Microbiology-cell chemistry

chemistry of cells and molecules between them

elements

composed of a single type of atom

atomic number

number of protons in the nucleus

atomic mass/atomic weight

sum of masses of protons, neutrons and electrons

electronegativity

atoms attraction or affinity for electrons

why do bonds form between atoms?

stability

when are atoms most stable?

electrons in the lowest energy level and outermost energy level (valence shell) is filled to its max (either 2 or 8)

to achieve stability, what do atoms do?

gain, lose or share electrons

after atoms form bonds, what are they called?

molecules

what determines the chemical properties of atoms?

electron configuration

chemical bonds

electrostatic forces between positively charged protons of one atom and negatively charged electrons of another atom that hold these atoms together within a molecule or between molecules

intramolecular bonds

hold atoms in the same molecule together

what are some examples of intramolecular bonds?

• ionic bonds

• covalent bonds

• hydrogen bonds

• hydrophobic bonds

intermolecular bonds

form between two different molecules

what are some examples of intermolecular forces?

• hydrogen bonds

• hydrophobic interactions

• electrostatic (ionic forces)

• van der Waals forces

ionic bonds

occur between oppositely charged ions

when do ionic bonds occur?

form between oppositely charged ions

what is it called when ions have a positive charge?

cation

what is it called when ions have a negative charge?

anions

what do ionic bonds usually form?

salts

covalent bonds

strognbondks between where electrons are shared between atoms to fill the valence shell

what are the three types of covalent bonds?

1. single

2. double

3. triple

single bonds

allow rotation to occur

double bonds

do not allow rotation to occur but they do allow bending to occur

triple bonds

do not allow for movement to occur and they are not found in biological systems

electronegativity

refers to the force of attraction of a nucleus on the electrons moving around it or for the electrons in a chemical bonds

non polar

electrons that are equally shared and there is no polarity

• occurs between atoms of similar or identical electronegativity

polar bonds

electrons that are shared unequally between two atoms so there is a positive and a negative pole

• net charge is zero

• not an ion

  • occurs between atoms with different electronegativities

what are ionic bonds mostly composed of and what is their water solubility?

• composed mostly/all ionic bonds

• generally water soluble to the point of saturation

what are non polar bonds composed of and what is their water solubility?

• composed on non polar covalent bonds

• not water soluble

what are amphipathic molecules composed of and what is their water solubility?

• composed of part hydrophilic (ionic or polar) and part hydrophilic (non polar) regions

• they are partially water soluble and partially water insoluble

what are solutions composed of?

solute and solvent

why are hydrogen bonds considered weak?

due to electrostatic interactions between hydrogen atoms (with positive polarity) and more electron attraction (electronegative) atoms (negative polarity)

what type of polarity does hydrogen have and why?

• positive polarity

• due to polar covalent bonds with larger, more elctronegtiave atoms

what important role do hydrogen bonds play?

considerable stability to other molecules

• biological properties of protein solubility and other properties of water

what are hydrophobic interactions?

weak bonds occurring when non polar molecules, or non polar regions of molcules associate tightly together in a polar solvent , disrupting hydrogen bonding among water molecules

• are pushed or squeezed tougher by water molecules to minimize their volume

what important roles do hydrophobic interactions play?

• enzymes binding substrates

• protein conformation

• stabilization of RNA and cell membranes

van der Waals forces

weak attractive forces that occur between atoms

what important roles do van der Waals forces play?

• enzymes binding substrates

• protein-nucleic acid interactions

• membrane fluidity

hydrocarbons

molecules of carbon and hydrogen

• backbones of molecules

functional groups

groups of atoms that when bonded to organic compounds impart unique chemical properties

monomers

small molecules that are the building locks of larger molecules

macromolecules

large molecules

polymers

large molecules composed of covalently bonded similar or identical monomers

what are some inorganic molecules found in all cells?

• water

• salts

• acids

• bases

• buffers

what are some organic molecules found in all cells?

• carbohydrates

• lipids

• polypeptides/proteins

what are the three most abundant molecules in the composition of a prokaryote cell?

• water

• protein

• RNA

salts

ionic compounds consisting of a cation and an anion held together by an ionic bond

what do salts do in water?

dissociate

cations and anions of salts are electrolytes that do what?

create electrical differences inside and outside of cell transfer electrons from one location to another

• they form important components of many enzymes

what kind of molecule is water?

polar

acids

proton (H+) donors and they increase the concentration of H+ ions in a solution

bases

proton acceptors and decrease the concentration of the H+ ions in a solution

buffers

composed that resist changes in pH

• can behave like an acid or a base

• found in all cells

the macromolecules of lipids

• fats

• oils

• sterols

fats, oils and sterols

non polar and hydrophobic

what important role do the macromolecule of lipids play?

• crucial in most membranes

• energy storage molecules

what are the macromolecules of carbohydrates?

• monosaccharides

• polysaccharides

how are are polymers of monosaccharides (carbohydrates) held together?

glycosidic bonds

what important role do the macromolecules of carbohydrates play?

• cell walls

• energy storage molecules

what are the macromolecules of proteins?

polymers of amino acids

what important role do the macromolecules of proteins play?

structural and enzymatic roles

what forms do nucleic acids come in?

DNA and RNA

what are the monomers of carbohydrates?

monosaccharides and disaccharides

• sugars

what are the two most important monosaccharides and disaccharides?

5 carbons (pentose) and 6 carbons (hexose)

pentose

c5 sugar

• structural backbone of nucleic acids

hexose

c6 sugar

• monomeric constituents of cell wall polymers and energy reserves

what are the functions of monomers of carbohydrates?

• energy storage

• building blocks for polysaccharides and nucleotides

what are some examples of pentose?

ribose and deoxyribose

eat are some example of hexose?

glucose and fructose

polysaccharides

carbohydrates that contain many monomeric units (monosaccharides) that are connected by glycosidic bonds

glycosidic bonds

covalent bonds linking adjacent sugar together

orientations of glycosidic bonds

alpha and beta

what are the types of polysaccharides?

starch and functional polysaccharides

starch

polysaccharide composed of glucose monomers joined to each other by alpha glycosidic bonds

• tend to be hydrophobic

structural polysaccharides

polysaccharides composed of glucose monomers and joined to each other by beta glycosidic bonds

• hydrophobic

• structural strength of cell walls

glycoproteins

polysaccharides and proteins together

glycolipids

polysaccharides and lipids together

what is the function of glycoproteins?

eukaryotic cell-surface

• receptor molecules

• typically reside on external surfaces of the membrane

what is the function of glycolipids?

important in cell walls of gram negative bacteria

triglycerides

simple fats composed of 3 fatty acids bonded to the carbon alcohol and glycerol

what is the function of triglycerides?

energy storage

what bonds do triglycerides have and where are they located?

ester bonds between glycerol and fatty acids

what do fatty acids consist of?

carboxyl groups and hydrocarbon chains

saturated fatty acids

no double bonds between carbon chain

• straight and linear molecule

unsaturated fatty acids

have one or more double bonds tween the carbons

• bent or kinked molecule

complex lipids

simple lipids that contain additional elements such as phosphorus, nitrogen, sulfur or small hydrophilic organic compounds

phospholipids

complex lipids that contain two fatty acid, glycerol, and a phosphate group and something attached to the phosphate group

• amphipathic

what is the function of phospholipids?

play a major structural role I cytoplasmic membranes

nucleic acids

polymer of nucleotides

DNA (deoxyribonucleic acid)

polymer of deoxyribonucleotides

• genetic material found in all cells and some viruses

RNA (ribonucleic acid)

polymer of ribonucelotides

• play a role in protein synthesis

• genetic material of some viruses

nucleotides are composed of?

• pentose sugar

• ribose or deoxyribose

• nitrogen base

• phosphates

nucleotides

nitrogenous base attached to pentose sugar by N-glycosidic linkage and bonded to a phosphate

nucleotides

• major components of nucleic acids

• key form of chemical energy (ATP)

• carriers of sugars in biosynthesis of polysaccharides

• regulatory molecules for certain enzymes or metabolic events

what are the two types of nitrogenous bases of nucleic acids?

purine and pyrimidine

purine bases

adenine and guanine

• contain two fused heterocyclic rings

pyrimidine bases

thymine, cytosine and uracil

• contain a six member heterocyclic ring

phosphodiester binds

covalent bonds that connect two adjacent nucleotides on the same strand

DNA

double stranded in cells

• complementary strands are held together by hydrogen bonds

RNA

single stranded

• demonstrates secondary structure

• four classes: m, t, r and small