Topic 2: Chemical foundations for cells 

         Chapter 2 The chemistry of living things

           

Objectives

1.       Be able to identify the structure of an atom

2.       Define and relate matter with energy

3.       compare and contrast 3 types of bonds Covalent, Ionic and Hydrogen

4.       List the 4 most abundant elements in the body.

5.       Describe the importance of water to life.

6.       Differentiate between Acids ,Bases and buffers (the pH scale)

7.       Describe an organic molecule

8.       Be able to identify the major types of organic molecules, Carbohydrates, lipids, protiens
and Nucleic acids.  What does each of these do?

9.       What is denaturation?

10.    What are enzymes and why are they so important in our metabolism?

11.   What is ATP?

Figures  2.2, 2.5-2.10, 2.15-2.18, 2.20-21, 2.23

Table 2.1, 2.2               

Lecture Notes

1.     Sadly, you will have to learn some chemistry in order to understand human biology

A.    All living organisms including humans depend on chemical reactions

(the sum of all the chemical reactions in the body is your metabolism.)

B.    Modern Chemistry has produced products that provide benefits and problems for
our world.  Chemicals or drugs can both do good and great harm to a body.
2.     Organization of Matter:  The smallest substances that make up the body.

A.   Matter is anything that occupies space and has mass

1)     It includes solids, liquids and gases

2)     Matter is made of some ninety-two naturally occurring elements: the four most
abundant in humans are Oxygen, Carbon, Hydrogen, and Nitrogen in decreasing
order (Know these elements)

3)     Elements are fundamental forms of matter.  They cannot be broken down any
further.  They are the building blocks used to make molecules (an associaiton of two
or more elements)

4)     Energy is the capacity to do work  combining elements to make a molecule is a

type of work and so is breaking apart a molecule.  Your body gets energy to move
and metabolize by breaking complex molecules into simpiler ones.  (sugar
(complex) and oxygen to Carbon Dioxide and water, simple)

B.    The Structure of Atoms   (be able to draw a typical atom)

1)     An atom is the smallest unit of matter that is unique to a particular element

2)     Atoms are composed of three particles:

a)     Protons (p+) are part of the atomic nucleus and have a positive charge.  Their
quantity is called the atomic number (unique for each element).

b)    Neutrons are also a part of the nucleus: they are neutral.  Protons plus neutrons =
atomic mass

c)     electrons (e-) have a negative charge.  Their quantity is equal to that of the
protons.  They move around the nucleus

3)     Electron activity is the basis for organization of materials and the flow of energy in
living things.

C.    Isotopes--variant forms of atoms

1)     Atoms with the same number of protons (for example, carbon with six) but
different number of neutrons (carbon can have six, seven, or eight) are called
isotopes. (12C,13C ,4C)

2)     Some radioactive isotopes are unstable (radioisotopes) and tend to decay (give off
energy)into more stable atoms.

a)     They can be used to date rocks and fossils

 b)    some can be used as tracers to follow the path of an atom in a series of reactions
or to diagnose disease

c)     Used as sources of radiation for radiation therapy, like in an X-ray machine or
for radiotherapy for cancer

D.    Combinations of Atoms

1)     A molecule is a bonded unit of two or more (usually the same) atoms

2)     A compound is a substance in which the relative percentage of two or more

different elements never vary

3)     A mixture is an intermingling of molecules in varying proportions

3.     Chemical bonds

A.   A chemical bond is an attraction between the electron structure of two (or more)
atoms.  Interactions that cause atoms to be gound to each other  by actractive forces are
called chemical bonds.  These bonds occur,  when the outermost electron shell of the
combining atoms are filled.

B.     electrons and Energy Levels

1)      Electrons are attracted to protons, but are repelled by other electrons.

2)     Orbitals permit electrons to stay as close to the nucleus and as far from each other
as possible.

3)     Orbitals can be thought of a occupying shells around the nucleus.

a)     The shell closest to the nucleus has one orbital holding a maximum of two
electrons.

b)    The next shell can have four Orbitals with tow electrons each for a total of eight
electrons.

c)     Atoms with “unfilled” Orbitals in their outermost shell tend to be reactive with
other atoms to fulfill the octet rule (maximum of eight electrons in outer shell).

4.     Important Bonds in biological Molecules

A.   Ionic Bonding: Electrons Gained or Lost  (these chemicals are not stable in water, take
table salt for an example, what happens to a salt crystal in water)

1)     When an atom loses or gains one or more electrons, it becomes positively or
negatively charged-an ion

2)     In an ionic bond, (+) and (-) ions are linked by mutual attraction of opposite
charges, for example, NaCl
 3)     Whenever a substance taking part in a chemical reaction gives up electrons, it is
said to be oxidized

4)     Ionic bonds are not stable in water because the ions are separated by the polar
water molecules.

B.    Covalent Bonding:  Most of the molecules in your body use this type of bonding, it is
very stable in water.

1)     A covalent bond holds together two atoms that share one or more pairs of electrons

2)      In a nonpolar covalent bond atoms share electrons equally

3)      In a polar covalent bond, because atoms share the electron unequally, there is a
slight difference in charge (electron electronegativity) between the two atoms
participating in the bond, water is an example.

C.    Hydrogen Bonding

1)     In a hydrogen bond, a slightly negative atom of a polar molecule interacts weakly
with a hydrogen atom already taking part in a polar covalent bond.  While the
overall charge of water is neutral (no charge at all) if one was to look at the
individual atoms that make up this molecule the oxygen (larger) is slightly negative
and the hydrogens (smaller) is slightly positive because the oxygen shares the
electron for a bit longer than the hydrogen.

2)      These bonds impart structure to liquid water and stabilize nucleic acids and other
large molecules.

5.     Some Water Chemistry that is important to life

A.   Properties of water

1)     The human body is about two thirds water, a substance that is critical to the
chemical reactions that occur in the body

2)      Water
is a polar molecule because of a slightly negative charge at the oxygen end
and a slightly positive charge at the hydrogen end

a)     Water molecules can form hydrogen bonds with each other .

b)     Polar substances are hydrophilic (water loving): nonpolar ones are
hydrophobic (water dreading) and are repelled by water

3)     Water displays properties useful to living systems:

a)     Water tends to stabilize temperature because it can absorb considerable heat
before its temperature changes.  This is an important property in evaporative and
freezing processes
 b)     The solvent properties of water are greatest with respect to polar molecules
because “spheres of hydration” are formed around the sought (dissolved)
molecules.

6.    pH values and Buffers

A.   The pH Scale

1)     pH is a measure of the H+ concentration in a solution: the greater the H+ the lower
the value on the pH scale

2)     The scale extends form 0 (acidic) to 7 (neutral) to 14 (basic)

B.    Buffers and the pH of body fluids

1)     Buffer molecule combine with , or release H+ to prevent drastic changes in pH.

2)     Bicarbonate is one of the body’s major buffers

7.     Properties of Organic compounds

A.   The Molecules of life are organic compounds, meaning that they consist of atoms of
carbon and one or more other elements, held together by covalent bonds.

B.     Effects of Carbon’s bonding Behavior

1)    Living organisms are mostly oxygen, hydrogen, nitrogen  and carbon(test
quesiton?)

2)      Much of the hydrogen and oxygen are linked as water

3)     Carbon can form four covalent bonds with other atoms to form organic molecules
of several configurations

C.    Hydrocarbons and functional Groups

1)     A hydrocarbon has only hydrogen atoms attached to a carbon backbone (e.g.
gasoline)

2)     Functional groups, atoms or groups of atoms covalently bonded to a carbon

backbone, convey distinct properties, such as solubility, to the complete molecule

3)    

D.    The Molecules of life

1)     These include simple sugars, fatty acids, amino acids and nucleotides

2)     They are used as an energy source or as building blocks for the synthesis of
macromolecules: polysaccharides, lipids, proteins and nucleic acids
8.    Carbohydrates http://esg-www.mit.edu:8001/esgbio/lm/sugars/sugars.html

A.    A carbohydrate is a simple sugar or a larger molecule composed of sugar units

1)     Carbohydrates are the most abundant biological molecules

2)     Carbohydrates serve as energy sources or have structural roles

B.    Monosaccharides

1)     A monosaccharide one sugar unit- is the simplest carbohydrate

2)     Sugars are soluble in water and may be sweet tasting

3)     Ribose and dextroribose (five carbon backbones) are building blocks for nucleic
acids

4)      Glucose (six carbon backbone) is a primary energy source and precursor of many
organic molecules

C.    Oligosaccharides

1)     A oligosaccharide is a short chain resulting form the covalent bonding of two or
three monosaccharides

2)     Sucrose (table sugar) is glucose plus fructose

3)     Lactose (milk sugar) is glucose plus galactose

4)      Maltose (grain sugar) is composed of two glucose units

D.    Polysaccharides

1)     A polysaccharide consists of many sugar units (same or different) covalently linked

2)      Glycogen is a storage form of glucose found in animal tissues

3)    Starch (energy storage in plants) and cellulose (structure of plant cell walls) are
made of glucose units but in different bonding arrangements

9.     Lipids

A.   Lipids are composed mostly of hydrocarbon and are hydrophobic

1)     They form the basic structures of membranes and have roles in energy metabolism

2)      The sterols are important in the formation of hormones

B.    Fatty Acids

 1)     A fatty acid is a long, unbranched hydrocarbon with a -COOH group at one end.

2)     Fatty acids that have only single C-C bonds in their tails, are solids at room
temperatures, and are derived form animal sources

3)     Fatty acids with one or more double bonds between the carbons permit “kinks” in
the tails :they tend to come form plants

C.    Neutral Fats (triglycerides)

1)     Triglycerides, which have three fatty acids attached to one glycerol, are the body’s
most abundant lipids

2)     On a per weight basis, these molecules yield twice as much energy as
carbohydrates

D.    Phospholipids

1)     Phospholipids have a glycerol backbone, two fatty acids, a phosphate group and a
small hydrophilic group

2)     They are important compounds of cell membranes

E.     Waxes

1)     Waxes are special molecules with fatty acid chains attached to alcohol’s

2)     They confer extraordinary waterproofing qualities

F.     sterols and their Derivatives

1)     Steroids have a backbone of four carbon rings.

2)     Cholesterol is a component of cell membranes in animals and can be modified to

form sex hormones

10. Amino Acids and Proteins http://esg-www.mit.edu:8001/esgbio/lm/proteins/aa/aminoacids.html

A.   Proteins function as enzymes, in cell movements, as storage and transport agents, as
hormones, as anti disease agents, and as structural material throughout the body

B.    Proteins are polymers of amino acids: small organic molecules with an amino group,
an acid group, a hydrogen atom and one of twenty varying “R” groups

C.    Primary structure of Proteins

1)     Primary structure is defined as the chain (polypeptide) of amino acids

2)      The amino acids are linked together in a definite sequence by peptide bonds
between an amino group of one and an acid group of another
 D.    Three-dimensional Structure of Proteins are important in its structure

1)     The primary structure determines the protein’s shape, and ultimately its function in
two ways

a)      By positioning groups so that hydrogen bonds can form between different
amino acids in the chain

b)    By putting r groups in positions that force them to interact

2)     During a process called denaturation the three demensional struture of a protein
can be ireversibley changed.  This is what happens when you cook an egg white. 
The properties of the protein change and the eggwhite goes from clear to white.

11.  Nucleotides and Nucleic acids http://esg- www.mit.edu:8001/esgbio/lm/nucleicacids/nucleicacids.html

A.   Nucleotides with roles in Metabolism

1)     Each nucleotide has a five carbon sugar (ribose or deoxyribose), a nitrogen
containing base and a phosphate group

2)     Examples of these kinds of molecules include

a)     Adenosine phosphates are chemical messengers (cAMP) and energy carriers
(ATP)

b)    Nucleotide coenzymes transport hydrogen atoms and electrons (examples:

NAD+ and FAD)

B.    Nucleic Acids-DNA and RNA

1)     In nucleic acids four different kinds of nucleotides are bonded together to form
large single or double stranded molecules

2)      RNA is single stranded: it functions in the assembly of proteins

3)      DNA is double strained: genetic messages are encoded in its base sequences.

12.  ATP (Adenosine triphosphate) is the principal energy carrying molecul of the cell.

A.   Its chemical structure consists of  an Adenosine molecule attached to 3 phosphates.

B.    Your cells can store energy by using energy to put these three phosphates on an
adenosing molecule.

C.    The cell then can gain energy by removing one or all of the phosphates from this
molecule.
 D.    This molecule acts like energy currency in your body.  Chemical bond energy is
converted into ATP from which the energy is gained to move substances in to a cell or
to move fibers past one another.

13. Metabolic Pathways

1)     Metabolism is the controlled capacity to acquire energy and use it to build, break
apart and eliminate substances, and is made up of a series of chemical reactions.

2)     Metabolic pathways form series of reactions that regulate the concentration of
substances within cells by enzyme-mediated linear and circular sequences

a)     In biosynthetic pathways also called anabolism small molecules are assembled
into large molecules for example, simple sugars are assembled into complex
carbohydrates

b)    In degradative pathways (called catabolism), large molecules such as

carbohydrates, lipids, and proteins are broken down to form products of lower
energy.  Released energy can be used for cellular work.

3)     Some terms used in describing metabolism:

a)      Substrates (reactants) are substances that enter a reaction

b)    Intermediates are substances that form between the start and conclusion of a
metabolic pathway

c)     End products are the substances present at the conclusion of the pathway

d)    Enzymes  are proteins that speed up a reaction

e)     Cofactors are organic molecules that assist enzymes in their action

f)      Energy carriers donate energy to substances by transferring functional groups to

them

g)    Transport proteins adjust concentration gradients at cell membranes in ways that
influence the direction of metabolic reactions

4)     “redox” reactions

a)     Many metabolic pathways involve oxidation-reduction reactions (=redox)

b)    The donor molecule loses an electron and is oxidized

c)     The receptor molecule gains an electron and is reduced

A.   Enzymes

1)      Enzymes are protein that serve a catalysts: they speed up reactions
 2)     Enzymes have four features in common

a)     Enzymes do not make anything happen that could not happen on its own.  they
just make it happen faster

b)    Enzymes can be reused

c)     Enzyme actions are reversible

d)     Enzymes are selective and act upon specific substrates, which are the molecules
that enzymes (at their active sites) recognize and bind to.

3)     Because enzymes operate best within defined temperature ranges, high
temperatures decrease reaction rate by disrupting the bonds that maintain three-
dimensional shape (denaturation occurs).

4)     Most enzymes function best at pH near 7: higher or lower values disrupt enzyme
shape and halt function

B.     Enzyme cofactors

1)     These are nonprotein groups that bind to many enzymes and make them more
reactive.

2)     Coenzymes are large organic molecules such as NAD+, FAD, and HADP+ (partly
derived form vitamins), which transfer protons and electrons form one substrate to
another.

3)     Inorganic metal ions such as Fe++ also serve as cofactors when assisting membrane
cytochyrome proteins in their electron transfers in mitochondria

C.     Control of Enzyme Function

1)      Enzyme activity can be controlled by cellular regulation of enzyme synthesis,

stimulation, and inhibition.

2)     Hormones also have significant enzyme regulating effects

Possible Questions: things to think about

1.        Draw an atom of carbon and distinguish the parts   hint

2.        What properties of water make it important to life  hint

3.        What is the difference between hydrophobic and hydrophilic?  hint

4.        Name the 4 basic elements of life  hint

5.        Name the 4 basic molecules of life hint

6.        What are the properties of the four basic molecules of life?

7.        What provides more energy a pound of carbohydrate or a pound of fat?

8.        Which bond dissolves in water? hint

9.        Describe the difference between a polymer and a monomer.  Give  examples of each.
hint

Multiple choice Questions

1.        Which of the following are considered subatomic particles present in an atom?

d)    Electron        b) Proton               c) neutron              d) mass                  e) space

2.        Which of the following elements are present in the body in the greatest amounts?

a) plutonium                  b) oxygen              c) nitrogen             d)hydrogen           e)trillium

3.        Which of the following organic molecules make up the body

a) lipids          b)oxygen                               c) nucleic acids     d) hydrogen         

e)carbohydrates

4.        How many ionic bonds does carbon usually make

a) 0                  b)1                                          c)2                           d)3                          e)4

5.        Human blood is considered

a) Neutral       b) basic                  c) acidic                                 d) blue                    e)

covalent

Answers 1) a,b,c 2)b,c,d 3)a,c,e 4) a 5) a

A physics site that is worth visiting  http://www.Colorado.EDU/physics/2000/index.pl

Online chemistry web book set up by NIH you can look for chemicals by a number of
characteristics.  http://webbook.nist.gov/chemistry/

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