Chemistry Basics PDF

Here's the conversion of the provided text into a structured markdown format: # CHEMISTRY BASICS ## Vocab * **Element** - A pure substance found on the periodic table * **Atoms** - Made of subatomic particles * Simplest unit of an element * **Compounds** - 2 or more elements combined...

Here's the conversion of the provided text into a structured markdown format: # CHEMISTRY BASICS ## Vocab * **Element** - A pure substance found on the periodic table * **Atoms** - Made of subatomic particles * Simplest unit of an element * **Compounds** - 2 or more elements combined $H-O, HOH$ * **Molecules** - 2 atoms (or more) combined * e.g., $2O, CO_2, H_2, O_2$ * **Electron arrangement** - Where electrons fill the orbitals * 2 electrons fill the first shell, then 8, 8, 18... ### Matter * All objects are made of atoms. * Atoms are made of protons, neutrons & electrons. * Every atom is made of different variations of atoms * Atoms combine to make molecules. * The electrons in the outmost orbital are known as valence electrons, and form bonds with other atoms. ### Intramolecular bonds There are 3 types: * Covalent bonds (non-polar) * Polar covalent bonds * Ionic bonds #### Covalent bonds * formed by sharing valence electrons between non-metals * most organic molecules have this bond * $NaCl$: $[Na]^+ [Cl]^-$ * shared pair of e- lowers energy forming bonds must add energy, breaking a bond releases energy #### Polar covalent bonds * a pair of valence e- is unequally shared between non-metals * The atom with the higher E-neg attracts the e-, giving it a neg. charge ($\delta^-$). The other atom is slightly pos. ($\delta^+$) #### Ionic bonds * Between a metal and non-metal * Formed by the transfer of e- from atom to atom ### Polarity #### Polar bonds * Occur if the electronegativity diff. between the 2 elements is >0.5 * Creates partial pos/partial neg to bonds * $CO, H_2O, NH, CN$ are polar bonds (only ones we need in biochem) #### Non-polar bonds * Any bond between the same element is non polar * $Cl_2, N_2$ ### Lone pair of electrons * Lone pairs create neg charges, causing partial neg in their location * Molecules are polar if it has lone pairs and asymmetrical ### Molecule Shapes * If a molk. has polar bonds, it can be non-polar if the polar bonds are synometrical * Synmetrical cancels each other out, making the mole. non-polar #### Polarity & Properties ##### Non polar * Tends not to attract on another * Not aqueous/ soluble in $H_2O$ (hydrophobic) (e.g. fats) * Low melting & boiling point ##### Polar * Attracts one another * Aqueous/ dissolves in $H\_20$, (hydrophilic) (e.g. liquids) * Higher melting and boiling point. * e.g., of polar & non polar compounds Diagrammatic representation for polarity of $H_2O$, $NH_3$ and $CO_2$. $$ \begin{aligned} &H_2O - \text{partial charges shown} - polar \\ &NH_3 - \text{lone pairs shown} - polar \\ &CO_2 - \text{dipole moments canceling} - non-polar \end{aligned} $$ *Isotopes* - A version of an element with different mass * diff number of electrons * $C-12$ $C-13$ $C-14$ *Ion* - An element with a charge * Cation: pos. Anion: neg. *Charge on atoms* - Based on electrons removed (+) or added (-) * Purpose is to fill outer valence shell to become stable Examples: Unstable $\xrightarrow{\text{add e-}}$ Stable! $MgCl^+ \longrightarrow MgCl_2$ *Electron* - in orbit, Charge -1, mass o amu *Neutron* - nucleus, charge 0, mass 1 amu *Proton* - nucleus, charge +1, mass 1 amu * Combes of atoms are held tgt by covalent bonds (Sharing): * Many molecules are organic (contains $C$ and $H$), some are inorganic. (no combo of $C$ and $H$) Compounds. Notes on Atomic Interactions: * Atoms form compounds to become more stable * compounds are either ionic or covalent * The elements of life - a mold + non-metal * Covalent: share electrons and made of 2 non-metals * Ionic: electrons are given from one atom to another, + made of a mold + nan-Metal * Atoms have stable valence shells by losing / gaining electrons * This loss/gain of electrons causes it to become charged, aka an ion * Ions are held tgt by electrostatic at traction * Cations positively charged Anion: negatively charged * In biochem ionic compounds (salts) are considered ions since they are in an aqueous environment #### The Basis of Life is Carbon: * Due to its variety of structures that it can form due to its four valence e- * There are 92 natural elements, 25 are essential for life, but 6 fundamental elements * 98% of living things are made of: C,N,O, P, H, S * $O$ -2 bonds * $C$ -4 bonds * $H$ -1 bond * $P$ -3 bonds * $N$ -3 bonds * $S$ -2 bonds * All of life is water based; we are 75% $H_2O$ * $H_2O$ has a slight charge to tht $O$ is more neg, $H$ is more pos. The slight charge causes it to be polar. * Polar molecules con pond with other polor mols. to form H bonds * water and Intermolecular Bonds - bonds between molecules e.g. H bonding. * Hydrophobic hydrophilic interactions & Intramolecular bonds - bonds within a molecule any covalent & ionic bonds * "Like dissolves like". $H_2O$ is polar and will dissolve (aqueous?) other polar substances * Hydrophilic: likes water, dissolves in $H_2O$ and polar substances, Hydrophobic: hates water, doesn't dissolve in $H_2O$ and non-polar Polarity- * polar molecules will dissolve in polar solvents (like water) * non-polar molecules will dissolve in non-polar solvents (like fats) a molecule is polar if the electronegativity difference between 2 elements is >0.5 [This creates a bond partial positive ($\delta^+$) and a partial negative ($\delta^-$) between the molecule Diagrammatic representation of polarity in $CO_2$ molecule. * Polar bonds, * not Symmetrical! ## Properties of water! * Molecular formula - $H_2O$ * Structural formula - $H-O-H$ * $H_2O$ molecules con make 4 H bonds ### Properties of $H_2O$ * There are 6 properties 1. Adhesion and cohesion (to forman one / cling) 2. lower density solid compared to liquid (molecules create space between them, causing lower density) 3. High specific heat capacity (Needs laige amt. of heat energy to raise temp) 4. High heat of Vapourization/Fusion (converting liquid to gas/melting a solid) (Needs large amt's of energy to change phases/ Vapour mools boore energy than fusion) 5. A good solvent (Capable of dissolving more substances than any liquid) 6. Ionization (Atom / molecule gets pos. /neg charge from gaining or losing electrons) ### Cohesion & Adhesion * **Cohesion**- The Clinging of a substance to itself. * e.g., H-bonds between the molecules hold water molecules tight * **Adhesion**- The clinging of one substance, to another * e.g., the miniscus (curve in water) when measuring water in a graduated cylinder ### Relevance of Cohesion & Adhesion: * Adhesion- In plants, adhesion within the plants con walls of xylen as well. * Water molecules allow for capillary action and allows water to be drawn ve. * Cohesion - cohesion between the molecule causes now theo molecules to be drawn up by the xylem with the help of this molecules ahead of them #### Surface tension Measurement of how difficult it is to break the surface of a liquid. e.g., some ipsecssrely on surface tension to stay on top of water ## Diagrammatic *High density solid vs. $H_2O$: $Ice$ is only liquid more dense than its solid *Ice is most dense at 4°c, Ice is less dense than $H_2O$ Biological significance - *Aquatic life:* when the lamp of the atmosphere drops to are or lower, the Ice freezes on the surface level, but within the int, Water is still danse at 4°C. Heat - The amt. of energy needed to heat lg of substance by 1°c *Water can absorb a lot of heat before raising in temp (.: $H\_20$ has a high specific heat Capacity) Biological significance - Animals Con Reepa constant internal tempias the H₂O in their bodies acts as a heat sink. Large bodies of water have an effect on nearby lemp too. Vaporization - LOT of energy is needed to change Het from liquis to gas Biological significance - -Sweating (liquid) draws a large amt of heat from our body as suvent evaporates, cooling us down! *High Heat of fusion*: A LOT of energy is needed to chance ice from solid to liquid *Solubility* - $H_2O$ is a versatile solwent due to its polarity. *Many molecules con dissolve in water if it has semi polar regions on its surface. Biological Significance - solutes include: salts, Sugars, vitamins & proteins $\text{Ionization - Ionization of }H_2O\text{ is rare but reversible}$ are very active & control the ph balance of the baby. Biological Significance - ions help the mitochondrion produce ATP ## Functional Groups! ### Vocab * **Hydrocarbons** - contain carbon and hydrogen * $CH_4$ - Methane (1C) * $C_2H_6$ - Ethane (2C) * **Saturated**: Hydrocarbons with Single bonds * **Unsaturated**: Hydrocarbons with double or Single bands of H * $C_3H_8$ - Propane (3C) * **Functional group**: A group of atoms attached to carbon skeletons * usually involved in chemical reactions **Family - # of Carbons Prefix** * 1 - Meth * 2 -Eth * 3 - Prop * 4 - But * 5 - Pent * 6 - Hex * 7 - Hept * 8 - Oct ### Types of functional groups. * **Hydroxyl group** - Polar, Keeps dissive organic compounds, H- bonding * $-O-H$ * Alkanol family * e.g. Methanol, $CH_3OH$ * **Carbonyl group** - chrgles are diwings on the terminds (enol of a carleon Chain * Aldehyde Family \ * $H-C=O$ * Ketone Family \ * $R-C=O - R$ * **Carboxyl group** - polar tendencies, H-branding, possible for the 's atoms to dissociate due to electrons quing chars e away from thom (Electronegativity diff.) * Carboxylic acids family \ * $R-C=O - OH$ * **Amino group** - important in proteins, H-banding * $H-N-H$ * **Sulfhydryl group** - Helps Howtine wtiate structures of proteins * Thiel family * $- S-H$ * **Phosphate group** - * very polar regions due to $O$ & H-bonding, Found in ATP & BHA * Phosphates family * $O=P - (OH)_3$ * **Ether linkage - forms from condensation** * Ester Linkage- forms from the condenselion of an alcohol * of tum authors, comb button by adding Condensation Reactions & Hydrolysls- water plays a pivotal role in condensation sonations and hydrolysis Condensation Reactions - The subunits merge together into one buge mascule by removing by HO -One large molecule can be broken into two sabuni 13 by adding HO Carbohydrates Carbohydrates- are Sugars Carbohydrates- Contains carbon, hydrogen and oxygen - The ratio is 1:2:1(1:2:1) Glucose- Basic Sugar made by plants during photosynthesis / primary snergy source in cellular respication - A simple Sugar, or monosaccharide Most other complex Sugars are made of gluwose chains Complex Sugars must be broken down back into glucose before entering the small intestine There are two types of glucose : aleha lasland Beta (Biwith the OH being off has the o = A monosaccharide carb round in fruits and honey = Fructose CHO has the Some formula As glucose, but dirl structure can Isumer - Galactose-The ideatifying molecule between human blood types A and B only differ by blood type a dive to one monosaccharice - Canteins N-aretugalutrans, and Sconkan, -Surnse-Adiccharide formed by glucose & Frictose -Sugar hand sold instores made to plants for transport in pholem ester Diagram representing condensation reaction leading to anhydride, ether and phosphate ester linkage ### Condensation (making disaccharides) * 2 monosaccharides form a synyle disaccharide, connaled by condensatim reallin (romove of water) * The joining or linking of the two molecules * e.g. of disaccharides: maltare lactase & Sucrose * #carbons are displayed *Lactose:* $$Glucose + Galactose \xrightarrow[remove H_2O]{condensate}$$ *Sucrose:* $$Glucose + Frutose \xrightarrow[remove H_2O]{condensate}$$ ### Polymers * many monosaccharide carbs Linked in a long change known as polysaccharides *in plants and in plants: - Very common - is a polysaccharide made by many chains aligh - Starthes donit dissolve in HO and plants use these long chubs for Starcy -Forms stuch chains: one alpha is an Straight Chain of a bonded gluwose with 1, b bonded gruase, casing it creates benders this is better because these bondros leaves more "hells (Glagen cond stock that guase at Shared in the liver) ### Hydrolysis * Reverse reaction of condensation (water's and ded) * Mese being added branches glycosidic link and bynd's -cawasenpály saccharise Celulose plants build Skelton celutose These plants is one * Besigama matte straight chor * The first chain has and bottom and H-bon's -celd we the plant, peraving