1. BSC 2010 - Exam I Lectures and Text Pages I. Intro to Biology (2-29) II. Chemistry of Life – Chemistry review (30-46) – Water (47-57) – Carbon (58-67) – Macromolecules (68-91) III. Cells and Membranes – Cell structure (92-123) – Membranes (124-140) IV. Introductory Biochemistry – Energy and Metabolism (141-159) – Cellular Respiration (160-180) – Photosynthesis (181-200)

2. THE CELL – The Fundamental Unit of Life Cell Theory 1. All organisms consist of one or more cells. 2. Cells are the smallest functional unit of life. 3. All cells arise from pre-existing cells. History of cell theory: 1. Robert Hooke - 1665 - first described and named cells, looking at cork 2. Loreza Oken - 1805 - “all life comes from and is made of cells” 3. Schleiden & Schwann - 1839 - credit for cell theory 4. Virchow - 1855- “cells come from pre-existing cells”

3. Cell structure is correlated to cellular function All cells are related by descent from previous cells. They have been modified over time by evolution. 10 µm Figure 6.1

4. Microscopy and Biochemistry Cytology – The Study of Cells To study cells, biologists use microscopes and the tools of biochemistry

5. Microscopes: used to view cells too small to see with our eyes Different types of microscopes can be used to visualize different sized cells and cellular structures. 1 m 0.1 nm 10 m 0.1 m 1 cm 1 mm 100 µm 10 µ m 1 µ m 100 nm 10 nm 1 nm Length of some nerve and muscle cells Chicken egg Frog egg Most plant and Animal cells Smallest bacteria Viruses Ribosomes Proteins Lipids Small molecules Atoms Nucleus Most bacteria Mitochondrion Unaided Eye Light microscope Electron microscope Figure 6.2 Human height Measurements 1 centimeter (cm) = 10  2 meter (m) = 0.4 inch 1 millimeter (mm) = 10 –3 m 1 micrometer (µm) = 10 –3 mm = 10 –6 m 1 nanometer (nm) = 10 –3 mm = 10 –9 m

6. Light Microscopes Light microscopes – Pass visible light through a specimen – Magnify cellular structures with lenses

7. Visualization Enhancement – There are several methods for enhancing visualization of cellular structures TECHNIQUE RESULT Brightfield (unstained specimen). Passes light directly through specimen. Unless cell is naturally pigmented or artificially stained, image has little contrast. [Parts (a)–(d) show a human cheek epithelial cell.] (a) Brightfield (stained specimen). Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved). (b) Phase-contrast. Enhances contrast in unstained cells by amplifying variations in density within specimen; especially useful for examining living, unpigmented cells. (c) 50 µm Figure 6.3

8. Visualization Enhancement Differential-interference-contrast (Nomarski). Like phase-contrast microscopy, it uses optical modifications to exaggerate differences in density, making the image appear almost 3D. Fluorescence. Shows the locations of specific molecules in the cell by tagging the molecules with fluorescent dyes or antibodies. These fluorescent substances absorb ultraviolet radiation and emit visible light, as shown here in a cell from an artery. Confocal. Uses lasers and special optics for “optical sectioning” of fluorescently-stained specimens. Only a single plane of focus is illuminated; out-of-focus fluorescence above and below the plane is subtracted by a computer. A sharp image results, as seen in stained nervous tissue (top), where nerve cells are green, support cells are red, and regions of overlap are yellow. A standard fluorescence micrograph (bottom) of this relatively thick tissue is blurry. 50 µm (d) (e) (f)

9. Electron microscopes: focus a beam of electrons through a specimen or onto its surface The scanning electron microscope (SEM) – Provides for detailed study of the surface of a specimen TECHNIQUE RESULTS Scanning electron micro- scopy (SEM). Micrographs taken with a scanning electron micro- scope show a 3D image of the surface of a specimen. This SEM shows the surface of a cell from a rabbit trachea (windpipe) covered with motile organelles called cilia. Beating of the cilia helps move inhaled debris upward toward the throat. (a) Cilia 1 µm Figure 6.4 (a)

10. Electron microscopes The transmission electron microscope (TEM) – Provides for detailed study of the internal ultrastructure of cells Transmission electron micro- scopy (TEM). A transmission electron microscope profiles a thin section of a specimen. Here we see a section through a tracheal cell, revealing its ultrastructure. In preparing the TEM, some cilia were cut along their lengths, creating longitudinal sections, while other cilia were cut straight across, creating cross sections. (b) Longitudinal section of cilium Cross section of cilium 1 µm Figure 6.4 (b)

11. Isolating Organelles by Cell Fractionation Cell fractionation – Takes cells apart and separates the major organelles from one another by size and density A centrifuge – Is used to fractionate cells into their component parts

12. Cell Fractionation Tissue cells Homogenization Homogenate 1000 g (1000 times the force of gravity) 10 min Differential centrifugation Supernatant poured into next tube 20,000 g 20 min Pellet rich in nuclei and cellular debris Pellet rich in mitochondria (and chloro- plasts if cells are from a plant) Pellet rich in “microsomes” (pieces of plasma mem- branes and cells’ internal membranes) Pellet rich in ribosomes 150,000 g 3 hr 80,000 g 60 min Figure 6.5 First, cells are homogenized in a blender to break them up. The resulting mixture (cell homogenate) is then centrifuged at various speeds and durations to fractionate the cell components, forming a series of pellets.

13. Cell Fractionation In original experiments, researchers used microscopy to identify the organelles in each pellet, establishing a baseline for further experiments. In the next series of experiments, researchers used biochemical methods to determine the metabolic functions associated with each type of organelle. Researchers currently use cell fractionation to isolate particular organelles in order to study further details of their function.

14. Features all cells have in common – They are bounded by a plasma membrane – They contain a semifluid substance called the cytosol – They contain chromosomes – They all have ribosomes

15. There are two major cell types Prokaryotic Eukaryotic – Eukaryotic cells have internal membranes that compartmentalize their functions

16. Prokaryotic cells B acteria and cyanobacteria (blue-green algae); appeared about 3.5 billion years ago. a.small, 1-10um b.usually have a cell wall c.no membrane-bound organelles d.no membrane-bound nucleus e. circular DNA concentrated in nucleoid region f.have a plasma membrane, cytoplasm, & ribosomes g. some have outer capsule, pili, and/or flagella

17. Prokaryotic cells (b) A thin section through the bacterium Bacillus coagulans (TEM) Pili: attachment structures on the surface of some prokaryotes Nucleoid: region where the cell’s DNA is located (not enclosed by a membrane) Ribosomes: organelles that synthesize proteins Plasma membrane: membrane enclosing the cytoplasm Cell wall: rigid structure outside the plasma membrane Capsule: jelly-like outer coating of many prokaryotes Flagella: locomotion organelles of some bacteria (a) A typical rod-shaped bacterium 0.5 µm Bacterial chromosome Figure 6.6 A, B

18. Eukaryotic cells All other living organisms (protists, fungi, plants, animals); appeared about 2.2 billion years ago. a. have membrane-bound organelles b. larger, 10-100um (limited by surface area/volume ratio) c. complex chromosomes d. true nucleus with a membranous nuclear envelope

19. Cell size is restricted by metabolic needs The logistics of carrying out cellular metabolism sets limits on the size of cells. Cells exchange materials and energy with the environment. This is accomplished across the plasma membrane.

20. A smaller cell – Has a higher surface area to volume ratio, which facilitates the exchange of materials into and out of the cell Surface area increases while total volume remains constant 5 1 1 Total surface area (height  width  number of sides  number of boxes) Total volume (height  width  length  number of boxes) Surface-to-volume ratio (surface area  volume) 6 1 6 150 125 12 750 125 6 Figure 6.7

21. Exchanges with the environment The plasma membrane – Functions as a selective barrier – Allows sufficient passage of nutrients and waste Carbohydrate side chain Figure 6.8 A, B Outside of cell Inside of cell Hydrophilic region Hydrophobic region Hydrophilic region (b) Structure of the plasma membrane Phospholipid Proteins TEM of a plasma membrane. The plasma membrane, here in a red blood cell, appears as a pair of dark bands separated by a light band. (a) 0.1 µm

22. The Origin of Eukaryotic Cells There are 2 evolutionary theories of the origin of eukaryotic cells. They are both supported by evidence, and they probably both contributed to the formation of eukaryotic cells. (For additional info: See chapters 26 and 28) 1. Invagination of cell membranes formed membrane-bound organelles. – Evidence? Small invaginations in modern bacteria, called mesosomes 2. Endosymbiotic theory (Lynn Margulis, 1967) - one prokaryote ate another without digesting, and came to live together. – Evidence? Mitochondria and chloroplasts have their own DNA as well as double membranes. They can replicate independently of cell division.

23. Advantages of membrane-bound organelles 1. partitions the cell into compartments 2. unique chemistry in different compartments 3. participate in metabolic reactions (membranes themselves have enzymes embedded) 4. provides localized environment with conditions for metabolism 5. sequesters reactions so they don’t interfere with other reactions in the cell

24. Processes cells undergo that allow for multicellularity 1. Specialization of cells into specific types allows for the formation of different tissues. 2. Differentiation: the process leading to specialized cells with different functions.

25. A Panoramic View of the Eukaryotic Cell Eukaryotic cells – Have extensive and elaborately arranged internal membranes, which form organelles Plant and animal cells – Have most of the same organelles

26. An Animal Cell Rough ERSmooth ER Centrosome CYTOSKELETON Microfilaments Microtubules Microvilli Peroxisome Lysosome Golgi apparatus Ribosomes In animal cells but not plant cells: Lysosomes Centrioles Flagella (in some plant sperm) Nucleolus Chromatin NUCLEUS Flagelium Intermediate filaments ENDOPLASMIC RETICULUM (ER) Mitochondrion Nuclear envelope Plasma membrane Figure 6.9

27. A Plant Cell In plant cells but not animal cells: Chloroplasts Central vacuole and tonoplast Cell wall Plasmodesmata CYTOSKELETON Ribosomes (small brwon dots) Central vacuole Microfilaments Intermediate filaments Microtubules Rough endoplasmic reticulum Smooth endoplasmic reticulum Chromatin NUCLEUS Nuclear envelope Nucleolus Chloroplast Plasmodesmata Wall of adjacent cell Cell wall Golgi apparatus Peroxisome Tonoplast Centrosome Plasma membrane Mitochondrion Figure 6.9

28. Basic Parts of a Eukaryotic Cell All eukaryotic cells have: – A nucleus – Cytoplasm – everything outside the nucleus but still inside the plasma membrane, includes various cytoplasmic organelles. – A plasma membrane

29. The Nucleus: Genetic Library of the Cell The nucleus – Contains most of the genes in the eukaryotic cell in the form of chromosomes Chromosomes are made of chromatin (DNA and proteins). – Has a double membrane with pores in it – Has dense regions called nucleoli - where ribosome subunits are made

30. The Nucleus The nuclear envelope – Encloses the nucleus, separating its contents from the cytoplasm Figure 6.10 Nucleus Nucleolus Chromatin Nuclear envelope: Inner membrane Outer membrane Nuclear pore Rough ER Pore complex Surface of nuclear envelope. Pore complexes (TEM). Nuclear lamina (TEM). Close-up of nuclear envelope Ribosome 1 µm 0.25 µm

31. Ribosomes: Protein Factories in the Cell Ribosomes – Are particles made of ribosomal RNA and protein – Function in protein synthesis – Are not membrane bound (also found in prokaryotic cells) – Subunits are created in the nucleoli, but assembled in the cytoplasm. – use mRNA and translate the genetic code into amino acids, building proteins. This process is translation and happens in the cytoplasm.

32. 2 Types of Ribosomes Free ribosomes- make proteins that stay in the cytoplasm and are used there. Bound ribosomes- make proteins for export or for membrane construction. ER Endoplasmic reticulum (ER) Ribosomes Cytosol Free ribosomes Bound ribosomes Large subunit Small subunit TEM showing ER and ribosomes Diagram of a ribosome 0.5 µm Figure 6.11

33. The Endomembrane System The endomembrane system regulates protein traffic and performs metabolic functions in the cell. The endomembrane system – May have evolved as an invagination of the plasma membrane – Includes many different structures Nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles and the plasma membrane.

34. The Endoplasmic Reticulum: Biosynthetic Factory The endoplasmic reticulum (ER) – Accounts for more than half the total membrane in many eukaryotic cells – Is a membranous network enclosing the lumen or cisternal space. – The ER membrane is continuous with the outer nuclear membrane. Smooth ER Rough ER ER lumen Cisternae Ribosomes Transport vesicle Smooth ER Transitional ER Rough ER 200 µm Nuclear envelope Figure 6.12

35. Two Distinct Regions of ER – Smooth ER, which lacks ribosomes – Rough ER, which has ribosomes embedded in the membrane Smooth ER Rough ER ER lumen Cisternae Ribosomes Transport vesicle Smooth ER Transitional ER Rough ER 200 µm Nuclear envelope Figure 6.12

36. Functions of Smooth ER The smooth ER – Synthesizes lipids – Metabolizes carbohydrates – Stores calcium – Detoxifies poison

37. Functions of Rough ER The rough ER – Has bound ribosomes – Produces peptide hormones, secretory proteins, and membranes, which are distributed by transport vesicles