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    • Organ Systems
    • Portal to the Skeletal system
      • The SKULL ANATOMY
      • the Thoracic Cage
      • the vertebral column
      • The Appendicular Skeleton
      • BONES AND SKELETAL TISSUES
      • joints
    • The Muscular System Portal
      • Muscle Tissue
      • Muscles - Intramuscular Injection Sites - WCU
      • Muscles of the Body - Review
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    • dissection of the fetal pig
  • Physiology
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    • Portal to the Skeletal system
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    • Female Reproductive System
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    • The Male Reproductive System and Male Contraception
    • Fertility and Conception
    • In-Vitro Fertilization
    • Infertility
    • Genetics of Reproduction
    • Prenatal and Maternity Care
    • The Pregnant Body
    • fetal development
    • Development of the Nervous System
    • Stages of Labor
    • Postpartum Issues
    • Twins
  • Chemistry
    • pH Lab
    • The Chemistry of Cells - ORGANIC
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    • Volcano Project
  • College/Life Skills
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    • Advising Resources
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      • Predation
    • Time Management
  • Environmental Science
    • MIDTERM 2 STUDY GUIDE
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    • ENVS 105 Home Page
      • Midterm 3 Study Guide Population Ecology
      • Ecology II - Communities and Ecosystems
      • Module 1 Assignments
      • Module 2 Assignments
    • Inrtoduction to ENV SCI
    • Historical Perspective of ​Environmental Science
    • Biomes
    • FOOD CHAIN and FOOD WEB
    • Biogeochemical Recycling
    • Evolution - Our Beginning
    • Genetic Inheritance
    • Evolution: How Populations Change over Time
    • Symbiosis
    • Population Ecology
    • Competition in Nature
    • Herbivory
    • Niches
    • Fossil Fuels
  • Environmental Biology Laboratory
    • SOILS AND GROUNDWATER
    • Ecological Roles of Living Organisms
      • The Basics
      • Bacteria - Ecological Roles
      • Protists - Ecological Roles
      • Fungus - Ecological Roles
      • Plantae and Animalia - Ecological Roles
    • Virtual FIELD TRIP TO THE RIO HONDO COLLEGE ​WILDLIFE SANCTUARY - Adaptations to Dry Climates
    • Microscopic Plant Adaptations
    • Natural Selection
    • GROWTH CURVES
    • SOILS AND GROUNDWATER
    • LC50 and LD50
    • How to Make a Solar Water Heater
    • WATER QUALITY ANALYSIS
  • General Biology
    • Characteristics of Life
    • Chemistry of Life - Inorganic
    • The Chemistry of Cells - ORGANIC
    • Introduction to The Cell
    • Photosynthesis and cellular Respiration
    • Cell Membranes and Osmosis
    • The Cell Cycle
    • REGULATION of The Cell Cycle
    • Mitosis
    • Meiosis
    • The Structure of DNA
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    • GENERAL BIOLOGY 101 LABORATORY HOME PAGE
      • Enzymes
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      • Lab 1 - Bacteria, Protista and Fungi
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      • Lab 8 - Enzymes
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      • Lab 10 Fermentation, Aerobic Cellular Respiration and Associated Major Organ Systems
    • GENERAL BIO 1110L Labs
      • lab 2 - CELLS - BIO 111L
      • lab 3 - DIFFUSION and OSMOSIS - BIO 111L
      • lab 4 - The Circulatory System - BIO 111L
      • lab 6 - Photosynthesis and Cellular Respiration
      • lab 7 - Reproduction - BIO 111L
      • DNA, GENES AND GENETIC INHERITANCE
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      • lab 10 - ADAPTATIONS - BIO 111L
      • lab 11 - ECOSYSTEMS AND BIODIVERSITY
  • Human Biology
    • A History of Human Biology
    • Levels of Organization
    • The Chemistry of Cells - ORGANIC
    • Cells
    • Cartilage SAC
    • BONES AND SKELETAL TISSUES
  • Human Biology Lab
    • Testing for Sugar, Starch and Proteins
    • Osmosis, Diffusion and Filtration
    • buffers
    • OSMOSIS LAB
    • Anatomical Planes
    • Body Cavities and Membranes
    • Anatomical Positions
    • The Appendicular Skeleton
    • The SKULL
    • the Thoracic Cage
    • the vertebral column
  • Human Sexuality
    • Course Information
    • Course Calendar
    • Lesson 1 - Introduction to Human Sexuality
    • Lesson 2 - Genetic Inheritance of Human Sexuality
    • Lesson 3 - The Male Reproductive Tract
    • Lesson 4 - The Female Reproductive Tract
    • Lesson 5 - The Menstrual Cycle
    • Midterm Exam Study Guide
    • Lesson 6 - Fetal Development and Sexual Differentiation
    • Lesson 7 - Disorders of Sexual Development
    • Lesson 8 - Gender Identity and Sexual Attraction
    • Lesson 9 - Fetishism
    • Lesson 10 - Sexuality Throughout the World
    • ​Lesson 11 - Sexuality Through the Ages
    • Lesson 12 - Sexual Harassment, Coercion and Violence
    • Final Exam Study Guide
  • Microbiology PORTAL
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      • ​Intro to Microorganisms
      • Diseases
      • EPIDEMIOLOGY
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      • Bacteria versus Archaea
      • Intro. to Bacteria
      • Viruses and Prions
      • Microbial Genetics
      • Microbial Nutrition and Growth
        • Nutritional Categories
        • Microbial Metabolism
        • CONTROL OF BACTERIA GROWTH AND ANTIBIOTICS
      • Eukaryotic Organisms
      • Archaeal Diversity
      • Prokaryotic and Eukaryotic Cells
      • Bacteria vs Archaeal Structures
      • Taxonomic Classifications
      • Archaea, Bacteria and Eukaryotic Cells
      • MIC- CPP Course Calendar
    • Cell Theory
    • Chemistry of Life
      • Chemical Bonds
      • Chemical Reactions
    • Biofilms
    • Definition of Terms
  • Microbiology Laboratory
    • Cell Culture and Inoculations
    • aseptic technique
    • WET MOUNT
    • Streak Plate
    • Mannitol salt agar (MSA) Test
    • Eosin Methylene Blue (EMB)
    • Blood Agar
    • Dilution Series and Calculations
    • Phage Plaque Assay
    • MICROBIOLOGY UNKNOWN LAB
    • Microbiology Lab -study guide exam one
    • Ex 2 - Microorganisms
    • EX 3 - aseptic technique
    • Ex 4 - Smear Prep
    • Ex 5 - Simple Stains
    • Ex 6 - Negative Staining
    • Ex 8 - Gram Stain
    • Ex 9 - Acid-Fast Stain
    • Ex 10 - Endospore Stain
    • Ex 11 - Motility Test
    • ex 12 -​ Pure culture technique
    • ex 13 - UV Radiation
    • Ex 14 - Enumeration of Bacteria : Standard Plate Count
    • ex - 15 Effects of Temperature on Growth
    • ex 16 - Hand-washing
    • ex 17 - pH and microbial growth
    • ex 18 - Evaluation of Antiseptics
    • ex 19 - Antibiotic Sensitivity : Kirby-Bauer Method
  • HISTOTECHNOLOGY
  • The Brain
  • The Brain
  • The Structure of DNA
  • Contact
  • FUN ZONE
    • GAMES
    • Video Vault
    • Population Ecology - ACTIVITY
    • The Carbon Cycle - ACTIVITY
    • Evolution - ACTIVITY
    • The Cell Game
    • SYMBIOSIS ACTIVITY
    • THE LORAX ACTIVITY
    • Brittney the Kidney
    • From Soup to Poop
    • MITOSIS - THE NURSERY RHYME
    • Verne the Sperm and friends
      • Verne the Sperm pg1
        • Verne the Sperm pg2
        • Verne the Sperm pg3
        • Verne the Sperm pg4
        • Verne the Sperm pg5
  • Lab 6 - The Chemistry of Cells
  • A History of Anatomy
  • List of Pages
    • Microscopes
  • Cell Membranes and Osmosis
  • Chemistry of Life
  • Muscle Movements
  • The Muscles of the Head, Trunk and Shoulders
  • The Muscles of the Limbs
  • Nervous Tissue
  • The Brain - Anat and Physiology
  • Instructions for Taking BIO 3070
  • MTH 121 Algebra A - Course Schedule and Info
  • Laboratory Calendar CMC Spring 2019
  • Genetics Lab
  • Chemistry and Conversions Lab
  • Digestion and Enzymes Lab
  • Endocrine and Homeostasis Lab
  • Muscles and Reflexes Lab
  • Sensory Lab
  • Immunohistochemistry
  • Blood Lab
  • Heart Rate, Blood Pressure, Electrocardiogram Lab
  • Respiratory Lab
  • Lab 11 Renal Lab
  • Blood Typing Game
  • Body Systems Interactive
  • Ch 9 - The Central Nervous System
  • Ch 10 - Sensory Systems
  • Neuron Virtual Laboratory
  • Virtual Eye Lab
  • Virtual pH Lab
  • Chemical Bonds Virtual Lab
  • Beer's Law Virtual Lab
  • Build-an-Atom Virtual Lab
  • Diffusion Virtual Lab
  • Ohm's Law Virtual Lab
  • New Page
  • Ch 8 - Nervous System

The Chemistry of Cells - ORGANIC

ORGANIC CHEMISTRY
​The Chemistry of Life


The Chemistry of Cells

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MEET CARMEN THE CARBON!!!
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     Let's take a look at the unique properties of Carbon that give rise to the vast majority of molecules necessary for life. The number of electrons in the outermost shell determines an atom’s chemical properties. A carbon atom has 4 electrons in a valence shell that holds 8. Carbon completes its outer shell by sharing electrons with other atoms in four covalent bonds. This allows for a huge variety of possibilities and possible structures. This is why we observe large organic molecules with complex and elaborate shapes.
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Life’s Diversity is due to being carbon-based.  Most of the molecules in cell makes are made up of carbon atoms bonded to one another and to atoms of other elements. Carbon is able to form large and complex molecules, which build the structures and carry out the functions required for life. Carbon-based molecules are called organic compounds, and they usually contain hydrogen atoms as well.

The shape of the organic molecule (and any molecule for that matter,) determines its function. Carbon chains form the backbone of most organic molecules. The diagram at the end of this section illustrates some of the possible shapes organic molecules can take. These molecules can differ in length and angle. For example, they can be straight, branched, or arranged in rings. Carbon skeletons may also include double bonds, which can vary in number.

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Hydrocarbons

    Hydrocarbons are composed of carbon and hydrogen. In nature, hydrocarbons take the form of crude oil and natural gas. That being said, hydrocarbons are the primary energy source for most of the world today. Hydrocarbons can be found in living organisms in the form of hydrocarbon chains within certain molecular structures. A good example of this are the hydrocarbon chains found in lipids (fats) that provide fuel to your body.  Hydrocarbons are very good at forming covalent bonds with other hydrocarbons to form long chains or rings.

​     There are two types of covalent bonding; polar and non-polar. In any covalent bond, electrons are SHARED between the bonded atoms. In a polar covalent bond, these electrons are unequally shared and they spend more of their time towards one of the bonded atoms than the other. This results in a "polar" molecule which will carry a partial negative near the atom with the higher electronegativity value (and, thus, the electrons preferentially will be located by that atom more often) and a partial positive charge at one end in which the electrons spend less time. In hydrocarbon chains, H and C have very similar electronegativties and from non-polar covalent bonds, and  when C binds to another C they share their electrons completely equally since they have the same electronegativity value. We consider any bond between two elements with the same or similar electronegativities (within ~ 0.30) a non-polar bond. Hydrocarbons are considered hydrophobic meaning they are “afraid” of water! Hydrocarbons are the world's leading source of electrical and thermal energy, due to the amount of energy produced when burnt. This burning is a combustion reaction in which oxygen from the air becomes a reactant with the hydrocarbon, to form a new chemical product. Common products of hydrocarbons combustion reactions include steam, carbon dioxide and heat.



​
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ELECTRONEGATIVITY = Electronegativity is the tendency of an atom to attract electrons towards itself. 
​We know from C position on the periodic table, that it is in group 4. all group 4 elements react in such a way that they can form up to 4 bonds. The atomic number of C is 6. The first shell can hold up to 2 electrons. The second shell can hold up to 8 electrons. Atoms have a tendency to ionize in such a way that their outer-most shell is filled. They can do this either by gaining or losing electrons, but it will always take the “path of least resistance”.
Organic compounds are those that have carbon atoms. Remember carbon? It has 4 Valence electrons = 4 electrons in the outer shell = 4 electrons are available for bonding.  Thus, carbon is able to make up to 4 strong bonds. carbon-based molecules can form a wide variety of shapes and long chains. Carbon is the element that we believe is necessary for LIFE.

Carbon Bonding
Carbon has 4 electrons available to form bonds with other atoms. This is why you will always see four lines connecting a carbon atom to other atoms.  Each line represents a BOND that is formed by a pair of shared electrons (one electron from carbon and one from another atom).  Each line represent a bond made with 1 valence electron from each atom participating in the bond. For example,  methane (CH4)  is a small organic molecule made up of one Carbon atom bound to 4 Hydrogen atoms. 
 
CHEMICAL EVOLUTION
The first organic molecules were small . they were carbon-based molecules made up of only a few atoms. These small carbon-based molecules evolved to combined with other simple molecules to form more complex molecules. Over many years and probably trillions and trillions of chemical reactions, more complex molecules, and more stable molecules, formed.

All living things consist of organic molecules, centered around the element carbon. Organic molecules evolved before cells, perhaps as long as 4 billion years ago. Complex molecules can be formed by stringing carbon atoms together in a straight line or by connecting carbons together to form rings. The presence of nitrogen, oxygen, and other atoms adds variety to these carbon molecules.
C H O N = 96% of living things

 How did these carbon-based molecules necessary for life first form? The first organic molecules formed about 4 billion years ago. Scientists believe lightening sparked chemical reactions in Earth’s early atmosphere. The early atmosphere contained gases such as ammonia, methane, water vapor, and carbon dioxide. Paleolightning is the study of lightning activity throughout Earth's history. Some studies have speculated that lightning activity played a crucial role in the development of not only Earth's early atmosphere, but also early life. Lightning, a non-biological process, has been found to produce biologically useful material through the oxidation and reduction of inorganic matter. Scientists hypothesize that this created a “soup” of organic molecules from inorganic chemicals. In 1953, scientists Stanley Miller and Harold Urey used their imaginations to test this hypothesis. They used a mixture of gases to represent Earth’s early atmosphere.  Then, they passed sparks through the gases to represent lightning. Within a week, several simple organic molecules had formed. 
 
RNA World Hypothesis

RNA may have been the first organic molecule to form as well as the basis of early life.
 
Primitive cells
The first cells consisted of little more than an organic molecule such as RNA inside a lipid membrane.
One cell (or group of cells), called the last universal common ancestor (LUCA), gave rise to all subsequent life on Earth.
Photosynthesis evolved by 3 billion years ago and released oxygen into the atmosphere.
Cellular respiration evolved after that to make use of the oxygen.
 
 
Complex molecules can be formed by stringing carbon atoms together in a straight line or by connecting carbons together to form rings.
The presence of nitrogen, oxygen, and other atoms adds variety to these carbon molecules.
 
 
Complex molecules can be formed by stringing carbon atoms together in a straight line or by connecting carbons together to form rings. The presence of nitrogen, oxygen, and other atoms adds variety to these carbon molecules.
MAKE SURE YOU KNOW THESE!!
Four important classes of organic molecules
Carbohydrates (sugars)
Lipids (fats)
proteins
nucleic acids ( RNA and DNA )
 
Carbohydrates

Sugar molecules have the formula (CH2O) n , where n is any number from 3 to 8. For glucose, n is 6, and its formula is C6H12O6. The formula for fructose is also C6H12O6, but as you can see in Figure 1, the placement of the carbon atoms is different. 
Carbohydrates are classified into three groups according to the number of sugar (or saccharide) molecules present:

1) monosaccharides  ( mono = 1,   saccharide = sugar )
2) disaccharides ( di = 2,   saccharide = sugar )
3) polysaccharides  ( poly = many,   saccharide = sugar )

Artificial Sugars
Aspartame is a common sugar substitute used in brands like Equal, and Nutrasweet, as well as diet soft drinks and chewing gums. Aspartame is not a sugar at all. It is a dipeptide (two amino acids joined together, as in a protein). But it's is a very slightly modified dipeptide.
180 times as sweet as sugar (sucrose). In this case, the artificial sweetener sucralose looks very similar to the natural sugar sucrose.
Sucralose is in some soft drinks and is marketed as an alternative to aspartame.
 
What is high-fructose corn syrup (HFCS)? Let’s start with the corn syrup part. The main carbohydrate in corn is starch, a polysaccharide built from glucose monomers. Industrial processing hydrolyzes starch into these monomers, producing corn syrup. Glucose, however, does not taste as sweet to us as sucrose. Fructose, on the other hand, tastes much sweeter than both glucose and sucrose. When a new process was developed in the 1970s that used an enzyme to rearrange the atoms of glucose into the sweeter isomer, fructose, the high-fructose corn syrup industry was born. (High-fructose corn syrup is a bit of a misnomer, because the fructose is combined with regular corn syrup to produce a mixture of about 55% fructose and 45% glucose, not much different from the proportions in sucrose.)



MAYO CLINIC - Research has shown that high-fructose corn syrup is chemically similar to table sugar. Controversy exists, however, about whether the body handles high-fructose corn syrup differently than table sugar. At this time, there's insufficient evidence to say that high-fructose corn syrup is any less healthy than other types of sweeteners. It is known, however, that too much added sugar of all kinds — not just high-fructose corn syrup — can contribute unwanted calories that are linked to health problems, such as weight gain, type 2 diabetes, metabolic syndrome and high triglyceride levels. All of these boost your risk of heart disease.
 
Lipids

Lipids are a class of substances that are insoluble in water. They are hydrophobic (water-fearing).
There are three major groups of lipids:
 1)  Triglycerides - fats, oils, and waxes.
 2) Phospholipids – makes up cell membranes. Will spontaneously form a membrane in water in the lab!
 3) Steroids - hormones

Triglycerides consist of three fatty acids bonded to a glycerol molecule. Fatty acids are hydrocarbons (chains of covalently bonded carbons and hydrogens) with a carboxyl group (–COOH) at one end of the chain. A saturated fatty acid the maximum possible number of hydrogens bonded to it. The carbon back bone contains only single bonds. Unsaturated fatty acids have less hydrogen bonded to it due to having one or more double bonds. This double bond is a the CIS configuration. “Transfats” are unsaturated fats that have one or more double bonds in a TRANS configuration. [CIS (same) vs TRANS (opposite)] CIS fats are healthy fats that promote good cholesterol. TRANS fats, on the other hand, can be harmful and can contribute to a decrease in cardiovascular health. Examples of TRANS fats include substances that are made from unnatural sources like hydrogenated oils. In November 2013, the U.S. Food and Drug Administration (FDA) put forth a mandate that food companies eliminate TRANS fats from their products over time. 
 
Phospholipids are the major component of cell membranes. Phospholipids are structurally similar to fats, except that they contain only two fatty acids attached to glycerol instead of three. they consist of a hydrophillic (polar) head and 2 hydrophobic (non-polar) tails.
Amphiphilic.
Phospholipids
Phospholipids spontaneously form a double-lipid bilayer (like the cell membrane) in water.
Chemistry may have brought forth “life”.
 
Steroids
PROTEINS
Nearly every dynamic function in your body depends on proteins.
A protein is a polymer of small building blocks called amino acids.
 Of all of life’s molecules, proteins are structurally and functionally the most elaborate and varied.
 
Proteins
Proteins are polymers of amino acids.
 
Proteins perform a vast array of functions within organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another.
Making Polymers - dehydration reaction
One monomer loses a hydroxyl group (OH-) and the other monomer loses a hydrogen (H) atom to form H2O.
 
As this occurs, a new covalent bond forms, linking the two monomers.
Breaking Polymers
HYDROLYSIS
“hydro” = water
“lysis” = to cut
 
Cells not only make macromolecules but also have to break them down.
Most of the organic molecules in your food are in the form of polymers that are much too large to enter your cells.
Nucleic Acids
DNA and RNA are built from single units (monomers) of nucleic acids.
DNA = Deoxyribonucleic acid
RNA = Ribonucleic acid
 
 
 


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