Chem basics and Biomolecules

Covalent bonds

two atoms share one (or many) electrons

Oxygen electronegativity

3.5

Nitrogen electronegativity

3.0

Sulfur and Carbon electronegativity

2.5

Phosphorus and Hydrogen electronegativity

2.1

Non-polar covalent bonds

atoms with similar electronegativity, electrons are equidistant

polar covalent bond

dissimilar electronegativity between atoms, electrons are closer to the atom with higher electronegativity

Potential energy in covalent bonds

PE is greater in bonds with w/ equal electronegativity (polar) than bonds w/ unequal electronegativity (non-polar)

Build up of the cell system

electrons—> atoms —> molecules —> macromolecules —> organelles —> cell!

Structural isomer

same chemical formula, differs in structure (ex: branch point)

Cis-trans isomers

same formula, different geometric (3-D) structure due to double bonds restricting rotation

enantiomers

same formula, inverted/right and left hand images of each other

Hydroxyl group

—OH, hydrophilic (hydrogen bonds w/ water) alcohols

Carboxyl group

hydrophilic acids, can donate H+ bc O—H is polar

Amino group

—NH2, hydrophilic amines, act as base and can pick up H+,

Phosphate group

phosphate, polar and hydrophilic

Polysaccharides

Sugars

Lipids

Glycerol and fatty acids

Amino acids

proteins

Nucleic acids

sugars and nucleotides

Carbohydrates functions

fuels (source of energy, breaking down sugar, glucose hydrolysis), storing energy (ex: glycogen, starch), structure (maintain integrity of cells, ex: cellulose)

Triose sugar

Pentose sugar

Hexose sugar

Aldose vs. ketose sugar

C-O group (carbonyl) location

Glycosidic linkage

Bond connecting monosaccharides, caused by dehydration reaction connecting C 1-4 (maltose) or C 1-2 (sucrose)

1-4 linkage orientations

alpha consistent orientation, beta alternating orientation

Cellulose traits

beta glucose, 1-4, No branching

Starch- amylose

alpha glucose, 1-4, no branching

Starch- amylopectin

alpha glucose, 1-4 and 1-6, branching ~ 20 units

Glycogen

animals, alpha glucose, 1-4 and 1-6, branching ~ 10 units

Lipid functions

strongly hydrophobic bc of lots of non-polar C-H bonds, fuel (break down lipids slowly), storage (store in adipocytes/fat), some support structure of cell membranes

Triglyceride structure

glycerol and fatty acids, ester linkages bond fatty acids to glycerol (3 carbon alcohol)

Phospholipid structure

2 fatty acids bonded to a glycerol bonded to a phosphate and functional group (hydrophillic head, hydrophobic tail)

Steroid structure

Generally a 4 ring hydrophobic structure, hydrophilic hydroxyl left side, functional group right side

Sex hormones

derived from cholesterol

Peptide bond

connects amino acids into a polypeptide chain with a dehydration reaction

polypeptide and proteins

made of amino acid/peptide chains

amino acid

composed of an amino group (NH2), carboxyl group (COOH), variable side chain (“R”), a hydrogen, all connected to a central carbon

Nonpolar hydrophobic side chains

-CH bonds

Polar hydrophillic side chains

C-O, C-S, C-N

Electrically charged side chains

negative= acidic, positive=basic

polysaccharides vs proteins

glycotic linkages vs. peptide bonds (w/ dehydration reactions)

Primary structure

amino acid sequence (peptide bonds), hydrophobic interactions

secondary structure

hydrogen bonds, alpha helices and pleated sheets

tertiary structure

all bonds (ionic, hydrogen, covalent disulfide), overall 3-D shape

quaternary structure

all bonds (ionic, hydrogen, covalent disulfide), connection of multiple subunits/multiple peptide chain

glycoprotein

macromolecule linking a protein and a small polysaccharide

nucleic acid functions

forms basis of inheritance/instructions to make proteins

nucleic acid composition

nucleotides—> polynucleotides/nucleic acids linked by phosphate group and pentose sugar (ribose or deoxyribose)

nucleotides

include phosphate group, pentose sugar, and nitrogenous base

pyrimidines

nitrogenous bases with 1 ring, cytosine, thymine, and uracil

purines

nitrogenous bases with 2 rings, adenine and guanine

ribose sugar structure

pentose with -OH at carbon 2

deoxyribose sugar structure

pentose with -H at carbon 2 (more stable)

central dogma 😛

DNA→RNA→Protein, DNA→mRNA (leaves nucleus)→ribsome translates into protein in cytoplasm