The Chemical Level of Organization Martini Chapter 2.

The Chemical Level of Organization

Martini Chapter 2

Chemistry

• The study of matter– anything that takes up space and has mass

• Mass refers to the amount of a substance.• Weight refers to the force exerted on a

substance by gravity.

• The smallest units of matter are called ATOMS

Atoms• All matter is composed of

atoms.– Protons (+) and neutrons

(neutral) are found in the atom’s nucleus, while electrons (-) circle the nucleus.• Atomic number - number

of protons– Atoms with the same

atomic number belong to the same element, and thus have the same inherent properties.

Nucleus

Atoms

Atomic Weight

• Atomic mass of an atom refers to the sum of the masses of protons and neutrons.– measured in Daltons– 1 Proton – 1.009 Daltons– 1 Neutron – 1.007 Daltons– 1 Electron – 1/1840 of a dalton - negligible

Elements

Trace Elements

Isotopes• Isotopes - Atoms of an element that

possess a different number of neutrons.– Have the same atomic # b/c # of protons

stays the same – Radioactive isotopes - Spontaneously

decay into elements of lower atomic number.• emit energy and/or subatomic particles

– Half-life refers to the amount of time necessary to decay half the atoms of a given sample.

Neutral Atoms

• Atoms with the same number of protons as electrons are electrically neutral.

Ions

• Atoms in which the number of protons and electrons differ.

• Cation - Contains more protons than electrons, and carries a positive charge.

• Anion - Contains fewer protons than electrons, and carries a negative charge.

Electrons and Atomic Behavior

• Orbital refers to the area around a nucleus where an electron is most likely found.– Chemical behavior of an atom is determined by the

number and arrangement of its orbitals.• Electrons are attracted to the positively charged nucleus,

thus it takes energy to hold electrons in place.

Stability of Atoms

• The outermost energy level determines an atoms stability– if the orbital is full, the atom will be

stable and not likely interact

Octet rule• atoms want to have 8 electrons in

their outer shell

– Inert atoms have outer level filled • already fulfilled this rule

– Reactive atoms do not have outer level filled • react in order to fulfill this rule

Chemical Bonds

• Atoms can be joined by chemical bonds.– ionic– covalent– hydrogen

• A molecule refers to a group of atoms held together by a covalent bond.

• Compound is composed of two or more different types of atoms held together by any kind of bond

Chemical Bonds

• Ionic bonds are formed because ions of opposite charge attract one another.– table salt – Sodium

Na+ – Chlorine Cl-

• formed when two or more atoms share pairs of valence electrons.

– Strength depends on number of shared electrons.

one pair = single bond two pairs= double bond three pairs = triple bond

Covalent bonds

Hydrogen Bonding

• Between a covalently bound H and a covalently bound O or N.

Water

• Hydrogen bonds form between the O and H of water molecules giving water its interesting properties

Chemical Reactions• A chemical reaction occurs during the

formation or breaking of chemical bonds.

• Chemical reactions can be influenced by:– temperature– concentration of reactants and products– catalysts (e.g., enzymes)

• know what an enzyme is and how it works!!!

Enzymes• protein catalysts:

– proteins that lower the activation energy of a chemical reaction

– are not changed or used up in the reaction

– Substrates: reactants in enzymatic reactions– Active site: a location on an enzyme that fits a

particular substrate

Break Down, Build Up• Decomposition reaction (catabolism):

AB A + B• Synthesis reaction (anabolism):

A + B AB• Exchange reaction (reversible):

AB A + B

Water In, Water Out• Hydrolysis:

A—B—C—D—E + H2O A—B—C—H + HO—D—E

• Dehydration synthesis (condensation):A—B—C—H + HO—D—E A—B—C—D—E

+ H2O

Redox Reactions• During some chemical reactions,

electrons are transferred between atoms, while still retaining their energy of position.– Oxidation - loss of an electron– Reduction - gain of an electron

Energy• Energy:

– the power to do work

• Work: – a change in mass or distance

Forms of Energy

• Kinetic energy: – energy of motion

• Potential energy: – stored energy

• Chemical energy: – potential energy stored in chemical

bonds

What is the difference between organic and inorganic compounds?

• Organic: – molecules based on carbon and hydrogen

• Inorganic: – molecules not based on carbon and hydrogen

Most important inorganic compounds in the body

• carbon dioxide • oxygen• water• inorganic acids, bases and salts

• Solubility: – water’s ability to dissolve a solute in a

solvent to make a solution

• Reactivity: – most body chemistry uses or occurs in water

• High heat capacity: – water’s ability to absorb and retain

heat

• Lubrication: – to moisten and reduce friction

Properties of Water

Aqueous Solutions

Figure 2–8

• Polar water molecules form hydration spheres around ions and small polar molecules to keep them in solution

Electrolytes• Inorganic ions which conduct electricity in

solution• Electrolyte imbalance seriously disturbs

vital body functions

What is pH and why do we need buffers?

• pH: – the concentration of hydrogen ions (H+) in a

solution

• Neutral pH: – a balance of H+ and OH— – pure water = 7.0

• Acid (acidic): pH lower than 7.0 – high H+ concentration,

low OH— concentration

• Base (basic): pH higher than 7.0– low H+ concentration,

high OH— concentration

Acids and Bases

pH Scale

Figure 2–9

• Has an inverse relationship with H+ concentration: – more H+ ions mean

lower pH, less H+ ions mean higher pH

• pH of body fluids measures free H+ ions in solution

• Excess H+ ions (low pH): – damages cells and tissues– alters proteins– interferes with normal physiological functions

• Excess OH— ions (high pH) also cause problems, but rarely

Acid and Alkaline• Acidosis:

– excess H+ in body fluid (low pH)

• Alkalosis: – excess OH— in body fluid (high pH)

Controlling pH• Salts:

– positive or negative ions in solution– contain no H+ or OH— (NaCl)

• Buffers: – weak acid/salt compounds– neutralizes either strong acid or

strong base

What kinds of organic compounds are there, and how do they work?

Carbohydrates

• Monosaccharides: simple sugars with 3 to 7 carbon atoms (glucose)

Carbohydrates

• Disaccharides: 2 simple sugars condensed by dehydration synthesis (sucrose)

Carbohydrates

• Polysaccharides: Chains of many simple sugars (glycogen)

Carbohydrates

• Carbohydrates are quick energy sources and components of membranes

Lipids

• hydrophobic molecules

• Made mostly of carbon and hydrogen atoms

• Lipids have many functions, including membrane structure and energy storage

• Long carbon chains with hydrogen atoms attached

– always has COOH at end

– saturated with hydrogen (no covalent bonds)– unsaturated (1 or more double bonds)

Fatty Acids

• derived from arachidonic acid– Leukotrienes: active in

immune system– Prostaglandins: local

hormones, short-chain fatty acids

Eicosanoids

• are the fatty acids attached to a glycerol molecule– Triglyceride: are the 3 fatty-acid tails

• bodies main fat storage molecule

Glycerides

Figure 2–15

– Cholesterol• component of cell membranes

– Estrogens and testosterone

– Corticosteroids and calcitrol

Steroids

Phospholipids and Glycolipids

Proteins

• Proteins are the most abundant and important organic molecules

• Basic elements: carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)

• Basic building blocks: 20 amino acids

Protein Functions

• 7 major protein functions:– support: structural proteins– movement: contractile proteins– transport: transport proteins – buffering: regulation of pH– metabolic regulation: enzymes– coordination and control: hormones– defense: antibodies

Amino Acid Structure

1. central carbon bound with

1. hydrogen

2. amino group (—NH2)

3. carboxylic acid group (—COOH)

4. variable side chain or R group

Peptide Bond

• A dehydration synthesis between:– the amino group of

1 amino acid– and the carboxylic

acid group of another amino acid

– producing a peptide

Figure 2–20a

Primary Structure• Polypeptide: a long chain of amino acids

Secondary Structure• Hydrogen bonds form spirals or pleats

Figure 2–20c

Tertiary Structure• Secondary structure

folds into a unique shape

Quaternary Structure • Final protein shape:

several tertiary structures together

Shape and Function• Protein function is based on shape

• Shape is based on sequence of amino acids

• Denaturation: loss of shape and function due to heat or pH

Protein Shapes• Fibrous proteins: structural sheets or

strands• Globular proteins: soluble spheres with

active functions

Nucleotides

• Are the building blocks of DNA

• Have 3 molecular parts: – sugar

(deoxyribose)– phosphate

group– nitrogenous

base (A, G, T, C)

The Nitrogenous Bases

Nucleic Acids

• Polymer of nucleotides (aka RNA and DNA)• found in the nucleus• stores and processes genetic information

Deoxyribonucleic Acid (DNA)

• Determines inherited characteristics• Directs protein synthesis• Controls enzyme production• Controls metabolism

Ribonucleic Acid (RNA)• Codes intermediate steps in protein synthesis

Differences between DNA and RNA structure

• DNA– double helix– sugar group is deoxyribose– nitrogenous bases used: C, G, A, T

• RNA– single stranded– sugar group is ribose– nitrogenous bases used: C, G, A, U

• purines pair with pyrimidines:

• DNA:– adenine (A) and thymine (T) – cytosine (C) and guanine (G)

• RNA: uracil (U) replaces thymine (T)

Complementary Bases

High Energy Compounds - ATP

• adenosine triphosphate (ATP): – 3 phosphate

groups

Phosphorylation

• Adding a phosphate group to ADP with a high-energy bond to form the high-energy compound ATP

• ATPase: the enzyme that catalyzes phosphorylation

The Cellular Level of Organization

Martini Chapter 3

The Cytoskeleton

• A network of proteins that gives a cell shape and strength

– microfilaments– intermediate

filaments– microtubules– thick filaments

(muscle cell)

Microvilli

• core of microfilaments

• increases cell surface area

Centrioles

• made of 9 microtubule triplets

• only found in cells that divide

• centrosome is the area surrounding these

Cilia

• made of 10 microtubule pairs

• anchored to basal body

• important for movement of fluids across cell surface

Ribosomes

• necessary for protein synthesis

• free– make proteins

that stay in cytosol

• fixed– attached to ER –

make secreted proteins

Proteosomes

• contain proteases

• recycle damaged and abnormal proteins

Endoplasmic Reticulum (ER)

Functions:

1. molecular synthesis

2. storage

3. transport

4. detoxification

Endoplasmic Reticulum (ER)

Functions:

1. molecular synthesis

2. storage

3. transport

4. detoxification

Endoplasmic Reticulum (ER)

SER Functions:

1. membrane synthesis

2. steroid synthesis

3. glyceride synthesis

4. glycogen synthesis

Endoplasmic Reticulum (ER)

RER Functions:1. post-translational

protein modification

2. packaging of secreted proteins storage

3. transported to golgi apparatus in transport vesicles

Golgi Apparatus

Functions:1. modifies and packages

molecules for secretion

2. renews/modifies cell membrane

3. puts special enzymes in lysosomes to be used within the cell

Mitochondria

• Responsible for energy production

Mitochondrial Energy Production

The Nucleus

Functions as the control center for a cell.

contains the entire genome

for that organism in the form of DNA

directs protein synthesis thereby determining the function of a cell

The Plasma Membrane

Functions of the Plasma Membrane

The main function of the plasma membrane are:

1. To separate the cytoplasm from the extracellular fluid

2. To regulate exchange between the cytoplasm and extracellular fluid

3. To sense changes in the environment

4. To provide the cell with structural support

What are the components of the plasma membrane?

• Lipids– phospholipids and carbohydrates

• Carbohydrates– the glycocalyx

• Proteins– integral (transmembrane), peripheral

6 functions of plasma membrane proteins

1. membrane transport

2. cell to cell communication3. structural stability4. signal receptor5. enzyme reaction6. recognition

The plasma membrane is selectively permeable

Martini pg 85

impermeable membrane

selectively permeable membrane

The plasma membrane is selectively permeable

Factors that determine permeability:

1. size2. electrical charge3. shape4. lipid solubility

Martini pg 85

Membrane Transport

Two categories define transport:

2.Transport process diffusion carrier-mediated vesicular

1.Energy requirement active passive

Martini pg 85

Membrane Transport

Martini pg 94

Diffusion Across the Cell Membrane

• Simple– lipid soluble

molecules

• Channel-mediated– small water soluble molecules and ions

Martini pg 86-87

Osmosis:the special case for water

diffusion• The movement of water across a

membrane, DOWN its concentration gradient.

Martini pg 87

Osmosis and Osmotic Pressure

Martini pg 88

Osmolarity

• Osmolarity is the solute concentration of an aqueous solution.

• The impact of osmolarity on a cell depends on the specific solutes.

• Tonicity is the word used to describe how a solution can impact a cell.

Martini pg 88

Tonicity

Isotonic: when the net flow of water is equal

Martini pg 88

Tonicity

• Hypotonic: water flows into a cell

Martini pg 88

Tonicity

• Hypertonic: water flows out of a cell

Martini pg 88

Carrier-Mediated TransportCharacteristics:1. specificity

each carrier protein will only

transport a specific molecule

2. limited by saturationif the membrane only has 10 carrier proteins and they are all being use, no more transport can take place.

3. ability to regulatethe cell can determine how many carrier proteins it puts in the membrane and their activity can be increased or decreased by chemical changes (for example, phosphorylation)

Facilitated Diffusion

No energy is required (passive) and molecules move down their concentration gradients.

Active Transport requires energy

The Sodium-Potassium Exchange Pump as an Example

Secondary Active Transport

Vesicular Transport

1. receptor-mediated2. pinocytosis3. phagocytosis

endocytosis

requires

ATP

The Transmembrane Potential

• The inside of a cell is relatively negative in charge (-70mVolts) due to the presence of negatively charged ions and proteins.

Why is the Transmembrane Potential important?

It provides potential energy.

Neurons (brain cells) communicate through electrical spikes made possible by their transmembrane potentials.

Hence – thought, movement and perception all depend on this potential energy!!!!