human biology

element

fundamental (pure) form of matter that cannot be broken down to a simpler form (iron, oxygen, hydrogen)

atom

elements are made up of particles, called atoms, the smallest unit of any element that still retains the physical and chemical properties of that element

protons - neutrons - electrons

amount of protons is often also the amount of neutrons (exception = hydrogen, nucleus has only 1 proton, no neutons)

amount of protons = atomic number

neutrons + protones = atomic mass (close to)

electrons have a negligible mass

electrons = protons = electrically neutral atom

shells (chemistry)

spherical clouds which inhabit electrons, first shell, closest to the nucleus = 2 electrons, 2nd has place for 8, 3rd has place for 8

isotopes

number of neutrons in an atom can vary, a few or more neutrons than usual = isotope. (vb: carbon-12 is standard, 2 more electrons = carbon-14) indicated in superscript before the symbol of the element

radioisotopes = unstable isotope, they tend to give off energy ( in the form of radiation) and particles until they reach a more stable state/ dangerous for living organisms (the energy can damage tissue)

decay rate of some isotopes is known, this is used to determine when rocks and fossils were formed (14C is often used for this)

in medicine isotopes are used to “tag“ molecules so that radiation sensors can track their location in the body. (locating damaged tissue in a patient’s heart after a heart attack).

radioisotopes are also used to kill certain kinds of cancer

certain isotopes that emit energy for a long period of time are used as a power supply for pacemakers.

free radical

an atom/molecule with 1+ unpaired electrons (but is still indipendent)

highly reactive, will take electrons from other molecules or will give electrons to other molecules

small amounts of free radicals are made as a toxic waste product of metabolism

molecule

stable association between 2 or more atoms (molecule of water is 2 atoms hydrogen and 1 atom oxygen)(hydrogen gas molecule = 2 atoms hydrogen)

energy (2 forms)

energy is the capacity to work/cause change in matter

potential energy = stored (dam holds water) (stored in bonds that hold atoms

kinetic energy = energy in motion (dam breaks)

chemical bonds

atoms bound together by attractive forces

(covalent, ionic and hydrogen)

covalent bond

strong, sharing electrons to having a maximally filled outermost shell of electrons (h2o, bond between an h and the o)

ionic bond

moderate, bond between 2 oppositely charged ions (atoms or molecules that were formed by the permanent transfer of 1 or more electrons (nacl)

hydrogen bond

weak, bond between oppositely charged regions of molecules that contain covalently bonded hydrogen atoms (bonds between molecules of water)

polar molecules

partially charged regions in a molecule (h2o, o=-, h2=+)

solvent

liquid in which other substances dissolve (water is ideal solvent)

solute

dissolved substance in a solvent

hydrophillic

water-loving, polar

hydrophobic

water-fearing, nonpolar/neutral molecules that do not dissolve in water

acid

any molecule that can donate an h+ ion. more acid = acidic solution

base

any molecule that can accept an h+ ion. more base = more alkaline solution

Ph scale

measure of hydrogen ion in a solution. scale form 0 to 14, water = 7, neutral point

acidic = less than 7 Ph, lot of h+

basic/alkaline = more than 7, not a lot of h+

buffer

any substance that tends to minimize the changes in Ph that might otherwise occur when an acid/base is added to a solution.

in biological solutions (urine and blood) buffers are in pairs with opposite effects (vb: bicarbonate, hco3-, can accept an h+. h2co3 can donate an h+ ion to counterbalance if needed)

organic molecules

molecules that contain carbon and other elements held together by covalent bonds

living organisms synthesize 4 classes of organic molecules: carbohydrates, lipids, proteins, nucleic acids.

dehydration synthesis/condensation reaction

multiple simple sugars bound together, h2o is a product that is formed next to a polysachharide

hydrolysis

h2o is used to deconstruct a polysachharide into simple sugars

carbohydrates

used for energy and structural support

backbone of carbon atoms with hydrogen and oxygen attached in the same proportion (2 to 1)

monosaccharide

ribose, deoxyribose, fructose, (5-rings) glucose (6-ring)

oligosachharide

a few monosachharides linked together

sucrose (glucose + fructose, disachharide, table sugar)

lactose (glucose + galactose, most common disachharide in human milk)

some oligosachharides are covalently bound to certain cell-membrane proteins (called glycoproteins). participate in linking adjacent cells together and in cell cell recognition and communication

polysachharide

convenient way for cells to store extra energy by locking it in the bonds of the polysachharide molecule

most important polysachharides in living organisms are long chains of glucose monosachharides. in animals, the storage polysachharide is glycogen. in plants it is starch. starch is broken down to glucose so we humans can use it.

are we not using the glucose on short term? then glucose is used to create glycogen or lipids and stored in our cells for later use.

cellulose is a slightly different form of glucose polysachharide. plants use it for structural support rather than for energy storage. most animals (including humans) can’t break cellulose down to glucose units (which is why we cannot digest wood) wood has a lot of potential energy stored in the chemical bonds, demonstrated by the heat generated by a wood fire.

undigested cellulose in the food we eat contributes to the fiber or roughage in our diet, certain amount of fibers is beneficial because it increases the movement of wastes through the digestive tract (more rapid excretion of wastes decreases the time of exposure to any carcinogens (cancer-causing agents) that may be in the waste material)

lipids

insoluble, do not dissolve in water, 3 calsses, triglycerides, phospholipids, steroids

triglycerides

also called fats or neutral fats

synthesized from a molecule of glycerol and three fatty acids (chains of hydrocarbons (often 16-18 carbons long) that end with a carboxyl group (ho-c=o))

fats vary in the length of their fatty acid tails and the ratio of hydrogen atoms to carbon atoms in the tails

saturated fats = straight tails, no double covalent bonds (solid at room temperature) diet rich in saturated fats contributes to the development of cardiovascular diseases.

unsaturated fats (oils)= no straight tails, some double covalent bounds (liquid at room temperature)

triglycerides are stored in adipose (fat) tissue and are an important source of stored energy in our bodies. most of the energy is located in the bonds between carbon and hydrogen in the fatty acid tails.

phospholipids

modified form of lipid, the primary structural component of cell membranes.

like fats a glycerol head, but only 2 fatty acid tails, replacing the 3rd tail is a phosphate group (po4-) and another group that varies depending on the phospholipid, but usually positively charged, this creates charged groups (polar head and nonpolar tail)

steroids

relatively insoluble in water, which is the reason they are classified as a lipid

3 6-rings and 1 5 ring

cholesterol

high levels of this is associated with cardiovascular diseases, but we d need some cholesterol, it is an essential structural component of animal cell membranes and the source of several important hormones, including the sex hormones estrogen and testosterone. our bodies manufacture cholesterol even though we generally get more than we need from our diet

proteins (polypeptides/proteins)

macromolecules constructed from long strings of single units called amino acids

each amino acid has an amino group (nh3) and a carboxyl group, COH group in the middle and a restgroup labeled R, differences in the charge and structure of the amino acids affect the shape and functions of the proteins constructed from them. our bodies can construct 11 amino acids if necessary, but we generally get enough of most of them ( including the 9 we cannot synthesize) in the food we eat

the weak hydrogen bonds that determine the structure can break easily, so the shape (and function/behaviour) can change when a charged/polar molecule passes by (essential to the function of certain proteins

can also be damaged, sometimes permanently, by high temperature/changes in Ph (denaturation)

most proteins are soluble (dissolve in water), but many many proteins that are part of our cell membranes are either insoluble in water or have water-insoluble regions. water-insolubility allows them to associate with the water-insoluble regions of the phospholipids that comprise most of te cell membrane’s structure

a singe string of 3-100 amino acids = polypeptide

a single string of 100+ amino acids (+ complex structure and function) = protein

some proteins consist of multiple polypeptides linked together

proteins (structure)

primary structure

amino acids in sequence, indicated by a 3-letter code

secundairy structure

how the amino chain is oriented in space

alpha helix: stabilized by hydrogen bonds between amino acids at regular intervals (with itsself)

beta sheet: formed when hydrogen bonds join 2 primary sequences of amino acids side by side (with another string)

in addition to these 2 structures, proteins can coil into an almost infinite variety of seemingly random shapes depending on which amino acids make up the sequence

tertiary structure

proteins acquire their tertiary structure by a folding process that occurs during synthesis or shortly after. Is how the protein twists and folds to form a 3d shape. this 3d shape depends on

1. its sequence of amino acids (locations polar + charged groups determine where the hydrogen bonds form that hold the complete sequence)

2. occasionally a covalent bond called a disulfide (S-S) bond forms between the sulfur molecules of 2 cysteine amino acids

3. proteins tend to fold in a way where neutral amino acids end up more in the interior, whereas polar and charged amino acids are more likely to face the outside (aqueous environment).

quaternary structure

refers to how many poly peptide chains the proteine has and how they associate with eachother

enzymes

proteins that regulate the rates of biochemical reactions within the cell (biological catalyst)

can also change shape, which makes them a good catalyst (change shape when the reactants bind, joining or seperating them before returning to it’s original shape)

some enzymes break molecules apart, some join molecules together

enzymes take 2 or more reactants/substrates and turns them into one or more products

denaturation

permanent disruption of protein structure, leading to a loss of biological function. (egg exposed to high temperatures, soluble proteins in the egg become damaged and clump together as a solid mass, causing the egg to harden

catalyst

speeds up chemical reaction without being altered or consumed by the reaction

nucleic acids

store genetic information (DNA and RNA)

DNA contains instructions for producing RNA

RNA contains instructions for producing proteins

proteins direct most of life’s processes

RNA and DNA consist of smaller molecular subunits called nucleotides

nucleotides

smaller units that make DNA and RNA

consist of

1. 5-carbon sugar (deoxyribose in DNA, ribose in RNA)

2. single/double ringed structure containing nitrogen (base)

3. one or more phosphate groups

8 nucleotides exist, 4 in DNA and 4 in RNA

DNA

4 bases DNA

1. A, adenine

2. T, thymine

3. C, cytosine

4. G, guanine

phosphate and sugar groups link together to form 1 strand, 2 intertwined complementary (A-T, C-G)strands form DNA, held together by weak hydrogen bonds

A-T = 2 hydrogen bonds required

C-G = three hydrogen bonds required

portions of DNA are transcribed into smaller fragments of RNA

RNA

portions of DNA are transcribed into smaller fragments of RNA

RNA is structurally like DNA, with a few exceptions

1. sugar unit in RNA is ribose, not deoxyribose like in DNA

2. U, uracil is substituted for T, thymine

3. RNA is a single strand, complementary to a part of 1 string of dna

4. RNA is shorter, representing only a small segment of DNA that codes for one or more proteins

ATP

nucleotide (Like ATGCU) with an important function, carries energy

identical to Adenine in RNA (with o), except that ATP has 2 additional phosphate groups (Adenosine TriPhosphate)

ATP → ADP + Pi + energy