I. Why Study Cells?

A. Body is made up of cells:

1. RBC

2. Nerve Cells

3. Skin Cells

4. Muscle Cells

B. Some more examples

5. White Blood Cells

6. T Cells & B Cells

7. Reproductive Cells

8. Stem Cells

C. Certain Cells can make us sick

Bacterial Cells

Cancer Cells

Protists

II. History of Cell Biology

1. Zacharias Janssen

A. 1595 – invented 1st optical compound microscope

2. Robert Hooke

A. 1665 – used a light microscope to look at non-living cork cells

3. Anton van Leeuwenhoek

A. Made microscopes with magnification 10x greater B. Observed living cells

IV. Cell Theory

A. 150 years later….(early 1800’s), three German scientists developed a theory about cells

from their observations.

CELL THEORY

1.) All living organisms are composed of one or more cells

2.) Cells are the basic units of structure and function in an organism.

3.) Cells come only from the reproduction of existing cells.

V. Microscopes

A. COMPOUND MICROSCOPE

B. STEREO MICROSCOPE

- Gives 3D images of specimen

C. SCANNING ELECTRON MICROSCOPE (SEM)

- Uses electrons instead of light to project surface image of specimen

D. TRANSMISSION ELECTRON MICROSCOPE (TEM)

- Works like light microscope except uses electrons

E. ELECTRON MICROSCOPES

- Can magnify up to 200,000 x

CHAPTER 2

The Chemical Basis of Life

Modules 2.1 – 2.8

Thomas Eisner and the Chemical Language of Nature

• Thomas Eisner pioneered chemical ecology

– the study of the chemical language of nature

• He studies how insects communicate via chemical messages

• Rattlebox moths release a chemical that spiders don’t like

2.1 The emergence of biological function starts at the chemical level

• Everything an organism is and does depends on chemistry

• Chemistry is in turn dependent on the arrangement of atoms in molecules

• In order to understand the whole, biologists study the parts (reductionism)

• Molecules and ecosystems are at opposite ends of the biological hierarchy

2.2 Life requires about 25 chemical elements

• A chemical element is a substance that cannot be broken down to other substances by ordinary chemical means

• About 25 different chemical elements are essential to life

• Carbon, hydrogen, oxygen, and nitrogen make up the bulk of living matter, but there are other elements necessary for life

• Goiters are caused by iodine deficiency

2.3 Elements can combine to form compounds

• Chemical elements combine in fixed ratios to form compounds

• Example: sodium + chlorine sodium chloride

2.4 Atoms consist of protons, neutrons, and electrons

• The smallest particle of an element is an atom

• Different elements have different types of atoms

• An atom is made up of protons and neutrons located in a central nucleus

• Each atom is held together by attractions between the positively charged protons and negatively charged electrons

• Atoms of each element are distinguished by a specific number of protons

2.5 Connection: Radioactive isotopes can help or harm us

• Radioactive isotopes can be useful tracers for studying biological processes

• PET scanners use radioactive isotopes to create anatomical images

2.6 Electron arrangement determines the chemical properties of an atom

• Electrons are arranged in shells

– The outermost shell determines the chemical properties of an atom – In most atoms, a full outer shell holds eight electrons

• Atoms whose shells are not full tend to interact with other atoms and gain, lose, or share

electrons

2.7 Ionic bonds are attractions between ions of opposite charge

• When atoms gain or lose electrons, charged atoms called ions are created

– An electrical attraction between ions with opposite charges results in an ionic bond

• Sodium and chloride ions bond to form sodium chloride, common table salt

2.8 Covalent bonds, the sharing of electrons, join atoms into molecules

• Some atoms share outer shell electrons with other atoms, forming covalent bonds

– Atoms joined together by covalent bonds form molecules

• Molecules can be represented in many ways

2.9 Water is a polar molecule

• Atoms in a covalently bonded molecule may share electrons equally, creating a nonpolar molecule

• If electrons are shared unequally, a polar molecule is created • In a water molecule, oxygen exerts a stronger pull on the shared electrons than

hydrogen 2.10 Overview: Water’s polarity leads to hydrogen bonding and other unusual properties

• The charged regions on water molecules are attracted to the oppositely charged regions on nearby molecules

– This attraction forms weak bonds called hydrogen bonds

• Like no other common substance, water exists in nature in all three physical states:

2.11 Hydrogen bonds make liquid water cohesive

• Due to hydrogen bonding, water molecules can move from a plant’s roots to its leaves

• Insects can walk on water due to surface tension created by cohesive water molecules

2.12 Water’s hydrogen bonds moderate temperature

• It takes a lot of energy to disrupt hydrogen bonds

– Therefore water is able to absorb a great deal of heat energy without a large increase in temperature

– As water cools, a slight drop in temperature releases a large amount of heat – A water molecule takes a large amount of energy with it when it evaporates

2.13 Ice is less dense than liquid water

• Molecules in ice are farther apart than those in liquid water

– Ice is therefore less dense than liquid water, which causes it to float

2.14 Water is a versatile solvent

• Solutes whose charges or polarity allow them to stick to water molecules dissolve in water

– They form aqueous solutions

2.15 The chemistry of life is sensitive to acidic and basic conditions

• A compound that releases H+ ions in solution is an acid, and one that accepts H+ ions in solution is a base

• Acidity is measured on the pH scale: – 0-7 is acidic – 8-14 is basic – Pure water and solutions that are neither basic nor acidic are neutral, with a pH

of 7 • Cells are kept close to pH 7 by buffers

2.16 Connection: Acid precipitation threatens the environment

• Some ecosystems are threatened by acid precipitation

• Acid precipitation is formed when air pollutants from burning fossil fuels combine with water vapor in the air to form sulfuric and nitric acids

– These acids can kill fish, damage buildings, and injure trees

2.17 Chemical reactions rearrange matter

• In a chemical reaction: – reactants interact – atoms rearrange – products result – Living cells carry out thousands of chemical reactions that rearrange matter in

significant ways

MACROMOLECULES OF LIFE

Found in all living things

Building blocks of all cells

Made up of the atoms: Carbon, oxygen, hydrogen, Nitrogen, Phosphorus, and Sulfur

There are 4

1. Carbohydrates C, H, & O

2. Lipids C, H, & O

3. Proteins C, H, O, N, & S

4. Nucleic Acids C, H, O, N, & P

Carbohydrates

Basic units: sugars

Provide energy and structural support Fiber is a carbohydrate that prevents constipation Foods: breads, cereals, vegetables, fruits, & seeds Extra glucose is converted into glycogen in the liver

Lipids/Fats

Basic units: fatty acids Functions: provides energy & structure, cushions the body, and prevents heat

loss Found in butter, margarine, candy made of fatty acid molecules that consist two distinct regions:

a long hydrophobic hydrocarbon chain

a hydrophilic head

Saturated Fats

contain single carbon-to-carbon bonds has lots of hydrogen solid at room temperature (beef, pork, chicken, dairy) found in animal products Reduce Intake! can clog blood vessels

Unsaturated Fats

contain double or triple carbon-to-carbon bonds & fewer hydrogen atoms Liquid at room temperature (oils, nuts, & seeds) found in plant products Better Intake!

DNA Structure discovery

James Watson and Francis Crick with DNA Model in 1953.

Nucleic Acids

Atoms: C, H, O, N, P

Basic units: nucleotides composed of

Sugar Phosphate group Base: cytosine, guanine, adenime, thymine, uracil

There are two types:

DNA (deoxyribonucleic acid) RNA (ribonucleic acid)

Function: DNA directs & controls all activities of all cells in an organism – RNA helps

DNA –DeoxyriboNucleic Acid

DNA is the hereditary material passed on from parents to offspring

Structure: double-stranded

Phosphate group Sugar deoxyribose Bases

Cytosine – Guanine Adenine – Thymine

RNA

RNA helps the DNA Structure: single-stranded

Basic units: nucleotides

Phosphate group

Sugar ribose

Bases

Cytosine – Guanine Adenine – Uracil Nitrogenous Bases

Proteins

Atoms: C, H, O, N, P, S Basic units: amino acids (20)

Provide energy & structure, repairs body tissues

Some are called hormones, enzymes, neurotransmitters, etc.

Foods high in protein: meat, eggs, poultry, milk & milk products, nuts, dried beans, peas, & lentils

Tertiary Structure

Interaction between alpha helices and beta-sheets.

These protein domains for small globular proteins. Quaternary Structure

Small globular proteins form protein aggregates.

A famous example is hemoglobin. Enzymes

Are proteins

Speed up chemical reactions without being consumed or using energy Enzymes

- Amylase - breaks down sugar - Proteases - break down proteins - Lipases - break down lipids - Catalase - breaks down hydrogen peroxide - Enzyme Action Models

Factors that affect enzyme action:

1. Temperature – 37oC best for human enzymes

2. pH – different for each enzyme

a. 7 for amylase in the mouth

b. 2 for pepsin in the stomach

c. 8 for trypsin in the intestines

3. Concentration of enzyme and substrate

4. Coenzymes – helpers such as minerals and vitamins

Cell theory

1. All living things are made of cells

2. Cell can only come from other cells

3. All functions of a living thing are carried out in cells

• Reminder: the functions of living things are: respiration, metabolism, growth, adaptations to the environment, reproduction, homeostasis and interdependence

Different Types of Cells

- There are two main groups of cells, prokaryotic and eukaryotic cells. Similarities: all are alive, all belong to one of the five life kingdoms. Differences: appearance, structure, reproduction, and metabolism.

Where to begin?

Prokaryotes are simpler, so we will start with them.

Prokaryotes were formed about 3.5 billion years ago, or 3,500,000,000 years.

Prokaryotes from the Greek meaning “before nuclei”

Why “before nuclei?”

- Prokaryotic cells have no nucleus. - Prokaryote’s DNA is circular (it has no ends). - Small circlets of DNA are called Plamids. - Prokaryotic DNA is “naked” – it has no histones associated with it and does

NOT form chromosomes - All Prokaryotes are in the monera kingdom domains Bacteria and Archaea

Bacteria

Cyanobacteria also known as blue-green algae

Prokaryote Characteristics

1. Simplest organisms: Very small size.

2. Lack membrane-bound organelles inside the cell

3. have few internal structures that are distinguishable under a microscope.

4. genetic information is in a circular loop called a plasmid (instead of having chromosomal DNA)

5. Strong cell walls: resistant to environmental changes

1. Size - Bacterial cells are very small, - about 1-2µm in diameter and 10 µm long

o One micrometer = 1/1000 mm. o Imagine looking at a dime from its thinnest side and trying to slice it into a

thousand pieces; that is the same as 1 µm.

2. Lack membrane-bound organelles inside the cell 3. have few internal structures that are distinguishable under a microscope. 4. genetic information is in a circular loop called a plasmid

E. coli cell dividing.

E. Coli Grows in human intestine;

Has a single, circular chromosome contains DNA as plasmids Plasmids are extra-chromosomal DNA

5. Strong cell walls: resistant to environmental changes

Shapes

3 basic shapes

Cocci - sphere Bacilli - rods Spirilla – spirals

2 basic groupings

Staph - in clusters Strep - in chains

Replication

- Binary fission o one cell splits into two cells, see diagram o offspring are genetically identical to parent

Bacterial conjugation

- a form of sexual reproduction where bacteria exchange genetic information before dividing

o offspring have new genes (and new traits) Transformation

- bacteria incorporate genes from dead bacteria

Transduction

- viruses insert new genes into bacterial cells. - This method is used in biotechnology to create bacteria that produce valuable

products such as insulin Movement

- Some prokaryotes can't move, while others have long threadlike flagella. - If bacteria doesn’t move, how does it get from person to person?

Prokaryote Functions decomposers

- agents of fermentation - play important roles in digestive systems - involved in many nutrient cycles

o ex: the nitrogen cycle, which restores nitrate into the soil for plants. - diverse array of metabolic functions.

o For example, some bacteria use sulfur instead of oxygen in their metabolism.

Eukaryotes From the Greek for “true nucleus” Eukaryote characteristics

All eukaryotes have …

1) A Cell membrane 2) A Central nucleus 3) Organelles in cytoplasm (like ER, vacuoles, mitochondria, etc.) Theories of the Origin or organelles

Symbiosis: two organisms live closely together Endosymbiosis: one organism lives inside another (bacteria in us) Theory explaining why mitochondria and chloroplasts are found in cells:

- It's thought that mitochondria (m) and chloroplasts (c) were types of prokaryotic cells that lived inside other cells. The m & c helped keep the cell alive and so were retained.

Evidence on relationship of mitochondria and chloroplasts to prokaryote cells:

a. mitochondria and chloroplasts are both surrounded by double membranes (like bacteria are). b. mitochondria and bacteria have similar size. c. mitochondrial ribosomes resemble bacterial ribosomes. d. mirochondria and chloroplast DNA is circular like bacteria.

size and shape are related to cell function.

1. birds’ eggs are large because they contain all the nutrient material that the developing bird embryo will need during its growth to a young chick.

2. Muscle cells are long, so that they can contract and shorten up, thereby moving body parts.

3. Nerve cells are also long — they need to transmit nerve signals to different parts of the body

4. epithelial cells are broad and flat

5. red blood cells are especially small because they need to get through the smallest capillaries of the circulatory system.

Reproduction

*Mitosis – body cells *Meiosis – gametes (egg & sperm)

Movement

Internal

1. The centriole 2. The cytoskeleton 3. Actin and tubulin proteins

External

4. Flagella 5. cilia Prokaryote & Eukaryote Similarities

1. DNA 2. A cell membrane 3. Ribosomes 4. Diverse forms (meaning a lot of shapes and sizes)

Prokaryotes & Eukaryotes differences

Prokaryotes Eukaryotes

• Plasmid DNA

• No membrane-bound organelles

• Few things inside (are simple)

• Nuclear bound DNA

• Has membrane bound organelles

• Many things inside (Are complex)