Water Molecules To Hydrogen Bond example essay topic

Chapters 2 & 3 Study Guide (Chapter 2) Atoms: Consist of Protons (+), Neutrons, and Electrons (-) - Number of Protons = Number of Electrons - Protons + Neutrons = Mass Number - Number of Protons = Atomic Number Isotopes: Same number of protons but different number of neutrons - All isotopes of an element interact with other atoms in the same way Orbitals: - Can house 1 or at most 2 electrons - More electrons (higher the atomic number) = more orbitals - Shell Model: Simple but not quite accurate way of thinking about how electrons are distributed in orbitals in an atoms - You can tell if two atoms will interact by looking at the number of electrons in the outermost shell o Vacancies mean it might give up, gain, or share electrons under suitable conditions. o Inert atoms: atoms that show little tendency to enter into chemical reactions due to the lack to vacancy in their outermost shells o Atoms fill up vacancies in their outer shells by bonding with other atoms (forming molecules) Covalent Bonds: A sharing of paired electrons - Can be single, double or triple bonds - They can be polar or non polar o Non-polar Covalent Bond: participating atoms exert the same pull on the electrons and both share them equally. "Non polar" implies that there is no difference in charge between two ends of the bond (its 2 poles). Example: molecular Hydrogen Its 2 H atoms, each with one proton, attract the shared electrons equally. o Polar Covalent Bond: Atoms of different elements (which have different numbers of protons) do NOT exert the same pull on shared electrons. The more attractive atom ends up with a slight negative charge; the atom is "electronegative" balanced out by the other atom which ends up with a slight positive charge.

Atoms interacting in a polar covalent bond have NO net charge but the charge is distributed evenly between the bond's 2 ends. Hydrogen Bonds: a weak attraction between an electronegative atom and a hydrogen atom taking part in a second Polar Covalent bond. Hydrogen's slight positive charge weakly attracts that atom with the slight negative charge. Ionic Bond: a positive ion and a negative ion stay together because of a mutual attraction of their opposite charges o Life depends on hydrophobic interactions o Membrane organization that separates a cell's watery surroundings with the watery interior A water molecule has no net charge, yet it shows polarity allows water molecules to hydrogen bond with on another and with other polar (hydrophilic) substances. -Water molecules tend to repel nonpolar (hydrophobic) substances An example of a large biological molecule within which hydrogen bonds exist: - 2 DNA chains are held together by hydrogen bonds pH: measurement of the H+ concentration - water molecules break apart into hydrogen ions and hydroxide ions (ionization of water) basis of pH scale Bases: accept H+ when dissolved in water and OH- forms directly or indirectly after they do this - also called "alkaline" fluids - pH above 7 Acids: donate H+ protons to other solutes or to water molecules - Have pH below 7 - Either weak or strong o Weak: are reluctant H+ donors Depending on the pH, they just as easily accept H+ after giving it up, so they alternate between acting as an acid and a base o Strong: totally give up H+ when they dissociate in water Buffer System: a partnership between a weak acid and the base that forms when the acid dissolves in water the two work as a pair to counter slight shifts in pH. - The action of a buffer system cannot make new hydrogen ions or eliminate ones that already are present.

It can only bind or release them - Help in metabolic reactions (Chapter 3) - Only living cells synthesize carbohydrates, lipids, proteins, and nucleic acids molecules characteristics of life (organic compounds) - Organisms consist mainly of oxygen, hydrogen, and carbon much of the oxygen and the hydrogen is in the form of water Carbon atoms are so important because of their versatile bonding capabilities - A chain of carbon atoms bonded together covalently forms a backbone from which other atoms can project Functional Groups: various kinds of atoms or clusters of them covalently bonded to the backbone - The backbone of a protein forms by reactions between amino groups and the carboxyl groups backbone is the start of bonding patterns that produce the proteins 3-D structure How do cells build organic compounds: Using carbon (from carbon dioxide), water, and sunlight (energy source), they photosynthetic cells put together simple sugar molecules as a starting point for assembling other small molecules, especially the fatty acids, amino acids, and nucleotides. - They require more than one energy input o Also require proteins called enzymes which make specific metabolic reactions proceed faster than they would on their own. Different enzymes mediate different kinds of reactions: Functional-Group Transfer: One molecule gives up a functional group, which another molecule accepts Electron Transfer: One of more electrons stripped from one molecule are donated to another molecule Rearrangement: A juggling of internal bonds converts one type of organic compound into another Condensation: Through covalent bonding, two molecules combine to form a larger molecule Cleavage: One molecule splits up into 2 smaller ones Polymer: a large molecule having three to millions of subunits which may or may not be identical - Subunits are called monomers Carbohydrates: The most abundant or all biological molecules which cells use as structural materials and transportable or storage forms of energy - Consist of Carbon, Hydrogen, and Oxygen in a 1: 2: 1 ratio - There are 3 classes of Carbs o Monosaccharides = one monomer of sugar, simplest carb o Oligosaccharides (sucrose) = short chain of 2 or more sugar monomers that are bonded covalently Disaccharides = just 2 sugar units o Polysaccharides = complex carbs, straight or branched chains of many sugar monomers of the same or different types (cellulose, starch) "Saccharide" = sugar Glucose: has 6 carbon atoms in the backbone and is the main source of energy for most organisms - is also a parent molecule of many compounds and a building block for larger carbohydrates Lipids: show little tendency to dissolve in water yet they readily dissolve in nonpolar substances. (greasy or oily to touch) They are mostly hydrocarbon - Fats - Phospholipids - Sterols - Waxes Unsaturated: incorporate one or more double bonds Saturated: contain single bonds only Triglycerides: neutral fats having three fatty acids tails attached to a glycerol head - They are the body's most abundant lipids and its richest energy source Phospholipids: main materials of cell membranes which have 2 layers of lipids Sterols: Lipids that have no fatty acids. All have a backbone of 4 fused together carbon rings - Cholesterol - Is a parent molecule of steroids Proteins: the most diverse biological molecule of the class called enzymes which make metabolic events occur much faster than they otherwise would - Consist of one or more polypeptide chains in which amino acids are strung together Amino Acid: a small organic compound that consists of an amino group, a carboxyl group, a hydrogen atom, and one or more atoms known as its R group. - When a cell synthesizes a protein, amino acids become linked, one after the other, by peptide bonds - When peptide bonds join two amino acids together, it is a Dipeptide - When three or more peptide bonds join amino acids together, it is a polypeptide chain. carbon backbone in for-C Most enzymes are globular proteins (one or more polypeptide chain folded in compact, round shapes) The primary structure gives rise to a proteins shape in 2 ways: - It allows hydrogen bonds to form between different amino acids along the length of a polypeptide chain - It puts R groups into positions that allow them to interact through these interactions the chain is forced to bend and twist Secondary Structure: - in many amino acids hydrogen bonds readily form between every third amino avid which forces the peptide groups to coil helically like a spiral staircase - In other amino acids hydrogen bonds hold 2 amino acids side by side in a sheet like array Third Level of Protein Structure: - polypeptide chains that have a coiled secondary structure undergo more folding the amino acids bend a chain at certain angles and in certain directions to make the chain loop out - Third structure level: Tertiary Structure 4th Level: - Two or more polypeptide chains have become joined together by numerous weak interactions (such as hydrogen bonds) and sometimes by covalent bonds between sulfur atoms and R groups. o Example: Hemoglobin: an oxygen transporting protein that has 4 polypeptide chains globular o Many other proteins having quaternary structure are fibrous Denaturation: Breaking weak bonds of a protein or any other large molecule that disrupts the 3 D shape Nucleotides: small organic compounds with a sugar (ribose or deoxyribose with a 5 carbon ring structure), at least one phosphate group, and a base. - ATP: has three phosphate groups attached to its sugar that can readily be transferred to many other molecules inside the cell central to metabolism - Nucleotides are building blocks for RNA and DNA.