Bio 204 vocab

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pinocytosis: type of endocytosis where liquids are "drank" using smaller vesicles
anabolism: builds large molecules from simple ones; requires energy
catalyst: a chemical agent that changes the rate of a rection without being consumed by the reaction
codon: a three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal ; the basic unit of the genetic code
ionic bond: an electrical attraction between oppositely charged ions
peptide backbone: regular structure that forms when amino acids link together through making an amide bond
centriole: a structure in an animal cell composed of cylinder of microtubule triplets arranged in a 9 + 0 pattern. an animal cell usually has a pair of centrioles involved in cell division
disulfide bridge: formed by reactions between sulfhydryl groups in two cystine amino acids; a strong covalent bond formed when the sulfer of one cystine monomer bonds to the sulfer of another cysteine monomer
genetic code: chain of nucleotides coding for a chain of amino acids. Triplet (3 nucleotides code for one amino acid. 64 possible combinations. It is a degenerate code meaning there is more than one way to say the same thing. It is not ambiguous because each codon always stands for the same amino acid. It is universal (almost).
Intron: a noncoding, intervening sequence within a eukaryotic gene
molarity: concentration is often expressed as this; (M) moles of solute per liter of solution
eukaryotic: a cell with membrane enclosed nucleus and membrane enclosed organelles; protists, plants, fungi, and animals
Spliceosome: a complex assembly that interacts with the ends of an RNA intron in splicing RNA, releasing the intron and joining the two adjacent exons
integral protein: typically a transmembrane protein with hydrophobic regions that completely spans the hydrophobic region of the interior of the membrane
technology: taking scientific discoveries and making something useful
acidity: measured on the pH scale-concentration of H+
phosphate: PO4^ -2, functional group
transition state: bonds are being broken and others are being formed
enzyme: allow reactions to happen without additional heat
Uracil: the nucleotide in RNA that pairs with A instead of instead T
polar covalent bond: a covalent bond between atoms that differ in electronegativity; the shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other slightly positive
carboxyl: COOH, functional group
cofactor: any nonprotein molecule or ion that is required for the proper functioning of an enzyme. can be permanently bound to the active site or may bind loosely with the substrate during catalysis
transcription unit: a region of a DNA molecule that is transcribed into an RNA molecule
atom: smallest unit of matter
tetrahedron: three sides and a triangle base; charateristic shape of small molecules
enzyme substrate complex: a temporary complex formed when an enzyme binds to its substrate molescules
wobble: a violation of the base pairing rules in that the third nucleotide (5' end) of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position (3' end) of a codon
centrosome: material present in the cytoplasm of all eukaryotic cells, important in cell division; the microtubule organizing center
nanometer: nm 10^ -9m
valence electrons: electrons in the outermost electron shell
stop codon: UAA, UGA, UAG
signal peptide: a stretch of amino acids on a polypeptide that targets the protein to a specific destination in a eukaryotic cell
ion: an atom (simple ion) or a covalent molecule(complex ion) with a net charge; an atom that has gained or lost electrons, thus acquiring a charge
ATP: energy that is used and created in cells; adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed. this energy is used to drive endergonic reactions in cells
transfer RNA (tRNA): an RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA
P site: one of a ribosomes three binding sites for tRNA during translation. It holds the tRNA carrying the growing polypeptide chain
flagellum: long cellular appendage specialized for locomotion
membrane: order in cells due to compartmentalization; barrier around cell allowing certain things in and out
element: pure substance made up of one kind...
alpha-helix: looks like a slinky; one form of the secondary structure of proteins arising from a specific hydrogen bonding structure
electron shell: an energy level represented as the distance of an electron from the nucleus of an atom; the likely number of bonds depends on the position of the electrons in the shell; the less energetic shells fill first, only outer shell deals with bonding
sodium-potassium pump: found in every animal; Na out of the cell, K into the cell, both normally against concentration gradient
salt: a compound resulting from the formation of an ionic bond; also called an ionic compoud
functional group: attaches to the hydrocarbon skeletons; hydroxyl (OH), sulfhydroxyl (SH), phosphate (PO4^-2), amino (NH2), carboxyl (COOH), cabonyl (CHO), ketone (CO)
substrate: the reactant on which an enzyme acts, converting it to products
A site: one of a ribosomes three binding sites for tRNA during translation. It holds the tRNA carrying the next amino acid to be added to the polypeptide chain
RNA processing: modification of RNA before it leave the nucleus, a process unique to eukaryotes
endergonic: anabolic, not spontaneous, unfavorable, energy requiring, uphill
ribonucleic acid (RNA): a type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine, cytosince, guanine, and uracil, usually single stranded; functions in protein synthesis and as the genome of some viruses
reading frame: the way a cells mRNA translating machinery groups the mRNA nucleotides into codons
RNA polymerase: an enzyme that links together the growing chain of ribonucleotides during transcription
gated channel: a protein channel in a cell membrane that opens or closes in response to a particular stimulus
electrochemical gradient: the diffusion gradient of an ion, representing a type of potential energy that accounts for both the concentration difference of the ion across a membrane and its tendency to mvoe relative to the membrane potential
translation: the synthesis of a polypeptide using he genetic information encoded in an mRNA molecule. There is a change of language from nucleotides to amino acids
cilium: a short cellular appendage specialized for locomotion, formed from a core of nine outer doublet microtubules and two inner single microtubules enheathed in an extension of plasma membrane
valence: the number of bonds an atom is likely to form, the number of unpaired electrons; the bonding capacity of an atom
start codon: AUG, start signal also codes for Met
double bond: two covalent bonds between the same two atoms, four electrons are shared
cytoskeleton: proteinaceous network throughout cytoplasm involved in cell shape and movement; consists of at least three rod like or fiber like elements ( microtubules, microfilaments, intermediate filaments), can assemble rapidly, disassemle. throughout the cytoplasm and a variety of mechanical and transport functions
structural formula: a type of molecular notation in which the constituent atoms are joined by lines representing covalent bonds
allosteric regulation: the binding of a molecule to a protein that affects the function of the protein at a different site
coenzyme: an organic molecule serving as a cofactor. most vitamins function as coenzymes in important metabolic reactions
catabolism: breaks down complex molecules to simpler ones; releases energy
hydrocarbon skeleton: carbons bonded to other carbons; increases polarity,
tertiary structure: irregular twisting and looping of the primary and secondary structure due to interactions among the side chain; this level gives each individual polypeptide its overall shape; hydrophobic and hydrogen bond interactions stabilize tertiary structure
tubulin: protein found in microtubules,
fluid mosiac model: proteins are embeded in the phospholipid bilayer and can move laterally within
competitive inhibitor: a substance that reduces the activity of an enzyme by entering the active site in place o the substrate whose stryctyre it mimics
amino: NH2, functional group
peripheral protein: stick on surface of membrane but do not embed within
hydroxyl: OH, functional group
5'-cap: nucleotide containing 3 phosphates and a guanine attached backwards to protect the RNA from exonuclease which degrates nucleotides from one end, Also serves as the recognition site for ribosomes.
poly-A tail: 50 to 250 adenine nucleotides added post-transcription to the 3' end. Involved in getting mRNA out of the nucleus and arranging it for efficient translation
inductive reasoning: type of logic in which generalizations are based on a large number of specific observations
microvillus: contain actin, increase surface of cell, in small intestine
carbonyl: CHO, functional group
polar molecule: a molecule (such as water) with opposite charges on opposite sides; one that contains significant charge separation due to polar bonding
chaperonin: a protein molecule that assists the proper folding of other proteins
transmission electron microscope: see layers, expensive, no color, no limit on resolution (clarity)
acid: lowers pH and increase H+ (hydrogen ions)
scanning electron microscope: see surface, expensive, no color, no limit on resolution
aquaporin: a transport protein in the plasma membrane of a plant or animal cell that specifically facilitates the diffusion of water across the membrane (osmosis)
glycoprotein: a protein covalently attached to a carbohydrate
hypertonic: the side with more solute, making a cell shrivel, loose water, water moves to hypertonic side
sulfydryl: SH, functional group
Ribose: the sugar component of RNA
proton: a subatomic particle with a single positive electrical charge, found in the nucleus of an atom
elongation factor: requires cytoplasmic proteins
actin: protein found in microfilaments, muscle and other contractile elements
osmosis: diffusion of water across membranes, most water movement is facilitated diffusion through membrane-bound water channel proteins called aquaporins. solutes affect the net direction of movement. always toward the side of the memebrane where solutes are more concentrated
anticodon: a specialized base triplet at one end of a tRNA molecule that recognizes a particular complementary codon on an mRNA molecule
passive transport: simple diffusion and facilitated osmosis/diffusion-downhill, losing free energy, end with less free energy
amino acid: an organic molecule possessing both carboxyl and amino groups; serve as the monomers of proteins
active site: the place on an enzyme where the substrate binds
cotransport: the coupling of downhill diffusion of one substance to the uphill transport of another against its own concentration gradient
secondary structure: regular coiling or folding of an amino acid chain due to hydrogen bonding within the polypeptide backbone
quaternary structure: interactions between two or more polypeptides creating a functional protein; coded by genes and amino acids; three dimensional arrangement
translocation: an aberration in chromosome structure resulting from attachment of a chromosomal fragment to a nonhomologous chromosome. During protein synthesis, the third stage in the elongation cycle when the RNA carrying the growing polypeptide moves from the A site to the P site.
atomic number: number of protons
science: funded even if results are not immediate; trying to learn something
turgid: very firm, a walled cell becomes this if it has a greater solute concentration than its surroundings, resulting in entry of water
polymer: molecule consisting of identical of similar subunits linked together end to end
noncompetitive inhibitor: a substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing its conformation so that it no longer binds to the substrate
pH: a measure of hydrogen ion concentration equal to -log[H+] and ranging in value from 0 to 14
monomer: subunit that serves as the building block of a polymer
electron: a subatomic particle with a single negative charge, one or more move around the nucleus of an atom
messenger RNA (mRNA): type of RNA synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure or a protein
signal transduction pathway: mechanism linking a mechanical or chemical stimulus to a specific cellular response
phagocytosis: type of endocytosis where soilds get encorporated into the cell
lipid: a class of macromolecules. mostly hydrocarbon, largely nonpolar-hydrophobic, not soluble in water, three most important to living systems are fats, phospholipids and steroids
ribosome: a cell organelle constructred in the nucleolus and functioning as the site of protein synthesis in the cytoplasm; consists of rRNA and protein molecules, which make up two subunits
activation energy: the amount of energy that reactants must absorb before a chemical reaction will start
plasmolysis: due loss of water in a hypertonic solution the membrane pulls away from the cell wall
electrogenic pump: an ion transport protein that generates voltage across a membrane
macromolecule: made in living systems from smaller building blocks covalently bonded; four classes: proteins, nucleic acids, carbohydrates, and lipids
peptide bond: covalent bonds between amino acids; connect the amino nirtogen of one monomer witht he carboxyl carbon of the next; the result of dehydration reactions
endocrine signals: hormonal, long distance. signal released travels through blood vessels to target cell, affects only target cell with correct receptor
systems biology: an approach to studying biology that aims to model the dynamic behavior of whole biological systems; knowing how the higher level works by knowing about the lower levels, a lot of data typically with computers
prokaryotic: a cell that lacks membrane enclosed nucleus and membrane enclosed organelles. bacteria and archaea
dehydration reaction: removes water molecule forming a new bond in the synthesis of a polymer
initiation factor: to correctly bring together the translation complex; both ribosomal subunits, 5' end of the mRNA, the tRNA carrying the correct amino acid for the first codon, to establish a reading frame
amphipathic: molecule that has both a hydrophilic region and a hydrophobic region such as a phosopholipid
micrometer: um; 10^ -6m
intermediate filament: 8-12 nm protein-variable, very little dynamic properties, lead to stability rather than change, reinforce cell shape and fix organelles in position
hydrophilic: having an affinity for water; likes water; soluble in water; hydrogen bonds, polar, ions
exergonic: classification of chemical reactions; catabolic, stpontaneous, favorable, energy yielding, downhill
fatty acid: a long carbon chain carboxylic acid. fatty acids vary in length and in the number and location of double bonds; three fatty acids linked to a glycerol molecule form fat.
paracrine signals: target cells nearby the signal releasing cell
polypeptide: a polymer consisting of many amino acids linked together by peptide bonds
selective permeability: membranes control the types of substances that can cross, the rate of transport, the direction of transport. they are also dynamic meaning their transport properties can change
freeze fracture microscopy: freeze a collection of membranes, fracture them with a dull blade. prepare the fractured surfaces for scanning, electron microscope
motor protein: powered by ATP, proteins are located on an organelle or cytoskeletal element; walk along another cytoskeletal element by changing shape
free energy: the portion of a systems energy available to do work; less is more stability and less capacity to do work
neutron: an electrically neutral particle found in the nucleus of an atom
cholesterol: steroid that forms an essentail component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids
neurotransmittors: a chemical messenger released from teh synaptic terminal of a neuron at a chemical synapse that diffuses across the synaptic cleft and binds to and stimulates the postsynaptic cell
isotonic: the solute concentration is the same on both sides
exocytosis: the cellular secretion of macromolecules by the fusion of vesicles witht he plasma membrane using cellular energy
release factor: a cytoplasmic protein that binds to the A-site. It catalyzes the hydrolysis of the polypeptide from the last tRNA after which the translation complex comes apart
active transport: use of transport proteins and cellular energy to move against the concentration gradient; moves molecules or ioins across membranes using transport proteins; cell supplies the energy in the form of ATP; the carrier proteins are unidirectional and called pumps
phospholipid: molecule that is a constituent of the inner bilayer of biological membranes, having a polar, hydrophilic head and a nonpolar, hydrophobic tail. consists of five smaller building blocks attached by dehydration reactions
aminoacyl-tRNA synthetase: an enzyme that joins each amino acid to the correct tRNA
basal body: extension of microtubules into the cell
exon: a coding region of a eukaryotic gene. They are expressed and separated frome ach other by introns.
Promoter: a specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing DNA
diffusion: passive movement of a substance from an area of high concentration (or activity) to low concentration dur to the random motion of its particles; always toward equilbrium
microtubule: 25nm, protein-tubulin, dynamic(can change length and action)
cooperativity: an interaction of the constituent subunits of a protein whereby a conformational change in one subunit is transmitted to all the others
base: increases pH and removes H+ creating OH
glycerol: three carbons with a hydroxyl; eliminating hydrophobia, component of phospholipids
molecule: two or more atoms attached by a bond
phospholipid bilayer: the hydrophilic heads are on the outside in the water and the hydrophobic tails point inside
matter: has mass; takes up space
ribosomal RNA (rRNA): the most abundant type of RNA, which together with proteins forms the structure of ribosomes. Ribosomes coordinate the sequential coupling of tRNA molecules to mRNA codons.
denaturation: in proteins, a process in which a protein unravels and loses it native conformation, thereby becoming biologically inactive. Occurs under exteme conditions
induced fit: the change in shape of the active site of an enzyme so that it binds more snugly to the substrate, induced by entry of the substrate
hydrogen bond: weak electrical attraction between a hydrogen in one polar bond and an electronegative oxygen or nitrogen in another; formed when slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule
signal receptors: on the surface of cells where the signal must attach
saturation kinetics: effect of various factors; study of rates; how fast does an enzyme work under different conditions
endocytosis: the cellular uptake of macromolecules and particulate substances by localized regions of the plasma membrane that surround the substance and pinch it off to form an intracellular vesicle using cellular energy
metabolism: the total of all the chemical activity in a call or organism
covalent bond: sharing of electrons, pair of electrons shared between two atoms, a strong chemical bond
electronegativity: how strongly a particular atom holds the electrons in a covalent bond; the attraction of an atom for the electrons of a covalent bond
receptor-mediated endocytosis: give endocytosis specificity derived from a protein controlled process; movement of specific molecules into a cel by the inward budding of membranous vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific substances
microfilament: 7nm, protein-actin, dynamic (can change length and action)
beta-pleated sheet: one form of the secondary structure of proteins in which the poly peptide chain folds back and forth. Two regions of the chain lie parallel to each other and are held together by hydrogen bonds
hydrophobic: having an aversion to water; tending to coalesce and form droplets in water; nonpolar, no electrical charge separation
compound: substance of two or more elements, different combinations
hydrolysis: polymers are broken down by adding water to a molecule
amino acid activation: attaching a free amino acid to the right tRNA and thus activating it for use in translation. Done by cytoplasmic enzymes called aminoacyl-tRNA synthetases
Transcription: the synthesis of RNA on a DNA template
metabolic pathway: a group of enzymes that cooperate to accomplish some task; versatility is a major benefit because of branching
transport protein: allow diffusion of hydrophilic substances, called channels or carriers; used in facilitated diffusion
polyribosome: an aggregation of several ribosomes attached to one messenger RNA molecule
DNA: instructions for cell structure and function
deductive reasoning: a type of logic in which specific results are predicted from a generalization
primary structure (of protein): linear sequence of amino acids in a protein
feedback inhibition: a methood of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway; an allosteric strategy used by cells to regulate metabolic pathways; the end product of a pathway is an allosteric inhibitor of an early reaction in the pathway

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