Chemistry, Cellular Structure, and Function

Concorde Career College, PortlandST110

Learning Objectives

• After you have completed this chapter, you should be able to:

1. Define the terms atom, element, molecule, and compound.

2. Describe the structure of an atom.3. Compare and contrast ionic and covalent

types of chemical bonding.4. Distinguish between organic and inorganic

chemical compounds.

Learning Objectives

5. Discuss the chemical characteristics of water.6. Explain the concept of pH.7. Discuss the structure and function of the

following types of organic molecules:carbohydrate, lipid, protein, and nucleic acid.

What is chemistry and why is it important?

• Chemistry– The science that deals with the composition and

properties of matter and applies to the studies of:• Physiology – study of function• Microbiology – study of microscopic plants and animals• Pharmacology - study of drugs and their actions

Elements

• Elements are the substances that make up matter.– Matter is anything that takes up space

• Elements are identified on the Periodic Table and include:– Gasses– Liquids– Solids

Structure of Matter

A. Elements and Atoms:1. Matter is anything that has

mass (Weight) and occupies space.

2. All matter is composed of elements, 92 of which occur naturally.

* Oxygen, carbon, hydrogen, and nitrogen make up 96% of the human body.

* Elements are composed of atoms; atoms of different elements vary

in size and in how they interact.

Periodic Table of Elements

• Periodic Table of Elements – Chart that arranges the elements by atomic number and by property– Arranged by atomic number – Which is the

number of protons and electrons in an element• O=8• H=1• C=6

Atoms

Atomic Structure

1. An atom consists of a nucleus containing protons and neutrons, with electrons in orbit around the nucleus in shells.

2. Protons, with a positive charge, are about equal in size to neutrons, which have no charge.

3. Electrons are much smaller and bear

a negative charge.4. An electrically neutral atom

has equal numbers of protons and electrons.

5. The number of protons denotes the atomic number of an element; the number of protons plus the number of neutrons equals the atomic weight.

Molecules and Compounds

1. A molecule is formed when two or more atoms combine.

2. If atoms of different elements combine, the molecule can also be called a compound.

3. Compounds always have a definite kind and number of atoms.

Molecule Formation

• Molecules form when electrons in the outer energy levels (valences) combine

Water

• The most abundant substance in living cells• Participates in key cellular reactions– Universal solvent– Functions in:• Respiration• Temperature control• Protects fetus, brain and spinal cord• Body lubricant

Chemical Bonding• Chemical bonds form to make atoms more

stable1 .Atoms form bonds by gaining, losing, or sharing

electrons.2. Electrons are found in shells around the nucleus. a. The first energy shell holds two electrons; the other

energy shells each hold up to eight electrons when on the outside.

(unpaired electrons can become stable by: sharing and donating electrons)

Bonds and Energy

• Atoms combine by bonding together and sharing electrons

• When atoms combine and bond together a molecule or a compound is formed (CO2 or H2O)

Types of Bonds

• Ionic bonds – One atom gains electrons while another atom loses electrons (positive and negative ions bond together)– Ions – positively or negatively charged atoms

• Sodium – Na+ is a positively charged ion (cation)• Chlorine – Cl- is a negatively charged ion (anion)

• What are electrolytes?– Ions in solution

– Ionic molecules dissolve (dissociate/break apart) in water.

– Water molecules wedge between the ions to force them apart.

* Electrolyte —molecule that dissociates (breaks apart) in water to form individual ions.

Ionic Bonds

Types of Bonds

• What are electrolytes?– Ions in solution

• What is the importance of electrolytes in the body?– Blood clotting– Muscle contraction– Acid/base balance (pH)

• What type of diagnostic testing is performed using ions (electrolytes) in the body?

Types of Bonds

• Covalent Bonds – Electrons are shared between atoms of the molecule– Electrons in the outer energy levels (valences) of the atom

bind together– Covalent bonds exist between atoms that are the same or

different– Nonpolar covalent bond – charges are equally distributed– Polar covalent bond – one part of the bond is more

positive or more negative at a given time

Nonpolar Covalent Bond

Polar Covalent Bond

Types of Bonds

• Hydrogen bonds – hold molecules (rather than atoms) together– Weak in comparison to ionic or covalent bonds– Positive hydrogen atoms attract negative

molecules– Hydrogen bonds hold water molecules together in

the liquid form

Hydrogen Bond

Water molecules held together with a hydrogen bond

Types of Bonds

• Time permitting, view this animation from the UC Davis Bioscience Department

http://www.youtube.com/watch?v=QqjcCvzWwww

Donors and Acceptors

Electron terminology• Electron donor-donates an electron• Electron acceptor-accepts an electron• Electron carriers-accepts electrons for a short

time then loses them

Formulas1. A molecular formula represents the numbers and types of atoms in a molecule.

2. Various representations, called structural formulas, can be used to illustrate molecules.

Inorganic Chemistry

• Organic molecules contain carbon– carbon covalent bonds and/or carbon hydrogen covalent bonds; inorganic molecules do not

• Examples of inorganic molecules: water and some acids, bases, and salts

Inorganic Chemistry

• Water–Water is a solvent (liquid into which

solutes are dissolved), forming aqueous solutions in the body

–Water is involved in chemical reactions– Dehydration synthesis — chemical

reaction in which water is removed from small molecules so they can be strung together to form a larger molecule

Hydrolysis —chemical reaction in which water is added to the subunits of a large molecule to break it apart into smaller molecules

• Oxygen Oxygen is needed to release energy

from nutrients and is used to drive the cell's metabolism.

• Carbon DioxideCarbon dioxide is released as a waste product during energy-

releasing metabolic reactions.

• Chemical reactions always involve energy transfers, as when energy is used to build ATP molecules• Chemical equations show how

reactants interact to form products; arrows separate the reactants from the products

Acids and Bases

1. Substances that release ions in water are called electrolytes.

2. Electrolytes that release hydrogen ions in water are called acids.

3. Electrolytes that release hydroxide ions in water are called bases.

pH scale• Measures acidity

• Acids are compounds that produce an excess of H+ ions (less than 7)

• Bases (alkaline) are compounds that produce an excess of OH- ions

pH scale

4. The concentrations of H+ & OH- in the body is very important to physiology.

5. pH represents the concentration of hydrogen ions [H+] in solution.

6. A pH of 7 indicates a neutral solution with equal numbers of hydrogen ions and

hydroxide (OH-) ions.

a. A pH of zero to less than 7 indicates the presence of more hydrogen ions, and thus the

solution is more acidic; a pH greater than 7 to 14 indicates more hydroxide ions, or a basic solution.

b. Between each whole number of the pH scale there is a tenfold difference in hydrogen ion

concentration.

Buffers Buffer• “Any substance or mixture of compounds that,

added to a solution, is capable of neutralizing both acids and bases without appreciably changing the original acidity or alkalinity of the solution.”

buffer. (n.d.). Dictionary.com Unabridged (v 1.1). Retrieved November 10, 2007, from Dictionary.com website: http://dictionary.reference.com/browse/buffer

Buffers

Why is aspirin buffered?

Salts

Strong acids mixed with strong Bases can neutralize each other.

When this happens usually a salt and water remains.

Buffers prevent sudden changes in concentration of hydrogen ions.

Chemical Constituents of Cells A. Compounds that contain carbon are called organic, the others are inorganic

Organic Chemistry

• More complex than inorganic compounds

• Larger than organic compounds

• Four type of major organic compounds– Carbohydrates– Lipids– Proteins– Nucleic Acids

1. Carbohydrates

a. Carbohydrates provide energy for cellular activities and are composed of carbon, hydrogen, and oxygen.

Organic Chemistry

Organic Chemistry

• Carbohydrates —sugars and complex carbohydrates– Contain carbon (C), hydrogen (H), oxygen (O)–Made up of six carbon subunits called

monosaccharides or single sugars (e.g., glucose)

– Disaccharide —double sugar made up of two monosaccharide units (e.g., sucrose, lactose)

Organic Chemistry

– Polysaccharide —complex carbohydrate made up of many monosaccharide units (e.g., glycogen made up of many glucose units)

– Function of carbohydrates is to store energy for later use

• Humans synthesize the polysaccharide glycogen.

Organic Chemistry

• Lipids —fats and oils– Trigylcerides• Made up of one glycerol unit and

three fatty acids• Store energy for later use

Organic Chemistry

– Cholesterol• Molecules have a steroid structure

made up of multiple rings • Cholesterol stabilizes the phospholipid

tails in cellular membranes • Makes steroid hormones such as

estrogen, testosterone and corisone

Proteins: Made of amino acids held together by peptide bonds creating a polypeptide chain. 2 types:

Structural Proteins – forms essential structures

Collagen – holds body tissues together

Keratin – forms outer layer of skin

Functional Proteins – play a part in chemical processes within body.

Examples: hormones, cell membrane channels and receptors, enzymes.

c. Nucleic acids are of two major types: DNA (with deoxyribose) and RNA (with ribose).

d. RNA (ribonucleic acid) functions in protein synthesis; DNA (deoxyribonucleic acid)

stores the molecular code in genes.

Organic Chemistry

– RNA (ribonucleic acid)• Used as temporary “working copy” of

a gene• Uses ribose as the sugar and A, U (not

T), and G as bases• Forms a single strand

Organic Chemistry

– DNA (deoxyribonucleic acid)• Used as the cell’s “master code” for

assembling proteins• Uses deoxyribose as the sugar and A,

T (not U), and G as bases• Forms a double helix

ATP

ATP

• Active Transport requires ATP• ATP is the fuel/energy needed for Active

Transport

*just like a vehicle needs fuel to transport*Pg. 25 AP4ST

Cell and Tissues

ST110Concorde Career College, Portland

Learning Objectives• After you have completed this chapter, you should

be able to:1. Identify and discuss the basic structure and function of the three major

components of a cell.2. List and briefly discuss the functions of the primary cellular organelles.3. Compare the major passive and active transport processes that act to

move substances through cell membranes.4. Compare and discuss DNA and RNA and their function in protein synthesis.5. Discuss the stages of mitosis and explain the importance of cellular

reproduction.6. Explain how epithelial tissue is grouped according to shape and

arrangement of cells.7. List and briefly discuss the major types of connective and muscle tissue.8. List the three structural components of a neuron.

Composition

– Cytoplasm containing specialized organelles surrounded by a plasma membrane

– Organization of cytoplasmic substances important for life

Structure of a typical cell

Structure of a typical cell

• Plasma membrane

• Cytoplasm

• Nucleus

(all parts are called Organelles)

Three Main Parts of the Cell

Parts of cell

• Organelle – “little organ” like structure. Highly specialized cellular structure that carries out a specific cellular activity. Pg. 22 AP4ST

Structural Parts

– Plasma membrane• Forms outer boundary of cell• Thin two-layered membrane of

phospholipids containing proteins• Is selectively permeable • Separates the inside from the outside pg. 27

AP4ST Table 2-1

Structure of Plasma Membrane

– Cytoplasm-materials that lie within the boundary of the cell.• Organelles (part with a specific

function; a cell organ)–Ribosomes»May attach to rough ER or lie

free in cytoplasm»Manufacture proteins»Often called protein factories

Structural Parts

– Endoplasmic reticulum (ER)• Network of connecting sacs and

canals• Carry substances through cytoplasm• Types are rough and smooth• Rough ER collects and transports

proteins by ribosomes• Smooth ER synthesizes chemicals;

makes new membrane

Structural Parts

–Mitochondria• Composed of inner and outer

membranes• Involved with energy-releasing

chemical reactions• Often called power plants of the cell• Contain one DNA molecule

Mitochondria

Structural Parts

– Golgi apparatus• Group of flattened sacs near nucleus• Collect chemicals that move from the

smooth ER in vesicles• Called the chemical processing and

packaging center

Structural Parts

– Lysosomes• Membranous-walled organelles• Contain digestive enzymes• Have protective function (eat

microbes)• Formerly thought to be responsible for

apoptosis (programmed cell death)

Structural Parts

– Centrioles• Paired organelles• Lie at right angles to each other near

the nucleus• Function in cell reproduction

Centrioles

Structural Parts

– Cilia• Fine hairlike extensions found on free

or exposed surfaces of some cells• Capable of moving in unison in a

wavelike fashion

Cilia

Structural Parts

– Flagella• Single projections extending from cell

surfaces• Much larger than cilia• “Tails” of sperm cells are the only

example of flagella in humans

Flagella

Structural Parts

– Nucleus• Controls cell because it contain the

genetic code—instructions for making proteins, which in turn determine cell structure and function• Component structures include nuclear

envelope, nucleoplasm, and chromatin granules• 46 chromosomes contain DNA, which

contains the genetic code

Nucleus

Modes of Transportation

• Separates: The inside from the outside of the cell.• Selectively permeable, allows certain substances

in, keeps other substances out. Keeps cytoplasm in, lets waste out, lets nutrients in.

• Molecules of water• Foods• Gases• Waste

Plasma Membrane

• Passive transport

• Active transport

Transportation

Passive Transport

• Isotonic

• Hypertonic

• Hypotonic

– EX• 0.9% NaCl=isotonic to RBC• Sterile water=hypotonic to RBC

Tonicity

Active Transport

• “Phago”-• “Pino”

• Ion pumps-uses ATP to move ions across the membrane against the concentration gradient

• Phago - permits a cell to engulf foreign material

• Pino - used to incorporated fluids or dissolved substances

(Requires cell energy in the form of ATP)

Active Transport

Click for Animation

Mitosis and Meiosis

• Interphase

• Prophase

• Metaphase

• Anaphase

• Telophase

5 Stages of Mitosis

Stages of Mitosis

Interphase• DNA replicate• Process by which each half of a DNA molecule becomes a whole molecule Process by which each half of a DNA molecule becomes a whole molecule

identical to the original DNA molecule; precedes mitosisidentical to the original DNA molecule; precedes mitosis

Centrioles

• Two rod-shaped organelles that migrate and participate in cell division.

Stages of Mitosis

• Prophase—first stage

– Chromatin granules become organized– Chromosomes (pairs of linked

chromatids) appear– Centrioles move away from nucleus– Nuclear envelope disappears, freeing

genetic material– Spindle fibers appear

Stages of Mitosis

Stages of Mitosis

• Metaphase—second stage– Chromosomes align across center of cell– Spindle fibers attach themselves to each

chromatid

Metaphase

Stages of Mitosis

• Anaphase—third phase– Centromeres break apart– Separated chromatids now called

chromosomes– Chromosomes are pulled to opposite

ends of cell– Cleavage furrow develops at end of

anaphase

Anaphase

Stages of Mitosis

• Telophase—fourth stage– Cell division is completed– Nuclei appear in daughter cells– Nuclear envelope and nucleoli appear– Cytoplasm is divided (cytokinesis)– Daughter cells become fully functional

Telophase

Types of Cells

Interactive Cell

• http://www.wisc-online.com/objects/ViewObject.aspx?ID=ap11403

• http://www.cellsalive.com/cells/cell_model.htm

• http://learn.genetics.utah.edu/content/begin/cells/insideacell/

Cellular Metabolism

ST110Concorde Career College

Objective

• Describe the process of cellular metabolism.

Cellular Metabolism Terminology

• Metabolism– Total chemical changes that happen inside a cell• Anabolism-builds larger molecules from smaller ones-

requires energy• Catabolism-breaks down large molecules to smaller

ones-releases energy

Cellular Metabolism Terminology

• Aerobic– Needing oxygen to produce energy

• Anaerobic– Without oxygen

• Calories– Measurement of the energy in food

• Specifically, a calorie is the amount of energy, or heat, it takes to raise the temperature of 1 gram of water 1 degree Celsius (1.8 degrees Fahrenheit). One calorie is equal to 4.184 joules, a common unit of energy used in the physical sciences.

A Gallon of Gas contains 31,000,000 calories

Calories Defined

• Most of us think of calories in relation to food, as in "This can of soda has 200 calories." It turns out that the calories on a food package are actually kilocalories (1,000 calories = 1 kilocalorie). The word is sometimes capitalized to show the difference, but usually not. A food calorie contains 4,184 joules. A can of soda containing 200 food calories contains 200,000 regular calories, or 200 kilocalories. A gallon of gasoline contains 31,000 kilocalories.

• The same applies to exercise -- when a fitness chart says you burn about 100 calories for every mile you jog, it means 100 kilocalories.

What do Calories do?

• Our bodies "burn" the calories in food through metabolic processes, by which enzymes break the carbohydrates into glucose and other sugars, the fats into glycerol and fatty acids and the proteins into amino acids. These molecules are then transported through the bloodstream to the cells, where they are either absorbed for immediate use or sent on to the final stage of metabolism in which they are reacted with oxygen to release their stored energy.

Cellular Metabolism

• Energy created in the Mitochondria– Post Glycolysis– Contain their own DNA– Thought to be prehistoric symbioticbacteriaCellular Respiration!

Cellular Respiration

• Oxidative Metabolism• Basic Steps:– Food Breakdown• Catabolism

– Glycolysis– Kreb’s Cycle– Electron Transport System

Glycolysis-aerobic process

• Glucose is transformed to pyruvic acid• Requires ATP• Phosphorylation-1st step of glycolysis• Glucose + 2xADP + 2xNAD+ -> 2xPyruvate +

2xATP + 2xNADH

Glycolysis

• Glycolysis- All in all the purpose of glycolysis is to break down one molecule glucose into two molecules of pyruvate. The pyruvate molecules are then individually sent to the transition reactions. Glycolysis has two Products, H20 and NADH. Overall Glycolysis makes four ATP but its net gain is two ATP due to the fact that it uses two ATP in the process.

Transition Reactions

• Transition Reactions- The purpose of the transition reactions is to take two hydrogen electrons and one carbon dioxide away from the pyruvate and add a coenzyme called Coenzyme A. The new acetyl Co-A is ready to be sent to the Krebs Cycle.

The Kreb’s Citric Acid Cycle-aerobic

• Next process in metabolism or respiration• Pyruvic acid Citric and

Oxaloacetic Acid• Glycolysis and Kreb’s is for the purpose of

forming ATP

Kreb’s Cycle

• Krebs Cycle- The purpose of the Krebs Cycle is basically to produce NADH+H and FADH2. Pyruvate enters the Krebs Cycle than goes through a series of reactions and the final product is six NADH+H and two FADH2. These energy carriers are than sent to the electron transport chain. The Krebs cycle Goes around twice for every molecule of acetyl Co-A.

Electron Transport Chain• Electron Transport Chain- The purpose of the electron transport chain is

to make the majority of ATP created in cellular respiration. The NADH and FADH2 from the Krebs Cycle drop their electrons at the starting of the electron transport chain. As the electrons move along the electron transport chain they give it power to pump hydrogen across the membrane from the matrix into the intermediate space. This creates a concentration gradient forcing the hydrogen through ATP synthase bounding ADP with Pi ( inorganic Phosphate). As the electrons move along the transport chain they lose their energy and at the end are picked up by oxygen and bonding with hydrogen making the bi-product H20.

• Yields about 32 ATP!

Fermentation-anaerobic

• Used by yeast and muscles• Less efficient process• Produces ATP• Produces Lactic acid and causes muscle

soreness