AP Biology Chapter 6

A Tour of the Cell

Light Microscope

Visible light is passed through  a specimen and then through glass lenses to magnify the image, allowing for the observation of small details in biological samples.

Electron Microscope

The microscope that focuses a beam of electrons through the specimen or over the specimen to create an image, providing much higher resolution than light microscopes.

Scanning Electron Microscopy (SEM)

A photography of the topography

Transmission Electron Microscopy (TEM)

A type of microscope that uses a beam of electrons to pass through a very thin sample, allowing scientists to see the tiny details inside it-down to the level of atoms.

Cell Fractionation

Takes cells apart and separates major organelles and other subcellular structures form one another.

Prokaryotic cells

Cells that have no membrane bound nucleus or organelles, but rather the DNA is concentrated in the nucleoid, often consists of bacteria and archaea.  

Eukaryotic cells

Cells that have a nucleus and membrane bound organelles, consists animals, plants, fungi, and Protists.

Bacterial chromosome

The area in the bacterium that contains the DNA, the nucleoid.

Nucleoid

The area of the cell where the DNA is stored, but it is not enclosed in a membrane.  Mostly found in prokaryotes.

Cytosol

The organelle that is the fluid portion of the cytoplasm, it’s the broth of the soup.

Nucleus

The “control center” of the cell.  Stores the DNA inside of Eukaryotic cells, the largest organelle.

Cytoplasm

A combination of the cytosol and the cytoskeleton, all of the soup.

Plasma Membrane

The membrane that encloses the cytoplasm and holds the organelles, provides some structure and form for the cell.  Selectively permeable and made from a double phospholipid bilayer.

Flagella

A few long arrangements of microtubules that are used for cell motility.  Prominent in bacteria and sperm cells.

Cillia

Many little microtubules put together that are used for cell motility.  Have a power stroke, and a recovery stroke.

Rough ER

A network of flattened, membrane-bound sacs studded with ribosomes, giving it a “rough” appearance, and is primarily responsible for synthesizing and folding proteins destined for secretion, membranes, or organelles. It also plays a key role in quality control, ensuring proteins are properly assembled before being transported to the Golgi apparatus

Smooth ER

A network of interconnected, ribosome-free membranes that specializes in lipid and steroid synthesis, detoxification of harmful substances, and calcium ion storage. Unlike the rough ER, it does not make proteins but instead regulates metabolic processes crucial for cell function and signaling.

Nuclear envelope

A double membrane that surrounds and protects the nucleus, separating its contents from the cytoplasm while allowing controlled exchange of molecules through nuclear pores. It provides structural support, regulates gene expression traffic, and connects to the endoplasmic reticulum for communication within the cell

Nucleolus

A dense, spherical structure inside the nucleus that is not membrane-bound and is mainly responsible for producing and assembling ribosomal RNA (rRNA) and ribosomal subunits. It also plays roles in cell cycle regulation, stress responses, and the organization of nuclear activities

Chromatin

The complex of DNA and proteins, mainly histones, found in the nucleus that packages genetic material into a compact, organized form. It regulates gene expression and DNA replication, with euchromatin being loosely packed and active in transcription, while heterochromatin is tightly packed and largely inactive.

Ribosomes

Small, non-membrane-bound structures made of ribosomal RNA (rRNA) and proteins that serve as the cell’s protein factories. They can float freely in the cytoplasm or attach to the rough ER, translating messenger RNA (mRNA) into polypeptide chains that fold into functional proteins

Golgi apparatus

A stack of cristae that modifies, sorts, and packages proteins and lipids received from the endoplasmic reticulum. It prepares these molecules for transport to their final destinations inside or outside the cell, acting like the cell’s “post office.”  It has the cis face which takes in the vesicles, and the trans face that ships out the vesicles.

Lysosome

A membranous sac of hydrolytic enzymes that many eukaryotic cells us to digest (hydrolyze) macromolecules.  Work best in an acidic environment.

Mitochondria

Double-membrane-bound organelles that serve as the primary site of cellular respiration, generating ATP through the breakdown of glucose and other molecules. They also regulate metabolic activity, apoptosis, and contain their own DNA and ribosomes, supporting the endosymbiotic theory

Peroxisome

Small, membrane-bound organelles that contain enzymes to break down fatty acids and detoxify harmful substances, such as hydrogen peroxide, by converting it into water and oxygen. They play an essential role in metabolism, cellular protection, and maintaining homeostasis

Microvilli

Microscopic, finger-like projections of the plasma membrane that greatly increase a cell’s surface area for absorption and secretion. They are especially abundant in cells lining the small intestine, where they enhance nutrient uptake.

Microtubules

Hollow tubes made of tubulin proteins that form part of the cytoskeleton, providing structural support and serving as tracks for the movement of organelles and vesicles. They also play critical roles in cell division by forming the mitotic spindle and in motility by making up cilia and flagella

Intermediate filaments

Durable, rope-like fibers of the cytoskeleton that provide mechanical strength to cells, helping them resist tension and maintain shape. They anchor organelles in place and are composed of various proteins, such as keratin in epithelial cells

Microfilaments

Thin, flexible fibers made of actin proteins that form part of the cytoskeleton, providing structural support and enabling changes in cell shape. They are essential for processes such as cell movement, cytokinesis, and intracellular transport

Cy

Centrosome

The main microtubule-organizing center of animal cells, containing centrioles and essential for spindle formation during cell division

Flagella

A whip-like structure made of microtubules in a 9+2 arrangement that propels cells using dynein-driven bending. Used for cell motility.

Cell Wall

A rigid protective layer outside the plasma membrane, made of cellulose in plants, that maintains cell shape, supports turgor, and resists mechanical stress.

Plasmodesmata

Chloroplast

A double-membrane organelle in plant and algal cells where photosynthesis occurs, converting light energy into chemical energy.

Central Vacuole

Located in plant cells, A large, membrane-bound compartment storing water, ions, and nutrients, maintaining turgor pressure, and aiding in growth and waste disposal

Food Vacuoles

Membrane-bound compartments formed when a cell engulfs food particles or microorganisms through phagocytosis. They later fuse with lysosomes so that hydrolytic enzymes can digest the contents and release nutrients to the cytoplasm

Chromatin

DNA wrapped around histone proteins in the nucleus, existing as euchromatin (loosely packed, transcriptionally active) or heterochromatin (tightly packed, inactive)

Nuclear Lamina

A dense protein network under the inner nuclear membrane that maintains nuclear shape and organizes chromatin

Chromosomes

Condensed, thread-like structures of DNA and proteins that carry genetic information, especially visible during cell division

Vesicles

Small, membrane-bound sacs that transport, store, or digest materials within cells.

Glycoproteins

Proteins with carbohydrate chains covalently attached, important for cell recognition, signaling, and adhesion

Transport Vesicles

Vesicles that shuttle proteins and lipids between organelles, especially from the ER to the Golgi and beyond

Phagocytosis

A form of endocytosis in which cells engulf large particles or microorganisms into food vacuoles for digestion

Contractile Vacuoles

Organelles in freshwater protists that pump excess water out of the cell to maintain osmotic balance.

Endosymbiont Theory

The hypothesis that mitochondria and chloroplasts originated as free-living prokaryotes engulfed by ancestral eukaryotic cells, supported by their double membranes, DNA, and ribosomes

Cristae

The folds of the inner mitochondrial membrane that increase surface area for ATP production during cellular respiration

Mitochondrial Matrix

The fluid-filled space inside the inner membrane of mitochondria containing enzymes, DNA, and ribosomes for respiration

Thylakoids

Flattened membrane sacs inside chloroplasts where light-dependent reactions of photosynthesis occur

Granum

A stack of thylakoids that maximizes light capture during photosynthesis

Stroma

The fluid surrounding the thylakoids in chloroplasts that contains enzymes for the Calvin cycle

Plastids

A double-membrane organelle found in plant and algal cells that develops into specialized forms such as chloroplasts (for photosynthesis), chromoplasts (for pigment storage), and amyloplasts (for starch storage). Plastids have their own DNA and ribosomes, supporting the endosymbiont theory

Motor Proteins

Proteins (such as kinesin, dynein, and myosin) that move along cytoskeletal filaments to transport vesicles and organelles

Centrioles

Barrel-shaped structures of microtubules found in centrosomes that help organize spindle fibers in cell division

Cilia

Short, numerous hair-like projections made of microtubules in a 9+2 arrangement, used for movement or moving fluid across surfaces

Basal Body

The microtubule-based organizing center at the base of cilia and flagella, structurally similar to centrioles

Actin

A protein that forms microfilaments, supporting cell shape, movement, and intracellular transport.

Cortex

A specialized region beneath the plasma membrane rich in actin filaments that reinforces the cell’s shape

Myosin

A motor protein that interacts with actin filaments to produce cellular movements such as muscle contraction and cytokinesis

Psuedopodia

Temporary extensions of the cytoplasm formed by actin remodeling, used for cell movement and phagocytosis

Cytoplasmic Streaming

The directed flow of cytoplasm, often driven by actin-myosin interactions, that helps distribute nutrients and organelles in large cells

Cell Motility

The ability of a cell or organism to move, often powered by the cytoskeleton and motor proteins

Primary Cell Wall

In plants, the primary wall is thin and flexible for growth

Secondary cell wall

In plant cells, a wall that is thicker, stronger, and deposited after growth for structural support.

Middle Lamella

A pectin-rich layer between plant cell walls that glues adjacent cells together.

Extracellular matrix

A network of glycoproteins and other molecules outside animal cells that provides support, adhesion, and signaling (ECM)

Collagen

A structural glycoprotein that is the most abundant protein in the ECM, providing tensile strength

Proteoglycans

Extracellular Matrix molecules with small core proteins and many attached carbohydrate chains that provide hydration and cushioning

Fibronectin

An extracellular matrix glycoprotein that connects cells to the ECM by binding collagen, proteoglycans, and integrins

Integrins

Transmembrane proteins that connect the ECM to the cytoskeleton and mediate cell signaling and adhesion

Chlorophyll

The green pigment in chloroplast thylakoids that absorbs light energy for photosynthesis

Paramecium

A ciliate protist covered with thousands of cilia used for locomotion and feeding; it exhibits complex cellular processes such as contractile vacuole function, oral groove feeding, and cytoplasmic streaming, making it a model organism for studying unicellular eukaryotic biology

Magnification

The process of enlarging the apparent size of an object under a microscope, determined by the product of the objective and eyepiece lens powers, which allows observation of fine cellular structures beyond the resolution of the naked eye

Resolution

The ability of a microscope to distinguish two closely spaced points as separate, determined by wavelength of light or electrons and numerical aperture; higher resolution allows visualization of subcellular structures in greater detail

Contrast

The difference in light absorption, reflection, or scattering between a specimen and its background that makes structures visible under a microscope; it can be enhanced using stains, phase-contrast, or differential interference techniques

Super-Resolution Microscopy

A collection of advanced imaging methods (e.g., STED, PALM, STORM) that surpass the diffraction limit of light, enabling visualization of molecular arrangements and interactions at the nanometer scale within living cells

Cytology

The scientific study of cell structure, organization, and function, often using microscopy to examine organelles, membranes, and the cytoskeleton

Biochemistry

The branch of biology that examines the chemical components and processes of living organisms, including enzymes, nucleic acids, lipids, carbohydrates, and metabolic pathways

Pore Complex

Large multiprotein structures embedded in the nuclear envelope that regulate selective transport of RNA, proteins, and other macromolecules between the nucleus and cytoplasm

Nuclear matrix

A fibrous network within the nucleus that maintains nuclear shape, organizes chromatin, anchors nuclear pores, and coordinates DNA replication and transcription

ER Lumen

The enclosed internal space of the endoplasmic reticulum where nascent proteins are folded, glycosylated, and processed, and where calcium ions are stored for signaling

Autophagy

A regulated process in which cells degrade and recycle damaged organelles, misfolded proteins, or invading pathogens through lysosome-mediated digestion, maintaining cellular homeostasis and responding to nutrient stress

Amyloplast

A colorless plastid in plants that stores starch granules and can convert stored starch into sugars for energy, particularly during periods of low photosynthetic activity

Chromoplast

A plastid specialized for synthesizing and storing pigments such as carotenoids, giving color to fruits, flowers, and other plant tissues for attraction of pollinators or seed dispersal

Glyoxysomes

Specialized peroxisomes in plant seedlings that convert stored fatty acids into sugars via the glyoxylate cycle, providing energy and carbon for germination and early growth

Dimer

A molecular complex composed of two subunits, either identical (homodimer) or different (heterodimer), that often forms the functional unit of structural or enzymatic proteins

α-Tubulin

A globular protein that pairs with β-tubulin to form heterodimers, which then polymerize into microtubules for structural support, intracellular transport, and mitotic spindle formation

β-Tubulin

The tubulin subunit that partners with α-tubulin to form heterodimers, essential for building microtubules and enabling cytoskeletal dynamics and motility

Tubulin

A family of globular proteins (α- and β-tubulin) that assemble into microtubules, forming the cytoskeletal scaffold, supporting organelle movement, and facilitating cell division and intracellular transport

9+2 Pattern

The structural arrangement of microtubules in eukaryotic cilia and flagella, consisting of nine outer doublets surrounding two central single microtubules, crucial for motility and bending motion

Pectin

A polysaccharide abundant in the middle lamella of plant cell walls that promotes adhesion between adjacent cells and contributes to wall flexibility and mechanical strength

Glycosylation

The enzymatic attachment of carbohydrate groups to proteins or lipids in the ER or Golgi, which influences protein folding, stability, trafficking, and cell-cell recognition

Phosphorylation

The covalent addition of a phosphate group to a protein or other molecule by kinases, a reversible modification that regulates enzyme activity, signal transduction, and protein-protein interactions

Sulfation

The enzymatic addition of sulfate groups to proteins, carbohydrates, or lipids, often modifying extracellular matrix components or secreted molecules to regulate structure, signaling, and interactions

Endomembrane system

A coordinated network of membranes within a eukaryotic cell, including the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, and the plasma membrane. It functions to synthesize, modify, transport, and degrade proteins and lipids, maintaining cellular organization and homeostasis

Tight Junctions

The plasma membranes of cells are very tightly pressed against each other, bound by specific proteins. Forming continuous seals around the cells, establish a barrier that prevents leakage of extracellular fluid across a layer of epithelial cells

Desmosomes

Function like rivets, fastening cells together into strong sheets. Intermediate filaments made of sturdy keratin proteins anchor desmosomes in the cytoplasm. Attach muscle cells to each other in a muscle.

Gap Junction

Provide cytoplasmic channels from one cell to an adjacent cell and in this way are similar in their function to the plasmodesmata in plants. Consist of membrane proteins that surround a pore through which ions, sugars, amino acids, and other small molecules may pass.