Introduction To Biology: Cells

The Cell Wednesday, July 01, 2009 9:59 PM

Name/part

Structure/ description

1. Prokaryotic Cell

• Cell with no nucleus • Bacteria and arcaea are procaryotes (pro= before + karyon=nucleus) • Bounded by plasma membrane • With cytosol where organelles are suspended • With chromosomes that carries the genes in the form of DNA • DNA concentrated on the nucleoid, but no membrane that separates the rest of the cell, thus more prone to

2. Eukaryotic cell

• Eu=true + karyon, thus cell • Protists, fungi, animals, and plants with true nucleus. • Bounded by plasma membrane • With cytosol where organelles are suspended • With chromosomes that carries the genes in the form of DNA • Chromosomes are found in a membrane-enclosed organelle (nucleus) • Within the cytoplasm are membrane-bound organelles with specialized form and function • Bigger than prokaryotes

3. Cytosol

• Semi-fluid structure

• Where the organelles are found

4. Cytoplasm

• The entire region between the nucleus and plasma membrane • Interior of the prokaryotic cell

•

5. metabolism

Function

Remarks

• Size relates to function: the smaller the object, the greater it's ration of surface area to volume. High surface-to-volume ratio facilitates the exchange of materials between a cell and it's environment. That's why cells are microscopic.

If the protoplasm is the cell minus the cell wall, is the gap between the cell wall and protoplast when the cell has undergone plasmolysis still part of the cytoplasm?

The totality of an organism's chemical reactions, consisting of catabolic and anabolic pathways.

Catabolic pathway: a metabolic pathway that releases energy by breaking down complex molecules to simpler compounds. Anabolic pathway: a metabolic pathway that synthesizes a complex molecule from simpler compounds.

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compounds. 6. Plasma Membrane • Lipid bilayer with proteins and carbohydrates

• Selective barrier that allows sufficient passage of oxygen, nutrients, and wastes to service the entire volume of the cell

Fluid mosaic model: the membrane is a fluid structure with various proteins embedded in or attached to a double layer of phospholipids.

• Membranes are fluid. Needs to be fluid in Proteins determine the membrane's order to function properly. Cells can alter the function. lipid composition of their membranes as an a. Integral proteins: those that penetrate the adjustment to changing temperature. phospholipid bilayer b. Peripheral proteins: not embedded in the • Membranes are mosaics of structure and lipid bilayer; they are appendages loosely function. A collage of different proteins bound to the surface of the membrane, often embedded in the fluid matrix of the lipid to the exposed parts of integral proteins. bilayer. Some functions of membrane proteins: 1. Transport. For either facilitated or active diffusion 2. Enzymatic activity: may be an enzyme with its active site exposed to substances in the adjacent solution. In some cases, several enzymes in a membrane are ordered as a team that carries out sequential steps of a metabolic pathway. 3. Signal transduction. Lock-and-key; usually for hormones, then it will transmit the message to the inside of the cell. 4. Intercellular joining. As in gap junctions (see #40) 5. Cell-cell recognition. Some glycoproteins serve as identification tags that are specifically recognized by other cells. 6. Attachment to the cytoskeleton and ECM. Microfilaments or other elements of the cytoskeleton may be bonded to membrane proteins, a function that helps maintain cell shape and fixes the location of certain membrane proteins. Proteins that adhere to the ECM can coordinate extracellular and intracellular changes.

Transport along the plasma membrane

1. Passive transport: no other energy is needed for transport to occur. a. Simple diffusion: molecules pass through the lipid bilayer b. Facilitated diffusion: molecules pass through the membrane through proteins.

Diffusion: the tendency for molecules of any substance to spread out into the available space. : result of thermal motion : Diffusion is the moving of molecules from an area of high concentration to an area of low concentration to reach equilibrium.

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Glycoproteins: proteins with short chains of sugars

Thermal motion: intrinsic kinetic energy of molecules. Hypotonic solution Isotonic solution Hypertonic solution Plasmolysis Hemolysis

proteins. 2. Active transport: the cell must expend its own metabolic energy for transport

Osmosis: passive transport of water through a semi-permeable membrane, from a hypotonic environment towards a hypertonic environment to achieve equilibrium. 1. Exocytosis: inside-out. Vesicles fuse with plasma membrane. 2. Endocytosis: outside-in. Vesicles bud off from the plasma membrane. a. Phagocytosis: cellular eating b. Pinocytosis: cellular drinking; unspecific in substance that it transports. c. Receptor-mediated endocytosis: embedded in the membrane are proteins with specific receptor sites exposed to the extracellular fluid.

Hemolysis Crenation Aquaporins: water channel proteins that facilitate the massive amounts of diffusion Gated channels: a stimulus causes them to open or close. The stimulus may be electrical or chemical; if chemical, it is a substance other than the one to be transported. Ligand: extracellular substance that bind to the receptors

7. phospholipid

Amphiphatic molecule: Hydrophobic molecules: hydrocarbons, CO2, Consists of: O2 a. Hydrophilic head (polar) b. Hydrophobic tail (non-polar)

Lipid: One of a family of compounds, including fats, phospholipids, and steroids, that are insoluble in water.

8. Polypeptide

A polymer (chain) of many amino acids linked together by peptide bonds.

Polymer: a long molecule consisting of many similar or identical monomers linked together. Peptide bond: the covalent bond between two amino acid units, formed by a dehydration reaction.

9. Nucleus

Made up of: a. Nucleolus b. Chromatin c. Nuclear envelope

10. Nuclear envelope Double membrane, each a lipid bilayer

11. Nuclear matrix

A framework of fibers extending throughout the nuclear interior.

12. Chromatin

Fibrous material

13. Chromosomes

Coiled chromatin fibers that is recognized at cell division

14. Nucleolus

A mass of densely stained granules and fibers adjoining part of the chromatin

Contains most of the genes in the eukaryotic cell

Encloses the nucleus, separating its contents from the cytoplasm

Where DNA is organized along with proteins

Where the ribosomal RNA is synthesized and assembled with proteins imported from the cytoplasm into the main components of

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Contains: a. Pore complex: protein structure that lines each pore and regulates the entry and exit of certain large macromolecules and particles. b. Nuclear lamina: lines the membrane on the nuclear side; : net-like array of protein filaments (intermediate filaments) that maintains the shape of the nucleus.

15. Ribosome

part of the chromatin

cytoplasm into the main components of ribosomes

• Particles made of ribosomal RNA and proteins • Composed of two sub-units (large and small)

• Organelles that carry out protein synthesis • Higher the rate of protein synthesis, the higher the number of ribosomes • The more active the protein synthesis, the more prominent nucleoli

Ribosomal sub-unit: main components of ribosomes that pass through the nuclear pores to the cytoplasm, where they can combine to form ribosomes With free and bound ribosomes: the cell adjusts the number of free and bound depending on metabolism changes

16. Free ribosomes

Suspended in cytosol

17. Bound ribosomes

Can be found on the • For insertion into membranes endoplasmic reticulum, or the • For packaging within certain organelle such nuclear membrane as lysosomes • For export from the cell (secretion)

18. Endomembrane system

Composed of the different membranes of the eukaryotic cell: a. Nuclear envelope b. Endoplasmic reticulum c. Golgi Body/Apparatus d. Lysosomes e. Vacuoles f. Plasma membrane

19. Endoplasmic reticulum (ER)

20. Smooth ER

Sugar breakdown

related through direct physical continuity or by Vesicles: sacs made of membrane the transfer of membrane segments called vesicles. Synthesis of secretory proteins in rough ER --> transport vesicle contains inactive hydrolytic enzymes --> received at the cis face of the golgi body --> proteins are modified and stored --> exit the golgi body through the trans face --> lysosomes are formed --> autophagy: recycles organic materials; digest food vacuoles from phagocytosis

• Membranous labyrinth • Separates the internal compartment of the ER from the cytosol • Accounts for more than half of the total membrane in many eukaryotic cells • Consists of cisternae, a network of membranous tubule and sacs

Endoplasmic: means "within the cytoplasm"

• It's cytoplasmic surface lacks • Involved in different metabolic processes: ribosomes a. Synthesis of lipids - Release of enzymes to synthesize oils, phospholipids, steroids - Ex: sex cells of vertebrates and hormones that secrete steroids to the adrenal gland are rich in smooth ER

Hydrolysis: a chemical process that lyses, or splits, molecules by the addition of water. : an essential process in digestion.

b. Metabolism of carbohydrates - Ex: liver cells store carbohydrate (glycogen, a polysaccharide). It's hydrolysis leads to the release of glucose from the liver cells. - The release of glucose is important in the

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Reticulum: means "little net" Cisternae: Latin, cisterna, a reservoir of liquid Cisternal space: internal compartment of the ER

Hydroxyl group: a functional group consisting of a hydrogen atom joined to an oxygen atom by a polar covalent bond. Molecules possessing this group are soluble in water and are called alcohols.

- The release of glucose is important in the regulation of sugar concentration in the blood. c. Detoxification of drugs and poisons - Big help especially in liver cells - Involves adding hydroxyl groups to drugs, making them more soluble and easier to flush from the body - Phenobarbital and other barbituates help proliferate smooth ER and its enzymes, thus causing one's tolerance to these drugs, and others as well (such as antibiotics used to cure addiction to the said drugs). • In muscle cells: there ER pumps Ca ions from the cytosol to the cisternal space. When a muscle cell is stimulated by a nerve impulse, the Ca ions rushes back to the cytosol, causing contraction of the muscle cells. 21. Rough ER

• Ribosomes stud the cytoplasmic surface

• Synthesis of secretory proteins Ribosomes --> proteins --> carbohydrates are attached to the proteins --> secretory proteins --> depart from the region of the ER called transitional ER wrapped in transport vesicles. • Membrane production - Membrane factory that grows in place by adding proteins and phospholipids

22. Golgi • Composed of a stack of Apparatus/ Body cisternae, not physically connected to each other

• Center of manufacturing, warehousing, sorting, and shipping. • Products of ER are modified and stored and then sent to other destinations. • Especially extensive in cells specialized in secretions

Glycoproteins: proteins that are covalently bonded with carbohydrates, which is an oligosaccharide; : most secretory proteins are glycoproteins. Oligosaccharide: relatively small polymer of sugar units. Transport vesicles: vesicles in transit from one part of the cell to another. Lumen: cavity Cellulose: made by enzymes located within the plasma membrane, which directly deposit polysaccharide on the outside surface.

Pectin: component of the middle lamella which is broken down by the enzyme pectinase. • Has receiving and transport end (the cis and trans face respectively) - From the ER, the membrane of the transport vesicles merge with the cis face and the proteins contained in the lumen are modified. @ proteins and phospholipids of membranes may be altered @ modification of oligosaccharide portions of glycoproteins. It removes some sugar monomers and substitutes others, producing a large variety of oligosaccharide. - Manufactures macromolecules that are secreted by the cell

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secreted by the cell @ pectins @ other noncellulose polysaccharide which is incorporated to cellulose into the plant's cell wall. - Proteins travel from one cisterna to another via vesicles. - Before releasing the product via trans face, it sorts the products and targets specific parts of the cell where it is supposed to go 23. Lysosomes (found only in animal cells)

Membrane-bound sac of hydrolytic enzymes

• Used to digest macromolecules • Maintains an acidic environment by pumping hydrogen ions from the cytosol to the lumen. • Provides space where macromolecules can be digested safely. • Autophagy happens when the lysosome engulfs another organelle or a small portion of the cytosol. • Programmed destruction are useful: frog's tail, webs of the human embryo.

24. Vacuoles

Membrane-bound sacs within the cells

a. Food vacuoles: formed by phagocytosis b. Contractile vacuoles: pump excess water out of the cell (in freshwater protists) c. Central vacuole: found in mature plants

25. Central Vacuole (found only in plant cells)

• Enclosed by a membrane called the tonoplast • Develops by coalescence of smaller vacuoles

a. Storage - Reserves of important organic compound such as proteins and inorganic ions such as potassium and chloride. b. Waste disposal - Crystals c. Pigments for color - anthocyanin d. Protection - Compounds that are poisonous or unpalatable to predators - crystals e. Growth - Vacuoles absorb water

26. Mitochondria pl. • Enclosed by a double • Sites of cellular respiration (s. membrane, each a lipid Mitochondrion) bilayer • Outer membrane: smooth • Inner membrane: convoluted

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Autodigestion: when a large number lysosome leaks its contents, the hydrolytic enzymes, to the cytosol and destroy the cell Phagocytosis: from the Greek phagein, to eat, and kytos, vessel, referring here to the cell : a food vacuole pinches off the plasma membrane, enclosing food particle : ex. amoebas and white blood cells. Autophagy: hydrolytic enzymes are used to recycle the cell's organic material

Tonoplast: selective in transporting solutes Cell sap: solution inside the vacuole; differs in composition from the cytosol. Crystals: waste-product of the cell; can also serve as protection from predators 1. Calcium oxalate a. Raphides: sticks; found in bundles (Dieffenbachia, _____________________) b. Syloids: needles; found alone (Dieffenbachia, ______________________) c. Druse/ rosette: flower-like (Ixora-santan) d. Prismatic: rectangular (Begonia 2. Calcium carbonate a. Cystolith inlithocyst: found in the epidermis (Ficus) b. Worm-like cystolith: (Pilea) Respiration: catabolic process that generates ATP by extracting energy from sugars, fats, and other fuels with the help of oxygen. # of mitochondria is correlated to the level of

# of mitochondria is correlated to the level of metabolic activity

• Inner membrane: convoluted with infoldings called cristae • Intermembrane space: between inner and outer membrane • Mitochondrial matrix: enclosed by the inner membrane • Membrane proteins made by free ribosomes and ribosomes contained inside the organelle • Contains mitochondrial DNA • Either one large mitochondria or hundreds, even thousands, in a cell • Moves around the cell, divides, and change their shape 27. Chloroplasts

• A plastid • Found only in plants and algae • Enclosed by a double membrane, each a lipid bilayer • With intermembrane space • membrane protein made by free ribosomes and ribosomes contained inside the organelle • Contains chloroplast DNA • Contains the thylakoid, and stroma.

28. thylakoid

• Membranous system in the form of flattened sacs

Cristae: convolution in the inner membrane : gives a larger surface area Mitochondrial matrix: contains many different enzymes as well as mitochondrial DNA and ribosomes

• Sites of photosynthesis

Plastid: pigments and stores food. a. Chloroplast - chlorophyll b. Chromoplast - flowers, yellow, orange coloration c. Amyloplast: amylo: starch; found in roots d. Leucoplastid: colorless

Granum: (singular; grana, plural) a stack of thylakoid Thylakoid space: the space inside the thylakoid

29. stroma

• The fluid outside the thylakoid • Contains the chloroplast DNA and ribosomes

30. peroxisome

• Bound by a single membrane • Special metabolic compartment • Grow by incorporating • Use oxygen to break down fatty acids to proteins and lipids made in become fuel for respiration the cytosol • Increase in number by splitting in two when they reach a certain size.

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31. cytoskeleton

32. Microtubules

• Network of fibers that extend through the cytoplasm • Microtubules, microfilaments, and intermediate filaments

Cell motility: movement of both cell location, • Gives the cell mechanical support and the parts of the cell • Gives the cell its shape : requires interaction with motor • Cell motility molecules • Regulation of biochemical activities in the cell Motor molecules: proteins

• Found in all eukaryotic cells • Shape and support the cell • Hollow rods • Serve as tracks along which organelles • 25nm diameter; 200nm to 25 equipped with motor molecules can move. • Responsible for the separation of micrometers length chromosomes during cell division • Wall made up of tubulin

Tubulin: globular protein Centrosomes: where the microtubules grow out; in animal cells, the centrioles exist Centrioles: composed of 9 sets of three microtubules. They duplicate during cell division; function unknown. Cilia and flagella: locomotor appendages that protrude from some cells : has a core of microtubules sheathed in an extension of the plasma membrane Dynein: a protein; motor molecules extending from each microtubule to the next : responsible for the bending of flagellum and cilia

33. Microfilaments

• Solid rods • 7nm in diameter • Made up of actin proteins

34. Intermediate filaments

• Fibrous proteins supercoiled • Maintenance of permanent cell shape into thicker cables (tension-bearing elements) • 8-12 nm in diameter • Anchorage of nucleus and certain other organelles • Made up of proteins from • Formation of nuclear lamina the keratin family

35. Cell wall

• Made up of microfibrils that are in turn made up of the polysaccharide cellulose are embedded in a matrix of other polysaccharide and proteins. • Found only in plant cells. Also in prokaryotes, fungi and some protists.

Primary cell wall: thin and flexible wall Secondary cell wall: has a strong and durable matrix that affords the cell protection and support Middle lamella: glues the cell together; made up of pectin

36. Extracellular matrix (ECM)

• Made up of glycoproteins secreted by the cell (collagen, proteoglycans, fibronectins)

Collagen: most abundant glycoprotein : forms strong fibers outside the cells

• Bear tension (pulling force) to maintain cell shape • Changes in cell shape • Muscle contraction • Cytoplasmic streaming • Cell division (cleavage formation)

Actin: globular protein Cytoplasmic streaming: circulation of materials in the different parts of the plant cell : a circular flow of cytoplasm in within cells.

Proteoglycans: especially rich in carbohydrates and can form large complexes

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Fibronectins: bind receptor proteins called integrin Integrin: bind the cytoplasmic side to the microfilaments of the cytoskeleton : transmit changes in the ECM to the cytoskeleton and vice versa--to integrate changes occurring outside and inside the cell 37. Plasmodesmata pl. (s. Plasmodesma)

From the Greek: desmos, to bind

• Connects the living parts of plant cells • Plasma membrane lines the channel

38. Tight junctions

Membranes of neighboring cells are fused

Prevent leakage of extracellular fluid across a layer of epithelial cells

39. Desmosomes

• Also called anchoring junction • Intermediate filaments reinforce desmosomes

Fastens cells together into strong sheets

40. Gap junction

• Also called communicating junctions

• Provide cytoplasmic channels between cells • Allows the transfer of salt ions, sugars, amino acids, and other small molecules to pass through pores

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