The Chemical Level of Organization Martini Chapter 2.
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Transcript of 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!!!!