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Hydrogen bonds
Form between an electronegative atom (oxygen or nitrogen)
and a hydrogen atom that is covalently bonded to another
electronegative atom (oxygen or nitrogen)
TERM 2
Electrostatic bonds
DEFINITION 2
Basically interaction between two charges (ionic bonds, salt
bridges)
TERM 3
Van der Waals Interactions
DEFINITION 3
Weak noncovalent interaction caused by a transient dipole-
induced dipole interaction between neighboring atoms
TERM 4
Buffer
DEFINITION 4
Weak acid or base that resists change in pH of a solution
TERM 5
Respiratory acidosis
DEFINITION 5
Increase in CO2 levels will cause a decrease in blood pH
Respiratory alkalosis
Rapid breathing, blood pH increases because you are getting
rid of oxygen
TERM 7
L sterioisomers of amino acids are used
for
DEFINITION 7
Proteins
TERM 8
Protein Structure: Primary
DEFINITION 8
Amino acid sequence
TERM 9
Protein Structure: Secondary
DEFINITION 9
Local, ordered structure, stabilized by hydrogen bonds
TERM 10
Protein Structure: Tertiary
DEFINITION 10
3D structure of a single polypeptide
Peptide Nomenclature: Around 25 or more
amino acids
Oligopeptide (few)
TERM 17
Peptide Nomenclature: Around 100 amino
acids
DEFINITION 17
Polypeptide (many)
TERM 18
N Terminal
DEFINITION 18
The free amino end of a protein
TERM 19
C Terminal
DEFINITION 19
The free carboxyl end of a protein
TERM 20
Peptides are always written:
DEFINITION 20
N-terminal to C-terminal
Disulfide bond
Covalent linkage between the sulfur atoms on two cysteine
residues in different polypeptides or in different parts of the
polypeptide
TERM 22
Column Chromatography
DEFINITION 22
Separates proteins based on charge (ion exchange
chromatography), size (size exclusion chromatography), or
binding affinity (affinity chromatography)
TERM 23
Ion Exchange
Chromatography
DEFINITION 23
Proteins are separated based on differences in their charges. This
technique uses specially modified beads whose surface are
covered by amino groups or carboxyl groups that carry either a
positive or negative charge. In a column of positively charged
beads, only proteins with a net negative charge will adhere to the
beads and vice versa. The bound proteins are removed selectively
from the column by passing a solution of varying concentrations of
salt through the column
TERM 24
Size Exclusion (Gel Filtration)
Chromatography
DEFINITION 24
Proteins are separated on differences in their mass. Proteins
flow around spherical beads in the gel, smaller beads can
penetrate into these depressions more readily than larger
proteins, they will travel more slowly than larger proteins
TERM 25
Affinity Chromatography
DEFINITION 25
Column chromatography technique for purifying proteins. A
protein ligand is covalently attached to polymer beads. The
protein will preferentially bind to beads and contaminating
proteins will wash through the column. The protein can be
eluted using buffer containing the ligand or by changing the
pH and/or salt concentration.
Edman Degradation
Reacts with PITC at N-terminal. Specific cleavage of proteins
TERM 32
Longer peptides are specifically cleaved with:
DEFINITION 32
Trypsin, Chymotrypsin, Cyanogen bromide
TERM 33
Trypsin (bovine pancreas) cleavage points:
DEFINITION 33
Carboxyl side of Lys and Arg
TERM 34
Chymotrypsin (bovine pancreas) cleavage
points:
DEFINITION 34
Carboxyl side of Phe, Tyr, Trp
TERM 35
Cyanogen bromide (CNBr) cleavage points:
DEFINITION 35
Carboxyl side of Met
Protein folding is driven by:
Hydrophobic residues in interior and by maximizing the
number of hydrogen bonds and electrostatic interactions
TERM 37
Peptide bond
DEFINITION 37
Planar behaves as if double bond between carbon and
nitrogen
TERM 38
Secondary Structure
DEFINITION 38
First level of folding of proteins
TERM 39
Domain
DEFINITION 39
Distinct regions of protein tertiary structure; compact
globular structure
TERM 40
Protein denaturation:
DEFINITION 40
guanidinium, urea, beta-mercaptoethanol
Hemoglobin carries:
O2, CO2, and H+
TERM 47
Cooperactivity
DEFINITION 47
Binding O2 at 1 heme increases the affinity for O2 at another
heme
TERM 48
T (tense) state
DEFINITION 48
Low affinity for oxygen. Stabilized by electrostatic
interactions between subunits. F Helix is pulled away from
heme --> Fe2+ is pulled out of plane --> harder for O2 to
bind
TERM 49
R (relaxed) state
DEFINITION 49
High affinity for oxygen
TERM 50
2,3-biphosphoglycerate
(BPG)
DEFINITION 50
electrostatic interactions stabilize the T state. HbBPG + 4 O
<--> Hb(O2)4 + BPG
O2 binding to fetal
hemoglobin
baby hemoglobin binds BPG less tightly, so it binds oxygen
more tightly
TERM 52
Heterotrophic Allosteric Effectors of
Hemoglobin
DEFINITION 52
BPG, CO2, and H+
TERM 53
Antibodies
DEFINITION 53
Proteins with specific and high affinity for binding to an
antigen, bind to antigenic determinant (epitope)
TERM 54
Immunoglobulin
DEFINITION 54
glycoprotein molecules that are produced by plasm cells in
response to an immunogen and which function as antibody
TERM 55
IgG (Immunoglobulin G)
DEFINITION 55
important for the neutralization of virus particle, also helps
prepare particular antigens for acquisition by cells equipped
with receptors specific for the Fc portion of IgG molecules
Heraceptin
Monoclonal antibody against HER2 - inhibits HER2 and
induces killing of the cell
TERM 62
Western Blot
(immunoblot)
DEFINITION 62
Combines the resolving power of gel electrophoresis and the
specificity of antibodies. Used to separate proteins then
identify a specific proteins using SDS Gel
TERM 63
Cofactor
DEFINITION 63
Non-protein part of enzyme need for activity
TERM 64
Coenzyme
DEFINITION 64
Organic Cofactor
TERM 65
Covalently bound
cofactor
DEFINITION 65
Prosthetic group
Holoenzyme
A whole functioning enzyme
TERM 67
Apoenzyme
DEFINITION 67
Protein only
TERM 68
Enzymes are catalysts
which:
DEFINITION 68
Alter the rates of the reaction they catalyze but not the
equilibrium between substrates and products or the free
energy available from the reaction
TERM 69
Transition State
DEFINITION 69
Point at top of the energy hill at which decay to the S or P
state is equally probable
TERM 70
Activation energy
DEFINITION 70
The difference between the energy levels of the ground state
and the transition state
Competitive inhibition:
inhibitor often resembles the substrate, it binds at the active
site
TERM 77
Competitive Inhibition can be overcome
at:
DEFINITION 77
high substrate concentration
TERM 78
Irreversible inhibitors:
DEFINITION 78
acetylcholinesterase, suicide inhibitors
TERM 79
Suicide inhibition
DEFINITION 79
enzymes mechanism attack on inhibitor causes enzyme to
permanently inhibit itself (forms a covalent bond)
TERM 80
Clavulanate/Amoxicillin
DEFINITION 80
suicide inhibitor of beta lactamase
pH dependence of enzyme activity
catalytic groups, conformation
TERM 82
Allosteric
DEFINITION 82
first enzyme in a pathway, usually more than one subunit
TERM 83
Allosteric activators and inhibitors
DEFINITION 83
ATP - heterotrophic allosteric activator; CTP heterotrophic
allosteric inhibitor
TERM 84
ATP
DEFINITION 84
Adenosine triphosphate
TERM 85
ADP
DEFINITION 85
Adenosine diphosphate
Beta Anomer
OH on same side as CH2OH
TERM 92
Aldose
DEFINITION 92
monosaccharide containing one aldehyde group per
molecule
TERM 93
Ketose
DEFINITION 93
sugar containing one ketone group per molecule
TERM 94
Glycosidic bond
DEFINITION 94
type of covalent bond that joins a carbohydrate (sugar)
molecule to another group which may or may not be
attached to another carbohydrate
TERM 95
N-glycosidic bond
DEFINITION 95
Has N attached
O-glycosidic bond
Has O attached
TERM 97
Composition of sucrose:
DEFINITION 97
fructose + glucose
TERM 98
Composition of lactose:
DEFINITION 98
galactose + glucose
TERM 99
Composition of trehalose:
DEFINITION 99
glucose + glucose
TERM 100
Composition of
maltose:
DEFINITION 100
glucose + glucose
