The Chemical Basis of Life

The Chemical Basis of Life
P The Chemical Basis of Life C O N Na Fe O

Essential Questions: 1. What is the connection between chemistry and biology? 2. What do you already know about this question? 3. Are there some connections that come to mind immediately?

We will be learning: 1. to appreciate the basic principles of chemistry which are involved in life processess. By: 1.1 being able to recognize that organisms are made of atoms.

How would you organize the words below from smallest to greatest?
Organisms Elements Atoms Cells

Atoms All living things are made up of atoms. Atoms Elements Cells
Organisms The smallest particles of matter, they cannot be broken down  further by ordinary means. They are made up of smaller  subatomic particles called neutrons, protons, and electrons.

Atoms Structure i) Nucleus: is the inner portion of the atom. It can contain both protons and neutrons. ii) Energy Levels (also called the orbitals or electron cloud): These levels contain negatively charged particles  called electrons. Example:

Nucleus = central core -very small & dense (little empty spaces) -give an atoms its weight -made up of: 1) Protons 2) Neutrons Electron Cloud = surrounds the nucleus -gives an atom its volume -composed of electrons -orbit the nucleus in energy levels (like a magnet)

Definition of an Element
Elements are groups of the same type of atoms. The  greatest portion of living organisms are made up of 4  elements: Carbon, Hydrogen, Oxygen and Nitrogen C H N O If elements are made up of different atoms, how do we determine the specific structure of a carbon atom? Or an oxygen atom? What tool do we have to help us?

The Periodic Table: Atomic Number: the number of protons.
Neutrons: atomic number subtracted from the atomic mass. Ion: An atom that has either lost or gained electrons. Cation: Positively charged ion. Anion: Negatively charged ion. Isotope: Atoms of the same element having different atomic mass numbers. Example:

Valence Electrons... A biologists, we are not just interested in determining the number of protons, electrons, and neutrons of specific atoms, but we are more interested in knowing how many electrons atoms have in their outer orbital--the electrons known as valence electrons. Why are we interested in these electrons? How do we determine the number of valence electrons of each atom?

Valence Electrons... We determine the number of valence electrons by numbering the vertical columns of our periodic table from left-right (we skip the columns in the middle). This number then corresponds to the number of valence electrons of each of the elements in that column. Example: Li: Mg: Se: Si: Br: Using this information, we can create a diagram of the number of valence electrons of several different elements.

Lewis Dot Structures draw the symbol determine the number of valence electrons place them around the symbol, start at the top and go around clockwise, each side must have 1 dot before any of the four sides can be given a second dot. Cl Please use the information learned in today's class to draw a Lewis dot structure for the first 18 elements. When you're finished, predict which elements would be likes to "bond: with other elements, based on the number of valence electrons each one has.

Review... 1. Draw a Lewis dot structure for He, Li, and F.
2. How many electrons does an element want to have in its outer shell? Why? 3. Based on the Lewis dot diagrams of He, Li, and F, what can we predict will happen to their valence electrons?

We will be learning: 1. to appreciate the basic principles of chemistry which are involved in life processes. By: 1.2 realizing the relationship between the electron structure of atoms and the type of bond which forms

Chemical Bonding 2 types of Chemical Bonds:
Atoms are most reactive when their outermost shell or energy level is  incomplete. 2 types of Chemical Bonds: i) Ionic Bonds:  deals with ions  Deals with the transfer of electrons between two atoms. Example: "Sodium-Chloride"

ii) Covalent Bonds:  Are formed when atoms share an electron pair or pairs.  Diatomic molecules are held together by covalent bonds. Examples: H2, Cl2, I2, Br2 Another compound held together by covalent bonds is water (H2O). One line between elements symbols represents one pair of shared  electrons (Cl Cl) Two lines represents two pairs of shared electrons (O O) Three lines represent three pairs of shared electrons (C N)

Let's do a few more covalent bond diagrams:
1. I + I 2. C + H4 3. Br + Br 4. Se + O

In-Class Assignment: 1. Decide and write whether each pair will form an ionic or a covalent bond. 2. Use arrows/lines to indicate what electrons will be transferred or shared. Pairs of elements: 1. Mg + S 5. Ca + F2 2. Li2 + O 6. C + O2 3. Li + Br 7. S + O 4. Na2 + S 8. H2 + O2

We will be learning: 1. to appreciate the basic principles of chemistry which are involved in life processes. By: 1.3 understanding the relationship between chemical bonds and stored energy. 1.4 recognizing the importance and ongoing nature of various chemical reactions in the body. 1.5 discussing a chemical reaction-the reactants, products, and energy either required or produced. 1.6 illustrate with examples the simlarities and differences between synthesis and decomposition reactions. 1.7 describe some relationships which exist between synthesis and decomposition reactions in relation to the functioning of the body.

Thought-Provoking Question:
When two elements combine, through a covalent or an ionic bond, what word can we use to describe this process???

Chemical Reactions A + B AB Reactants Products Synthesis Reaction
Synthesis is the combination of 2 or more substances to  form a new compound. It is when two or more elements or  compounds unite to form one. Examples: 2Na(s) Cl2(aq) NaCl 2H2(g) O2(g) H2O(g)

Decomposition Reaction
Opposite of synthesis. One substance breaks down  (decomposes) to form 2 or more simpler substances. Example: 2H2O(g) H2(g) O2(g)

So What? How does everything we have learned connect to biology, especially our human bodies?

Chemical or Bond Energy
In order for life processes to occur, energy is needed. When chemical reactions occur in which bonds are broken,  energy is released. When bonds form energy is needed. Green plants can transform light energy into potential bond  energy of plant compounds (glucose). Heterotrophs, depend on the chemical compounds (glucose)  produced in the bodies of green plants or other organisms. The energy in chemical compounds which animals take in, is  actually in the bonds which holds molecules together. Bond energy is the energy in covalent and ionic bonds.

What are some other examples of synthesis and decomposition reactions that occur in our body?

Review... 1. Why are synthesis and decomposition reactions said to be opposite? 2. What is homeostasis?

We will be learning: 2. To investigate the properties of carbohydrates, lipids, and proteins. By... 2.1 explaining how carbon-based molecules interact with each other through hydrogen bonding.

Polar Bonding A special type of covalent bond where the sharing of electrons is not equal As a result of this unequal sharing, the molecule has positive and negative ends Example: Water (H2O) + H O + H O + H O + - - - + +

HYDROGEN BONDING Deals with polar molecules
Hydrogen bonds are formed between a hydrogen proton  and the negative end of another polar molecule. In DNA the nitrogen base from one spine of the ladder are  connected to the nitrogen bases from the other spine of the  ladder by means of hydrogen bonds. H O + _ Ex. = hydrogen bond

Review... 1. What is polar and hydrogen bonding? 2. What is an example of a substance that displays hydrogen bonds?

We will be learning: 2. to investigate the properties of carbohydrates, lipids, and proteins. By: 2.1 explaining how carbon-based molecules interact with each other through hydrogen bonding. 2.2 comparing mono-, di-, and polysaccharides and then provide expamples of their usefulness to a living system. 2.3 describing the relationship between fatty acids and fats by providing examples to illustrate when they are useful to a living system. 2.4 describing the relationship between amino acids and proteins with reference to the peptide bond. 2.5 discussing enzymes using a series of key words which should be included in a concept web with the heading of proteins. 2.6 indicating the component parts of a fat molecule. 2.7 recognizing the value of proteins by using examples from the body.

Organic Compounds (Biological Molecules or Macromolecules)
Inorganic Chemistry: Compounds that do not contain the element carbon (C). Organic Chemistry: Compounds that contain the element carbon (C). Carbon can link with other carbon atoms or with other atoms to form  chains which can be long, branched, or in the form of rings. Carbon forms for covalent bonds with other atoms. Examples: C H C O CH4 CO2

4 Groups of Organic Molecules
1. Carbohydrates 2. Lipids (fats and oils) 3. Proteins 4. Nucleic Acids

Organic Molecules These organic molecules are absolutely essential to life as they provide us with energy and as they fulfill various other needs...we will study carbohydrates first.

Carbohydrates Made up of sugar units.
Composed of the 3 elements: C, H, and O, usually in a 1:2:1 ratio. The bodies most important source of energy. The human body can not produce carbohydrates on its own, the  body must get them from an external source (plants). Carbohydrates are either single sugar units or polymers (long chains)  of many sugar units. Usually end in the suffix "ose". There are 3 types of carbohydrates: Monosaccharides,  Disaccharides, and Polysaccharides.

1.  Monosaccharides Simplest of the sugars, they are made up of one sugar unit (Mono = 1). They are found in the form of a ring. Examples: glucose (found in human blood), fructose (plant sugar found in  fruit) and galactose (found in dairy products). They all have the chemical formula of C6H12O6. They are isomers. The structure of glucose is the following: H C O

2.  Disaccharides Formed by the combination of 2 monosaccharides (di = two). All are formed by a chemical process called dehydration synthesis because water is removed from the two monosaccharides. Ex) glucose glucose maltose water C6H12O6 C12H22O11 H2O Sucrose (one glucose + one fructose), lactose(one glucose + 1 galactose), and  maltose (one glucose + one glucose) are examples. Sucrose is white table sugar, extracted from sugar cane and beet. Lactose is milk sugar. Maltose is malt sugar found in seeds of germinating plants.

3.  Polysaccharides Formed by the union of many monosaccharides (poly = many). Polysaccharides are very long chains. Some examples are:  I) Starch: found in plant bodies and often stored in roots and  seeds.  II) Cellulose: provides strength and support to plant body.  Plant cell wall.  III) Glycogen: found in animal bodies. Animals can't make  carbohydrates, but they store them in the form of glycogen. It can be  converted back to glucose.

Review: 1. What are the 3 elements that make up all carbohydrates? 2. List and explain the usefulness of one carbohydrate.

Lipids: composed of C, H, and O; with a ratio of 1:2:1. have more covalent bonds and therefore contain more energy than carbohydrates. most are non-polar molecules = do not dissolve in water.

Lipids What do Lipids do for the human body????
1) are a reserve supply of energy or fuel for the body. 2) take part in building certain cell parts (cell membrane). 3) help to form vitamins and hormones. 4) act as hormones themselves (steroids). 5) can be stored just under the skin to act like an insulating area. 3 main lipids: triglycerides, phospholipids, waxes Most if not all have a 2 part structure; glycerol and fatty acids. They combine by dehydration synthesis in different ratios.

Types of Lipids Triglycerides
formed by the union of one glycerol and 3 fatty acids triglycerides that are solid at room temperature are called fats and  liquid at room temperature are called oils. a glycerol = chain of C and H with OH- groups; a fatty acid = chain of C and H with -COOH (carboxyl) group formed by dehydration synthesis

Differ in the type of fatty acids they are made up of:
Triglycerides Differ in the type of fatty acids they are made up of: a) Saturated (animal fats) all atoms are joined by single covalent bonds, therefore harder to break down solid or semisolid at room temperature bad fat b) Unsaturated (plant fats) contains at least 1 double bond, therefore easier to break down and digest oil or liquid at room temperature

Phospholipids contains a phosphate molecule (PO4) attached to one GLYCEROL + 2 FATTY ACIDS (the phosphate molecule replaces once of the fatty acids). the phosphate molecule has a negative charge, giving it a polar end and making it soluble in water. one end is soluble in water (hydrophilic end; water loving) and one end that is insoluble (hydrophobic end; water fearing). phosopholipids are parts of cell membranes.

Waxes long chain fatty acids + long chain alcohol or long chain fatty acids + carbon rings. insoluble in water. make a waterproof coating for plant leaves or animal feathers/fur.

Review: 1. What is the main differences between triglycerides, phospholipids, and waxes?

Proteins What Proteins Do:
1) Organelles in the cytoplasm of cells are made up of protein  (mitochondria, ribosomes). 2) Most parts of muscles, nerves, skin and hair are made up of protein. 3) Antibodies are specialized proteins that help the body defend itself  against disease. 4) Enzymes are proteins that speed chemical reactions. 5) Proteins are essential for the building, repair, and maintenance of cell  structure. 6) Proteins can supply energy for the tissues. 7) Proteins make up hormones which are used for body regulation  (homeostasis). 8) Proteins form a large part of chromosomes.

Protein Structure: -Proteins are made up of 20 different amino acids. The amino acids bond in  a variety of different orders, this gives a great variety of proteins. -Each amino acid has 2 parts   an amino group  an acid group N H C O OH Amino Group Acid Group Could be a variety of atoms, it changes with the type of amino acid. Where dehydration synthesis or bonding with other molecules occurs.

A bond forms between the nitrogen of the amino group of one amino acid  and the carbon of the acid group of the other amino acid. This is a peptide  bond. Amino acids that make up proteins are held together by peptide  bonds. N H C O OH N H C O OH + Glycine Alanine Peptide Bond -2 amino acids join to form a dipeptide, while 3 or more amino acids form a polypeptide. Most proteins have 2 polypeptide chains. -as there are 20 different amino acids, the possible combinations to form different proteins is almost immeasurable.

Since proteins consist of amino acids, held together by peptide bonds,  proteins are often call polypeptides. The human body can make many amino acids, but there are 8 the body  can't make. They are called essential amino acids, we must get them from  our food. The lack of any one of the 8 will lead to protein deficiency and  disease. Proteins have very complex patterns and bond arrangements - this makes  them very sensitive to changes in temperature, oxygen and pH level. These  changes would cause a protein to change shape or denature.

Review: 1. What makes proteins "polypeptides"? 2. What important functions do proteins carry out in our bodies?

Enzymes - A Type of Protein
Catalysts: are chemicals that speed up the rate of a chemical reaction,  without altering the products formed by the chemical reactions. Catalysts  remain unchanged after the reaction. Enzymes: are protein catalysts that speed up/or allow chemical reactions to occur in living organisms. Enzymes allow low temperature reactions to occur in  organisms, by reducing the activation energy. Every reaction (200,000 different reactions in the cell) uses a certain enzymes  to catalyze it.

The molecules on which an enzyme works are called the substrate
The molecules on which an enzyme works are called the substrate. Each substrate molecule combines with a specific enzyme. They are sometimes  called the enzyme - substrate complex. The active site of the enzyme is the area that joins with the substrate molecules. Each enzyme has a specially shaped active site, so only specific  substrate molecules can fit in. Coenzymes help some enzymes bind to substrate molecules. They are organic molecules made from vitamins.

Factors that effect enzyme activity:
1) Temperature: Proteins (enzymes) change shape when the temperature is too high or low. This will cause a change in shape of the active site therefore  the substrate and enzyme do not fit together. 2) pH: A change in pH levels can alter the shape of an enzyme. 3) Concentration of Substrate Molecules: Increase the concentration of the substrate molecules and you increase the number of collisions between the  substrate and enzyme. This will increase the rate of reaction. 4) Inhibitor Molecules: Inhibitor molecules have shapes very similar to the substrate molecules. The inhibitors compete with the substrate molecules for  the active site of the enzyme.

We will be learning to: 3. describe the structures of nucleic acids. By: 3.1 describing the similarities and differences in the structure of DNA and RNA. 3.2 describing the process of replication and transcription.

Nucleic Acids There are two types of nucleic acids:
1) DNA -- deoxyribonucleic acid 2) RNA -- ribonucleic acid

Structure of Nucleic Acids:
They are made up of repeating units of nucleotides. All nucleotides are made up of 3 parts:  1) 5 carbon sugar  2) phosphate group  3) nitrogenous base: 5 types of nitrogen bases; adenine, guanine,   thymine, cytosine and uracil

i) DNA has the bases adenine, guanine, thymine and cytosine
i) DNA has the bases adenine, guanine, thymine and cytosine. In DNA  adenine (A) always bonds with thymine (T) and guanine (G) always bonds with  cytosine (C). ii) RNA has the bases adenine, guanine, uracil and cytosine. In RNA adenine  (A) always bonds with uracil (U) and guanine (G) always bonds with cytosine  (C). iii) Adenine and Guanine are called purines, they are in the category of  nitrogenous bases that are comprised of two rings bonded together. iv) Cytosine, thymine uracil are called pyrimidines, they are in the category of  nitrogenous bases that are comprised of one ring.

DNA The order of the nitrogen base in DNA determines the genetic code.
The arrangements of the DNA bases in the nucleus acts as patterns for the  building and functioning of all other cell parts. Nucleotide Diagram Phosphate Group Nitrogenous Base

DNA is located in the nucleus
DNA is located in the nucleus. It has a shape of a double helix or a  twisted ladder. DNA Single Strand Diagram

DNA Double Strand Diagram

Review: 1. What is the structure of DNA? 2. What are two differences between DNA and RNA?

We will be learning to: 3. describe the structures of nucleic acids. By: 3.1 describing the similarities and differences in the structure of DNA and RNA. 3.2 describing the process of replication and transcription.

Replication of DNA Replication: The process in which a single strand of nucleotides acts as a template for the formation of a complementary strand. A single strand of DNA  can make a complimentary strand. DNA is capable of duplicating itself, this  happens through a process called replication.

THE STEPS OF REPLICATION
(Remember DNA is a double helix. Both sides of the ladder are attached by  nitrogen bases) 1) The hydrogen bonds that hold the complementary nitrogen bases together are  broken. 2) The two edges of the ladder unzip, leaving 2 single parent strands. 3) The 2 parent strands act as a template or a mold. Free-floating nucleotides in  the cell attach to the parent strands. The free floating nucleotides attach  themselves at their matching bases (A-T, C-G) 4) Enzymes called polymerazes then come fuse the free floating nucleotides to the parent strand. The result is 2 complimentary strands of DNA. The 2 new  strands of DNA are identical to the parent strand. 5) Sometimes mistakes can happen when the bases match up. There are special  enzymes that act as proof-readers and they run the strands of DNA to look for  mistakes. Once a mismatch is noted, another enzyme comes in, snips the error  out and the right nucleotide is added.

RNA RNA is a single stranded nucleic acid used to translate the information of  DNA into protein structure. It acts as a messenger by taking the instructions of the DNA out of the  nucleus and into other parts of the cell. There are two types of RNA: 1) mRNA: reads the code from the DNA molecule and is called  the messenger RNA. 2) tRNA: called the transfer RNA, picks up codes from the amino  acids circulating in the cytoplasm and shuttles them to the mRNA  to be used in the translation process in the making of proteins.

Transcription/Translation
Protein Synthesis: Transcription/Translation Transcription: the process by which the genetic code is transferred from the DNA molecule to the mRNA molecule. Transcription is also known as protein  synthesis or the making of proteins. Things to Remember: Proteins are made from amino acids. DNA is involved in transcription and it never leaves the nucleus. RNA and DNA have very similar structures. mRNA reads the DNA code in the nucleus and carries it to the ribosomes  where the making of proteins will be completed in a process called translation.

Steps to TRANSCRIPTION
1. The double stranded DNA molecule in the nucleus unzips. 2. Once the DNA molecule unzips, nucleotides from the mRNA match up with  the appropriate base on the DNA. The single DNA strand is acting as a blue  print.  DNA RNA   C G   A  U 3. The mRNA nucleotides, that have attached to the single strand of DNA, join  into a long chain. 4. The mRNA strand moves away from the parent DNA strand. 5. The two strands of original DNA then rejoin. 6. The process of transcription has been completed. The single stranded  mRNA molecule moves out of the nucleus through the nuclear membrane and  carries the nitrogen-base code to the ribosomes in the cytoplasm. This happens  in a process called translation.

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