I. Atoms

A. Matter

1. Conventional issue - defined as a problem that has mass and occupies an are - is composed of atoms.

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2. There are 94 different species of naturally arising atoms - characterized by distinctions in the number of protons in the nucleus. These are the naturally developing elements. Atom are additionally defined as the the smallest unit the a pure problem (one element) that retains the nature of that substance and also cannot be subdivided further by chemical means. 3. Compounds room substances written of two or much more types of facets in a addressed ratio, through a particular structure/spatial setup maintained by chemical bonds (ionic or covalent). So, NaCl (table salt) is an ionic compound. H2O (water) is a covalent compound. 4. Molecules space substances of two or much more atoms bound together by covalent bonds. So, the is unreasonable to describe a "molecule" the NaCl (which is ionic). 2 atoms that hydrogen bound with each other by a covalent shortcut is a molecule that hydrogen. That is no a compound, as it only consists of one form of element. For compounds consists of covalently tied atoms, a molecule is the the smallest unit the the compound the maintains the nature of that compound. So, we can have one molecule that water, which is also a compound.

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B. Properties of Atoms

We will usage a really simplistic "Bohr" version of atomic structure, emphasizing the particulate nature of issue (rather than the tide nature) and excluding a consideration of quarks. For a an ext detailed account, feel complimentary to view this attach from the university of Oregon and Wikipedia.

1. Atoms have a nucleus containing protons (mass ~ 1 atomic mass unit; elementary fee = +1 ) and neutrons (mass ~ 1 atomic mass unit; elementary fee = 0). The number of protons specifies the kind of atom - the aspect - and it"s atomic number. The mass of one atom is largely figured out by the fixed of protons and also neutrons. Although all atoms that an facet have the same variety of protons, the variety of neutrons can vary. These atoms through variable numbers of neutrons are referred to as isotopes. Those through an excess number of neutrons are much less stable and also will loose them end time. These space radioisotopes, and they emit power when they loose a neutron. They loosened them in ~ a consistent rate, so girlfriend can date how old they are by how countless have changed to the much more stable state. Atoms v unequal number of protons and also electrons have actually a network charge and also are dubbed ions. 2. The nucleus is surrounded by a cloud of electrons (mass ~ 0; elementary charge = -1), represented as shells and also orbitals: Shells 1, 2, 3 have 1, 4, 4orbitals, "containing" a best of 2, 8, 8 electrons, respectively. The orbitals are 1000"s of time the broad of the nucleus, for this reason an atom (and hence, all matter) is mainly space. Because that comparison, if you envision the cell nucleus of a carbon atom together a basketball (about 12 customs in diameter), the outermost electrons would be orbiting 5 miles away.

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3. The distance in between the orbital and the cell core correlates with the energy of the electron (in regards to a wave function). 4. Together electrons get energy, castle "orbit" farther indigenous nucleus. Without an intake of energy, an atom will lose energy and approach it"s lowest energy state, occupying the closest "unoccupied" orbit available. 5. Transforming orbitals - and also energy claims - is a discrete process. Electron must obtain or lose discrete quantities of power (quanta) to change position to another orbital. 6. Binding nature are greatly governed through the variety of electrons in the outermost orbital/shell. They accomplish greater stability when the outermost orbitals/shells room full. They accomplish this stability by losing, gaining, or sharing electrons with other atoms.

II. Binding

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A. Covalent Bonds

Atoms share electons in pairs: H2, H2O, etc. These room the primary bonds in biologically necessary molecules - they have the right to be non-polar (shared evenly) prefer H2 - or polar (shared unevenly...creating a charge difference across the molecule - as in water, wherein the common electrons are held an ext tightly through the larger oxygen nucleus, pulling the electron cloud turn off the hydrogen nucleu, revealing several of its positive charge).

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B. Ions and also Ionic Bonds

If the attraction between nuclei is really unequal, the shared electrons deserve to be stripped from among the atoms and taken by the other. This creates fee particles (ions) which might then be attracted to one another based on your opposite charge. (NaCl)

C. Hydrogen Bonds

These room weak ionic bonds, weak forces of attraction in between a partially charged Hydrogen Atom (+ charge) and also a negatively fee molecule or the an adverse portion the a molecule.

III. Molecules

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A. Water 1. Structure - H2O is a polar molecule v partially positive hydrogen ends and also a partially an adverse oxygen end - thus, water develops hydrogen binding with other water molecules, and also other fee substances (polar or ionic). 2. Properties and Their Importance a. Often referred to as a "universal" solvent due to the fact that polar and ionic compound dissolve in water; as soon as dissolved, they can communicate with various other solutes. By "dissolving", we typical the separation of molecules or ion from one another. This happens due to the fact that the water molecules have the right to get in between the molecules/ions and bind come them, separating this molecules/ions in solution. B. Water has a "high particular heat" - an interpretation that it takes too many of energy to readjust its temperature and state. So, aqueous options (cells and also aqueous environments) room thermally stable. c. Water dissociates into H+ and OH- ions, in ~ a concentration that 1 x 10-7 molecules in pure water = pH of 7. d. Water is "cohesive", in that it "sticks" to iself; and also it is"adhesive", in the it rod to fee surfaces. Capillary action in vascular plants and tiny blood ship is a function of these properties.
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B. Carbohydrates

1. Structure: - monomer - monosaccharide (simple sugar) - CnH2nOn (glucose, galactose, fructose space 6 carbon sugars; ribose, ribulose, deoxyribose room 5 carbon sugars) - disaccharides: sucrose (glucose + fructose); maltose - (2 glucose) - polymer - polysaccharide - chain of street starch, glycogen, chitin, cellulose

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- monomers are connected together into polymers utilizing dehydration synthetic - a removal of a water molecule (dehydration) and the synthesis of a bond. This requires energy and is catalyzed by enzymes in living systems. 2. Function: a. Power storage: - all huge biomolecules have actually lots the bonds and also thus store several energy. But, the larger the molecule, the more time that takes come harvest every the power by metabolic failure (catabolism). So, polysaccarides serve much better as "longer-term" energy storage 보다 monosaccharides, conversely, monosaccarides, due to the fact that they can be metabolized much more quickly, serve much better as a short term power supply. (starch in plants andglycogen in the liver of pets are much longer term storage molecules; glucose is the short-term power molecule in all of life) b. Structural: - cellulose is just a lengthy chain the glucose. And decomposers malfunction wood to produce the street they will usage for metabolic energy. - chitin is the main component the exoskeletons in arthropods.
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C. Proteins
- (we will cover this in much more detil throughout the class on protein synthesis) 1. Structure: monomer - amino acid - amine (NH2) team at one end and also carboxyl team (COOH) at other there space 20 various amino acids that are uncovered in living systems. polymer - polypeptide - 100 come 300 amino mountain long. The AA"s are attached by dehydration synthetic reactions right into a long straight chain. Due to the fact that there are 20 Amino mountain ("letters") that deserve to be offered in their construction, proteins deserve to have a limitless number of different combine (like letter in different combinations do differnt "words"). This selection in kind means selection in function. **Higher level of structure: 1. The major structure of a polypeptide/protein is the linear sequence that amino acids

2. This linear sequence deserve to take a helical or "pleated" sheet shape, depending upon bond angles and also soforth. These are second levels structure

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3. Some proteins then wrinkles upon themselves, taking a globular shape. This globular form is preserved by bonds between different functional groups of differnt amino acids. Enzymes and cell membrane protein are typical globular proteins.this is dubbed tertiary structure.

4. Sometimes, single proteins room not sensible on their own - they should be an unified with various other proteins to forma a protein through a quaternary structure. Hemoglobin, with 2 alpha and 2 beta globular polypeptides, is one example. Collagen is another, composed of number of helical polypeptides.

2. Function: a. Power Storage: (all biomolecules deserve to be damaged down for power harvest. Typically, because proteins are doing miscellaneous else, too, they are damaged down last so that the organism have the right to maintain this duty that the protein performs for as lengthy as possible). b. Structural: after ~ water, pets are largely proteinaceous collagen, elastin, muscle proteins, etc. c. Metabolic: all organic reactions room catalyzed. Most organic catalysts space proteinaceous enzymes d. Transport: cell membrane - there room proteins that aid transport across the membrane biology - hemoglobin, because that instance, move oxygen e. Immunity: antibodies space proteins.

D. Fats and Lipids:

1. Structure: monomer - fatty acid - lengthy carbon chain with a carboxyl group (COOH) - have the right to be saturation (with H - no dual bonds in between C"s) or unsaturated (a dual bond) - animal fats are usually saturated, and also are solid in ~ room temp. Plant and fish fats room usually unsaturated, and also are fluid at room temp and also are referred to as "oils". By saturating a plant fat, it deserve to be made solid - hydrogenated fat or oil. (changing peanut oil right into peanut butter, or vegetables oil right into "crisco"). Throughout this process, trans-fats are additionally created. These are unsaturated fats through a trans (not cis) conformation. Trans-fats have actually been linked with atherosclerosis
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polymer - fat (triglyceride) - 3 fatty mountain attached by dehydration synthesis to a glycerol molecule - phospholipid: glycerol through 2 fatty acids and a phosphate (PO4) group. The PO4 is negatively fee (thus, polar), while the fatty acids space non-polar. This account for how these molecules orient in aqueous solutions, forming membranes. A "choline" groups is generally attached to the phosphate. 2. Function: a. Energy storage: saturated fats are really dense - the fatty acids to the right together, in parallel, really snugly. So, to save the most energy in the the smallest space, fats room the desired medium. b. Cabinet membranes - barrier to water soluble materials. The non-polar lipid "bilayer" is a barrier to water soluble materials (that are ionic or polar). So, ionic and polar compounds can"t just circulation into the cell; the cell can regulate how much the what gets in and also out. c. Insulation d. Hormones - obtained from fats, lipid soluble, slip best theough cabinet membranes right into cells, therefore they can duty at an extremely low concentrations.

E. Main point Acids (DNA/RNA)

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DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acids - polymers consists of a straight sequence of connected nucleotide monomers. Us will explain the framework of the monomers first, and then define how they are attached into direct polymers. Finally, we will explain the double-stranded framework of ds-DNA.

1. The monomers room "nucleotides"

three components:

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- Pentose (5 carbon) sugar: either ribose (RNA) or deoxyribose (DNA). The carbons room numbered clockwise. The difference between the street is the ribose has an -OH group on the 2" carbon, vice versa, deoxyriboes has only 2 H groups and thus is "deoxygenated" loved one to ribose. BOTH sugars have actually an -OH group on the 3" carbon, which will be connected in binding. The 5" carbon is a sidegroup off the ring.

- Nitrogenous Base: each nucleotide has a single nitrogenous base attached to the 1" carbon the the sugar. This nitrogenous base might be a double-ringed structure (purine) or a solitary ringed (pyrimidine) structure. The purines room adenine (A) and also guanine (G). The pyrimidines space thymine (T), cytosine (C), and also uracil (U). DNA nucleotides may carry A, G, C, or T. RNA nucleotides bring either A, G, C, or U.

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- The third component that a nucleotide is a phosphate group, which is attached come the 5" carbon of the sugar. When a nucleotide is incorporated into a chain, it has a solitary phosphate group. However, nucleotides can take place that have two or three phosphate groups (dinucleotides and trinucleotides). ADP and also ATP are important examples the these types of molecules. In fact, the precursors of incorporated nucleotides space trinucleotides. As soon as two phosphates are cleaved, energy is exit that have the right to be provided to include the remaining monophosphate nucleotide come the nucleic mountain chain.

2. Polymerization is by "dehydration synthesis"

As through all various other classes the biologically vital polymers, monomers are connected into polymers through dehydration synthesis. In nucleic acid formation, this requires binding the phosphate group of one nucleotide to the -OH team on the 3" carbon of the existing chain. For the objectives of seeing just how this reaction works, we can envision one H+ on one of the negatively fee oxygens the the phosphate group. Then, a molceule of water can be eliminated from these two -OH groups, leave an oxygen binding the street of one nucleotide come the phosphate of the next.

This creates a "dinucleotide". It has actually a polarity/directionality; the is various at that is ends. In ~ one end, the reactive team is the phosophate top top the 5" carbon. This is dubbed the 5" end of the chain. In ~ the other end, the reactive team is the free -OH ~ above the 3" carbon; this is the 3" finish of the chain. So, a nucleic acid strand has actually a 5" - 3" polarity.

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3. Most DNA exists together a "double helix" (ds-DNA) comprise two direct nucleic mountain chains.

a. The nitrogenous bases on the 2 strands space "complementary" to each other, and type weak hydrogen bonds in between them. A always pairs with T, and C always pairs with G. As such, there is always a double-ringed purine pairing through a single-ringed pyrimidine, and also the width of the double-helix is continuous over its entire length.

b. The 2 strands (helices) space anti-parallel: they room arranged with opposite polarity. One strands point out 5" - 3", when the various other points 3" - 5". The direction that the pentose sugars and also the type of reactive group at the ends of the chains show this relationship.

4. RNA performs a wide range of attributes in life cells:

a. M-RNA (for "messenger") is the copy the a gene. That is the sequence of nitrogenous bases in m-RNA that is actually check out by the ribosome to identify the framework of a protein.

b. R-RNA (for "ribosomal") is made the very same way, as a copy of DNA. However, the is not transporting the recipe because that a protein; rather, it is sensible as RNA. It is inserted IN the Ribosome, and also it helps to ‘read’ the m-RNA.

c. T-RNA (for "transfer") is likewise made as a copy that DNA, but it is additionally functional together an RNA molecule. Its duty is to tie to a details amino acid and incorporate it into the amino mountain sequence as instructed by the m-RNA and also ribosome.

d. Mi-RNA (micro-RNA) and si-RNA (small interfering RNA) tie to m-RNA and splice it; inhibiting the synthetic of the protein. This is a regulatory function.

e. Sn-RNA (small nuclear RNA) are short sequences that process initial m-RNA products, and also regulate the manufacturing of r-RNA, preserve telomeres, and also regulate the action of transcription factors. Regulation functions.

Study Questions: 1) What is the simple structure of an atom (mass, charge, and also location that its components)? 2) What is the relationship between electrons, orbital distance, and also energy? 3) What space isotopes and ions? 4) What space covalent, ionic, and hydrogen bonds? 5) draw the framework of water, consisting of all electron in your shells. Likewise identify the covalent bonds, and also the place of the partial dues on the molecule. 6) What two large classes of link dissolve in water? Why? 7) What is the an easy structure the a monosaccharide?8) What type of molecule room chitin and also cellulose?9) display how 2 monosaccharides are connected together. What is the surname of this reaction?10) What is the structure of a fat acid? A triglyceride?11) What is the monomeric unit of proteins? draw one, without specifying the change group.12) present how two amino acids are connected together. What is the name of the reaction? 13) diagram the components of one RNA nucleotide.
14) display how 2 nucleotides are attached together by dehydration synthetic reactions. 15) Why walk the purine - pyrimidine framework relate to the safety nature that double-stranded DNA? 16) draw a DNA dual helix, showing three basic pairs and also the antiparallel nature the the helices.

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17) explain the greater levels of eukaryotic chromosome structure, consisting of the terms nucleosome and also solenoid.