyrosine Tyr Y Tryptophan Trp W
Hexokinase
Phosphorylates hexoses. (a)-D-Glucose-6-Phosphate is the most important product - from glucokinase
Cysteine Properties
Polar Uncharged 5.07
Serine properties
Polar Uncharged 5.68
Threonine properties
Polar Uncharged 5.87
Asparagine properties
Polar uncharged 5.41
Glutamine properties
Polar uncharged 5.65
P
Proline
RS system
Right is clockwise S is counterclockwise Assign priority around the chiral center
Entropy
S. Randomness of a system.
Draw serylglycyltyrosylalanylleucine.
Ser-Gly-Tyr-Ala-Leu SGYAL
Polar Uncharged R Groups
Serine Ser S Threonine The T Cysteine Cys C Asparagine Asn N Glutamine Gln Q
Protein containing only amino acid residues
Simple Proteins
What contributes to the overall acid-base properties of polypeptides?
The R groups
Delta G definition
The chemical potential that is minimized when a system reaches equilibrium at constant pressure and temperature
Affinity chromatography
The column has molecules that bind tightly to your protein. Then your protein binds, everything else gets washed out. Next flush with ligand solution
Molecular Confirmation
The spatial arrangement of substituent groups that are free to assume different positions in space because of freedom of bond rotation (single bonds)
T
Threonine
W
Tryptophan
Y
Tyrosine
V
Valine
Multisubunit proteins
a protein consisting of more than one polypeptide chain associated noncovalently. If at least PP chains are identical the protein is Oligomeric; each identical unit is a Protomer. Hemoglobin has four polypeptide subunits: two identical a chains and two identical B chains.
Amino Acid Residue
an amino acid in a polypeptide that is not the N or C terminal AA. This refers to every amino acid in a polypeptide chain.
B
asparagine
Auto vs Heterotroph
autotrophs obtain all their carbon straight from CO2 or their etc. from methane; heterotrophs have to oxidize food
Endomembrane system
segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reactions occur.
Peptide Bond
two amino acids covalently joined through a substituted amide linkage. Formed by dehydration: remove ~OH from carboxyl group and ~H from the amino group. This is a condensation reaction. Equilibrium favors the amino acids over the dipeptide. Carboxyl group must be chemically modified or activated so the hydroxyl can be eliminated more easily.