Biology of the Cell

Dr. K. Yu School of Biological Sciences NTU

Reference textbook
Campbell Essential Biology with Physiology, 3rd edition Simon, Reece & Dickey Pearson Education Chapters 4, 5, 6, 7

Define what is a Cell ?

It is the unit of structure, function & reproduction in living things.

General Properties of all Cells

Are complex n highly organized Contain a genetic blueprint n machinery as hereditary information Derive from the division of other cells Acquire n utilize chemical energy Perform & regulate a variety of chemical reactions Can engage in mechanical activities contain the following structures: plasma membrane, cytoplasm, genetic material.
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The light microscope an invaluable aid for viewing cells

Magnification: increase in the apparent size of an object compared to its actual size Resolving power: ability of an optical instrument to distinguish 2 objects as separate. Human eye 0.1 mm. Light microscope 0.2 m. Electron microscope 0.2 nm

Optical Train of a Light Microscope

Light Source Tungsten-halogen light LED Condenser: light rays from the illuminator are condensed & focused through this lens in the center of the stage, providing better image resolution. Disc Diaphragm or Iris Diaphragm: rotating disc fixed under the stage, designed to adjust amount of light entering objective lens. This type of diaphragm provides greater control of contrast and helps achieve high image resolution Objective lens: The second lens of the microscope. Adjust magnification. The standard objectives are 4x, 10x, and 40x for total 6 magnification of 40x, 100x.

Electron Microscope
Introduced in 1950s. 2 major types of electron Microscope Transmission electron microscope Scanning electron microscope

Principle of Electron Microscope

Electron gun: shoots electron beam. Electron lenses (magnetic coils) Condenser lens: direct the electron beam to the specimen. Objective & intermediate lens: collect the electron beam that has passed through the specimen. Projector lens: direct the electron beam onto a fluorescent screen. Scanning electron microscope
Transmission electron microscope

Type of Cells
Prokaryote Cell Eukaryote Cell
Prokaryote Cell cells that lack a nucleus or any other membrane-bound structures. Almost all are unicellular (single cell). Very few are multicellular such as myxobacteria 2 groups of prokaryote Cells Bacteria, Archaea. Eukaryote Cell cells that have a nucleus and are bound by a membrane. They have specialized membrane-bound structures called organelles that perform dedicated functions. 3 major groups animal, plant, fungi.
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Eukaryote Cell vs Prokaryote Cell

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Prokaryote Cells
Bacteria & Algae

Some common bacteria E. Coli Bacillus Salmonella Helicobacter pylori Streptomyces Lactobacillus Bifidobacterium Penicillum Anthrax
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Bad bacteria

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Eukaryotic cells
3 groups of eukaryotic cells: Animals, Plants, Fungi

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A typical eukaryotic cell

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All Eukaryotes have a number of common features. They are:

Plasma membrane (cell membrane) Nucleus Mitochondria Endoplasmic reticulum Golgi apparatus Ribosomes Cytoskeleton Cytoplasm all the contents (fluid, organelles) outside the cell nucleus & enclosed within the plasma membrane of the cell.

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Plant Cell
Cell Wall: composed of cellulose, hemicellulose, pectin & lignin. Plasma membrane: skin of the cell Chloroplasts: contain chlorophyll for photosynthesis. Mitochondria: producing energy Endoplasmic reticulum: site for producing proteins. Golgi apparatus: processing proteins Ribosomes: producing proteins Nucleus: contains genetic material of the cell & thus controls gene activity. Also controls cell division (cell cycle). Plasmodesmata: channels that lined the plasma membrane that connects with adjacent cells across the cell wall

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Animal cell
Plasma membrane: Skin of the Cell Chloroplasts: contain chlorophyll for photosynthesis. Mitochondria: producing energy Endoplasmic reticulum: site for producing proteins. Golgi apparatus: processing proteins Ribosomes: producing proteins Nucleus: contains genetic material of the cell & thus controls gene activity. Also controls cell division (cell cycle).

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Plant cell vs Animal Cell

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Closer look at the Cell

Plasma membrane Cell Wall Cell nucleus n Ribosomes Endomembrane system: endoplasmic recticulum n Golgi apparatus Lysosomes Vacuoles Chloroplasts n Mitochondria Cytoskeleton Cilia n Flagella
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Plasma Membrane
All animal n plant cells are bounded by a protective outer layer called the plasma membrane = Skin of the Cell. Plasma membrane regulates the traffic of substances between the interior of the cell n its surrounding.

Structure - Bilayer of phospholipids embedded with proteins & cholesterol

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Function of Membrane Lipids

Regulate membrane fluidity Fluidity refers to the viscosity of the lipid bilayer.

Function of Membrane Proteins

Transport carry molecules across the plasma memb. Cell-cell recognition conjugated with carbohydrates to form glycoproteins. Serve to recognize own cells from foreign cells. Cell-cell communication cells send memb proteins to talk to other cells. Intracellular signal transduction memb proteins sent to organelles (nucleus, golgi, endoplasmic recticulum) as signals. Adhesion cells stick to each other using memb proteins.
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The Cell Wall

Only in plant cells. Controls turgidity (stiffness). Extracellular structure surrounding plasma membrane. Primary cell wall: extremely elastic. Secondary cell wall forms around primary cell wall. Contains tiny openings call plasmodesmata, that contact with the cell wall of adjacent cells.

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Plasmodesmata

Provide an easy route for the movement of ions, small molecules like sugars and amino acids, and even macromolecules like RNA and proteins, between cells. Are sheathed by a plasma membrane that is simply an extension of the plasma membrane of the adjoining cells.

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3 layers in the Cell Wall

Middle lamella shared by 2 adjacent cells Primary wall Secondary wall

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Cell Nucleus: Structure

Spherical-shaped organelle present in every eukaryotic cells except red blood cells. In general, each cell has only 1 nucleus; except a very few species of slime molds & algae. It occupies 15 70% of the cells volume. Consists of a nuclear envelope-It is a double-layered membrane that encloses the contents of the nucleus. Contents in cell nucleus: nucleolus, chromatin, nucleoplasm, ribosomes. Nucleolus: produces ribosomes. Nucleoplasm: fluid in the nucleus. Outer membrane is connected to endoplasmic reticulum. Nuclear envelope has tiny openings called nuclear pores. Nuclear pores regulate passage of specific molecules (proteins & RNA) between the nucleus & cytoplasm.
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Cell Nucleus: Roles & Functions

Roles

Control center for regulation & coordination of genes & genetic & biochemical activities in the cell.
Functions Storage of hereditary material genes contained in DNA. DNA is coupled to histones & they are referred to as chromatins. Chromatin is packaged into chromosomes. Produce messenger RNA (mRNA) that code for proteins. Production of ribosomes (protein factories) in the nucleolus. Transport regulatory factors, ribosomes & mRNA via nuclear pores to outside the nucleus. Organize cell division for tissue & organ repair & development.

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Ribosomes

Ribosomes are composed of RNA & ribosomal proteins. Structurally, they are made up of 2 subunits: a large subunit (60S) & a small subunit (40S) They are the protein factories. They produce/manufacture proteins. Ribosomes are made in the nucleolus & are transported outside the nucleus into the cytoplasm.

In the cytoplasm, they attach to endoplasmic reticulum where they will

produce/manufacture proteins.

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Endomembrane system: endoplasmic recticulum n Golgi appararus

Endoplasmic recticulum (ER) structure: It contains many folds - but the membrane forms a single sheet enclosing a single closed sac. This internal space is called the ER lumen. ER functions as the site of production of the proteins. ER is additionally responsible for moving proteins & other carbohydrates to Golgi apparatus, to the plasma membrane, to the lysosomes, or wherever else needed. There are two types of ER - rough, which is coated with ribosomes, and smooth, which isn't. Rough ER is the site of protein synthesis. The smooth ER is where the vesicles carrying newly synthesized proteins (from the rough ER) are budded off.
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Golgi Apparatus
Golgi apparatus has a structure that is made up of cisternae, which are flattened stacks of membrane usually found in a series of five to eight Main functions of the Golgi apparatus are processing proteins synthesized in the endoplasmic reticulum (ER) & directing molecules made in various areas of the cell to their future locations in or out of the cell.
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Lysosomes
A lysosome is a specialized singlemembrane layer organelle that holds a variety of digestive enzymes. Digestive enzymes are first created in rough endoplasmic reticulum. They are packaged in a vesicle & sent to Golgi apparatus. The Golgi then does its final work to create the digestive enzymes & pinches off a small, very specific vesicle. That vesicle is a lysosome. From there the lysosomes float in the cytoplasm until they are needed. Lysosomes also act as cellular garbage trucks, hauling away unusable waste & dumping it outside the cell.

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Vacuoles
Structure of vacuoles is as follows: a single membrane layer that surrounds a mass of fluid. In that fluid are nutrients or waste products. Plants may also use vacuoles to store water. Those tiny water bags help to support the plant. They are closely related to objects called vesicles that are found throughout the cell. Vacuoles are storage bubbles found in cells. They are found in both animal & plant cells but are much larger in plant cells Vacuoles might store food or any variety of nutrients a cell might need to survive. They can even store waste products so the rest of the cell is protected from contamination. Eventually, those waste products would be excreted out of the cell.

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Chloroplast: Structure & Functions

Structure: Two membranes contain & protect the inner parts of chloroplast. Stroma is an area inside of chloroplast where reactions occur & starches (sugars) are created. One thylakoid stack is called a granum. Thylakoids have chlorophyll molecules on their surface. Chlorophyll uses sunlight to create sugars. Stacks of sacs are connected by stromal lamellae. Lamellae act like the skeleton of chloroplast, keeping all of sacs a safe distance from each other & maximizing efficiency. Functions: to make sugars & starches. They use a process called photosynthesis - process of a taking energy from the Sun & creating sugars. When the energy from the Sun hits a chloroplast, chlorophyll uses that energy to combine carbon dioxide (CO2) & water (H2O). The molecular reactions create sugar and oxygen (O2). Plants & animals then use the sugars (glucose) for food & energy.
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Mitochondria: Structure, Functions

Structure: Rod-shaped structures that are enclosed within two membranes - the outer membrane & the inner membrane. The space in between the two membranes is called the inter-membrane space which has the same composition as the cytoplasm of the cell. Inner membrane contains enzymes of the electron transport chain & the ATP synthetase enzyme which will produce ATP from fatty acids & sugars. It is permeable only to oxygen, carbon dioxide & water. The inner membrane has infoldings called cristae that increase the surface area for enzymes & proteins that produce ATP, the energy rich molecules. Matrix contains enzymes that are important for producing ATP molecules. Besides these, it has oxygen, carbon dioxide & other 33 recyclable intermediates.

Functions: Transport fatty acids (lipids) & sugars from cytoplasm into mitochondrial matrix for energy production (ATP). Detoxification of ammonia.

Cytoskeleton
Cytoskeleton serves several key functions:
It maintains structure to cells & acts as a scaffolding for the attachment of many organelles. Provides mechanical strength. Enables cells to move. Enables proper cell division for cellular reproduction. Enables movement of nutrients to the various organelles in the cell

Cytoskeleton is made up of 3 types of protein fibers

Actin filaments: solid thick rods that enable cells to move. Intermediate filaments: solid narrow short rods that hold & tie microtubules in specific arrangements Microtubules: hollow rods that enable cells to maintain their shape as well as enable movement of nutrients in the cell.
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 Both are whiplike appendages that extend out from the plasma membrane of many different types of eukarytoic cells. If there are many of them, they are called cilia. If only one, or a few of them, they are called flagella. Flagella tend to be longer in length than cilia.

Cilia n Flagella
They move liquid (fluid) past the surface of the cell. For single cells, for eg, sperm, this enables them to swim. For cells anchored to a tissue, for eg, epithelial cells lining our air passages, this moves liquid over the surface of the cell (eg, driving particle-laden mucus towards the throat.)

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The Working Cell

Metabolism Basic Energy Concepts ATP n Cellular Work Enzymes Membrane function

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Metabolism
Metabolism is the basis of life that arises from interaction between molecules within the orderly environment of the cell. All living things must carry out metabolism in order to live. Metabolism through metabolic pathways generate a variety of energies such as kinetic energy, potential energy, chemical (free) energy & thermal energy. Metabolism can be divided into 2 metabolic pathways catabolic pathways, anabolic pathways. Metabolic pathways are basically sets of biochemical reactions. Catabolic pathways: these pathways deal with cellular respiration in which the sugar called glucose & other organic foods are broken down in the presence of oxygen to give carbon dioxide n water. Anabolic pathways: these pathways deal with consumption of energy to build complicated molecules from simpler ones. An example of building muscles and storing fats.

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Basic Energy Concepts

Cell must WORK in order to live. WORK requires ENERGY. ENERGY is defined as the capacity to perform work. Work is performed whenever an objectis moved against an opposing force. Kinetic energy: Energy of motion. Potential energy: Energy that an object has because of its location or structure, such as the energy contained by water behind a dam or by a compressed spring. Conservation of Energy: Energy cannot be created or destroyed; instead energy is converted from one form (eg, oil) to another form (eg, electricity). Entropy: Entropy is a measure of randomness or disorder. Every energy conversion releases randomized energy in the form of heat. Chemical Energy: Molecules store varing amounts of potential energy in the arrangement of their atoms. Organic compounds are relatively rich in such chemical energy. Free energy: Energy that is extracted from a biological system. Food calories: Food calories are units used to measure the amount of energy in our foods and the amount of energy we expend in various 38 activities.

 ATP - universal carrier of energy in cells ATP = adenosine triphosphate Terminal phosphate of ATP can be broken (hydrolysed) to give ADP with the release of free energy This free energy is used for muscle contraction, biosynthesis of proteins, transport of proteins, etc. ADP is converted back to ATP by a process called rephosphorylation. Re-phosphorylation comes from oxidizing foods or by photosynthesis.

ATP

Energy from the food you eat is converted in mitochondria into ATP. Cells use ATP to power their chemical reactions. For example, muscle cells convert ATP energy into physical work, allowing you to lift weights, jog, or simply move your eyeballs from side to side.
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Chemical structure of ATP

Adenine bonded to ribose = adenosine. Adenosine bonded to 3 molecules of phosphate. Bond between the phosphate molecules has very high energy. Very high energy is released when 1 molecule of phosphate is broken off. ATP becomes ADP.

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Chemistry of ATP
Storing Energy in ATP - Energy is stored in the chemical bond between the outermost phosphate forming ATP from ADP

Releasing Energy from ATP - When energy is required, the bond between the outermost phosphate is broken releasing stored energy.

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Re-phosphorylation

Metabolism of food (or photosynthesis) generates intermediates that are able to phosphorylate ADP back to ATP (see phosphate transfer potential later). ATP is not a store of energy - it is the immediate donor of free energy that is continually being regenerated from ADP (40kg/day is turned over in humans). We store energy in the form of glycogen and fat.
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Enzymes
Are biological catalysts that increases the rate of biochemical reaction. In other words, they speed up the biochemical reaction. They are proteins. They are not changed or destroyed by the biochemical reaction they catalyze. In general, enzymes are specific in nature to the type of biochemical reaction they catalyze

Enzymes how they work

Function by binding to one or more of the reactants (substrates) in the reaction. Exact location on enzyme where substrate binding takes place is called the active site. The shape of the active site just fits the shape of the substrate, like a key fits a lock. In this way, the correct substrate binds to that specific enzyme.
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 A biochemical reaction has an activation energy. Activation energy is that which must be supplied in order for the substrates to be broken down in the biochemical reaction. The enzyme lowers activation energy, thus speeding up the biochemical reaction.

Enzymes how they work

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Enzymes how they work

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Some examples
Pepsin (Stomach): a digestive enzyme that breaks up the proteins of ingested food, splitting them into usable amino acids. Without pepsin, protein could not be used to build healthy skin, strong skeletal structure, rich blood supply, and strong muscles. Renin (intestine): a digestive enzyme that causes coagulation of milk, changing its protein into a usable form in the body. Renin releases the valuable minerals from milk, calcium, phosphorus, potassium, and iron that are used by the body to stabilize the water balance, strengthen the nervous system, and produce strong teeth and bones. Lipase (intestine): a digestive enzyme that splits fat, which is then utilized to nourish the skin cells, protect the body against bruises and blows, n ward off the entrance of infectious virus cells and allergic conditions. 46

Functions of the Plasma Membrane

Transport of Substances Cell Signaling cells communicating with each other

Transport of Substances
Plasma membrane functions to allow certain substances to enter or leave the cell. Some of these transport processes happens passively without the cell needing to expend any energy to make them happen. They are called passive transport processes. Other transport processes require energy from the cells metabolism to power them. They are called active transport processes.
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Passive Transport Processes

Two passive transport processes. Both processes do not require energy (use of ATP). They are
Simple Diffusion Facilitated Diffusion

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Simple Diffusion
Plasma membrane only allows certain molecules to cross it by simple diffusion. Plasma membrane is referred to as a selective permeable barrier or semipermeable barrier. Molecules that pass through the plasma membrane by simple diffusion: oxygen, nitrogen, carbon dioxide, ethanol, water, urea, benzene. Simple Diffusion is the movement of molecules from region of higher concentration to region of lower concentration. We call this moving down a concentration gradient.
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Facilitated diffusion

Similar to simple diffusion but requires a transport protein called a facilitated carrier. Molecules that cross the plasma membrane by facilitated diffusion: glucose, sucrose, fructose, Na+, K+, Mg2+, Ca2+. 50

 Is a special passive diffusion process. The diffusion of water through the plasma membrane. Osmosis is the movement of water from a region of high water concentration to a region of lower water concentration through the semipermeable membrane

Osmosis

Animal cells: imagine if we take a RBC which has an internal concentration of 0.9% salt solution & place it in various concentrations of varying salt concentrations. 51

How is osmosis affected in solutions of different tonicities

Hypotonic solution: the solution in which causes the cell volume to swell is referred to as hypotonic solution. Isotonic solution: the solution in which there is no change to the cell volume is referred to as isotonic solution. Hypertonic solution: the solution in which there is a decrease in cell volume is referred to as hypertonic solution.
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Active Transport
This transport processes require energy (uses ATP). Two types: Pumps, Endocytosis. They are mediated by protein pumps & receptors.

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Protein Pumps
Protein pumps pumps substances across the plasma membrane against the concentration gradient, i.e from low concentration to high concentration. Energy (in the form of ATP) must be used for these Protein pumps to work.

Hydrogen Pump: Pumping hydrogen ions out of the cell.

Sodium/Potassium Pump: Pumping sodium ions out of the cell and pumping potassium ions into the cell.

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Endocytosis
3 types of endocytosis processes

Phagocytosis Pinocytosis Receptor-mediated endocytosis.

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Endocytosis - definition
Transport of solid substances or liquid into the cell using a vacuole or vesicle. This is an active transport process; thus it uses energy (ATP). Entry of solid substance or liquid into the cell does not pass through the plasma membrane. Instead, the plasma membrane undergoes an inward protusion (invagination) that forms a vesicle. The vesicle contains the solid substance or liquid.
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Pinocytosis

Plasma membrane forms an invagination. Whatever solid substance or liquid within that area of invagination will enter into the cell. In general, this material will be dissolved in water; thus, this process is also referred to as cellular drinking to indicate that liquids n materials dissolved in liquids are ingested by the cell. 57

Phagocytosis

Cell changes shape by sending out projections which are called pseudopodia. Psuedopodium (plural) then surround the particle when the plasma membrane comes into contact with the particle. The tips of the psuedopodium fuse with each other. This results in formation of a vesicle.
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Receptor-mediated endocytosis

Receptors on the plasma membrane will bind only to specific substances (proteins) on the outside of the cell. In such an interaction, we call this a Receptor binding a ligand. Invagination occurs & a vesicle is formed. 59 The vesicle contains the receptor n ligand.

Cellular Respiration: Overview

Cellular Respiration is the production of energy from food. The Energy from food flows in a recycling manner between the organisms that respire & that of the environment in order to maintain a stable eco-system. Producers of energy are called autogrophs. They make organic molecules from inorganic molecules via photosynthesis. Consumers of organic molecules are called heterotrophs. Heterotrophs are divided into carnivores & herbivores. They consume organic molecules to make energy via cellular respiration

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Cellular Respiration Processes

Cellular respiration involves the process of oxidizing food molecules or breaking down chemical bonds of glucose into carbon dioxide & water. The energy released during the process is trapped in the form of ATP (Adenosine Tri-Phosphate) and used by different energy consuming activities of the cell. In other words, it's a set of the metabolic reactions that occur in the mitochondria of the cells of organisms to convert biochemical energy from nutrients into ATP, and release byproducts. The complete breakdown of glucose into carbon dioxide & water involves 3 major biochemical events: glycolysis, citric acid cycle, electron transport chain.

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Glycolysis, Citric Acid Cycle, Electron transport chain

Glycolysis: It's an anaerobic catabolism of glucose that occurs in all the cells & produces two molecules of pyruvate & two molecules of ATP. Citric Acid Cycle: A product of glycolysis called pyruvic acid is made into citric acid. Citric acid goes through a number of steps which is basically a cyle. This cycle is called the citric acid cycle. Carbon dioxide is formed at two of the steps in this process & hydrogen atoms are removed from the molecules along with their electrons at four of them. 2 molecules of ATP are formed. Electron transport chain: A product of glycolysis called NADH undergoes several biochemical reactions involving oxidation & reduction that result in production of hydrogen atoms (electrons) which are then made into ATP. 34 molecules of ATP are formed.

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Glycolysis, Citric Acid cycle, Electron transport chain

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Glycolysis
In glycolysis, the 6-carbon sugar, glucose, is broken down into two molecules of a 3-carbon molecule called pyruvate. This change is accompanied by a net gain of 2 ATP molecules and 2 NADH molecules.

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Citric Acid Cycle (Krebs Cycle)

Citric Acid Cycle begins after the two molecules of the three carbon sugar produced in glycolysis are converted to a slightly different compound (acetyl CoA). Through a series of intermediate steps, several compounds capable of storing "high energy" electrons are produced along with two ATP molecules. These compounds, known as nicotinamide adenine dinucleotide (NAD) & flavin adenine dinucleotide (FAD), are reduced in the process. These reduced forms carry the "high energy" electrons to the next stage. Citric Acid Cycle occurs only when oxygen is present but it doesn't use oxygen directly. Citric acid cycle occurs in mitochondria & generates a pool of chemical energy (ATP, NADH, FADH) from the oxidation of pyruvate, the end product of glycolysis.
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Electron Transport Chain

Electron Transport Chain is the final stage of cellular respiration. During glycolysis & Citric Acid Cycle, entire energy was not released from glucose. In this stage of cellular respiration, remaining energy from glucose will be released by the electron transport chain. The network of electrons carrying proteins to the inner membrane of the cell is known as electron transport chain. Eventually, in this stage the electrons along with the protons will be added to oxygen. When electrons & protons are added to oxygen, it produces water & not ATP (energy). Actually, ATP is produced when the protons are moved across the cell membrane.

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Photosynthesis - Overview

Carbohydrates produced by photosynthesis are used by the plants as a source of immediate energy for growth, reproduction, absorption of nutrients, etc. They also act as energy reserves & stored in the form of starch which enable the plants to survive in drastic conditions, like, extreme winters or droughts. Carbohydrates are also used in the formation of plant tissues to grow leaves, wood, flowers, fruits, roots, etc
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Photosynthesis - Overview
Is a chemical process that takes place in the presence of sunlight in which plants produce & store their own food. This occurs in chlorophyll containing plant cells. Chlorophyll is a pigment found in plant leaves that gives plants their green color. Chlorophyll absorbs the light energy & uses it to produce carbohydrates (sugars) & oxygen from carbon dioxide (CO2) & water (H2O). The chemical reaction can be described as follows Carbon Dioxide + Water + Sunlight Glucose + Oxygen 6CO2 + 6H2O + Sunlight C6H12O6 + 6O2 Glucose is converted into both cellulose & starch. Cellulose (fiber) & Starch is stored in the plant cell
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Photosynthesis
Chlorophyll is contained in chloroplasts. Thus, photosynthesis takes place in chloroplasts of plant cells. Glucose is converted into both cellulose & starch. Cellulose (fiber) & Starch is stored in the plant cell.

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