Learn: 1-5 BIOA

Four classes of biological macromolecules

Carbohydrates, lipids, nucleic acids, and proteins.

Nucleic acid monomers

Nucleotides, consisting of a nitrogenous base, a pentose sugar, and a phosphate group.

DNA vs RNA nitrogenous bases

DNA uses A, T, C, and G; RNA uses A, U, C, and G.

Pentose sugars in nucleic acids

DNA contains deoxyribose; RNA contains ribose.

Phosphodiester bonds

Covalent bonds connecting nucleotides to form the sugar-phosphate backbone.

Nucleic acid directionality

Chains run in a 5' to 3' direction based on the carbon atoms of the pentose sugar.

Complementary base pairing in DNA

Adenine (A) binds thymine (T) with 2 hydrogen bonds; guanine (G) binds cytosine (C) with 3.

DNA secondary structure

Antiparallel strands forming an alpha-helical structure held together by hydrogen bonds.

Polypeptide vs Protein

A peptide has 2-50 amino acids; a protein consists of one or more polypeptides with >50 total amino acids.

Peptide bond

A covalent bond formed between the amino and carboxyl groups of adjacent amino acids.

Amino acid R groups

Unique side chains grouped into non-polar, polar, and electrically charged (acidic/basic) categories.

Primary protein structure

The unfolded, linear sequence of amino acids with an N-terminus and a C-terminus.

Secondary protein structure

Alpha helices and beta-pleated sheets formed by hydrogen bonds along the polypeptide backbone.

Tertiary protein structure

A functional 3-D structure formed by interactions between amino acid R groups, including disulfide bridges.

Quaternary protein structure

The association of two or more polypeptide chains into a single functional protein.

Protein denaturation

Disruption of protein structure by heat or pH, breaking non-covalent bonds while leaving disulfide bridges intact.

Chaperone proteins

Proteins that assist in the proper and timely folding of other proteins.

Beta-amyloid misfolding

Protein misfolding caused by genetic and environmental factors, linked to diseases like Alzheimer's.

GC-rich DNA thermal stability

G-C base pairs form three hydrogen bonds, making GC-rich DNA more thermally stable.

Finding DNA complements

Write the base-by-base complement, then reverse it to find the antiparallel 5' to 3' strand.

Effect of amino acid swaps on folding

Replacing a small non-polar R group with a bulky charged R group severely disrupts protein folding.

Sickle cell disease mechanism

A single amino acid substitution of glutamic acid to valine changes hemoglobin folding and function.

L to D amino acid isomerization

L to D amino acid isomerization disrupts normal protein structure in chronic kidney disease.

Tau protein in Alzheimer's

Cis versus trans conformations of the tau protein alter its aggregation behavior.

Macromolecules

Large polymers composed of repeating subunits called monomers.

Monomers

Repeating subunits that serve as the building blocks of polymers.

Dehydration Reaction

A chemical reaction where two monomers bond together with the loss of a water molecule (H2O).

Hydrolysis

A chemical reaction where a polymer breaks apart through the addition of water (H2O) and enzymes.

Four Classes of Macromolecules

Carbohydrates, lipids, nucleic acids, and proteins.

Monosaccharides

Carbohydrate monomers, also known as simple sugars, such as glucose.

Polysaccharides

Carbohydrate polymers consisting of multiple monosaccharides linked by glycosidic bonds.

Glycosidic Linkage

A specific covalent bond joining two monosaccharides together.

Starch

A polysaccharide used by plants for energy storage.

Glycogen

A polysaccharide used by animals for energy storage.

Cellulose

A polysaccharide that provides structural support in plant cell walls.

Chitin

A polysaccharide used for structural support in insect exoskeletons.

Lipids

A diverse group of hydrophobic molecules mainly consisting of hydrocarbons.

Triglyceride

A fat molecule constructed from glycerol and three fatty acid tails joined by ester linkages.

Saturated Fats

Fats with no double bonds in their tails, having a straight 'no kink' structure and solid at room temperature.

Cis-Unsaturated Fats

Fats with double bonds causing a 'kink' in their tails, typically liquid at room temperature.

Phospholipids

Lipids with two hydrophobic fatty acid tails and a hydrophilic phosphate head, forming cell membranes.

Steroids

Lipids characterized by a carbon skeleton consisting of four fused rings, such as cholesterol.

Aldose vs. Ketose

Aldose has a carbonyl group at the end, while ketose has it in the middle.

Sugar Ring Form

Sugars mostly exist as rings in water because the ring form is more stable in aqueous environments.

Sucrose Formation

Formed when glucose and fructose join via a dehydration reaction creating a glycosidic linkage.

Glycogen and Diabetes

Glycogen releases glucose via hydrolysis; insulin suppresses this breakdown, and failure of this signal in diabetes keeps blood glucose high.

Trans Fats

Unsaturated fats with a double bond but no kink, allowing them to pack tightly and behave like saturated fats.

Phospholipid Bilayer Structure

Hydrophilic heads face outward toward water, while hydrophobic tails cluster in the interior.

Cholesterol Functions

Made in the liver, transported as LDL/HDL, serving as a membrane component and hormone precursor.

Carbon valence electrons

4 valence electrons allowing up to 4 covalent bonds.

Carbon bonding partners

Hydrogen, oxygen, and nitrogen.

Hydrocarbons

Organic molecules consisting of only carbon and hydrogen.

Isomers

Compounds with the same molecular formula but different structures.

Three main forms of isomers

Structural isomers, cis-trans isomers, and enantiomers.

Enantiomers

Isomers that are mirror images of each other.

Functional groups

Chemical groups that give organic molecules unique properties.

ATP function

Powers cellular processes and contains high-energy phosphate groups.

Four ways carbon skeletons vary

Length, branching, double bond position, and presence of rings.

Structural isomers

Isomers with atoms connected in a different sequence.

Cis-trans isomers

Isomers with the same bonds but different spatial arrangement around a rigid double bond.

Chiral carbon

A carbon atom attached to four different groups, required for enantiomers.

Biological importance of isomers

Biology is exquisitely sensitive to 3D shape; different isomers can have drastically different biological effects.

Carboxyl group (-COOH)

Polar, acidic group that donates H⁺; found in fatty acids and amino acids.

Amino group (-NH₂)

Polar, basic group that accepts H⁺; found in amino acids.

Phosphate group (-PO₄)

Polar, acidic group that donates up to 2 H⁺; backbone of DNA, RNA, and ATP.

Methyl group (-CH₃)

Nonpolar, hydrophobic group involved in gene regulation and modifying reactivity.

Four ways carbon skeletons vary

Length, branching, double bond position, and presence of rings.

Structural isomers

Isomers with the same molecular formula but atoms connected in different ways.

Cis-trans isomers

Isomers with the same bonds but different spatial arrangements around a rigid double bond.

Enantiomers

Isomers that are mirror images, requiring a carbon with 4 different attached groups.

Carboxyl group (-COOH)

A polar, acidic functional group that donates H+ ions.

Amino group (-NH2)

A polar, basic functional group that accepts H+ ions.

Phosphate group (-PO4)

A polar, acidic functional group that donates up to 2 H+ ions, found in ATP and nucleic acids.

Water molecule shape

Bent and polar, with oxygen at delta- and hydrogens at delta+.

Hydrogen bonds per water molecule

Up to four bonds with neighboring molecules.

Cohesion

Water molecules hydrogen bonding to each other.

Adhesion

Water hydrogen bonding to a different surface.

Water's high specific heat

Added heat first breaks hydrogen bonds rather than speeding molecules.

Effect of salt on water's specific heat

Decreases it by disrupting water-water hydrogen bonds.

Ice density vs liquid water

Ice is less dense due to a rigid hexagonal lattice.

Water hydration shell

Water molecules surrounding dissolved ions using polarity.

Hydrophilic

Polar or charged substances that love water and form hydrogen bonds.

Hydrophobic

Nonpolar substances that fear water and do not form hydrogen bonds.

Amphipathic

Molecules having both hydrophilic and hydrophobic regions, like phospholipids.

Water self-ionization equation

2H₂O ⇌ H₃O⁺ + OH⁻.

Acid

A substance that donates protons or H⁺ ions.

Base

A substance that accepts protons or H⁺ ions.

pH formula

Negative logarithm of hydrogen ion concentration (-log[H⁺]).

Buffer function

Keeps pH stable by absorbing or releasing excess H⁺ ions.

Heat of vaporization

The heat a liquid must absorb for 1g to be converted to gas.

Evaporative cooling

The process where the remaining surface of a liquid cools down as molecules evaporate.

Electronegativity in water

Oxygen (3.44) pulls shared electrons away from hydrogen (2.20) due to its higher electronegativity.

Strong acids and bases

Substances that completely lose or accept all H⁺ ions in water.

Carbonic acid buffer system

Consists of H₂CO₃ as a weak acid and HCO₃⁻ as a weak base to regulate pH in biological systems.

Matter

Anything with mass that takes up space.

CHONPS elements

Carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur (~96% of body mass).

Trace elements

Elements needed in tiny amounts, such as iron in hemoglobin.

Atomic number

The number of protons in an atom's nucleus.

Mass number

The total number of protons and neutrons in an atom.

Isotopes

Forms of an element with the same protons but different neutron counts.