Chapter 2: Atoms and Stuff But I'm Making this From Scratch

What elements are more than 90% of our bodies composed of?

Carbon, oxygen, nitrogen, and hydrogen

Inorganic compounds

water, minerals, phosphates, electrolytes

They lack a carbon to hydrogen bond, or they don’t contain carbon

Organic compounds

carbs, lipids, proteins, vitamins..

A covalently bonded compound that contains carbon, excluding carbonates and oxides

Involves carbon to hydrogen bonds

Element

defined by the atomic number

Atomic number

number of protons in the nucleus

Planetary model of atom

Electrons move around the nucleus in fixed cylindrical orbits- orbits are discrete

also called the bohr/shell model

Atomic Mass

the number of protons and neutrons in the nucleus

it’s the weighted average of all the isotopes in the element, so the atomic mass takes into account the different masses of the isotopes 

Isotopes

same element and same number of protons, but different number of neutrons in the nucleus,

Radioisotope

isotope with a radioactive unstable nuclei, with excess energy, that is released as an alpha particle, beta particle, gamma radiation or give an electron as it decays

Electron energy level

a location of electrons surrounding the nucleus in the atom

the shell at which the atom exists discretely- can’t exist between shells

Electron Shells`

an energy level of electrons at a characteristic average distance from the nucleus of an atom

First electron shell holds 2 electron, 2nd and 3rd shell hold 8, and 4th shell holds 18

Think of orbitals and how many each hold

Electron cloud

the cloud around which an electron can exist

Ionic bonds

When an atom gains or loses electrons, they form ions, becoming charged, and can be a positive cation or negative anion

Transfer of atoms 

Covalent Bonds

atoms bonded together by sharing electrons in their outer valence shells

Why are some elements reactive?

Reactivity is based on the electrons in the outermost energy shells, or valence electron

Elements that are closer to having a full valence shell are more reactive

Why are noble gases unreactive

they are unreactive because their outermost valence shell is unreactive with a full octet

Is CHON reactive?

Yes, as they have almost filled valence shells

How do ionic bonds form?

one element donates electron, other accepts it, they form ions, one positive, cation, and one negative, anion

the positive and negative charges attract, and this electrostatic attraction, or electrostatic forces is the ionic bond

What shape do ionic compounds typically take?

a crystal lattice, like with sodium chloride

Formation of a covalent bond

the proton of each atom attracts the electron of the other atom

the point at which attraction is the highest is the point when the covalent bond forms

the shells merge, and electrons are shared

Structural formula

displays atoms in molecule in the order they’re bonded

Molecular formula

shows the number and type of atoms of each element, but not how they are bonded

Heterogenous

composed of different kinds, diverse

Homogenous

of the same kind

Concentration

A measurement of how much solute exists within a certain volume of solvent

Sol-gel transformation

Reversible change of a colloid from a fluid (sol) to a more solid (gel) state.

Molecule

two or more atoms, usually of the same element, that are covalently bonded, so joined by strong bonds

Compound

2 or more atoms of different elements joined by strong or weak bonds

Molecular weight

the sum of the atomic weights of all the atoms in a molecule

eg. molecular weight of CO2 is 44g/mol

Chemical bonds

attraction between atoms from sharing valence electrons and forming covalent bonds, or the presence of opposite charges on an atoms, such as in ions, that have electrostatic attraction, or ionic bonds. The bonded atoms gain complete outer electron shells

chemical bonds can also be the intermolecular forces that exist between the polar molecules

Valence shell

The outermost energy shell of an atom, containing the valence electrons involved in the chemical reactions of that atom

the number of valence shell electrons determine the atom’s chemical properties

Octet rule/rule of eight

atoms react by gaining or losing electrons so as to acquire the stable electron structure of a noble gas, usually eight valence electrons

Polar molecules

caused by atoms of an element being more electronegative than others, so the molecule has an unequal sharing of electrons, causing the molecule to have a positive end and negative end, or dipoles

Non-polar molecules

atoms of an element have no difference, or very little difference in electronegativity, so the electrons are equally shared in molecule

No dipoles formed

Unstable free radicals

disrupt nearby molecules, leading to loss of function and cellular damage

free radicals are atoms with unpaired electrons

antioxidants are produced to counteract these

Electronegativity

the measure of an atom’s ability to attract a shared pair of electrons in a covalent bond

Electropositive

When an atom is not at all electronegative. Loses electrons rather than gaining them

Electropositive elements are usually group 1 or 2, and at the bottom, as easily lose valence shell electrons, as they only have one or two valence shell electrons

Basically, want to give away electrons

Dipole

a molecule that has two poles, or regions, with opposite charges

occurs in polar molecules, when one atom is more electronegative than the other

Hydrogen Bond

A type of weak chemical bond formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule.

Occurs when hydrogen is covalently bonded to a very electronegative element like oxygen, nitrogen, and fluorine

Avogadros number

6.02 × 10²3

Hydrogen bonding in water

water is a polar covalent molecule, has a negative dipole, oxygen, and positive dipole, hydrogen. The negative and positive dipoles are attracted to each other, forming hydrogen bonds

What does hydrogen bonding in water allow?

surface tension between water molecules

Acid and base definition

bases accept H+ ions, acids donate H+ ions

Normal pH range of human blood

7.35-7.45

What is an electrolyte?

a substances separates into cations and anions when dissolved in a polar substance, creating an electrically conducting solution

Can hydrogen bonds form between solutes and water?

Yes, if the solute is hydrophilic, or polar or charged, and form hydration spheres around the solute

Ionic compounds in a solution

ionic compounds dissolve into ions in a solution, or dissociate in water

Polar water molecules break ionic bonds 

Each ion is surrounded by water molecules, forming a hydration sphere

Glucose in a solution

glucose is hydrophilic, and is a polar covalent molecule, so has polar bonds, and water forms hydration sphere around glucose, dissolving it

glucose doesn’t dissociate in water, not an electrolyte

Solute

substance dissolved in a solution

Solvent

Substance that dissolves solute

Acids

dissociate H+ ions in water

Base 

substance that dissociates into OH- ions

Salts

dissociate into cations and anions

Mixtures

a combination of two or more substances that aren’t chemically combined

mixtures can be suspensions, solutions, or colloids

Solution

solute suspended in solvent, transparent, doesn’t settle out

Colloid

suspended large molecules that scatter light, and don’t settle out

eg. milk, because some proteins in milk scatter light

Suspension

settles out, large particles eventually settle out

Characteristics of water

Solvent, lubricant, cohesion, high heat capacity, high latent heat of vaporization, and required for catabolism

Lubricant

Foods, internal organs slippery

Cohesion

surface tension due to H bonds

High heat capacity

absorbs lots of heat with little change in temperature

Latent heat in vaporization

takes a lot of energy to vaporize, or change from liquid to gas

Required for catabolism

chemically breaks down molecules, often with hydrolysis reactions

What is ATP?

usable energy for cells, cells use energy from ATP to do biological work

captures energy from ingested molecules, and stores energy in phosphate bond of ATP

How do cells use ATP for energy?

use ATP by removing one of the phosphates, creating ADP, releasing energy, exergonic, used for physiological functions

Formation of ATP?

Formation of ATP from ADP requires energy, reverse releases energy

How many elements in ATP?

CHON and phosphate

Nucleobase and nucleoside difference

nucleobase is just the nitrogenous base in ATP, nucleoside is the nitrogenous base and the ribose sugar in ATP, adenosine 

The nitrogenous base = adenine

nitrogenous base and ribose sugar of nucleotide = adenosine

Nucleotides (relating to ATP)

Adenosine monophosphate AMP, diphosphate ADP, and triphosphate ATP are all nucleotides

Metabolism

describes all the chemical/energy transformations in the body, sum of all the enzyme catalyzed reactions in the body

Catabolism and anabolism

catabolism is the chemical breakdown of substances into smaller one for usable energy 

anabolism if the synthesis of complex substances, uses energy

Catabolism and anabolism energy use

catabolism is exergonic

anabolism is endergonic

Synthesis reactions

small molecules bond together using anabolism, usually endergonic

Decomposition reactions

breaking bonds, catabolism, usually exergonic

Exchange reactions

swaps

Reversible reactions

hydrolysis and dehydration

Types of chemical reactions

synthesis, decomposition, exchange, reversible

Redox

oxidation is loss of electrons

Reduction is gaining electrons

Nutrients

substance from food used by the body for life functions

nutrients provide energy and building blocks for cell components, and other molecules

Classes of nutrients

carbohydrates, lipids (fats), proteins, vitamins, minerals, water

Carbohydrates

sugars/starches, contain fixed proportions of oxygen, carbon, and hydrogen

Hexose (6c) or pentose (5c)

Body’s preferred energy source, like in glycogen/blood sugar, or structural role, like glycoproteins

What are simple sugars called?

monosaccharides

Ways to find carbohydrates in the body

monosaccharides, individual

disaccharides in pairs

polysaccharides in long chains or complex carbohydrates, such as starch

Disaccharide formation

dehydration synthesis forms it, hydrolysis breaks it down back into monosaccharides

Plants

starches, polyglucose of amylopectin and amylose, which is sucrose, glucose/fructose and cellulose fiber

Animals

glycogen, polyglucose, and lactose

How must sugars be absorbed?

must be broken down into monosaccharides to be absorbed

How are sugars stored and what sugar used in body?

glucose mostly used for ATP

carbs stored as glycogen in liver and muscle, and fat, or adipose tissue if not used

What can excess and reduced CHO intake lead too?

excess leads to obesity, and elevated blood lipid level, atherosclerosis

reduced leads to increased protein and fat metabolism, loss of muscle pass, and acidosis

Lipids general classes

hydrophobic/nonpolar

triglycerides, fatty acids, phospholipids, and steroids

Triglycerides

glycerol backbone and 3 fatty acids

glycerol has 3 carbon atoms

fatty acids are long hydrocarbon chains

What is specially found on the end of the FA tail?

carboxylic acid tail, COOH, gives it acid properties

Saturated vs unsaturated

all single bonds in FA means saturated

unsaturated means FA has double bonds, and less hydrogen bond

monounsaturated is one double bond

polyunsaturated is more than one double bond

States of unsat vs sat fats

unsaturated fats liquids are room temp, plant sources

saturated fats solid at room temperature, plant sources

hydrogenated oils

chemically altered oils, double bonds made into single bond with hydrogen addition

Makes unsaturated fats, saturated and solid at room temp

Recommended sources of fats

very little saturated fats, unsaturated fats better, and essential fatty acids are ones we must get from diet

we can’t synthesis the FA of linoleic acid or linolenic acid

Relationship between FA and atherosclerosis

increases saturated FA intake, increases atherosclerosis, or heart attacks

What do hydrogenated oils increase?

hydrogenated oils increase low density lipoproteins, LDL, and decrease high density lipoproteins, which help lead to heart disease and cancer

Where are triglycerides deposited?

stored in the form of fat, deposited in subcutaneous tissue, or other fat deposits, like adipose tissue

What is obesity?

a common side effect of excess triglyceride storage