bchem ch 3 MCAT

Proteins that provide shape and mechanical support to cells

Structural proteins

Major structural protein in connective tissue

Collagen

Structural protein that provides elasticity to tissues

Elastin

Structural protein forming intermediate filaments

Keratin

Cytoskeletal protein involved in cell shape and movement

Actin

Cytoskeletal protein forming microtubules

Tubulin

Proteins that convert chemical energy into mechanical work

Motor proteins

Motor protein that moves along actin filaments

Myosin

Motor protein that moves toward the plus end of microtubules

Kinesin

Motor protein that moves toward the minus end of microtubules

Dynein

Proteins that reversibly bind other molecules

Binding proteins

Protein that binds oxygen in blood

Hemoglobin

Protein that binds oxygen in muscle

Myoglobin

Protein that transports fatty acids in blood

Albumin

Proteins that bind DNA and regulate gene expression

Transcription factors

Proteins mediating cell-cell or cell-matrix interactions

Cell adhesion molecules/cam

Calcium-dependent cell adhesion proteins

Cadherins

Cell adhesion proteins involved in leukocyte trafficking

Selectins

Cell adhesion proteins connecting cells to extracellular matrix

Integrins

Proteins produced by B cells that bind antigens

Immunoglobulins

Another name for immunoglobulins

Antibodies

Region of antibody that binds antigen

Variable region

Region of antibody responsible for immune effector functions

Constant region

Most abundant antibody in blood

IgG

Antibody involved in allergic responses

IgE

Antibody found in mucosal secretions and breast milk

IgA

Proteins that transmit signals across cell membranes

Signal transduction proteins

Membrane proteins allowing ion passage

Ion channels

Ion channels opened by voltage changes

Voltage gated ion channels

Ion channels opened by ligand binding

Ligand gated ion channels

Ion channels opened by mechanical stress

Mechanically gated ion channels

Receptors that activate intracellular enzymes upon ligand binding

Enzyme linked receptors

Most common enzyme linked receptor type on the MCAT

Receptor tyrosine kinases

Process initiated when RTKs bind ligand

Dimerization and autophosphorylation

Common ligand for RTKs

Insulin

Receptors that signal through heterotrimeric G proteins

G protein coupled receptors

Number of transmembrane domains in GPCRs

Seven

Subunits of heterotrimeric G proteins

Alpha beta gamma

Inactive alpha subunit binds

GDP

Active alpha subunit binds

GTP

Second messenger produced by adenylyl cyclase

cAMP

Second messenger that activates protein kinase A

cAMP

Second messengers produced by phospholipase C

IP3 and DAG

Effect of IP3

Calcium release from endoplasmic reticulum

Effect of DAG

Activation of protein kinase C

Technique separating proteins by size using electric field

SDS PAGE

Detergent that denatures proteins and adds negative charge

SDS

What SDS PAGE separates proteins by

Molecular weight

Smaller proteins in SDS PAGE migrate

Farther

Electrophoresis technique separating proteins by charge and size

Native PAGE

Technique separating proteins by charge only

Isoelectric focusing

Point at which protein has no net charge

Isoelectric point

Technique combining isoelectric focusing and SDS PAGE

Two dimensional electrophoresis

Technique that identifies proteins using antibodies

Western blot

Technique detecting DNA sequences

Southern blot

Technique detecting RNA sequences

Northern blot

Antibody based assay used to quantify proteins

ELISA

Technique that pulls a protein out of solution using antibodies

Immunoprecipitation

Technique separating molecules based on interactions with a stationary phase

Chromatography

Chromatography separating proteins by size

Size exclusion chromatography

Proteins that elute first in size exclusion chromatography

Largest proteins

Chromatography separating proteins by charge

Ion exchange chromatography

Chromatography separating proteins by specific binding

Affinity chromatography

Chromatography commonly using antibodies or ligands

Affinity chromatography

Technique used to determine protein molecular weight and identity

Mass spectrometry

Level of protein structure defined by amino acid sequence

Primary structure

Protein structure stabilized by hydrogen bonds between backbone atoms

Secondary structure

Examples of secondary structure

Alpha helices and beta sheets

Protein structure stabilized by side chain interactions

Tertiary structure

Protein structure formed by multiple polypeptide chains

Quaternary structure

Bond stabilizing primary structure

Peptide bond

Covalent bond stabilizing tertiary structure

Disulfide bond

Noncovalent interactions stabilizing tertiary structure

Hydrophobic ionic hydrogen bonds

Loss of secondary tertiary or quaternary structure

Denaturation

Does denaturation break peptide bonds

No

Common causes of protein denaturation

Heat pH detergents

Analysis determining which amino acids are present

Amino acid composition analysis

Technique determining N terminal amino acid sequence

Edman degradation

Measurement of protein function

Activity assay

What activity assays measure

Biological or binding function

Measurement of protein concentration

Protein concentration determination

Technique measuring absorbance at 280 nm

UV spectroscopy

Amino acids contributing to 280 nm absorbance

Tryptophan tyrosine phenylalanine

Colorimetric protein assay using copper ions

Biuret assay

Highly sensitive dye based protein assay

Bradford assay

Law relating absorbance to concentration

Beer Lambert law

Equation for Beer Lambert law

A equals epsilon l c

Common MCAT protein analysis trap

Confusing SDS PAGE with native PAGE

Common MCAT signaling trap

Confusing GPCRs with receptor tyrosine kinases

Common MCAT protein structure trap

Thinking denaturation breaks peptide bonds