2.3: Carbon

A set of vocabulary-style flashcards covering carbon-related biomolecules, their structures, and key physiological concepts from the notes.

Functional groups

Groups of atoms that confer specific chemical characteristics or functions to hydrocarbon chains or rings.

Isomers

Molecules with the same molecular formula but different arrangements, giving them different properties.

Organic

Compounds containing carbon–hydrogen or carbon–carbon bonds.

Hydrocarbon

A molecule consisting only of hydrogen and carbon.

Aliphatic

Hydrocarbons in chains or rings with all single bonds (saturated) typically; non-aromatic.

Aromatic

Hydrocarbons arranged in rings with alternating double and single bonds.

-ane, -ene, -yne

Suffixes indicating single (alkane), double (alkene), or triple (alkyne) carbon–carbon bonds.

Structural isomers

Isomers with the same atoms but different covalent bond arrangements.

Geometric isomers

Isomers around a carbon–carbon double bond (cis/trans).

Enantiomers

Non-superimposable mirror-image isomers; can affect drug activity.

L & D (enantiomers)

Arbitrary left- and right-handed assignments used to distinguish enantiomers.

Acid (general)

Substance that ionizes to release H+ (proton donor).

Base (general)

Substance that accepts H+ (proton acceptor).

Carbohydrates: 1:2:1 ratio

Empirical ratio of carbon:hydrogen:oxygen (1:2:1) in carbohydrates.

Aldose

Monosaccharide with an aldehyde group at the end of the molecule.

Ketose

Monosaccharide with a ketone group (carbonyl within the molecule).

[number]-oses

Notation indicating the number of carbon atoms in a sugar (e.g., glucose has 6 carbons).

Dehydration synthesis

Removal of a water molecule to form a covalent bond (glycosidic bond) between monomers.

Hydrolysis

Addition of water to break a covalent bond (e.g., glycosidic bond).

Monosaccharides

Simple sugars; can exist as linear chains or cyclic rings (often rings in solution).

Glycosidic bond

Covalent bond formed between two monosaccharides during oligo- or polysaccharide formation.

Alpha vs beta anomer

Configuration of the hydroxyl group at the anomeric carbon (C1) in cyclic sugars; alpha typically has the OH/ H orientation opposite at C1; beta has the same side orientation.

Disaccharides

Two monosaccharides joined by a glycosidic bond (alpha or beta).

Sucrose

Disaccharide composed of fructose + glucose.

Maltose

Disaccharide composed of glucose + glucose.

Polysaccharides

Polymers of many monosaccharides linked by glycosidic bonds.

Amylose

Unbranched component of starch (plant storage polysaccharide).

Amylopectin

Branched component of starch (plant storage polysaccharide) with α-1,6 branches.

Glycogen

Animal storage form of glucose; highly branched.

Cellulose

Structural plant polysaccharide with β-1,4 linkages; linear and tough; not digestible by humans.

Chitin

Structural carbohydrate of exoskeletons; N-acetyl-β-d-glucosamine; found in fungi/insects.

Starch

Plant storage polysaccharide made of amylose and amylopectin with α-1,4 and α-1,6 bonds.

Fibers: insoluble vs soluble

Insoluble fiber (e.g., cellulose) is not readily dissolved; soluble fiber dissolves in water.

Glycosidic bonds (overall)

Covalent bonds linking monosaccharides in carbohydrates.

β-1,4 glycosidic bonds

Bonds in cellulose; lead to linear, rigid chains.

Starch composition

Mixture of amylose (unbranched) and amylopectin (branched) in plants.

Glycolipids and Glycoproteins

Carbohydrate groups attached to lipids or proteins on the cell surface (glycocalyx).

Insoluble fiber

Dietary fiber like cellulose that resists digestion and adds bulk.

Lipids

Diverse, mostly nonpolar molecules with long hydrocarbon tails or steroid rings.

Glycerol

Three-carbon alcohol: glycerol with three hydroxyl groups.

Fatty acid

Long hydrocarbon chain with a carboxyl group; typically 12–18 carbons.

Ester bond

Bond formed by dehydration synthesis between a fatty acid and glycerol.

Omega-3 fatty acids

Polyunsaturated fats with a double bond at the third carbon from the end; includes ALA, EPA, DHA.

Alcohols (hydroxyl group)

Compounds containing hydroxyl (-OH); in lipids, hydroxyls help form esters.

Fats (triglycerides)

Triacylglycerols: glycerol backbone + three fatty acids; energy storage.

Saturated vs unsaturated

Saturated fats have no double bonds; unsaturated have one or more; cis/trans geometry affects packing.

Cis vs trans

Geometric isomers in unsaturated fatty acids; cis has kinked shape; trans is straighter.

Polyunsaturated

Fatty acids with more than one double bond.

Hydrogenation

Addition of H2 to unsaturated fats, can convert cis to trans and harden fats.

Adipocytes

Fat-storing cells in adipose tissue.

LDL (low-density lipoprotein)

“Bad” cholesterol that can contribute to atherosclerosis.

Essential fatty acids

Fats the body cannot synthesize and must obtain from diet (omega-3 and omega-6).

Phospholipids

Phosphate group + glycerol + fatty acids; phosphate headed by alcohol; main membrane components.

Phospholipid bilayer

Two-layer arrangement forming the cell membrane; hydrophobic interior with hydrophilic heads.

Steroids

Lipids with four fused hydrocarbon rings; hydrophobic; include steroid hormones.

Steroid hormones

Hormones derived from steroids that regulate various physiological processes.

Proteins

Macromolecules made of amino acids; perform catalysis, structure, transport, signaling, defense.

Amino acids

20 standard building blocks of proteins; each has an amino group, carboxyl group, and R group.

Polypeptide

Chain of amino acids linked by peptide bonds.

Enzymes

Proteins that catalyze biochemical reactions; often require specific conditions.

Denaturation

Loss of protein structure and function due to pH, temperature, or chemicals.

Peptide bond

Covalent bond formed by dehydration synthesis between amino acids.

Amino acid structure

Amino group, carboxyl group, hydrogen, and R group attached to the alpha carbon.

Essential amino acids

Amino acids the body cannot synthesize and must be obtained from diet.

Post-translational modifications

Chemical modifications after translation (e.g., cleavage, phosphorylation) that affect function.

Chaperone proteins

Proteins that assist the folding of other proteins.

Primary structure

Linear sequence of amino acids in a protein.

Secondary structure

Regular folding patterns (alpha helix, beta pleated sheet) stabilized by hydrogen bonds.

Tertiary structure

Overall 3D shape of a single polypeptide; driven by side-chain interactions.

Disulfide linkages

Covalent bonds between cysteine residues that help stabilize folding.

Quaternary structure

Association of multiple polypeptide chains into a functional protein.

Protein interactions (types)

Ionic, hydrogen, dipole-dipole, and dispersion forces govern folding and stability.

Hydrophobic vs hydrophilic

Hydrophobic parts bury inward; hydrophilic parts face outward toward water.

Protein folding and chaperones

Process of folding assisted by chaperone proteins to avoid misfolding.

Active site

Region of an enzyme where substrates bind and reactions occur.

Substrate

Molecule or ion that participates in a chemical reaction with an enzyme.

N-terminus/C-terminus

Ends of a polypeptide chain: amino terminus (N-terminus) and carboxyl terminus (C-terminus).

Nucleic Acids

DNA and RNA; store/transfer genetic information and participate in protein synthesis.

DNA

Deoxyribonucleic acid; genetic material in most organisms; stores hereditary information.

RNA

Ribonucleic acid; participates in protein synthesis and regulation.

Central dogma

Flow of genetic information: DNA -> RNA -> protein.

Phosphodiester bond (nucleic acids)

Bond connecting nucleotides along a nucleic acid strand.

DNA in eukaryotes (chromatin)

DNA packaged with histones into chromatin; forms chromosomes.

RNA types (mRNA, rRNA, tRNA, miRNA)

Different RNA roles: mRNA (coding), rRNA (ribosomes), tRNA (translation), miRNA (gene regulation).

Nitrogenous bases

Purines (A, G) with two rings; Pyrimidines (C, T, U) with one ring.

Ribose vs deoxyribose

Ribose in RNA has extra oxygen at 2'; deoxyribose in DNA lacks it.

Antiparallel

DNA strands run in opposite 5' to 3' directions in a double helix.

DNA double helix

Two anti-parallel strands wound around each other with base pairing.

RNA structure

Typically single-stranded; can fold into complex structures.

mRNA, rRNA, tRNA, miRNA

RNA types with roles in coding, ribosome structure, translation, and gene regulation.

rRNA peptidyl transferase

Enzymatic activity of rRNA that catalyzes peptide bond formation.

Glycocalyx

Sugar-containing coating on cell exterior formed by glycoproteins and glycolipids.

Glycoproteins/Glycolipids

Proteins or lipids with attached carbohydrate chains on cell surface.

5.1 Plasma membrane

Phospholipid bilayer with proteins and carbohydrates; fluid mosaic model.

Fluid mosaic model

Membrane structure: a mosaic of lipids, proteins, and carbohydrates that can move laterally.

Integral proteins

Proteins that span the lipid bilayer and interact with its interior.

Peripheral proteins

Proteins associated with membrane surfaces or with integral proteins.

Glycoproteins/Glycolipids (surface roles)

Carbohydrate-bearing proteins/lipids important for cell recognition and signaling.

Aquaporins

Channel proteins that facilitate rapid water transport across membranes.

Diffusion

Passive movement of molecules from high to low concentration without energy.