Chapter 4: Cell Structure and Function
The Cell Theory:
1. All organisms are composed of cells, and the cell is the basic unit structure of organisms
2. Cells are capable of self-reproduction, and all cells arise from preexisting cells
In general, cells are very small (10 100 mm)
Cells maintain a large surface-area-to-volume ratio (to maximize its surface area) for adequate exchange of materials with its environment
Microscopes capable of viewing subcellular components:
Electron Microscope (EM): (max. magnification 100,000X)
Scanning EM surface (exterior) view of cell and/or organelles
Transmission EM slice or section through any part of cell
Microscopes capable of viewing subcellular components:
Confocal Microscope: (max. magnification 1200X)
- slice or section through any part of cell
- uses fluorophores (fluorescent molecules which absorb light of a specific wavelength, and transmit a specific color of light) which can be used to illuminate specific macromolecules or organelles within the cell using a separate color for each
Prokaryotic Cells: (bacteria/Kingdom Monera)
Features:
Outer Boundary: Flagella (motile bacteria)
Capsule or slime layer (some bacteria)
Cell Wall (contains peptidoglycan)
Plasma membrane
Cytoplasm: thylakoids (photosynthetic cyanobacteria)
ribosomes
many enzymes
(no mitochondria)
Nucleoid: chromosome (DNA only: no true nucleus)
(no nuclear membrane)
Eukaryotic Cells: (all other organisms)
- True nucleus with nuclear membrane
- Organelles: small, membrane-bounded bodies with a specific structure & function (e.g.: mitochondria, chloroplasts, lysosomes) in cytosol (semifluid medium between nucleus and plasma membrane)
Outer boundary:
Cilia and Flagella: composed of microtubules (9 + 2 pattern); used in movement
- Cilia present in some unicellular protists (Paramecium) and cells of respiratory tract in animals
- Flagella present in some unicellular protists (Euglena) and sperm cells
Cell Wall: only in plant cells
- composed of cellulose fibrils; porous; functions in support & protection
Plasma membrane: outer boundary of cells (except plant cells also cell wall)
- Phospholipid Bilayer: semipermeable and selectively permeable
- Functions in regulation of passage of molecules into and out of the cell
- See Chapter 5
Cytosol:
Cytoskeleton: composed of microtubules,
intermediate filaments, and actin filaments
- Functions in maintaining shape of cell and movement of subcellular structures
- Microtubules: composed of tubulin dimers coiled into tubelike structures
- Concentrated & arranged as rings of nine doublets or triplets in centrioles, cilia, and flagella
- Microtubules involved in movement associate with motor proteins kinesin and dynein
- Intermediate Filaments and actin filaments have structural roles throughout the cell
- Actin filaments combine with myosin in muscle cells to enable muscle movement
Centrioles: (animal cells only)
- 9+0 pattern of microtubules
- involved in organization of spindle fibers for chromosome movement during mitosis
Ribosomes:
site of protein synthesis
in the cell
- free in cytoplasm (polyribosomes) or associated with rough endoplasmic reticulum
- 2 subunits (large & small); mRNA is threaded through subunits during translation (protein synthesis)
Energy-related organelles:
Chloroplasts: plant cells and some unicellular protists
- site of photosynthesis in plant cells (use of solar energy to produce carbohydrates for food)
- contains a fluid-filled space (stroma) within which is a system of interconnected flattened membranes (thylakoids)
- several photosynthetic pigments (e.g.: chlorophyll) are within the thylakoid membranes of grana (stacks of thylakoids)
Mitochondria: all eukaryotic cells
- site of cellular respiration (ATP production from carbohydrates)
- also have folded membrane system (folds are cristae, inner fluid-filled space is the matrix)
- extensive membrane systems are important in both chloroplasts and mitochondria for ATP production
Endomembrane System: includes Golgi apparatus, endoplasmic reticulum, vesicles, and nuclear membrane
Endoplasmic Reticulum: (ER)
- Rough ER: associated with ribosomes; proteins translated on ribosomes associated with the rough ER will be transported and/or secreted outside cell
- begins processing & modification of these proteins
- Smooth ER: synthesizes phospholipids in all cells; various other cell type-specific functions
- synthesizes steroid hormones in testes, and detoxifies drugs in liver cells
Golgi Apparatus:
Completes modification of proteins from rough ER (transported to Golgi in vesicles (small membrane-bounded organelles for transport))
- modification of proteins & lipids (addition of carbohydrate chains (glycosylation))
-
also transports organic molecules in vesicles; some
become lysosomes
Lysosomes: vesicles with digestive enzymes to break down macromolecules & cell debris
Microbodies: smaller version of lysosomes with specific enzyme activities
- Peroxisomes are microbodies that contain enzymes for oxidizing certain organic molecules with the release of hydrogen peroxide (toxic, but breaks down into water & oxygen)
Vacuoles: larger membrane-bounded organelles
- function in storage (mainly in plant cells)
- some plant cell vacuoles store water (central vacuole) for support; some store pigments
Nucleus: stores genetic information in all eukaryotic cells
- DNA is organized into distinct chromosomes
- Chromosomes are packaged with proteins to form chromatin
- Chromatin exists in a semifluid medium called nucleoplasm
- Dark regions within the nucleus are nucleoli (1 or more per cell)
- Within each nucleolus, ribosomal RNA is produced and joins with ribosomal proteins to form ribosomes
- The nucleus is bounded by a porous membrane, the nuclear envelope, which regulates passage of molecules into & out of the nucleus
- The structure of the nucleus is maintained by the nuclear matrix, which contains a protein network called the nuclear lamina, which also provides chromatin attachment sites to maintain organization
Chapter 5: Membrane Structure & Function
Plasma Membrane
Models:
Sandwich Model: Phospholipid bilayer is a filling between 2 layers of protein
Unit Membrane Model: Outside & inside of membrane consist of uniform units of phospholipids and proteins, with fatty acids in between
Fluid Mosaic Model: the membrane is a fluid phospholipid bilayer, capable of lateral movement of membrane components, in which various protein molecules are either partially or wholly embedded
The fluid mosaic model seems to tell the story, since the plasma membrane is a dynamic environment, capable of changing based on the cell type, and that cellıs immediate needs (membrane protein components & passage of small molecules)
Membrane Structure & Fluidity
Membrane components:
- Phospholipids: create bilayer
- Glycolipids: protective function, and cell identity (specific for cell type)
- Cholesterol: bulky; controls (reduces) permeability
- Proteins: also glycoproteins; can be transmembrane (spans the entire membrane) or embedded in either the cytoplasmic or extracellular side of the membrane
- glycoproteins (and glycolipids) function in cell-cell recognition (cell fingerprint); important in transplantation
Fluidity: Both phosholipids and membrane proteins are capable of lateral movement in the plasma membrane
- phospholipids rarely change from cytoplasmic to extracellular side of the bilayer, or vice-versa, since the polar head group would have difficulty moving through the hydrophobic center
- the amount of movement is dependent on composition of phospholipids, glycolipids, & cholesterol
Types of Membrane Proteins:
Channel Proteins: create transient hydrophilic channel for small molecules & ions to flow into & out of cell
Carrier Proteins: selectively interact with small molecules or ions to assist them across the membrane
Cell Recognition Protein: Cell Identity; individual-specific groups of proteins on extracellular side of membrane (e.g.: MHC/HLA (Human Leukocyte Antigen) important to match with donor to avoid rejection of transplanted organ or tissue)
Receptor Protein: Interacts with specific molecule to transmit some type of signal or communication between cells (e.g.: hormone receptors)
Enzymatic Protein: Catalyzes (speeds up) some specific reaction which results in a cellular response
Plasma Membrane is semipermeable and selectively permeable: some molecules may pass through freely (e.g.: water); others must be assisted across
Diffusion: movement of molecules from a region of higher concentration to a region of lower concentration (down concentration gradient)
- lipid soluble molecules, gases (oxygen, carbon dioxide) and water can diffuse across the plasma membrane
Osmosis: diffusion of water across a differentially permeable membrane (plasma membrane)
- important in water retention
Tonicity: the strength (solute concentration) of a solution in relation to osmosis
- in cells, the solute concentration of a solution with respect to that solute concentration inside the cell
- Isotonic, Hypotonic, & Hypertonic solutions: Know what happens to both plant and animal cells when placed in each type of solution
Transport by Carrier Proteins:
Facilitated Transport: passage of small molecules (glucose, amino acids) across the plasma membrane even though they may not be lipid-soluble
-
a carrier protein
assists movement of molecules down concentration gradient
-
no energy
is required
Active Transport: movement of small molecules or ions across membrane assisted by carrier protein and against concentration gradient from region of lower concentration to region of higher concentration
- requires energy (ATP)
- (e.g.: sodium-potassium pump)
Membrane-assisted transport:
- transport of macromolecules into or out of cell in vesicles
- requires energy
- Exocytosis: moves macromolecules out of cell through vesicles budding off plasma membrane
- Endocytosis: moves macromolecules into cell through vesicles budding off plasma membrane
-
Endocytosis
- Phagocytosis: Endocytosis of large food particles or invading cells (bacteria)
- Common in macrophages of the immune system
- Pinocytosis: Endocytosis of a liquid or very small particles
- Receptor-mediated endocytosis: pinocytosis involving a receptor protein and its ligand (molecule it binds)
-
receptor proteins cluster together in clathrin-coated
pits
Cell-Cell Junctions & Communication:
Plants cells: plasmodesmata: channels of cytoplasm between cells (go through cell walls)
Animal Cells:
- Adhesion junctions (desmosomes): cytoplasmic plaques within two cells are joined by intercellular filaments
- Tight junctions: plasma membrane proteins of two adjacent cells attach, producing a zipperlike fastening
- important in forming barriers to neighboring cells of a different type (e.g.: digestive tract cells with very low pH)
- Gap junctions: Channel proteins from 2 adjacent cells join, forming a continuous channel between the 2 cells
- important in muscle cell communication
Chapter 6: Metabolism: Energy and Enzymes
Energy: the capacity to do work
- Forms of energy:
Light
energy (e.g.: sunıs rays)
Heat
energy often a conversion from
another form of energy, or dissipated as a result of an energy conversion
Kinetic
energy energy of motion
Potential
energy energy stored (often in the
bonds of chemical compounds (ATP))
Two Laws of Thermodynamics:
1. Law of conservation of energy: energy cannot
be created or destroyed, but can only change from one form to another
2. Energy cannot be changed from one form to another without a loss of usable energy
Entropy: a
measure of randomness or disorder
-
organized, usable energy (fossil fuel energy; chemical energy
of ATP) has low entropy
-
unorganized, less stable energy forms (heat) have high
entropy
-
nature tends toward high entropy usable energy is required to maintain order
in nature or within an organism
-
organisms require a
constant input of usable energy (ATP hydrolysis) to maintain order
-
The ultimate source of this usable energy in organisms is light energy from the sun
-
Plants use light energy
from the sun to produce carbohydrate molecules through photosynthesis
-
Animals consume
carbohydrates produced in plants, and convert them to the potential energy of
ATP molecules through cellular respiration
Metabolism: all the chemical reactions occurring in a cell
-
some reactions are spontaneous (energy independent), while others are not (energy
dependent)
-
a reaction will occur spontaneously if it increases the entropy of the universe (remember, nature tends toward high
entropy)
Free Energy: energy
available; energy free to do work after completion of a chemical reaction
-
The free energy of both
the reactants and the products of a chemical reaction can be measured
-
Exergonic reaction:
the free energy of products is less than that of the reactants
-
Endergonic reaction:
the free energy of the products is greater than that of the reactants
-
Equilibrium: the
free energy of the products and reactants are equal
-
Exergonic reactions are spontaneous; endergonic reactions are generally not spontaneous
Endergonic reactions require an input of usable energy (the free energy of the products is greater than that of the reactants; energy is absorbed during the reaction)
Coupling exergonic reactions, which release energy, to exergonic reactions, which absorb energy, allows energetically unfavorable reactions which require energy input (muscle contraction, synthesis of macromolecules, transport of molecules across membranes) to occur in cells
ATP (Adenosine Triphosphate) : nucleotide molecule with a high energy phosphate bond
-
hydrolysis of this bond (release of the terminal phosphate) is
an exergonic reaction (releases
energy)
-
Reaction: ATP Þ
ADP + P
(+ 7.3 kcal/mol energy)
-
Advantages of using ATP as common energy source in cells:
- same energy source is used for many different types of chemical reactions in cells
- amount of ATP hydrolyzed is specific for type of reaction minimal energy loss
Enzymes: organic catalysts that speed up chemical reactions
- Usually protein molecules
- ATP hydrolysis uses an enzyme called ATPase
- Often assist each step of a metabolic pathway
- Each enzyme reacts with a specific substrate to form a specific product
- Enzymes are not changed by chemical reaction (usually)
- Enzymes lower the energy of activation for a reaction (energy required to activate the reactants)
Enzymes (cont.):
- The part of an enzyme molecule where the substrate binds is called the active site
Synthetic reaction: two or more reactants combine to produce a larger product (combination of reactants)
Degradative reaction: Larger product is broken down into two or more smaller products
The rate of a chemical reaction is influenced by:
1. temperature: moderate is best; high temperatures often denature (inactivate) enzyme
2. pH: optimized for reaction conditions
3. amount of enzyme: usually increased enzyme concentration increases rate
4. time: usually increased time increases rate
Enzyme Inhibition: (slow rate)
Competitive Inhibition: competition of substrate analog for active site of enzyme
Noncompetitive Inhibition: binding of a molecule to a different site of enzyme (allosteric site) induces change of shape at active site substrate can no longer bind
Feedback Inhibition: product of reaction binds to enzyme (allosteric site), and stops reaction
Cofactors: inorganic ions or organic (nonprotein) coenzymes required by some enzymes for function
-
Vitamins are often components of coenzymes
Chapter 7:
Photosynthesis
Photosynthesis: conversion of solar energy to carbohydrate molecules using carbon dioxide and water
Overall reaction: solar energy + CO2 + H2O Þ carbohydrate + O2
Electromagnetic spectrum: solar radiation spectrum
- divides energy forms based on wavelength
- light energy (sunlight) is a portion of this spectrum
- short wavelength forms (ultraviolet (UV) light) have high energy; long wavelength forms have low energy (infrared light)
Photosynthesis uses the visible light portion of the electromagnetic spectrum
Photosynthesis uses pigments (chlorophylls, carotenoids, etc.) that absorb specific wavelength(s) of light
- Absorption spectrum: plots relative absorption of wavelengths of visible light for molecules
- Plants appear green (mostly) because the dominant pigments of plants (and photosynthesis) are chlorophylls
- chlorophylls transmit green light (absorb most other wavelengths of visible light)
Photosynthesis occurs in chloroplasts
Chloroplasts composed of 2 main parts:
- stroma: large central compartment
- thylakoid: membrane system within stroma
- grana: stacks of thylakoids
Photosynthesis consists of 2 major reactions:
Light-dependent reactions: capture solar energy in 2 photosystems
- occur in thylakoid membrane where pigments are located
- In each photosystem, the light-gathering antenna (chlorophylls & accessory pigments) absorb solar energy and transfer it to a reaction center chlorophyll a molecule, which then sends energized electrons to an electron acceptor molecule
- Cyclic electron pathway: utilized by some photosynthetic bacteria to produce only ATP from photosystem I
- Noncyclic pathway: noncyclic electron flow: water is oxidized (split) to yield H+, e-, and O2; ATP is produced, and NADP+ becomes NADPH (reduced)
-
utilizes both photosystems I and II
- most plants uses this pathway
Chemiosmosis: ATP production occurs in the stroma, tied to an electrochemical gradient produced by the flow of hydrogen ions from the thylakoid space into the stroma
- utilizes a membrane ATP synthase complex
Hydrogen ions in the stroma combine with NADP+ to yield NADPH
ATP and NADPH are utilized in the light independent reactions to produce carbohydrate molecules
Calvin Cycle (Light-independent reactions):
Carbon dioxide fixation: attachment of carbon dioxide to a 5 carbon sugar (RuBP (ribulose bisphosphate)) by RuBP carboxylase
This molecule immediately breaks down into 2 PGA (phosphoglyceraldehyde) molecules in 2 steps
- these reactions use ATP and NADPH formed by the light-dependent reactions
- The 2 PGA immediately break down into 2 PGAL (phosphoglyceraldehyde) molecules, which are used to synthesize glucose molecules
Cellular respiration includes both Aerobic Respiration and Anaerobic Respiration
-
includes all the various
metabolic pathways that break down carbohydrates and other molecules
resulting in the production of ATP
Aerobic
Respiration: the complete breakdown of glucose to carbon dioxide
and water
Fermentation (Anaerobic Respiration:) : Glycolysis followed by the reduction of pyruvate to either lactate or alcohol and carbon dioxide.
Glucose metabolism is an oxidation-reduction
reaction. Glucose is oxidized and oxygen is reduced
Energy released by metabolism of glucose is used to produce
ATP
- ATP synthesis is an endergonic reaction
Glycolysis: the
breakdown of glucose (6C) to 2 pyruvate (3C) molecules
- net gain of 2 ATP molecules (4 produced, 2 used)
-
no oxygen is required;
takes place in cytoplasm of
cell (outside mitochondria)
Transition reaction:
pyruvate (3C) is oxidized to acetyl group (2C) with release of carbon dioxide
Krebs cycle: series
of reactions that form a cycle, releasing carbon dioxide and producing ATP
- 2 ATP produced per glucose (1 for each acetyl group entering cycle)
Electron Transport System: accepts electrons from NADH (produced from NAD+ in glycolysis and Krebs cycle) and FADH2 (Produced from FAD during Krebs cycle), and is transferred to acceptors until it reaches the final acceptor in the chain, oxygen
Krebs cycle (cont.)
- 16 ATP produced per pyruvate released by glycolysis, for a total of 32 ATP produced (from a total of 10 NADH and 2 FADH2 produced by the complete breakdown of glucose)
- each NADH yields 3 ATP molecules
- each FADH2 yields 2 ATP molecules
The mitochondrion is an organelle with a double membrane and a fluid matrix in the middle, with an intermembrane space between the inner and outer membranes
- the membranes fold to form cristae, to increase surface area for transport, transfer of hydrogen ions and ATP
- ATP is produced in the matrix, and leaves the matrix through a channel protein
- Glycolysis occurs in the cytoplasm of the cell
- The Krebs cycle takes place in the matrix of the mitochondrion
- The electron transport system is located in the cristae of the mitochondrion, with electron carriers and an ATP synthase complex in the inner membrane
ATP is produced by an ATP synthase complex in the inner membrane of the mitochondrion
- an electrochemical gradient produced by the flow of H+ ions through membrane pores created by the electron acceptor complexes drives the production of ATP
- the H+ ions are released from reduced NADH and FADH2, following the electrons donated to the membrane carriers
The various metabolic reactions of cellular respiration result in a pool of metabolites metabolic intermediates which can be used in anabolic (synthesis) or catabolic (degradative or breakdown) reactions
Fermentation: used by yeast and bacteria to produce lactate (lactic acid fermentation) or ethyl alcohol (alcohol fermentation)
- only 2 ATP are produced (low energy yield)