Nonenzymatic Protein Function and Protein Analysis & Carbohydrate Structure and Function

Practice flashcards covering nonenzymatic protein function, protein analysis, and carbohydrate structure and function from MCAT Biochemistry chapters.

Motif (Protein Structure)

A super-secondary structure consisting of a repetitive organization of secondary structural elements together.

Collagen

A structural protein with a characteristic trihelical fiber that makes up most of the extracellular matrix of connective tissue.

Trihelical fiber (Collagen)

Structure consisting of three left-handed helices woven together to form a secondary right-handed helix.

Function of Collagen

Provides strength and flexibility throughout the body.

Osteogenesis imperfecta

Also known as brittle bone disease, a disorder where the replacement of glycine in collagen leads to improper folding and bone fragility.

Elastin

An extracellular matrix component of connective tissue whose primary role is to stretch and then recoil like a spring.

Keratins

Intermediate filament proteins found in epithelial cells that contribute to mechanical integrity and function as regulatory proteins.

Primary component of hair and nails

Keratin.

Actin

A protein making up microfilaments and thin filaments in myofibrils; it is the most abundant protein in eukaryotic cells.

Actin Polarity

Possesses a positive side and a negative side, allowing motor proteins to travel unidirectionally.

Tubulin

The protein that makes up microtubules, providing structure and aiding in chromosome separation and intracellular transport.

Tubulin Polarity

The negative end is usually adjacent to the nucleus, while the positive end is in the periphery of the cell.

Motor Proteins

Proteins that display enzymatic activity as ATPases to power conformational changes for motility.

Myosin

The primary motor protein that interacts with actin, serving as the thick filament in a myofibril.

Myosin structure

Each subunit has a single head and neck; movement at the neck is responsible for the power stroke of sarcomere contraction.

Kinesins

Motor proteins associated with microtubules that generally bring vesicles toward the positive end ($soma \rightarrow synaptic terminal$ in neurons).

Dyneins

Motor proteins associated with microtubules involved in the sliding movement of cilia and flagella; they bring vesicles toward the negative end.

Retrograde transport in neurons

Movement of waste or recycled neurotransmitter back toward the soma (negative end of microtubule) via dyneins.

Binding Proteins

Proteins like hemoglobin or DNA-binding proteins that transport or sequester molecules by binding to them.

Affinity curve (Binding Proteins)

A representation of how well a protein binds its target molecule across varying concentrations.

Sequestration Goal (Binding Protein)

High affinity across a large range of concentrations to keep the target bound at nearly $100\%$.

Cell Adhesion Molecules (CAMs)

Integral membrane proteins found on cell surfaces that aid in binding the cell to the extracellular matrix or other cells.

Cadherins

Glycoproteins that mediate calcium-dependent cell adhesion and often hold similar cell types together.

E-cadherin

A type-specific cadherin used by epithelial cells.

N-cadherin

A type-specific cadherin used by nerve cells.

Integrins

Proteins with two membrane-spanning chains ($\alpha$ and $\beta$) used for communicating with the extracellular matrix.

Integrin $\alpha_{IIb}\beta_{3}$

Allows platelets to stick to fibrinogen to stabilize a blood clot.

Selectins

CAMs that bind to carbohydrate molecules projecting from other cell surfaces; they form the weakest bonds of the CAMs.

Antibodies

Also called immunoglobulins ($Ig$), these are proteins produced by B-cells to neutralize targets like toxins and bacteria.

Antibody Structure

Y-shaped proteins made of two identical heavy chains and two identical light chains held by disulfide linkages.

Antigen-binding region

Located at the tips of the antibody 'Y,' containing specific polypeptide sequences that bind one unique antigenic sequence.

Constant region (Antibody)

The part of the antibody molecule involved in recruitment and binding of other immune cells like macrophages.

Opsonization

The function of an antibody marking a pathogen for destruction by other white blood cells.

Agglutination

Clumping together of antigen and antibody into large insoluble complexes for phagocytosis by macrophages.

Biosignaling

A process in which cells receive and act on signals, involving ligands, receptors, and second messengers.

Ion Channels

Proteins that create specific pathways for charged molecules to pass through the membrane via facilitated diffusion.

Facilitated diffusion

Type of passive transport moving molecules down a concentration gradient through a transmembrane protein pore.

Ungated Channels

Ion channels that have no gates and are unregulated, such as ungated potassium channels.

Voltage-Gated Channels

Channels regulated by membrane potential changes near the channel, such as voltage-gated sodium channels in neurons.

Ligand-Gated Channels

Channels where the binding of a specific substance causes them to open or close, such as $GABA$ binding to chloride channels.

Km (Transport Kinetics)

The solute concentration at which a transporter is functioning at half of its maximum activity.

Enzyme-Linked Receptors

Membrane receptors displaying catalytic activity in response to ligand binding, often initiating second messenger cascades.

Domains of Enzyme-Linked Receptors

Primary domains include the membrane-spanning domain, ligand-binding domain, and catalytic domain.

Receptor Tyrosine Kinases (RTK)

An enzyme-linked receptor that dimerizes upon ligand binding and performs autophosphorylation.

G Protein-Coupled Receptors (GPCR)

A family of integral membrane proteins characterized by seven membrane-spanning $\alpha$-helices involved in signal transduction.

Heterotrimeric G protein

The intracellular link to guanine nucleotides ($GDP$ and $GTP$) utilized by GPCRs to transmit signals.

$G_{s}$ Protein

Stimulates adenylate cyclase, which increases levels of $cAMP$ in the cell.

$G_{i}$ Protein

Inhibits adenylate cyclase, which decreases levels of $cAMP$ in the cell.

$G_{q}$ Protein

Activates phospholipase C, leading to the formation of $PIP_2$, $DAG$, and $IP_3$, and increasing cellular calcium.

$\alpha$ subunit (G protein)

In its inactive form, it binds $GDP$; when activated, $GDP$ is replaced by $GTP$, and it dissociates from $\beta$ and $\gamma$.

Cell Lysis and Homogenization

The process of crushing, grinding, or blending tissue into an evenly mixed solution to isolate proteins.

Electrophoresis

A method of separating compounds by subjecting them to an electric field, moving them based on net charge and size.

Anode (Electrophoresis)

The positively charged electrode toward which negatively charged particles (anions) migrate.

Cathode (Electrophoresis)

The negatively charged electrode toward which positively charged particles (cations) migrate.

Migration Velocity Formula

$v = \frac{Ez}{f}$, where $E$ is field strength, $z$ is net charge, and $f$ is the frictional coefficient.

Polyacrylamide gel

The standard porous matrix medium for protein electrophoresis.

Native PAGE

A method for analyzing proteins in their native states, limited by varying mass-to-charge and mass-to-size ratios.

Dalton ($Da$)

An alternative term for molar mass ($g/mol$); the average molar mass of one amino acid is $\sim 100\,Da$.

SDS-PAGE

A technique using sodium dodecyl sulfate to denature proteins and give them a uniform negative charge, separating them by mass alone.

Isoelectric Point ($pI$)

The $pH$ at which a protein or amino acid is electrically neutral (as a zwitterion).

Isoelectric Focusing

Separation of proteins based on $pI$ using a gel with a $pH$ gradient; proteins stop moving when $pH = pI$.

Anode in Isoelectric Focusing

Has acidic ($H^{+}$-rich) gel and a positive charge ($A+$).

Chromatography

A variety of techniques that require a homogenized protein mixture to be fractionated through a porous matrix.

Stationary Phase (Adsorbent)

The solid medium (e.g., silica beads) onto which a sample is placed in chromatography.

Mobile Phase

The solvent run through the stationary phase to allow the sample to elute.

Retention Time

The amount of time a compound spends in the stationary phase.

Partitioning

The separation of components within the stationary phase due to varying retention times.

Column Chromatography

Uses gravity to move solvent and compounds down a column filled with silica or alumina beads.

Ion-Exchange Chromatography

Beads are coated with charged substances to attract compounds with an opposite charge.

Size-Exclusion Chromatography

Beads contain tiny pores that trap small compounds, allowing large compounds to elute faster.

Affinity Chromatography

Customized columns with high affinity for a specific protein, often using receptors or antibodies.

X-ray crystallography

The most reliable method for determining protein structure, measuring electron density on a high-resolution scale.

Edman Degradation

Sequentially removes the N-terminal amino acid of a protein (up to $50$-$70$ residues) for analysis via mass spectroscopy.

Cleavage Enzymes for Large Proteins

Includes chymotrypsin, trypsin, and cyanogen bromide.

UV Spectroscopy (Proteins)

Used for concentration determination due to the presence of aromatic side chains (phenylalanine, tyrosine, tryptophan).

Bradford Protein Assay

A colorimetric method using Coomassie Brilliant Blue dye that turns from green-brown to blue upon binding to amino acids.

Bradford Reagent Shift

The dye gives up protons to the protein, stabilizing its blue ionic form; absorbance is then measured against a standard curve.

Monosaccharide

The simplest structural unit of carbohydrates, such as glucose or fructose.

Triose

A monosaccharide containing three carbon atoms.

Aldose

A carbohydrate with an aldehyde group as its most oxidized functional group.

Ketose

A carbohydrate with a ketone group as its most oxidized functional group.

Glyceraldehyde

The simplest aldose (an aldotriose).

Dihydroxyacetone

The simplest ketose (a ketotriose, with the carbonyl usually at $C\text{-}2$).

Glycosyl residues

Sugars acting as substituents via glycosidic linkages.

Stereoisomers (Optical Isomers)

Compounds with the same chemical formula that differ only in the spatial arrangement of atoms.

Enantiomers

Nonidentical, nonsuperimposable mirror images of each other.

Chiral Carbon

An atom attached to four different groups.

Number of Stereoisomers Formula

$2^n$, where $n$ is the number of chiral carbons.

D-sugar (Fischer Projection)

Has the hydroxide of the highest-numbered chiral center on the right.

L-sugar (Fischer Projection)

Has the hydroxide of the highest-numbered chiral center on the left.

Diastereomers

Stereoisomers that are not mirror images of each other.

Epimers

A subtype of diastereomers that differ in configuration at exactly one chiral center.

Hemiacetal

Produced by the intramolecular reaction of a hydroxyl group with an aldehyde group in a sugar.

Hemiketal

Produced by the intramolecular reaction of a hydroxyl group with a ketone group in a sugar.

Pyranose

A stable six-membered ring structure of a cyclic sugar.

Furanose

A stable five-membered ring structure of a cyclic sugar.

Anomeric Carbon

The new chiral center formed at the carbonyl carbon during ring closure.

Alpha-anomer (Glucose)

The $\text{-}OH$ group on $C\text{-}1$ is trans to the $\text{-}CH_2OH$ substituent (axial and down).

Beta-anomer (Glucose)

The $\text{-}OH$ group on $C\text{-}1$ is cis to the $\text{-}CH_2OH$ substituent (equatorial and up).

Haworth Projection

A method for depicting cyclic sugars as planar rings, though pyranose rings actually adopt chair-like configurations.