EXAM 1 KEY TERMS

Biology

The scientific study of life and living systems

Cell

The basic structural and functional unit of life

Cell Theory

All living organisms are composed of one or more cells, the cell is the basic unit of life, all cells come from preexisting cells

Spontaneous Generation

The incorrect idea that living organisms can arise directly from nonliving matter, ex: people thought maggots could spontaneously appear from rotting meat

Domain

The highest major taxonomic category used to classify organisms

Eukarya

Domain containing organisms whose cells are eukaryotic, contains a membrane bound nucleus

Archaea

Organism belonging to one of the 3 domains of life and is prokaryotic, molecularly and evolutionarily different from the other prokaryotic domain

Bacteria

Organism that belongs to one of the 3 domains of life and is prokaryotic

Cilium (-a)

A short, hair like structure that extends from the surface of some eukaryotic cells and can help with movement or moving material across the cell’s surface

Central Dogma of molecular biology

Information flow from DNA to protein is conserved in living things

Electron

A negatively charged particle around an atom, stores and transfers energy in cells

Valence

How many open slots an atom has for bonding, tells you how many bonds an atom can form

Orbital

Specific 3D space where an electron usually hangs out, each holds up to 2 electrons

Shell

The energy level where orbitals sit, the ones farther from the center have higher energy

Chemical Bond

An attraction between atoms caused by sharing, stealing, or losing electrons to fill their outer shell

Ionic Bond

A bond formed when one atom steals an electron from another, creating opposite charges that attract

Covalent Bond

A strong bond where two atoms share electrons

Hydrogen Bond

A weak attraction between partially positive hydrogen atom and a partially negative atom on another molecule

Van Der Waals Force

Super weak, temporary stickiness between nonpolar molecules when they get squeezed close together

Electronegativity

How “greedy” an atom is for electrons

Polar Covalent Bond

Unequal sharing of electrons, the greedier atom pulls electrons closer, creating tiny positive and negative spots on the molecule

Nonpolar Covalent Bond

Equal sharing of electrons, no charged spots are created

Hydrophilic

Water loving, polar or charged molecules that easily mix with and dissolve in water

Hydrophobic

Water fearing, non polar molecules that avoid water and clump together instead

Amphipathic

A molecule with both a water loving head and a water fearing tail

Carbon

The main building block of life, forms 4 stable bonds, allowing it to build complex rings and chains

Organic Molecule

Any molecule containing carbon bonded to hydrogem

Hydrocarbon

A molecule made of only carbon and hydrogen, it is non polar and packed with energy

Urea

A simple organic waste product produced when animals break down excess amino acids, often used in lab settings to denature proteins

Functional Group

A specific group of attached atoms that gives an organic molecule its chemical personality and reactivity

Macromolecule

A huge biological molecule made up of thousands of bonded atoms (carbohydrates, proteins, nucleic acids, lipids)

Monomer

A single building block molecule (one bead on a necklace)

Polymer

A long chain made by linking monomers together (the whole necklace)

Dehydration Linkage (synthesis)

The chemical reaction that builds polymers by linking monomers together, removing a water molecule in the process

Hydrolysis

The chemical reaction that breaks polymers apart into monomers by adding a water molecule

Glycosidic Bond

The covalent bond formed between two sugar monomers during a dehydration reaction

Monosaccharide

A single sugar molecule, the cell’s primary fuel source

Disaccharide

Two monosaccharides joined by a glycosidic bond

Storage Polysaccharide

A sugar polymer used to store energy for later, easily broken down via hydrolysis

Structural Polysaccharide

A tough sugar polymer used to build physical supports (plant cell walls, insect exoskeletons), hard to break down

Amino Sugar

A sugar molecule with an amino group (NH2) replacing a hydroxyl (OH) group, a key monomer unit in chitin

Cellulose

A structural polysaccharide made of glucose that forms plant cell walls, human cannot digest it (dietary fiber)

Chitin

A structural polysaccharide made of amino sugars that forms fungal cell walls and insect exoskeletons

Glycogen

An energy storage polysaccharide found in animal liver and muscle cells, highly branched for quick release of glucose

Starch

An energy storage polysaccharide found in plants (potatoes and rice)

Amino Acid

The monomer building block of proteins, consists of a central carbon bonded to an amino group, a carboxyl group, a hydrogen, and an R group

R group

The variable part of the amino acid, its specific chemistry (polar, non polar, charged), determines how the protein folds and behaves

Peptide Bond

The specific covalent bond formed between amino acids via a dehydration reaction

Peptide

A short chain of amino acids linked together (usually under 50)

Polypeptide

A long, unbranched chain of amino acids linked by peptide bonds

Protein

One or more polypeptide chains folded into a specific, functional 3D shape

N-Terminus

The free amino end (NH2) of a polypeptide chain, where protein synthesis begins

C-Terminus

The free carboxyl end (COOH) of a polypeptide chain, where new amino acids are added

Primary Structure

The unique linear sequence of amino acids in a polypeptide chain, determines how a protein folds

Secondary Structure

Local folding of the polypeptide backbone held together by hydrogen bonds, interactions between stretches of amino acids

Tertiary Structure

The overall 3D shape of a single polypeptide, driven by interactions between R groups

Quaternary Structure

The final protein shape that forms when two or more distinct polypeptide chains assemble together

Alpha-Helix

A spiral/coiled secondary structure held together by hydrogen bonds along the backbone

Beta-Sheet

A flat, pleated secondary structure where parallel or antiparallel strands align via backbone hydrogen bonds

Disulfide Bond

A strong covalent bond between the sulfur atoms of two cysteine R groups; helps lock tertiary and quaternary structures in place

Denaturation

Unfolding a protein (losing its 3D shape and function), using heat, pH changes, or chemicals (like urea)

Renaturation

Refolding the protein back into its active 3D shape when normal conditions are restored

RNAse

An enzyme that cuts up and breaks down RNA molecules

Nascent Polypeptide

A brand new protein chain that is currently being synthesized by a ribosome and hasn’t finished folding yet

Chaperone

A helper protein that provides a safe, sheltered environment for newly made or unfolded proteins to fold correctly without clumping together

Prion

An infectious misfolded protein that forces normal proteins of the same type to misfold into harmful aggregates

X-Ray Crystallography

A classic laboratory technique used to map out the exact 3D atomic structure of a crystallized protein or molecule

AlphaFold

An AI program developed by DeepMind that predicts a protein’s 3D tertiary structure directly from its 1D amino acid sequence with high accuracy

Nucleotide

The monomer building block of nucleic acids, made of 3 parts: a 5 carbon sugar, a phosphate group, and a nitrogenous base

Phosphoanhydride Bond

High energy chemical bonds connecting phosphate groups (like those in ATP), breaking them via hydrolysis releases energy to power cellular work

Ribose

The 5 carbon sugar found in RNA nucleotides (has an -OH group on its 2’ carbon)

Deoxyribose

The 5 carbon sugar found in DNA nucleotides (missing an oxygen atom, having an -H on its 2’ carbon instead)

Nitrogenous Base

The nitrogen containing ring structure on a nucleotide that carries the genetic code (Adenine, Thymine, Guanine, Cytosine, Uracil)

Purine

A nitrogenous base with a double ring structure

Pyrimidine

A nitrogenous base with a single ring structure

DNA

A double stranded nucleic acid that stores genetic information using deoxyribose sugar and base: A, T, C, G

RNA

A usually single stranded nucleic acid involved in protein synthesis using ribose sugar and bases: A, U, C, G

Base Pairing

Hydrogen bonding between specific nitrogenous bases across complementary nucleic acid strands (A with T/U, C with G)

Sugar/Phosphate Backbone

The repeating structural frame of a DNA or RNA strand formed by strong covalent phosphodiester bonds between sugars and phosphate groups

5’ End

The orientation and directionality of a nucleic acid strand: the end with a free phosphate group attached to the carbon #5 of the sugar

3’ End

The orientation and directionality of a nucleic acid strand: The end with a free -OH group on carbon #3 of the sugar (where new nucleotides are added)

Double Helix

The twisted ladder shape of the double stranded DNA, where two antiparallel strands wrap around a central axis

tRNA (transfer RNA)

A small RNA molecule that carries specific amino acids to the ribosome during translation to build a polypeptide chain

Phospholipid

Saturated Fatty Acid

A hydrocarbon chain with no double bonds, saturated with hydrogen atoms, straight structures allow for tight packing, solid at room temperature

Unsaturated Fatty Acid

A hydrocarbon chain with one or more double bonds

Cis Unsaturated Fatty Acid

Hydrogens are on the same side of the double bond, creating a noticeable kink that prevents tight packing, liquid at room temperature

Trans Unsaturated Fatty Acid

Hydrogens are on the opposite sides, keeping the chains straight like a saturated fat (rare in nature, articificial/unhealthy)

Glycerol

A 3 carbon alcohol backbone that anchors fatty acid chains in lipids via ester linkages

Tricylglycerol

One glycerol molecule bound to three fatty acid chains, highly hydrophobic molecule used primarily for long term energy storage

Cholesterol

A 4 ring steroid lipid embedded in animal cell membranes, acts as a temperature buffer for fluidity, keeps membranes from becoming too fluid at high temperatures and prevents them from freezing/solidifying at low temperatures

Low Density Lipoprotein

Bad cholesterol, a protein/lipid carrier that delivers cholesterol from the liver to body tissues, high levels lead to arterial plaque buildup

High Density Lipoprotein

Good cholesterol, a carrier that collects excess cholesterol from tissues and brings it back to the liver for excretion/recycling

Phospholipid Bilayer

An amphipathic lipid consisting of a hydrophilic (polar) phosphate head and two hydrophobic (nonpolar) fatty acid tails attached to a glycerol backbone

Integral Membrane Protein

A protein permanently embedded within the lipid bilayer, often spanning both sides (transmembrane protein) via hydrophobic amino acid regions

Peripheral Membrane Protein

A protein loosely attached to the inner or outer surface of the membrane (bound to integral proteins or phospholipid heads), easily detached

Fluid Mosaic Membrane

The standard model for describing the cell membrane, fluid because lipids and proteins draft laterally within the plane, and mosaic because it is a complex tapestry of proteins, lipids, and carbohydrates working together

Endocytosis

The process where a cell takes in large molecules or particles by folding its plasma membrane inward to form a pocket, which pinches off inside the cell

Vesicle

A smal, membrane bound sac inside a cell used to transport or store substances

Receptor-Mediated Endocytosis

A highly specific form of endocytosis where target molecules (ligands) bind to specific cell-surface receptors before being brought into the cell