I. Atoms

A. Matter

1. Conventional issue - defined as a problem that has actually mass and also occupies space - consists of atoms.

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2. There space 94 different varieties of naturally emerging atoms - characterized by distinctions in the variety of protons in the nucleus. These space the naturally emerging elements. Atoms are also defined together the smallest unit of a pure problem (one element) the retains the nature of that substance and cannot be subdivided more by chemical means. 3. Compounds space substances created of two or more types of elements in a resolved ratio, with a particular structure/spatial plan maintained by chemistry bonds (ionic or covalent). So, NaCl (table salt) is one ionic compound. H2O (water) is a covalent compound. 4. Molecules are substances of two or much more atoms bound together by covalent bonds. So, it is inappropriate to refer to a \"molecule\" of NaCl (which is ionic). 2 atoms that hydrogen bound with each other by a covalent bond is a molecule of hydrogen. It is not a compound, together it only includes one type of element. For compounds consists of covalently bound atoms, a molecule is the smallest unit the the compound that maintains the properties of that compound. So, we deserve to have one molecule of water, which is additionally 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 wave nature) and excluding a factor to consider of quarks. For a much more detailed account, feel totally free to check out this connect from the university of Oregon and Wikipedia.

1. Atoms have actually a nucleus containing proton (mass ~ 1 atomic mass unit; elementary charge = +1 ) and also neutrons (mass ~ 1 atom mass unit; elementary charge = 0). The number of protons defines the form of atom - the facet - and also it\"s atom number. The massive of an atom is largely identified by the mass of protons and also neutrons. Although every atoms of an aspect have the same number of protons, the variety of neutrons have the right to vary. This atoms v variable number of neutrons are referred to as isotopes. Those with an excess variety of neutrons are much less stable and also will loose them end time. These room radioisotopes, and they emit energy when they loosened a neutron. They loose them in ~ a consistent rate, so you can date how old they are by how plenty of have readjusted to the much more stable state. Atoms with unequal number of protons and also electrons have actually a network charge and also are dubbed ions. 2. The cell nucleus is surrounding by a cloud of electron (mass ~ 0; elementary charge = -1), stood for as shells and also orbitals: Shells 1, 2, 3 have actually 1, 4, 4orbitals, \"containing\" a preferably of 2, 8, 8 electrons, respectively. The orbitals room 1000\"s of time the width of the nucleus, for this reason an atom (and hence, every matter) is mostly space. For comparison, if friend envision the nucleus of a carbon atom as a basketball (about 12 inches in diameter), the outermost electrons would certainly be orbiting 5 miles away.

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3. The distance in between the orbital and the nucleus correlates through the power of the electron (in regards to a wave function). 4. As electrons gain energy, castle \"orbit\" farther indigenous nucleus. Without an entry of energy, one atom will lose energy and approach it\"s lowest power state, occupying the the next \"unoccupied\" orbit available. 5. An altering orbitals - and energy claims - is a discrete process. Electron must obtain or shed discrete quantities of energy (quanta) to readjust position to one more orbital. 6. Binding properties are largely governed through the variety of electrons in the outermost orbital/shell. They accomplish greater stability as soon as the outermost orbitals/shells space full. They accomplish this stability by losing, gaining, or sharing electrons with various other atoms.

II. Bonds

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A. Covalent Bonds

Atoms re-superstructure electons in pairs: H2, H2O, etc. These are the primary bonds in biologically essential molecules - they can be non-polar (shared evenly) like H2 - or polar (shared unevenly...creating a charge difference throughout the molecule - together in water, wherein the common electrons are held more tightly through the bigger oxygen nucleus, pulling the electron cloud turn off the hydrogen nucleu, revealing several of its optimistic charge).

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B. Ions and also Ionic Bonds

If the attraction in between nuclei is very unequal, the mutual electrons deserve to be stripped from one of the atoms and taken through the other. This creates charged particles (ions) which may then be attractive to one one more based on your opposite charge. (NaCl)

C. Hydrogen Bonds

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

III. Molecules

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A. Water 1. Structure - H2O is a polar molecule through partially optimistic hydrogen ends and also a partially negative oxygen finish - thus, water forms hydrogen bonds 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 since polar and also ionic compounds dissolve in water; as soon as dissolved, lock can connect with other solutes. By \"dissolving\", we mean the separation of molecules or ion from one another. This happens since the water molecules have the right to get between the molecules/ions and bind to them, separating these molecules/ions in solution. B. Water has actually a \"high specific heat\" - an interpretation that that takes lots of power to adjust its temperature and also state. So, aqueous solutions (cells and aqueous environments) space thermally stable. c. Water dissociates into H+ and OH- ions, at a concentration the 1 x 10-7 molecule in pure water = pH the 7. d. Water is \"cohesive\", in the it \"sticks\" come iself; and it is\"adhesive\", in that it pole to fee surfaces. Capillary action in vascular tree and little blood vessels is a duty of this properties.
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B. Carbohydrates

1. Structure: - monomer - monosaccharide (simple sugar) - CnH2nOn (glucose, galactose, fructose are 6 carbon sugars; ribose, ribulose, deoxyribose are 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 linked together into polymers utilizing dehydration synthetic - a removal of a water molecule (dehydration) and also the synthetic of a bond. This needs energy and also is catalyzed by enzymes in living systems. 2. Function: a. Power storage: - all huge biomolecules have lots the bonds and also thus store lots of energy. But, the bigger the molecule, the an ext time that takes come harvest all the power by metabolic failure (catabolism). So, polysaccarides serve much better as \"longer-term\" power storage than monosaccharides, conversely, monosaccarides, because they have the right to be metabolized an ext quickly, serve far better as a short term energy supply. (starch in tree andglycogen in the liver of animals are longer term storage molecules; glucose is the short-term energy molecule in every one of life) b. Structural: - cellulose is simply a long chain the glucose. And decomposers break down wood to develop the sugars they will usage for metabolic energy. - chitin is the main component that exoskeletons in arthropods.
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C. Proteins - (we will cover this in much more detil throughout the great on protein synthesis) 1. Structure: monomer - amino acid - amine (NH2) group at one end and carboxyl group (COOH) at various other there are 20 different amino acids that are uncovered in living systems. polymer - polypeptide - 100 come 300 amino mountain long. The AA\"s are attached by dehydration synthesis reactions right into a long direct chain. Due to the fact that there room 20 Amino acids (\"letters\") that deserve to be offered in your construction, proteins deserve to have a limitless number of different combine (like letters in different combinations make differnt \"words\"). This variety in kind means selection in function. **Higher levels of structure: 1. The main structure that a polypeptide/protein is the linear sequence the amino acids

2. This straight sequence can take a helical or \"pleated\" sheet shape, depending on bond angles and soforth. These are secondary levels structure

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3. Some proteins then fold upon themselves, taking a globular shape. This globular form is kept by bonds in between different functional teams of differnt amino acids. Enzymes and also cell membrane proteins are common globular proteins.this is called tertiary structure.

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

2. Function: a. Power Storage: (all biomolecules have the right to be broken down for power harvest. Typically, since proteins are doing other else, too, castle are broken down critical so the the organism can maintain this duty that the protein performs because that as lengthy as possible). b. Structural: after water, animals are largely proteinaceous collagen, elastin, muscle proteins, etc. c. Metabolic: all biological reactions room catalyzed. Most biological catalysts room proteinaceous enzyme d. Transport: cell membrane - there are proteins that assist transport throughout the membrane biology - hemoglobin, because that instance, move oxygen e. Immunity: antibodies room proteins.

D. Fats and also Lipids:

1. Structure: monomer - fatty mountain - lengthy carbon chain through a carboxyl group (COOH) - have the right to be saturation (with H - no dual bonds in between C\"s) or unsaturated (a twin bond) - pet fats are usually saturated, and also are solid in ~ room temp. Plant and also fish fats room usually unsaturated, and are liquid at room temp and are referred to as \"oils\". By saturating a plant fat, it can be make solid - hydrogenated fat or oil. (changing peanut oil right into peanut butter, or vegetable oil into \"crisco\"). During this process, trans-fats are likewise created. These space unsaturated fats through a infectious diseases worldwide (not cis) conformation. Trans-fats have been connected with atherosclerosis
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polymer - fat (triglyceride) - 3 fatty mountain attached by dehydration synthetic to a glycerol molecule - phospholipid: glycerol v 2 fat acids and also a phosphate (PO4) group. The PO4 is negatively charged (thus, polar), if the fat acids room non-polar. This accounts for how these molecules orient in aqueous solutions, creating membranes. A \"choline\" groups is commonly attached come the phosphate. 2. Function: a. Power storage: saturated fat are very dense - the fat acids fit together, in parallel, an extremely snugly. So, to save the most energy in the the smallest space, fats are the preferred medium. b. Cabinet membranes - barrier to water soluble materials. The non-polar lipid \"bilayer\" is a obstacle to water soluble materials (that are ionic or polar). So, ionic and polar link can\"t just flow into the cell; the cell deserve to regulate how much of what gets in and out. c. Insulation d. Hormones - obtained from fats, lipid soluble, slip best theough cell membranes right into cells, for this reason they can function 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 consisting of a straight sequence of linked nucleotide monomers. Us will explain the structure of the monomers first, and also then define how they are connected into straight polymers. Finally, us will explain the double-stranded framework of ds-DNA.

1. The monomers are \"nucleotides\"

three components:

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- Pentose (5 carbon) sugar: either ribose (RNA) or deoxyribose (DNA). The carbons are numbered clockwise. The difference in between the sugars is that ribose has an -OH team on the 2\" carbon, vice versa, deoxyriboes has only 2 H groups and also thus is \"deoxygenated\" family member to ribose. BOTH sugars have an -OH group on the 3\" carbon, which will certainly be associated in binding. The 5\" carbon is a sidegroup turn off the ring.

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

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- The 3rd component that a nucleotide is a phosphate group, i beg your pardon is attached come the 5\" carbon the the sugar. When a nucleotide is included into a chain, it has a single phosphate group. However, nucleotides can occur that have actually two or three phosphate groups (dinucleotides and trinucleotides). ADP and also ATP are essential examples that these species of molecules. In fact, the precursors of included nucleotides space trinucleotides. Once two phosphates room cleaved, power is released that deserve to be supplied to include the staying monophosphate nucleotide to the nucleic mountain chain.

2. Polymerization is by \"dehydration synthesis\"

As v all various other classes the biologically important polymers, monomers are attached into polymers by dehydration synthesis. In nucleic mountain formation, this involves binding the phosphate group of one nucleotide to the -OH group on the 3\" carbon of the present chain. For the functions of seeing how this reaction works, we deserve to envision one H+ on among the negatively charged oxygens that the phosphate group. Then, a molceule the water deserve to be removed from these two -OH groups, leaving an oxygen binding the sugar of one nucleotide come the phosphate the the next.

This creates a \"dinucleotide\". It has a polarity/directionality; that is different at that is ends. At one end, the reactive group is the phosophate on the 5\" carbon. This is referred to as the 5\" finish of the chain. In ~ the other end, the reactive group is the totally free -OH ~ above the 3\" carbon; this is the 3\" finish of the chain. So, a nucleic mountain strand has a 5\" - 3\" polarity.

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3. Most DNA exists as a \"double helix\" (ds-DNA) include two direct nucleic mountain chains.

a. The nitrogenous bases ~ above the 2 strands space \"complementary\" to each other, and form weak hydrogen bonds between them. A constantly pairs through T, and also C always pairs v G. Together such, there is constantly a double-ringed purine pairing with a single-ringed pyrimidine, and the width of the double-helix is continuous over its whole length.

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

4. RNA performs a wide variety of features in living cells:

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

b. R-RNA (for \"ribosomal\") is do the exact same way, together a copy of DNA. However, the is not carrying the recipe because that a protein; rather, the is sensible as RNA. It is inserted IN the Ribosome, and it help to ‘read’ the m-RNA.

c. T-RNA (for \"transfer\") is additionally made as a copy the DNA, yet it is likewise functional as an RNA molecule. Its duty is to bind to a certain amino acid and incorporate it into the amino mountain sequence as instructed by the m-RNA and ribosome.

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

e. Sn-RNA (small nuclear RNA) are brief sequences that procedure initial m-RNA products, and also regulate the production of r-RNA, preserve telomeres, and regulate the action of warrior factors. Regulatory functions.

Study Questions: 1) What is the basic structure of one atom (mass, charge, and location that its components)? 2) What is the relationship in between electrons, orbital distance, and also energy? 3) What are isotopes and also ions? 4) What are covalent, ionic, and hydrogen bonds? 5) attract the framework of water, including all electron in their shells. Also identify the covalent bonds, and also the position of the partial dues on the molecule. 6) What two huge classes of compound dissolve in water? Why? 7) What is the basic structure that a monosaccharide?8) What form of molecule room chitin and cellulose?9) display how 2 monosaccharides are linked together. What is the name 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) display how 2 amino acids are connected together. What is the surname of the reaction? 13) diagram the components of an RNA nucleotide. 14) display how two nucleotides are linked together through dehydration synthesis reactions. 15) Why go the purine - pyrimidine framework relate to the complementary nature of double-stranded DNA? 16) draw a DNA twin helix, mirroring three basic pairs and also the antiparallel nature the the helices.

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