Gen Bio Vocab (Unit 1)

Element

Distinct type of substance or matter. Each element has atoms that contain a unique number of Protons in the nucleus

Atom

Fundamental unit of an element. Composed of Protons, neutrons, and electrons

Ion

An atom/molecule that carries a full charge (Not partial)

Positive (+): More protons than electrons

Negative (-): More Electrons than problems

Molecule

Structure made of two or more atoms held together by covalent bonds

Covalent Bond

An attraction between two atoms based on shared electrons

Electronegativity

Tendency for an atoms nucleus to attract the shared electrons in a covalent bond

Polar Covalent Bond

An asymmetry in the position of shared electrons due to difference in atomic electronegativity of involved atoms. Creates partial positive and partial negative charges depending on the pull of the electrons

Ex: Water molecule

Nonpolar covalent bond

Equal sharing of electrons due to equal/ roughly equal electronegativity of involved atoms

Ex: Carbon bonds

Hydrogen Bond

Attraction between partial positive hydrogen and partial negative charge on a different atom

Lipid

Molecule that does not dissolve in water

Saturated (Lipid)

A Hydrocarbon chain that contains only single bonds

Unsaturated (lipid)

A hydrocarbon chain that contains one or more double bonds

Fat

A lipid comprised of three fatty acids (hydrocarbon chains with COOH group on one end) attached to a glycerol (3-carbon compound)

Steroid

A lipid containing a specific four fused ring structure

Phospholipid

A lipid consisting of:

• A hydrophilic “head” that includes a phosphate group and another polar group and…

• A Hydrophobic hydrocarbon tail that can vary in length

Amphipathic

A molecule having both a hydrophobic region and a hydrophillic region

I.E: A Phosphlipid

Nucleotide

Molecule made up of phosphate group and a nitrogenous base bonded to a 5-carbon sugar

Nucleic Acid

Molecule made up of nucleotides linked together to form a chain/strand

Phosphodiester bond

Covalent bond between the phosphate group on the 5’ carbon of one nucleotide and the -OH group on the 3’ end of a second nucleotide, creating the sugar-phosphate backbone

Complementary base pairing

DNA: Hydrogen bonding b/w A-T and G-C in a nucleic acid

RNA: Hydrogen bonding b/w A-U and G-C in a nucleic acid

Primary Structure (Nucleic Acids)

The sequence of nucleotides in a nucleic acid, read from 5’ to 3’ no matter what

Secondary Structure (Nucleic Acids)

Formation of a double helix in DNA or a Stem & Loop structure in RNA based on complementary base pairing

Sugar-Phosphate Backbone

The “spine” of 5 carbon sugars and phosphate groups in a nucleic acid (the nitrogenous bases project off of this backbone)

Antiparallel strands

Strands of DNA or RNA that align in opposite 5’ to 3’ orientation

Monomer

A small subunit molecule that can be linked to another via covalent bonds to form a larger molecule

Ex: nucleotides

Polymer

A Large molecule composed of strings of covalently bonded small molecules/monomers

Ex: DNA or RNA

Peptide Bond

Covalent bond that forms between carboxyl group of one amino acid & the amino group of another amino acid. Usually the bond follows a N-C-C repition

Protein Primary Structure

The sequence of amino acids linked via peptide bonds

Protein Secondary structure

formation of alpha helices and beta pleated sheets, stabilized by hydrogen bonds between backbone atoms

Protein tertiary structure

folding into 3-d shape stabilized by hydrogen bonds, ionic bonds, Sulfur-Sulfur bridges, and hydrophobic interactions

Ionic bond

Interaction that occurs when a positively charged ion is attracted to a negatively charged ion

Hydrophobic interactions

Interactions that stabilize hydrophobic regions of molecules by minimizing their contact with water

Protein Quaternary structure

assembly of multipart proteins from folded subunits, stabilized by hydrogen bonds, ionic bonds, sulfur-sulfur bridges, and hydrophobic interactions

Denaturing

“unfolding” or loss of 3-d structure (secondary, tertiary, and/or quaternary structure), often via environmental changes (heat or PH changes)

Gene

A Segment of DNA that contains the information required to produce a product that functions in the organism

Alleles

Different versions of a gene that have slight variations in the DNA sequence found in other alleles of the same gene

Transcription

The process that creates an RNA molecule from information stored in a gene

Comparison: IPA transcription. Taking base phonemes (Nucleotides) and forming them into a universally understandable code

Translation

The Process that uses the information in the messenger RNA (mRNA) to synthesize a protein

Comparison: Languages. From German into English is similar to mRNA into proteins

Diffusion

Movement of ions or molecules from an area of higher concentration to an area of lower concentration

Entropy

The tendency of systems to reach a state of higher disorder or randomness

Osmosis

Movement of water across a membrane, from an area of higher concentration (low solute concentration) to an area of lower concentration (higher solute concentration)

Concentration gradient

A difference in a substance’s concentration in space—usually across a cell membrane

Potential energy

The energy of position

Facilitated diffusion

Diffusion of substances across cell membranes through integral membrane proteins

Passive Transport

Movement of ions or molecules that does not require an input of energy; occurs down a gradient and is spontaneous because it increases entropy

Active Transport

Movement of ions or molecules that requires an input of energy; occurs against a gradient and is nonspontaneous because it decreases entropy

Channel protein

An integral membrane protein that forms a tunnel for a specific ion to diffuse across a membrane

Carrier protein

An integral membrane protein that facilitates diffusion of a specific molecule across a membrane by changing shape once the molecule binds to it

Pump

An integral membrane protein that transports specific ions or molecules against their concentration gradient across a membrane; uses energy input

Cell (plasma membrane)

The boundary of every cell on Earth, made of a lipid bilayer with proteins and carbohydrates.

Oligosaccharide

A chain of around 6-10 sugars long

Peripheral membrane protein

A protein found on the inner or outer surface of a cell membrane.

Integral membrane protein

A protein embedded, or integrated, into a cell membrane.

Transmembrane protein

A type of integral membrane protein that spans the lipid bilayer of a cell membrane.

Kinetic energy

The energy of motion

Vacuole

An organelle that stores key molecules; very prominent in most plant cells.

Chloroplast

An organelle that contains the molecular machinery required for photosynthesis.

Cell Wall

A stiff structure outside of many types of cells, usually made primarily of carbohydrates

Primarily seen in Plant cells and are specialized to have Cellulose as part of this.

Endoplasmic Reticulum (ER)

A eukaryotic organelle that forms a branching network of narrow tubes and flattened sacs. The place where proteins, membrane lipids, and other molecules are synthesized and/or processed. Can have ribosomes associated with it (rough) or not (smooth).

Golgi (body/apparatus)

An organelle comprised of stacked, flattened sacs, where proteins and other molecules are processed and packaged for shipment to specific destinations.

Actin Filaments

Small-diameter cytoskeletal fibers made of subunits of the protein actin.

Intermediate Filaments

Cytoskeletal fibers whose size is intermediate between those of actin filaments and microtubules and can be made from a variety of protein subunits.

Microtubules

Large-diameter, hollow cytoskeletal elements made of pairs of the proteins α-tubulin and β-tubulin.

Cell

The smallest thing that can function as an independent organism; also the building block of larger organisms.

Chromosome

A DNA molecule — circular or linear, depending on the species — usually associated with specific proteins that bind to the DNA.

Ribosome

A molecular machine consisting of RNA and proteins that is the site of protein synthesis.

Organelle

Any membrane-bound compartment inside a cell.

Cytoskeleton

Rod-like proteins inside cells that function in structural support, transport of materials, and movement in some species.

Cell Wall

A stiff structure outside the cell membrane composed of carbohydrates and other molecules.

Flagellum (plural: Flagella)

A long, flexible structure that extends from the cell and whips or rotates to propel the cell through water.

Nucleus

An organelle unique to eukaryotes enclosed by a double membrane and containing the cell’s chromosomes

Mitochondrion (Plural: Mitochondria)

An organelle found in all eukaryotes that functions in “burning” sugars to provide energy for the cell

Eukaryote

A lineage of species with cells that contain a nucleus and mitochondria

Prokaryote

 A species in the lineages Archaea and Bacteria, with cells that lack a nucleus

Endomembrane System

A collection of machines, cytoskeletal components, and organelles that together produce, process, and transport proteins and lipids destined for organelles, the cell membrane, or outside the cell

Signal Sequence

A series of amino acids at the start of a protein that allows that protein to enter the endomembrane system

Motor Protein

A protein that functions in cell movement through shape changes caused by phosphorylation or dephosphorylation

Phosphorylation

The addition of a phosphate group (PO₄^3-) to a protein or other molecule. In most cases, the phosphate group comes from ATP. Dephosphorylation is the reverse process (removal of a phosphate group)

Endergonic Reaction

One that results in an increase in free energy; another way of referring to a nonspontaneous reaction.

Exergonic Reaction

One that results in a decrease in free energy; another way of referring to a spontaneous reaction

Activation Energy

The amount of energy required to get a chemical reaction through its transition state

Transition state

During a chemical reaction, an intermediate state where old bonds are being broken but new bonds have not yet formed

Enzyme

A protein that catalyzes a chemical reaction

Active site

The place on an enzyme (or ribozyme) where a reaction is catalyzed

Reduction-Oxidation (redox) reactions

Chemical reactions involving the gain (reduction) or loss (oxidation) of an electron

Cellular respiration

A multi-step process that uses energy captured from carbon oxidation to power ATP production via an electron transport chain and ATP synthase

Electron Transport Chain (ETC)

A series of machines that uses an electric current to pump protons across a membrane, establishing a proton gradient that is then used to generate ATP. When the ETC uses oxygen as an electron acceptor, ATP production via the combined action of the ETC and ATP synthase is called oxidative phosphorylation

ATP Synthase

The multi-protein machine that transforms the kinetic energy in a flow of protons to mechanical energy that catalyzes the addition of a phosphate group to ADP to form ATP

Glycolysis

A sequence of ten enzyme-catalyzed reactions that begins with glucose and ends with pyruvate, producing 2 ATP and 2 NADH per molecule of glucose

Pyruvate Processing

A series of enzyme-catalyzed reactions that begins with pyruvate as a substrate and produces acetyl-CoA and NADH

Citric Acid Cycle

A sequence of nine enzyme-catalyzed reactions that begins with acetyl-CoA, completes the oxidation of glucose to CO₂, and produces ATP, NADH, and FADH₂

NADH, FADH₂, Q

Molecules that function as electron carriers during cellular respiration, meaning that they transport electrons to or within the electron transport chain