Cell Biology Exam 1

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Virus

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small, intracellular parasite, consisting of nucleic acid (DNA or RNA) enclosed in a protein coat. Can only replicate in susceptible host cell.

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Prokaryote

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class of organism including bacteria and archaea, lack a true membrane-limited nucleus and other organelles

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Eukaryote

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class of organism composed of one or more cells contain membrane-enclosed nucleus and organells. Constitutes one of three distinct evolutionary lineages of modern day organisms (also called eukarya)

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Archaea

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class of prokaryotes constitues one of the three distinct evoltionary lineages of modern-day organisms. (also called archaebacteria/archaens)

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Covalent Bond

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stable chemical force that holds atoms in molecules together by sharing one or more pairs of electrons

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Hydrogen Bond

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non covalent interaction between an atom (commonly O or N) carrying partial negative charge.

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Hydrophilic

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interacting effectively with water

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Hydrophobic

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not interacting effectivly with water, in general poorly soluble or insoluble in water

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Hydrophobic effect

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tendency of non-polar molecules or parts of molecules to associate with each other in aqueous solution so as to minimize their direct interactions with water; commonly called Hydrophobic interaction or bond

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Van der Waals interactions (forces)

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weak non covalent interaction due to small, transient asymmetric electron distributions around atoms (dipoles)

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Ionic interactions

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non covalent interaction between a positively charged ion (cation) and negatively charged ion (anion) (commonly called ionic bond)

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molecular complementarity

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lock and key kind of fit between the shapes, charges, hydrophobicity and/or other physical properties of two molecules or portion thereof that allow formation of multiple on-covalent interaction between them at close range

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non covalent interactions

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any relatively weak interaction that does not involve an intimate sharing of electrons

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amino acid

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organic compound containing at least one amino group and one carboxyl group. Aa are monomers for building proteins, amino group and carboxyl group covalently linked to central C atom (alpha carbon) to which variable side chain is attached.

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alpha carbon atom

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in aa, central carbon that is bonded to 4 different chemical groups (except glycine) including side chain (R group)

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side chain

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peptide bond

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covalent amide linkage between aa formed between amino group of one aa and the carboxyl group of another with the net release of a water molecule (dehydration)

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polypeptide

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linear polymer of aa connected by peptide bonds, usually containing 20 or more residues.

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primary structure

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in proteins = linear sequence (arrangement) of aa within a polypeptide chain

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secondary structure

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in proteins, local folding of a pp chain into regular structures, including alpha helix, beta sheet and beta turns

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tertiary structure

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in proteins, overall 3D form of a pp chain stabilized by multiple non-covalent interaction between side chains

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quaternary structure

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number and relative positions of pp chains in multimeric (multisubunit) proteins

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disulfide bond

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-S-S- a common covalent linkage between the sulfur atoms on two cysteine residues in different polypeptides or in different parts of the same polypeptide

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alpha helix

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common protein secondary structure in which linear sequence of aa is folded into a right-handed spiral stabilized by H-bonds between carboxyl and amide groups in the backbone

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beta sheet

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a flat, secondary structure in proteins that is created by hydrogen bonding between the backbone atoms in two different polypeptide chains or segments of a folded chain

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beta turn

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a short U-shaped secondary structure in proteins.

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chaperone

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prevent misfolding of a target protein or actively facilitate proper folding of an incompletely folded target protein

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conformation

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precise shape of a protein or other macromolecule in 3D resulting from spatial location of the atoms in the molecule.

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domain

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region of protein that has a distinct and often independent, function or structure that has a distinct topology relative to rest of the protein

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motif

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short, recurring patterns in DNA that are presumed to have a biological function. Often they indicate sequence-specific binding sites for proteins such as nucleases and transcription factors (TF).

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homology

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similarity in characteristics that reflects a common evolutionary origin. Proteins or genes that exhibit homology are said to be homologous and sometime are called homologs. Reflect a common evolutionary origin

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enzyme activation energy

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input of energy required to initiate a chemical reaction, enzymes increase rate of reaction by reducing the rate of reaction

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active site

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specific region of an enzyme that binds to a substrate molecule(s) and promotes a chemical change in the bound substrate

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Km

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Michaelisconstant

Km= (k-1+kcat) /k1

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Kd

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dissociation constant

Kd=(k-1)/k1

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ligand

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any molecule other than an enzyme substrate that binds tightly and specifically to a macromolecule usually a protein, forming a macromolecule-ligand complex.

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substrate

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molecule that undergoes a charge in a reaction catalyzed by an enzyme

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allostery

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change in the tertiary and/or quaternary structure of a protein induced by binding of a small molecule to a specific regulatory site causing a change in protein activity

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post-translational modification

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refers to the covalent and generally enzymatic modification of proteins during or after protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product.

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kinase

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an enzyme that transfer the terminal (γ) phosphate group from ATP to a substrate.

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phosphorylation

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covalent addition of a phosphate group to a molecule such as a sugar or protein. Hydrolysis of ATP often accompanies phosphorylation, providing energy to drive the reaction and the phosphate group that is covalently added to the target molecule. Enzymes that catalyze phosphorylation are called kinases.

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ubiquitin

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small protein that can be covalently linked to other intracellular proteins, thereby tagging these proteins for degradation by the proteasome, sorting to the lysosome or alteration in the function of the target protein

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proteasome

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large multifunctional protease complex in the cytosol which degrades intracellular proteins marked for destruction by attachment of multiple ubiquitin molecules

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amphipathic

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referring to a molecule or structure that has both hydrophobic and hydrophilic parts

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cytosolic face

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face of a cell membrane directed toward the cytosol

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exoplasmic face

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face of cell membrane directed away from the cytosol

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lumen

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aqueous interior of an organelle

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cholesterol

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lipid containing the 4-ring steroid structure with hydroxyl group on one ring. component of many eukaryotic membranes and precursor of steroid hormones, bile acids and vitamin D

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sterol

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any of a group of naturally occurring unsaturated steroid alcohols, typically waxy solids.

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lipid raft

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microdomain in the plasma membrane that is enriched in cholesterol, sphingomyelin and certain proteins

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sphingolipid

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major group of membrane lipids derived from sphingosine, that contain 2 long hydrocarbon chains, and either a phosphorylated head group (sphingomyelin) or carbohydrate head group (cerebrosides, gangliosides)

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phospolipid bilayer

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2 layer, sheet-like structure in which the polar head groups of phospholipids are exposed to the aqueous media on either side and the non-polar fatty acyl chains are in the centre. Foundation of all biomembranes

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phospoglyceride

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amphipathic derivatives of glycerol 3-phosphate that generally consists of 2 hydrophobic fatty acyl chains esterfied to the hydroxyl groups in glycerol and a polar head group attached to the phosphate. most popular lipid in biomembranes

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glycolipid

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any lipid to which a short carbohydrate chain is covalently linked, common in plasma membrane

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glycoprotein

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any protein to which one or more oligosaccharide chains are covalently linked. Most secreted proteins and many membrane proteins are glycoproteins

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fatty acid

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any long hydrocarbon chain that has a carboxyl group at one end; major energy source during metabolism and precursor of synthesis of phospholipids, triglyerides and cholesteryl esters

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saturated

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referring to a compound (e.g. fatty acid) in which all C-C bonds are single bonds.

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unsaturated

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referring to a compound (e.g. fatty acid) in which one C-C bonds is a double or triple bond

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trans-fat

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unsaturated fatty acid, typically found in margarines and manufactured cooking oils, result of hydrogenation.

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integral membrane protein

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any protein that contains one or more hydrophobic segments embedded within the core of the phospholipid bilayer

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lipid anchored membrane protein

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any protein that is tethered to a cellular membrane by one or move covalently attached lipid groups, which are embedded in phospholipid bilayer.

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peripheral membrane protein

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any protein that associates with the cytosolic or exoplasmic face of a membrane but does not enter the hydrophobic core of phospholipid bilayer

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fluorescencerecovery after photobleaching (FRAP),

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A type of fluorescent method which tracks the movement of cell surface proteins

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Cell Line

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a population of cultures cells of plant or animal origin which has undergone a genetic change allowing the cells to grow indefinitely

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cell strain

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a population of cultured cells of plant or animal origin that has a finite life span and eventually dies commonly after 25-50 generations

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cell culture

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removal of cells from animal or plants and subsequent environment

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medium

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nutrient-rich liquid

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plasma membrane

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membrane surrounding a cell that separates the cell from its external environment, consists of phospholipids and associated membrane lipids and proteins

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Endoplasmic Reticulum (ER)

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network of interconnected membranous structures within the cytoplasm of eukaryotes contiguous with the nuclear envelope.
rough ER = associate with ribosomes, functions in synthesis and processing of secreted and membrane proteins.
smooth ER = lacks ribosomes, functions in lipid synthesis

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Golgi Apparatus

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stacks of flattened interconnected membrane bound compartments (cisternae) in eukaryotes that function in processing and sorting proteins and lipids destined for other cellular compartments or for secretion.

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Lysosome

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small organelle that has internal pH of 4-5 contains hydrolytic enzymes, functions in degradation of materials internalized by endocytosis and of cellular components in autophagy.

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mitochondria

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large organelle that is surrounded by 2 phospholipid bilayer membranes, contains DNA, carries out oxidative phosphorylation, thereby producing most of the ATP in eukaryotic cells

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peroxisome

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small organelle containing enzymes for degrading fatty acids and aa by reactions generating hydrogen peroxide converted to water and oxygen by catalase

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organlles

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membrane-limited sub cellular structure found in eukaryotic cells

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light microscopy

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in bright field, light from tungsten lamp focussed on specimen (usually strained with dyes to enhance contrast) by a condenser lens below the stage

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fluorescence microscopy

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beam of light from a mercury lamp is directed to the excitation filter allowing the correct wavelength of light to pass through. light is then reflected off a dichroic mirror, through the objective lens which focuses it on the specimen. Fluoresce light emitted by specimen passes up through objective lens, then dichromic mirror, focussed and recorded on detector at image plane

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immunofluorescence

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most widely used method of detecting specific protein localization. Antibody covalently attached to a fluorescent dye used to stain cells fixed with chemical crosslinker.

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Deconvolution Microscopy

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yields high-resolution optical sections that can be reconstructed to create 1 3D image. uses calculated point-spread function of out-of-focus light to computationally remove fluorescence contributed to out of focus parts of the sample

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transmission electron microscope (TEM)

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electrons emitted from a heated filament, accelerated by electric field (anode) and focussed on specimen by a magnetic condenser lens. Some scattered by interaction with metal stain, then focussed by series of magnetic objective and projector lenses to form a magnified image

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scanning electron microscope (SEM)

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beam of electrons emitted, focussed by condenser, objective lenses on metal-coated specimen is scanned across a specimen by scanning coils. Electrons scattered from specimen metal coating are collected by photomultiplier tube detector to form an image

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cryoelectron (CryoEM) microscopy

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images hydrated, unfixed and unstained biological specimens avoiding artifacts introduced by fixation and dehydration. 3D structure computed from series of 2D projection images recorded from the 3D specimen as specimen tilted trough a semicircle.

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Forster resonance energy transfer (FRET)

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check protein-protein interaction. energy transferred between different fluorochromes on different proteins by FRET. excitation (433nm) of cyan fluro protein (CFP) used to protein x emits 475nm light, can excite fluores protein )YFP) fused to protein Y to emit 530nm light, if protein interaction brings CFP and YFP close enough together.

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high throughput screening

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siRNA/chemical libraries applied to multi-well plates, observed by automated microscope and analyzed by computer software.

high throughputs cell images: high content

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high content screening

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same as high throughput

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chemical biology

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small molecule inhibitors of proteins

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RNA interference

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inhibition of a protein: siRNA or other RNA interference

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Flow cytometry

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cell sorting, flow cytometer machine flows cells past a laser beam which measure the light that they scatter and the fluorescence that they emit. Thus can quantify the cells expressing the fluorescent protein in a mixture.

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fluorescence activated cell sorting (FACS)

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based on flow cytometry, can both analyze cells and select the few fluorescent cells from thousands of others and sort them into a separate culture dish. Cells mixed with a buffer and forced through a vibrating nozzle to generate tiny droplets.

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differentialcentrifugation

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purification of organelles, using centrifugation , most common initial step in protein purification from cells or tissues is the separationof water-soluble proteins from insoluble cellular material bydifferential centrifugation.

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equilibrium density-gradient centrifugation

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used to mainly separate DNA, lipoproteins that carry lipids through the circulatory system or organelles

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electrochemical gradient

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driving force that determines energetically favorable direction of transport of an ion (or charged molecule) across a membrane, represents the combined influence of the ions concentration gradient across the membrane and membrane potential

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simple diffusion

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net movement of a molecule across a membrane down its concentration gradient at a rate proportional to the gradient and the permeability of the membrane (also called passive diffusion)

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facilitated transport

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protein-aided transport of an ion or small molecule across a cell membrane down its concentration gradient at a rate greater than that obtained by simple diffusion

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channel

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membrane proteins that transport water, ions, or small hydrophilic molecules across membranes down concentration or electric potential potential gradients

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aquaporrin

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family of membrane transport proteins that allow water and a few other small uncharged molecules such as glycerol to cross biomembranes

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uniport

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transport of a single molecule type down its concentration gradient using a uniporter

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active transport

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protein mediated movement of an ion or small molecule across a membrane against its concentration or electrochemical gradient driven by coupled hydrolysis of ATP

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cotransport

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protein mediated movement of an ion or small molecule across a membrane against its concentration gradient driven by coupling to movement of a second molecule town its concentration in same or opposite direction

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symport

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type of cotransport in which membrane protein (symporter) transports 2 different molecules or ions across the membrane in the same direction

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antiport

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type of cotransport in which a membrane protein (antiporter) transports 2 different molecules across a cell membrane in opposite directions

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ATP-powered pumps

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any transmembrane protein that has ATPase activity and couples hydrolysis of ATP to the active transport of ion or small molecule across a biomembrane against its electrochemical gradient

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F-class pumps

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bacterial plasma membrane, inner mitochondrial membrane, thylakoid membrane of chloroplast

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P-class pump

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plasma membrane of plants, fungi, bacteria (H+ pump), plasma membrane of higher eukaryotes (Na+/K+ pump), apical plasma membrane of mammalian stomach (H+/K+ pump), plasma membrane of all eukaryotic cells (Ca2+ pump), sarcoplasmic reticulum membrane in muscle cells (Ca2+ pump)

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V-class pump

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Vacuolar membranes in plants, yeast, other fungi. Endosomal and lysosomal membranes in animal cells, plasma membrane of osteoclasts and some kidney tubule cells

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ABC superfamily

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large group of integral membrane proteins that often function as ATP-powered membrane transport proteins to move diverse molecules (e.g. phospholipids, cholesterol, sugars, ions, peptides) across cellular membranes

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multidrugresistance protein

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originally called MDR1, now known as ABCB1, uses energy derived from the cytosol to the extra-cellular medium.

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Flippase

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protein that facilities the movement of membrane lipids from one leaflet to the other leaflet of a phospholipid bilayer

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Membrane potentional

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Electric potential difference expressed in volts across a membrane due to the slight excess of positive ions (cations) on one side and negative ions (anions) on the other side.

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Na+/K+ ATPase

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a P-class ATP-powered pump that couples the hydrolysis of one ATP molecule to export of Na+ ions and import of K+ ions. Largely responsible for maintaining the normal intracellular concentrations of Na+ (low) and K+ (high) in animal cells

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resting (non-gated) K+ channel

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in the plasma membrane which in conjunction with the cytosolic K+ concentration produced by the Na+/K+ ATPase, are primarily responsible for generating the inside-negative resting membrane potential in animal cells

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Catabolism

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cellular degradation of complex molecules to simpler ones usually accompanied by the release of energy. (Anabolism is the reverse in which energy is used to synthesize complex molecules to simpler ones)

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Anaerobic

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referring to a cell, organism or metabolic processes that functions in the absence of gaseous oxygen (O2)

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Glycolysis

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metabolic pathway in which sugars are degraded anaerobically to lactate or pyruvate in the cytosol with the production of ATP

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Substrate level phosphorylation

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formation of ATP from ADP and Pi catalyzed by cytosolic enzymes in reaction that do not depend on a proton-motive force or molecular oxygen

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aerobic oxidation

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oxygen requiring metabolism of sugars and fatty acids to CO2 and H2O coupled to the synthesis of ATP

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citric acid cycle

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set of 9 coupled reactions occurring in the mitochondrial matrix in which acetyl groups are oxidized, generating CO2 and reduced intermediates used to produce ATP (krebs and TCA)

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mitochondria inner matrix

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The inner mitochondrial membrane (IMM) is the mitochondrialmembrane which separates the mitochondrial matrix from the intermembrane space.

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oxidative phosphorylation

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phosphorylation of ADP to form ATP driven by the transfer of electrons to oxygen (O2) in bacteria and mitochondria. involved the generation of a proton-motive force during ETC and subsequent use to power ATP synthesis.

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respiratory chain

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ETC

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electron transport chain (ETC)

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set of 4 large multiprotein complexes in the inner mitochondrial membrane plus diffusible cytochrome c and coenzyme Q through which electron flow from reduced electron donors (e.g. NADH) to O2. Each member of the chain contains one or more bound electron carriers

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prosthetic groups

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a nonprotein group forming part of or combined with a protein.

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reduction potential

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measure of the tendency of a chemical species to acquire electrons and thereby be reduced. Reduction potential is measured in volts (V), or millivolts (mV).

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electron carrier

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any molecule or atom that accepts electrons from donor molecule and transfers them to acceptor molecules in coupled oxidation and reduction reactions.

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hydrogen carrrier

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organic macromolecule that transports atoms of hydrogen from one place to another inside a cell or from cell to cell for use in various metabolical processes.

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NAD (nicotinamide adenine dinucleotide)

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a small organic molecule that function as an electron carrier by accepting two electron from a donor molecule and one H+ from the solution

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FAD (flavin adenine dinucleotide)

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small organic molecule that functions as an electron carrier by accepting 2 electrons from a donor molecule and 2 H+ from the solution

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coenzyme Q

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any of a class of compounds that occur in all living cells and that act as electron-transfer agents in cell respiration

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cytochrome

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group of colored heme-containing proteins some of which function as electron carriers during cellular respiration and photosynthesis

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ATP

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nucleotide that is most important molecule for capturing and transferring free energy in cells. Hydrolysis releases large amount of free energy which can be used to drive cellular processes

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ATP synthase

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multimeric protein complex bound to inner mitochondrial membranes, thylakoid membranes of cholorplasts and the bacterial plasma membrane that catalyzes syntheis of ATP during oxidative phophorylation and photosynthesis.

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chemiosmosis

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process whereby an electrochemical gradient (pH plus electric potential) across membrane used to drive an energy-requiring process such as ATP synthesis

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PMF - proton motive force

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energy equivalent of proton (H+) conc. gradient and electric potential gradient across the membrane used to drive ATP synthesis by ATP synthase, transport of molecules against their concentration gradient and movement of bacterial flagella

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Uncoupler

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any natural substance or chemical agent that dissipates the proton-motive-force across the inner mitochondrial membrane or thylakoid membrane of chloroplasts,thereby inhibiting ATP synthesis

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F0F1 complex

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also known as ATP synthase

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reactive oxygen species

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by-products of Electron Transport, forms radicals