Cell Chemistry

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Element

composed of a single type of atom

Atomic number

number of protons in the nucleus and determines the element

Atomic mass

sum of masses of protons, neutrons, and electrons

Electronegativity

attraction of atom for electrons

Intramolecular bonds

hold atoms within a molecule together; ionic, covalent, hydrogen, hydrophobic interactions

Intermolecular bonds

form between two different molecules; hydrogen bonds, hydrophobic interactions, electrostatic forces, van der waals forces

ionic bonds

forms between oppositely charged ions where one atom takes away an electron from another

covalent bond

strong bond between where electrons are shared between atoms to fill valence shell

ionic

hydrophilic

polar

hydrophilic

nonpolar

hydrophobic

amphipathic

part hydrophilic and part hydrophobic

Hydrogen bond

“weak” bond due to electrostatic interactions between hydrogen atoms (+) and more electronegative atoms

Hydrophobic interactions

weak bonds occuring when nonpolar molecules associate tightly together in a polar solvent

van der waals forces

weak attractive forces that occur due to temporary polarities in atoms and molecules

Hydrocarbons

molecules of carbon and hydrogen that are the backbones of all biomolecules

functional groups

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

monomers

small molecules that are the building blocks of larger molecules

macromolecules

large molecules

polymers

larger molecules composed of covalently bonded similar or identical monomers

water

major consitituent of all microbial cells, polar molecule, can form H-bonds, good solvent for polar and ionic molecules, high specific heat, cohesion and adhesion, participates in many chemical reactions

salts

ionic compounds consisting of a cation and an anion held together by an ionic bond, often dissociate in water; cations and anions are electrolytes that create electrical differences between inside and outside of cell, transfer electrons from one location to another, form important components of many enzymes

acids

H+ donors

Bases

H+ acceptors

Buffers

compounds that resist changes in pH found in all cells

Lipids

non polar compounds, hydrophobic, play crucial roles in most membranes and as energy storage molecules

Carbohydrates

polymers of monosaccharide units bonded together by glycosidic bonds that play important roles in cell walls and as energy storage molecules

Proteins

polymers of amino acids bonded by peptide bonds that are the most abundant macromolecules in cells, found throughout the cell, and have important structural and enzymatic roles

nucleic acids

polymers of nucleotides that can be RNA or DNA; amount of RNA>amount of DNA

Carbohydrate monomers

organic compounds that contain carbon, hydrogen, and oxygen at a 1:2:1 ratio; polar and hydrophilic

Pentoses

C5 sugars; structural backbones of nucleic acids

Hexoses

C6 sugars; monomeric constituents of cell wall polymers and energy reserves

Carbohydrate monomer functions

energy storage; building blocks for polysaccharides and nucleotides; break down sugars for energy to make ATP

Modified monosaccharides—derivatives

when other chemical species replace one or more of the hydroxyl groups on the sugar, derivatives are formed

Glycosidic bonds

covalent bonds linking adjacent sugars together

alpha glycosidic bond

occurs on the same side of the plane

beta glycosidic bond

crosses the plane

Starch

polysaccharide composed of glucose monomers joined to each other by alpha glycosidic bonds (tend to be hydrophobic); function is energy storage

structural polysaccharide

polysaccharid composed of glucose monomers joined to each other by beta glycosidic bonds; function is strength of cell walls

glycoproteins

polysaccharide + protein; includes eukaryotic cell-surface receptor molecules; typically reside on external surfaces of the membrane

glycolipids

polysaccharides + lipids; important in cell walls of gram-negative bacteria

triglycerides

simple fats; composed of three fatty acids bonded to the 3 carbon alcohol, glycerol; function is for energy storage

ester bonds

bond between glycerol and fatty acids

saturated fatty acids

no double bonds between Cs; straight, linear molecule

unsaturated fatty acids

one or more double bonds between C’s; bent or kinked molecule

phospholipids

complex lipids containing 2 fatty acids, glycerol, a phosphate group and something attached to phosphate; play a major structural role in cytoplasmic membranes; amphipathic

sterol

strucutral lipid found in all eukaryotes and very few prokaryotes

hopanoid

structural lipid found in many prokaryotes, but not in any eukaryotes

DNA (deoxyribonucleic acid)

polymer of deoxribonucleotides; genertic material in all cells and some viruses

RNA (ribonucleic acid)

polymer of ribonucleotides; plays role in protein synthesis in all cells; genetic material of some viruses

nucleotide composition

pentose (RNA or DNA), nitrogen base, phosphates

nucleotide

nitrogen base attached to C5 sugar by N-Glycosidic linkage and bonded to a phosphate

Nucleotide functions

major components of nucleic acid, key forms of energy (e.g. ATP), carriers of sugars in biosynthesis of polysaccharids, regulatory molecules for certain enzymes or metabolic events

Purine bases

adenine and guanine; contain two fused heterocyclic rings

Pyrimidine bases

thymine, cytosine, and uracil; contain a single six-membered heterocyclic ring

Phosphate ester

bonds phosphate to sugar in ATP

Phosphodiester bond

covalent bond that connects two adjacent nucleotides on the same strand

Primary structure

sequence of nucleotides in DNA or RNA molecule

Enzymes

catalytic proteins; cataysts for chemical reactions

Strucutral proteins

integral parts of cellular structures (such as eukaryotic chromosomes)

amino acids

monomers; most consist of C,H, O, N; 2 of 22 contain sulfur, 1 contains selenium; all contain carboxylic acid group (-COOH) and amino group (-NH2)

peptide bond

bond that holds adjacent amino acid monomers together

Ionizable side chains

hydrophilic

Nonionizable polar side chains

hydrophilic

Nonpolar side chains

hydrophobic

Isomers

related, but nonidentical molecules

optical isomers

enantiomers (sterioisomers or mirror image isomer); have same chemical properties but often have different physical properties

racemases

enzymes capable of interconverting specific enatiomers

polypeptide

many amino acids bonded by peptide bonds; each has an amino end and carboxyl end and can be a whole protein or subunit of a larger protein

primary structure (proteins)

linear array of amino acids in a polypeptide; determined by genes, held together by peptide bonds

secondary structure

localized folds or twists in parts of polypeptide that form a more stable structure; determined by primary structure, held together by hydrogen bonding between amino group Hydrogen and carboxyl Oxygen

Tertiary structure

overall, 3 dimensional shape of a polypeptide that forms exposed regions or grooves in molecule that are important for binding to other molecules; held together by hydrogen bonds, electrostatic interactions, hydrophobic interactions, and disulfide bonds

disulfide bonds

covalent bonds between -SH groups from two different amino acids

quaternary structure

overall arrangement of polypeptides in a protein; only found in proteins composed of two or more polypeptides

subunit

each polypeptide in the protein, held together by either/both covalent and noncovalent linkages

Denaturation

unfolding of polypeptide chains due to breaking of specific bonds as a result of extremes of pH, high temperatures, or certain chemicals which causes loss of biological function