Unit 2

Protein-Protein Interactions

The specific interactions between proteins that occur during many critical cellular processes

Genome

The complete genetic material of an organism or species

Gene

A unit of heredity. At the molecular level, it is an organized unit of base sequences in a DNA strand that can be transcribed into RNA and ultimately results in the formation of a functional product

Prokaryotic Cell

A cell lacking a membrane-enclosed nucleus and cell compartmentalization (the cells of members of the domains Bacteria and Archaea are examples of this)

Bacteria

One of the three domains of life (the other two are Archaea and Eukarya)

Archaea

One of the three domains of life (the other two are Bacteria and Eukarya)

Plasma Membrane

The biological membrane that separates the internal contents of a cell from its external environment

Cytoplasm

The region of the cell that is contained within the plasma membrane

Nucleoid

The site in a bacterial cell where the genetic material (DNA) is located

Ribosome

A structure composed of proteins and rRNAs that is the site where translation of mRNAs and synthesis of polypeptides occurs

Cell Wall

A relatively rigid, porous structure located outside the plasma membrane of prokaryotic cells and cells in plants, fungi, and certain protists (provides support and protection)

Glycocalyx

1. An outer viscous covering surrounding a bacterium that traps water and helps protect the bacterium from drying out

2. A carbohydrate-rich zone on the surface of animal cells (also called a cell coat)

Capsule

A very thick, gelatinous glycocalyx produced by certain strains of bacteria that may help them avoid being destroyed by an animal’s immune (defense) system

Pili (singular, pilus)

Threadlike surface appendages that allow bacteria to attach during conjugation or to move across surfaces

Flagella (singular, flagellum)

Relatively long cell appendages that facilitate cellular movement or the movement of extracellular fluids

Eukaryote

A member of the domain Eukarya. The distinguishing feature of this is cell compartmentalization, including a cell nucleus (they include protists, fungi, plants, and animals)

Organelle

A subcellular structure or membrane-bound compartment with its own unique structure and function

Compartmentalization

A characteristic of eukaryotic cells, in which many membrane-bound organelles separate the cell into different regions. This process in a cell allows it to carry out specialized chemical reactions in different places

Liquid-Liquid Phase Separation

The phenomenon in which aggregated solutes, such as proteins and RNA molecules, separate from the bulk solvent, and form a droplet

Droplet Organelle

An organelle that is not surrounded by a membrane but exists as a droplet formed by liquid-liquid phase separation

Proteome

The complete complement of proteins that a cell or an organism makes

Cytosol

The region of a eukaryotic cell that is inside the plasma membrane and outside the organelles

Metabolism

The sum of all bodily activities and chemical reactions that occur within an organism to maintain life. Also, a specific set of chemical reactions that occur at the cellular level

Enzyme

A protein that acts as a catalyst to speed up a chemical reaction in a cell

Catabolism

A metabolic pathway that results in the breakdown of larger molecules into smaller molecules. Such reactions are often exergonic

Anabolism

A metabolic pathway that results in the synthesis of cellular molecules and macromolecules (requires an input of energy)

Cytoskeleton

In eukaryotes, a network within the cytosol consisting of three different types of protein filaments called microtubules, intermediate filaments, and actin filaments

Microtubule

A type of hollow protein filament composed of tubulin proteins that is part of the cytoskeleton and is important for cell shape, organization, and movement

Intermediate Filaments

A type of protein filament of the cytoskeleton of animal cells that helps maintain cell shape and rigidity

Actin Filaments

A thin type of protein filament that is composed of actin proteins, forms part of the cytoskeleton, and supports the plasma membrane (plays a key role in cell strength, shape, and movement)

Dynamic Instability

The oscillation of a single microtubule between growing and shortening phases (important in many cellular activities, including the sorting of chromosomes during cell division)

Microtubule-Organizing Center (MTOC)

A site in a eukaryotic cell from which microtubules grow

Centrosome

A single structure often near the nucleus of a eukaryotic cell that forms a nucleating site for the growth of microtubules (also called a microtubule-organizing center)

Centrioles

A pair of structures within the centrosome of animal cells. Most plant cells and many protists lack this

Pseudopodia

Temporary, finger-like projections of the plasma membrane that are used for cell movement and for engulfing particles

Motor Protein

A type of cellular protein that uses ATP as a source of energy to promote movement (consists of three domains called the head, hinge, and tail)

Axoneme

An internal structure of eukaryotic flagella and cilia that contains microtubules, the motor protein dynein, and linking proteins

Basal Bodies

A site at the base of flagella or cilia from which microtubules grow. These are anchored on the cytosolic side of the plasma membrane

Nucleus

In cell biology, an organelle found in eukaryotic cells that contains most of the cell’s genetic material

Endomembrane System

A network of membranes that includes the nuclear envelope, the endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, peroxisomes, and plasma membrane

Nuclear Envelope

A double-membrane structure that encloses the cell’s nucleus

Nuclear Pore

A passageway for the movement of molecules and macromolecules into and out of the nucleus (formed where the inner and outer nuclear membranes make contact with each other)

Chromosome

A discrete unit of genetic material composed of DNA and associated proteins. Eukaryotes have this in their cell nuclei and in plastids and mitochondria

Chromatin

The complex of DNA and proteins that makes up eukaryotic chromosomes

Nuclear Matrix

A filamentous network of proteins that is found inside the nucleus and lines the inner nuclear membrane. It serves to organize the chromosomes

Nuclear Lamina

A collection of protein fibers that line the inner nuclear membrane (part of the nuclear matrix)

Chromosome Territory

A distinct area where each chromosome is located within the cell nucleus of eukaryotic cells (these do not overlap)

Nucleolus

A droplet organelle in the nucleus of nondividing cells where ribosome assembly occurs

Endoplasmic Reticulum (ER)

A convoluted network of membranes in a cell’s cytoplasm that forms flattened, fluid-filled tubules, or cisternae

Cisternae

Flattened, fluid-filled tubules of the endoplasmic reticulum and Golgi apparatus

Lumen

The internal space or hollow cavity of an organelle or an organ, such as the endoplasmic reticulum, the stomach, or a blood vessel

ER Lumen

A single compartment enclosed by the ER membrane

Rough Endoplasmic Reticulum (Rough ER)

The part of the ER whose outer surface is studded with ribosomes (this region plays a key role in the initial synthesis and sorting of proteins that are destined for the ER, Golgi apparatus, lysosomes, vacuoles, plasma membrane, or extracellular environment

Membrane Vesicle

A small sphere enclosed by a membrane

Glycosylation

The covalent attachment of a carbohydrate to a protein or lipid, producing a glycoprotein or glycolipid, respectively

Smooth Endoplasmic Reticulum (Smooth ER)

The part of the ER whose outer surface is not studded with ribosomes. This region is continuous with the rough ER and functions in diverse metabolic processes such as detoxification, carbohydrate metabolism, accumulation of calcium ions (Ca²⁺), and synthesis and modification of lipids

Golgi Apparatus

A stack of flattened, membrane-bound compartments that performs three overlapping functions: secretion, processing, and protein sorting

Proteolysis

A processing event within a cell in which enzymes called proteases cut proteins into smaller polypeptides

Protease

An enzyme that cuts proteins into smaller polypeptides

Secretory Vesicle

A membrane vesicle carrying different types of materials that fuses with the cell’s plasma membrane to release the contents extracellularly

Secretory Pathway

A pathway for the movement of larger substances, such as carbohydrates and proteins, from the ER to the outside of a cell

Lysosome

A small organelle found in animal cells that contains acid hydrolases that degrade molecules and macromolecules

Acid Hydrolase

A hydrolytic enzyme found in lysosomes that functions at acidic pH and uses a molecule of water to break a covalent bond

Vacuole

Specialized organelles found in eukaryotic cells that function in storage, the regulation of cell volume, and degradation

Central Vacuole

An organelle that often occupies 80% or more of the volume of a plant cell and stores a large amount of water, enzymes, and inorganic ions

Contractile Vacuole

A small, membrane-enclosed, water-filled compartment that eliminates excess liquid from the cells of certain protists

Peroxisome

A relatively small organelle that is found in all eukaryotic cells and that catalyzes detoxifying reactions

Catalase

An enzyme within peroxisomes that breaks down hydrogen peroxide to water and oxygen gas

Glyoxysome

A specialized organelle within plant seeds that contains enzymes needed to convert fats to sugars

Membrane Transport

The movement of ions or molecules across a biological membrane

Cell Signaling

A vital function of the plasma membrane in which cells sense changes in their environment and communicate with each other

Cell Adhesion

A vital function of the cell membrane that allows cells to bind to each other. This is critical in the formation of multicellular organisms and provides a way to convey positional information between neighboring cells

Mitochondrion

A semiautonomous organelle found in eukaryotic cells that supplies most of a cell’s ATP

Cristae

Projections of the highly invaginated (folded) inner membrane of a mitochondrion

Mitochondrial Matrix

A compartment enclosed by the inner membrane of a mitochondrion

Chloroplast

A semiautonomous organelle found in plant and algal cells that carries out photosynthesis

Photosynthesis

The process whereby light energy is captured by plant, algal, or photosynthetic bacterial cells and is used to synthesize organic molecules from CO₂ and H₂O (or H₂S)

Thylakoid Membrane

A membrane within the chloroplast that forms many flattened, fluid-filled tubules that enclose a single, convoluted compartment. The membrane contains chlorophyll and is the site where the light-dependent reactions of photosynthesis occurs

Granum

A structure composed of stacked membrane-bound thylakoids within a chloroplast

Stroma

The fluid-filled region of the chloroplast between the thylakoid membrane and the inner membrane

Plastid

A general name given to organelles found in plant and algal cells that are bound by two or more membranes and contain DNA and large amounts of either chlorophyll (in chloroplasts), carotenoids (in chromoplasts), or starch (in amyloplasts)

Proplastid

A type of unspecialized structure from which a plastid is derived

Mitochondrial Genome

The chromosome found in mitochondria

Chloroplast Genome

The chromosome found in chloroplasts

Nuclear Genome

The chromosomes found in the nucleus of a eukaryotic cell

Binary Fission

The process of cell division in bacteria and archaea in which one cell divides into two cells. It is also the process by which mitochondria and chloroplasts divide

Endosymbiosis

A symbiotic relationship in which the smaller species (the symbiont or endosymbiont) lives inside the larger species (the host)

Endosymbiosis Theory

A theory that mitochondria and chloroplasts originated from bacteria that took up residence within primordial eukaryotic cells

Sorting Signal

A short amino acid sequence in a protein that directs the protein to its correct location in a cell (also known as a traffic signal)

Cotranslational Sorting

The sorting process in which the synthesis of certain eukaryotic proteins begins in the cytosol and then halts temporarily until the ribosome has become bound to the ER membrane

Post-Translational Sorting

The uptake of proteins into the nucleus, mitochondria, chloroplasts, or peroxisomes that occurs after the protein is completely made in the cytosol (that is, completely translated)

ER Signal Sequence

A sorting signal in a polypeptide that is usually located near the N-terminus and is recognized by SRP (signal recognition particle), allowing the polypeptide to be directed to the ER membrane

Signal Recognition Particle (SRP)

A protein-RNA complex that recognizes the ER signal sequence of a polypeptide, pauses translation, and directs the ribosome to the ER to complete translation

Chaperone

A protein that keeps another protein in an unfolded state during the process of post-translational sorting or aids in the folding of a protein into its proper three-dimensional conformation

Biological Membrane

Any membrane made by living cells (can be the plasma membrane or an internal membrane that surrounds an organelle)

Phospholipid Bilayer

The basic framework of a biological membrane, consisting of two layers of phospholipids

Amphipathic

Refers to molecules containing a hydrophobic (water-fearing) region and a hydrophilic (water-loving) region

Fluid-Mosaic Model

The accepted model of a biological membrane (its basic framework is the semifluid phospholipid bilayer with a mosaic of proteins). Carbohydrates may be attached to the lipids or proteins

Leaflet

Half of a phospholipid bilayer

Transmembrane Protein

A protein that has one or more regions that are physically embedded in the hydrophobic interior of a membrane’s phospholipid bilayer