BICD 110 Midterm 1 - IA Review Session

Modern cell theory

The theory that states that all life forms are made from one or more cells, the cell is the structural and functional unit of all living things, cells only arise from pre-existing cells by division, cells contain hereditary information passed from cell to cell during division, all cells have the same basic chemical composition, and all energy flow of life occurs within cells.

Prokaryotic cell

A type of cell that is smaller in size, lacks organelles, has a nucleoid region instead of a nucleus, and is found in bacteria and archaea.

Eukaryotic cell

A type of cell that is larger in size, contains organelles, has a nucleus, and is found in eukaryotes.

Organelles

Structures within eukaryotic cells that have specific functions, such as the plasma membrane, nucleus, rough ER, smooth ER, Golgi, mitochondria, chloroplasts, lysosomes, and peroxisomes.

Endosymbiont hypothesis

The hypothesis that mitochondria and chloroplasts evolved from endocytosis of bacteria by the precursor of a eukaryotic cell, supported by evidence such as the presence of two membranes, their own DNA genome, and similarities to prokaryotic translation.

Phospholipid bilayer

The main component of cell membranes, consisting of two layers of phospholipids with hydrophilic heads facing outward and hydrophobic tails facing inward.

Lipids in cell membranes

Different types of lipids found in cell membranes, including phosphoglycerides (phospholipids), sphingolipids, and sterols.

Fluid mosaic model

The model that describes the movement and arrangement of lipids and proteins in the plasma membrane, where lipids move fluidly within the same leaflet and proteins are embedded or associated with the membrane.

Annexin staining

A method used to identify apoptotic cells by staining phosphatidylserine (PS) on the outer leaflet of the plasma membrane using fluorescent annexin V.

Integral membrane proteins

Proteins that span the entire width of the plasma membrane, often containing hydrophobic alpha helices or beta barrel structures.

Lipid-anchored proteins

Proteins that are covalently bonded to a lipid in the plasma membrane.

Peripheral membrane proteins

Proteins that are only associated with one side of the membrane and may interact directly or indirectly with the phospholipid head groups or other membrane proteins.

Concentration gradient

A difference in the concentration of a substance on different sides of the membrane.

Membrane potential

The electrical potential (voltage) across the membrane, based on the difference in charge made up of positive and negative ions/compounds.

Electrochemical gradient

The combination of concentration gradient and membrane potential, which determines the direction of a charged molecule.

Channels

Transmembrane proteins that transport water, specific ions, or hydrophilic small molecules across the membrane down their gradients through passive transport or facilitated diffusion.

Transporters

Transmembrane proteins that move a wide variety of molecules and ions across cell membranes, but at a slower rate than channels.

ATP-powered pumps

ATPases that use the energy of ATP hydrolysis to move ions or small molecules against a gradient, resulting in active transport.

Channels

Hydrophilic tubes that allow the movement of ions, water, and small hydrophilic molecules through passive or facilitated diffusion.

Gated Channels

Channels that can be opened or closed to control the movement of molecules.

Non-gated Channels

Channels that are always open and allow continuous movement of molecules.

Ligand-gated Channels

Channels that open or close in response to the binding of a specific molecule (ligand).

Voltage-gated Channels

Channels that open or close in response to changes in membrane voltage.

Transporters

Proteins that facilitate the movement of molecules across the membrane.

Uniporters

Transporters that allow the movement of a single molecule type down its gradient.

GLUT1 transporter

A specific uniporter that transports glucose.

Cotransporters

Transporters that use the energy from one molecule moving down its gradient to power the transport of another molecule against its gradient.

Symporter

A type of cotransporter where two molecules move in the same direction, even though their gradients are in opposite directions.

Glucose/Na+ symporter

A specific symporter that transports glucose and sodium ions.

Antiporter

A type of cotransporter where two molecules move in opposite directions, even though their gradients are in the same direction.

3 Na+/Calcium antiporter

A specific antiporter that transports three sodium ions in exchange for one calcium ion.

ATP-powered pumps

Proteins that transport ions and small molecules against their concentration gradient using the hydrolysis of ATP as a power source.

P-class pumps

ATP-powered pumps that require phosphorylation for their activity.

Na/K pump

A specific P-class pump that transports three sodium ions out of the cell and two potassium ions into the cell.

V-class ion pump

An ATP-powered pump that moves H+ ions from the cytosol into the lumen of lysosomes to decrease the pH.

F-class ion pump

An ATP-powered pump that uses the movement of H+ ions down their gradient to power the synthesis of ATP.

ABC superfamily

A diverse group of proteins that function as ATP Binding Cassette transporters.

CFTR gene

The gene responsible for cystic fibrosis. CFTR is an ABC transporter that moves chloride ions down their concentration gradient.

Transcellular transport

The import of molecules through the plasma membrane on the apical side and their export through the basolateral side.

Apical side

The top surface-facing side of a cell.

Basolateral side

The inside, bloodstream-facing side of a cell.

Secretory Pathway

The pathway in which proteins are synthesized on ribosomes bound to the cytosolic face of the ER and then transported to the plasma membrane or secreted.

N-terminal ER signal sequence (SS)

A hydrophobic sequence of amino acids on the N-terminus of a secreted protein that is recognized by the SRP.

Signal recognition peptide (SRP)

A protein-RNA complex that binds to the N-terminal ER signal sequence and targets the developing protein to the ER membrane.

SRP receptor

A protein embedded in the rER membrane that recognizes the SRP and facilitates the targeting of developing proteins to the ER membrane.

Cotranslational translocation

The process of targeting developing proteins to the ER membrane while they are still being synthesized.

Translocon

A transmembrane channel embedded in the rER membrane that facilitates the translocation and insertion of polypeptides.

Topology

The arrangement and orientation of membrane proteins within the membrane.

Type I membrane protein

A membrane protein with a cleavable N-terminal signal sequence in the ER lumen.

Type II membrane protein

A membrane protein with a signal-anchor sequence that remains in the membrane.

Type IV membrane protein

A multipass membrane protein with multiple membrane-spanning segments that alternate between the lumen and cytosolic side.

GPI anchor

A glycosylphosphatidylinositol anchor that attaches proteins to the membrane.

Cytosol

The fluid portion of the cytoplasm, excluding the organelles.

Hydropathy plot

A plot that shows the overall hydrophobicity in a protein.

Topology

The arrangement or structure of a protein, used to deduce the kind of sequence(s) present in a polypeptide chain.

Hydrophobic segments

Segments of a protein that have a positive value in a hydropathy plot, indicating their hydrophobic nature.

Hydrophilic segments

Segments of a protein that have a negative value in a hydropathy plot, indicating their hydrophilic nature.

Glycosylation

The covalent attachment of carbohydrates to a protein.

N-linked oligosaccharides

Carbohydrates that are attached to proteins through the nitrogen atom of asparagine residues.

O-linked oligosaccharides

Carbohydrates that are attached to proteins through the oxygen atom of serine or threonine residues.

Disulfide bonds

Covalent bonds formed between sulfides on cysteine residues in the lumen of the rough endoplasmic reticulum (rER).

Protein disulfide isomerase (PDI)

An enzyme in the lumen of the rER that forms disulfide bonds by stabilizing intermediates.

Chaperones

Proteins that aid in the proper folding of polypeptide chains and assembly of multisubunit proteins.

BiP

A type of chaperone (Hsp70) that binds to proteins on nascent chains and stabilizes them, preventing aggregation until the protein is folded correctly.

Calnexin/Calreticulin

Chaperones that bind to glycosylated carbohydrate chains on proteins, preventing aggregation and premature or incorrect folding.

Unfolded Protein Response (UPR)

A cellular response to the presence of unfolded proteins in the endoplasmic reticulum (ER).

Ire1

An ER membrane protein that dimerizes during UPR, leading to the production of more chaperones.

ERAD

Endoplasmic reticulum-associated degradation, a process that targets unfolded proteins for degradation in the cytosol.

p97 ATPase

An enzyme that pulls unfolded proteins across the ER membrane during ERAD.

Ubiquitination

The process of tagging proteins for degradation by attaching ubiquitin molecules to them.

Proteasome

A cellular complex that degrades polyubiquitinated proteins.

Modern cell theory

The idea that all life forms are composed of one or more cells, cells share the same biochemical composition, cells only arise from preexisting cells through cell division, and all energy flow of life occurs within cells.

Primary structure

The linear sequence of amino acids in a protein.

Secondary structure

The local folding patterns of a protein, such as alpha helices and beta sheets.

Tertiary structure

The overall three-dimensional conformation of a protein.

Quaternary structure

The arrangement of multiple protein subunits in a complex.

Integral membrane structure

A type of protein structure that spans the lipid bilayer of a membrane, with a hydrophobic surface and a hydrophilic core.

Peripheral protein

A protein that is bound to the surface of a membrane but does not span the lipid bilayer.

Symporters

Membrane transport proteins that move two molecules in the same direction across a membrane.

P-class pumps

A type of membrane protein pump that requires phosphorylation and undergoes conformational changes to transport ions or molecules.

V and F class pumps

Other types of membrane protein pumps that do not create ATP and have different functions compared to P-class pumps.

Transcellular transport

The movement of molecules or substances across a cell, from one side to another.

Glucose

A simple sugar that serves as an important source of energy in living organisms.

Na/K pump

A membrane protein that actively transports sodium ions out of the cell and potassium ions into the cell.

Symporter

A membrane protein that transports two different molecules or ions in the same direction across the cell membrane.

Antiporter

A membrane protein that transports two different molecules or ions in opposite directions across the cell membrane.

Transmembrane sequence

A sequence of amino acids in a protein that spans the cell membrane.

N-terminus

The end of a protein or polypeptide chain that contains the amino group.

C-terminus

The end of a protein or polypeptide chain that contains the carboxyl group.

SA sequence

A signal anchor sequence that directs the insertion of a protein into the cell membrane.

STA sequence

A stop-transfer anchor sequence that halts the insertion of a protein into the cell membrane.

ER lumen

The interior space of the endoplasmic reticulum, a network of membranes within the cell.

Cytosol

The fluid portion of the cytoplasm, excluding the organelles.

ER signal sequence

A sequence of amino acids at the N-terminus of a protein that directs its insertion into the endoplasmic reticulum.

SRP (Signal Recognition Particle)

A protein-RNA complex that recognizes and binds to the ER signal sequence of a protein.

SRP receptor

A membrane protein that binds to the SRP-ribosome complex and facilitates the targeting of the protein to the endoplasmic reticulum.

Sec61 translocon

A protein complex in the endoplasmic reticulum membrane that forms a channel for the translocation of proteins.

GTP hydrolysis

The process of breaking down GTP (guanosine triphosphate) into GDP (guanosine diphosphate) and inorganic phosphate, releasing energy.

ATP hydrolysis

The process of breaking down ATP (adenosine triphosphate) into ADP (adenosine diphosphate) and inorganic phosphate, releasing energy.

Signal peptidase

An enzyme that cleaves the ER signal sequence from a protein during its translocation into the endoplasmic reticulum.