bio 102 lec 2:cell & cell chemistry handout 1 cells and cell chemistry rev 12-12 all matter...

BIO 102 Lec 2:Cell & Cell Chemistry HANDOUT

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Cells and Cell Chemistry rev 12-12

• All matter consists of elements– Matter is anything that has mass and

occupies space– Element is a substance made of one kind of

atom • Periodic chart contains the 103 known elements,

arranged by similar properties

• Atoms: the smallest functional unit of an element that still retains the physical and chemical properties of the element


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– Elements of biological importance:• Carbon-C Oxygen-O• Hydrogen-H Sodium-Na• Nitrogen-N Calcium-Ca• Chlorine-Cl Potassium-K• Magnesium- Mg Phosphorous-P • Sulfur-S Iron-Fe


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Core of the atom is the cell nucleus.• It consists of:

– Protons: + (positive) charge, have mass (weight-1 AMU)

– Neutrons: have no charge (neutral particle), have mass (1 AMU)

– Protons and Neutrons are tightly bound together

• Electrons: - (negative) charge, orbit the nucleus, have no discernable mass (<0.001 AMU)

• Electrons are constantly moving so their actual location within their specific shell can not be determined

• Atoms and their parts are weighed by AMU-atomic mass units because they are so small.


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• All atoms are electrically neutral– Have an equal number of protons and electrons

• Number of protons and electrons determines behavior of each atom

The Periodic Table of the Elements identifies the 11 composition of each atom. Na

22.990

– Letters in the middle = the atom’s chemical symbol– Number on top = the atomic number (# of protons) (and also the number of electrons—Why?)– The number on the bottom is the atomic mass;

(use it to figure out the number of neutrons-How?)

• Subtract the atomic number (# of protons) from the atomic mass or subtract the top number from the bottom number.


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Isotopes• All atoms of a particular element have the same

number of protons and electrons HOWEVER, they can have a different number of neutrons, therefore a different atomic mass (weight)

• These atoms are called isotopes.• Isotopes tend to be unstable. They are called

RADIOISOTOPES because they give off energy as radiation until they reach a stable state– Some of this energy can damage the body– Some of this can be used in medicine to tag and track

molecules to determine their location in the body


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Electrons have potential energy– The term “shell” refers to the energy level of

electrons– The term “orbital” describes the probable

location of an electron within a “shell” • Each shell further away from the nucleus has a

higher level of energy-- When an electron moves to a shell closer to

the nucleus it loses energy

--When an electron moves to a shell further away from the nucleus, it gains energy


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• Atoms are most stable when their outermost occupied electron shell is completely filled– An atom with an unfilled outermost electron shell will

try to interact with other atoms in order to fill this outermost shell

– Atoms try to share electrons with other atoms• First shell can hold 2 electrons; second can hold 8 electrons; few

atoms have a third shell (can hold a maximum of 18 electrons)

• These interactions will typically cause the atoms to be bound to each other by a force called a “chemical bond”

• There are 3 principal types of chemical bonds:– Covalent– Ionic– Hydrogen


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• Covalent Bond– Strong-rarely break apart– Formed by the sharing of a pair or more of

electrons with another atom (in order to fill the outermost shell)

– Sharing of 1 pair of electrons is a single bond– Sharing of 2 pairs of electrons is a double

bond– Example: Hydrogen gas, oxygen gas, water

molecule


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• Ionic bond- bond between two oppositely charged atoms or molecules which was formed by the transfer of one or more electrons– Atom with nearly full outer shell gains the electrons;

gives the atom a net charge due to gain or loss of electrons

• + charge for each electron lost• - charge for each electron gained

– An electrically charged atom or molecule is called an ion. Examples: Na+, Cl-, Ca2+

– Bond is of moderate strength


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• Hydrogen Bond– Weak attraction which occurs between oppositely

charged regions of polar molecules that contain covalently bonded hydrogen. We see this most often in a water molecule.

– Water is electrically neutral overall but still has partially charged ends (called poles). This type molecule is called a polar molecule.

• Since opposites attract, polar molecules arrange themselves to that the negative pole of one molecule is facing the positive pole of another molecule.

– Hydrogen bonds between liquid water molecules are so weak that they break and reform allowing water to flow.

A polar molecule is formed when electrons are unequally shared between two atoms.

• This occurs because one atom has a stronger affinity for electrons than the other (yet not enough to pull the electrons away completely and form an ion) and the bonding electrons will spend a greater amount of time around the atom that has the stronger affinity for electrons. – An example of this is the hydrogen-oxygen

bond in water.


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Compounds

• Composed of molecules.– A molecule forms when 2 or more atoms

combine.

• Organic compounds contain the element carbon

• Inorganic compounds do not contain carbon


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Life depends on water

• Water is responsible for 60% of our body weight

• Water molecules are polar

• Water is liquid at body temperature

• Water can absorb and hold heat energy


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Two Biological Functions of Water

1. Water is the biological solvent because it is a polar liquid at body temperature

– A solvent is a liquid in which other substances dissolve

– Solute is any dissolved substance.


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2. Water helps regulate body temperature– Water can absorb and hold heat with only a

small increase in temperature. It prevents body temperature from rising suddenly.

– Water also holds heat when there is danger of too much heat loss (on a cold day for example).

– We can lose heat rapidly by evaporating water from our body surface.


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So, water is the substance in which many chemical reactions take place.– Water is the substance that carries solutes

from one place to another.– It also fills our intracellular and intercellular

spaces.• The term hydrophilic refers to polar molecules

attracted to water and interact with it.• The term hydrophobic refers to nonpolar

molecules that are not attracted to water and therefore don’t interact with it. (oil and water)


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The Importance of Hydrogen Ions

Despite the covalent bonds between water molecules, the bonds can be broken into H+ and OH-.– In pure water, there are only a few dissociated (broken

apart) molecules• Other sources of hydrogen ions in aqueous solutions:

– Acids are any molecule that can donate a hydrogen ion (H+ --proton). Produce an acidic solution (which has a higher concentration of H+ than water)

– Bases are any molecule that can accept hydrogen ions. Produce a basic or alkaline solution (which has a lower H+ concentration than water).

• Acids and bases have opposite effects on the H+ concentration of solutions so they “neutralize” each other


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How to indicate the acidity or alkalinity of a solution

• pH Scale = measure of hydrogen ion concentration in a solution– Scale goes from 0-14; pH of water is 7.0 or

neutral – Changes in pH of body fluids can affect how

molecules are transported across the cell (plasma) membrane and how rapidly certain chemical reactions occur. pH changes affect the body’s homeostasis.


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Buffers: minimize pH change• Buffers are essential to maintain homeostasis of

pH in body fluids

– Carbonic acid (H2CO3) and bicarbonate (HCO3

-) act as one of the body’s most important buffer pairs. They pick up H+ when fluids are too acidic and release them when fluids are too basic.


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Organic Molecules of Living Organisms

Organic molecules are molecules that contain carbon and other elements held together by covalent bonds.

Carbon is the building block of all organic molecules.– Comprises 18% of body weight– Forms four covalent bonds with other molecules– Can form single or double bonds– Can build micro- or macromolecules


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• Living organisms synthesize 4 classes of organic molecules:

• Carbohydrates• Lipids• Proteins• Nucleic acids


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Living organisms use carbohydrates for energy; plants also use them for structural support

• Monosaccharides are the simplest carbohydrate – Glucose, fructose, ribose and deoxyribose are 4 of

the most important monosaccharides in humans• Oligosaccharides: short chains of monosaccharides

linked together.• Disaccharides: consist of 2 linked

monosaccharides

examples: sucrose (table sugar), lactose• Some oligosaccharides are bonded to cell

membrane proteins; called glycoproteins– Glycoproteins participate in linking adjacent

cells together and in cell-cell recognition and communication


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• Polysaccharides: a complex carbohydrate formed when thousands of monosaccharides are joined together in long chains and branches

• Extra long chains; energy is stored in the bonds of the polysaccharide molecule

– Glycogen: most important polysaccharide made in animals; stores energy

– Starch: most important in plants; stores energy– Cellulose: Undigestible polysaccharide made in plants

for structural support• Undigested cellulose in the food we eat is called

“fiber”


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Lipids

• Are relatively insoluble in water

Most Important Subclasses of Lipids:

Triglycerides: energy storage molecules–Glycerol and 3 fatty acids make up triglyceride;

can be saturated or unsaturated• Saturated fats are usually solid at room temperature• Unsaturated fats are usually liquids at room

temperature

–Are stored in adipose tissue


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Phospholipids:• Are the primary structural component of cell

membranes

• Have a phosphate group (PO4-) at one end; this negative charge makes the phospholipid a polar molecule and thus one end of it is soluable in water. The other end is “neutral” and is not soluble in water


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Steroids: • Are classified as lipids because they are

relatively insoluble in water• Cholesterol is a steroid• We all need a certain amount of cholesterol

because it:– is an important part of the cell membrane– is used in making estrogen and testosterone


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– A string of 3-100 amino acids is called a polypeptide

– When a polypeptide is longer than 100 amino acids it is called a protein

Proteins are macromolecules constructed from long strings of amino acids


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The body has many different proteins; each serves different functions.– Structural support --Muscle contraction– Part of the cell membrane --Enzymes

• Protein shape can be changed in the presence of polar molecules.– The ability to change shape is essential to the

functions of certain proteins.• Protein structure can be damaged by high temperatures

or changes in pH.– Denaturation refers to permanent disruption of protein

structure which causes a loss of function i.e. boiling an egg


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• Enzymes:– are proteins that function as a biological catalyst (a

substance that speeds up the rate of a chemical reaction without itself being changed or consumed by the reaction)

– they speed up a reaction that would have happened anyway but it would have taken longer

• They serve as catalysts because, as proteins, they can change shape. This allows them to bind to other molecules and orient them so they can work with each other.

• The functional (or changeable) shape of an enzyme is dependent on:– temperature of reaction medium – pH – ion concentration– presence of inhibitors


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Other organic molecules:Nucleic Acids• DNA: deoxyribonecleic acid• RNA: ribonucleic acidFunctions:• DNA directs everything the cell does including the

instructions for producing RNA.• RNA is a closely related macromolecule and carries out

the instructions of DNA including how to produce proteins.

• Structure– Composed of Nucleotides consist of a phosphate

group, a sugar, and a nitrogenous base– DNA structure is a double helix: two associated

strands of nucleic acids– RNA is a single-stranded molecule


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Structure of DNA and RNA

• DNA: double-stranded helix– Sugar: deoxyribose– Nitrogenous bases: adenine, thymine,

cytosine, guanine (the protein code is actually contained in the sequencing of nucleotides)

– Pairing: adenine-thymine and cytosine-guanine

• RNA: single-stranded helix– Sugar: ribose– Nitrogenous bases: adenine, uracil, cytosine,

guanine– Pairing: adenine-uracil, cytosine-guanine


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• Adenosine Triphosphate (ATP)– Nucleotide– Made up of adenine+ ribose (which is a 5 carbon

sugar). Together these are called adenosine. There is also a 3 phosphate group called triphosphate.

– Is a universal energy source for cells• The bonds between the phosphate groups contain

a lot of potential energy

bio 102 lec 2:cell & cell chemistry handout 1 cells and cell chemistry rev 12-12 all matter...

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