plasma membrane
the selective barrier surrounding a living cell that enables the cell to concentrate nutrients, retain products, and excrete waste
enzyme
a protein that catalyzed a specific chemical reaction
transcription
the copying of one strand of DNA into a complentary RNA sequence
translation
process by which the sequence of nucleotides in an mRNA molecule directs the incorporation of amino acids into protein
gene
region of DNA that controls a discrete hereditary characteristic of an organism, usually corresponding to a single protein (or set of alternative protein variants) or to a structural, catalytic, or regulatroy RNA.
mRNA
RNA molecule that specifies the amino acid sequence of a protein
amino acids
the building blocks of proteins
genome
the total genetic information of a cell or ganism as embodied in its complete DNA sequence
virus
a small packet of genetic material that has evolved as a parasite on the reproductive and biosynthetic machinery of host cells
model organism
organism selected for intensive study as a representative of a large group of species
archaea
one of the two divisions of prokarytoes, typically found in the hostile environments such as hot springs or concentrated brine
homolog
the general term for genes that are related by descent
eukaryote
living organism composed of one or more cells with a distinct nucleus and cytoplasm
prokaryote
major category of living cells distinguished by the absence of a nucleus
(T/F) Genes and their encoded proteins are co-linear; that is, the order of amino acids in proteins is the same as the order of the codons in the RNA and DNA.
True
(T/F) DNA AND rna use the same four-letter alphabet.
False, DNA uses ATGC, while RNA uses AUGC. (Thyamine in DNA base pairs; Uracil in RNA base pairs)
(T/F) The vast majorite of CO2 fixation into the organic compounds need for further biosynthesis is carried out by phototrophs.
True
(T/F) Eukaryotic cells contain either mitochondria or chloroplasts, but not both.
Fals, some have either both or just mitochondria
Most of the DNA sequences in a bacterial genome code for proteins, whereas most of the DNA sequences in the human genome do not.
True
hydrophobic force
force exerted by the hydrogen-bonded network of water molecules that brings to nonpolar surfaces together by excluding water between them
hydrogen bond
noncovalent bond in which an electropositive hydrogen atom is partially shared by two electronegative atoms
acid
substance that releases protons when dissolved in water, forming a hydronium ion (H3O+)
van der Waals attraction
type of noncovalent bond that is formed at close range between non-polar atoms
activation energy
extra energy that must be possessed by atoms or molecules in addition to their ground-state energy in order to undergo a particular chemical reaction
standard free-energy change
free-energy change of two reacting molecules at standard temperature and pressure when all components are present at a concentration of 1 mole per liter
oxidation
loss of electrons from an atom, as occurs during the addition of oxygen to a molecule or when a hydrogen is removed
substrate
molecule on which an enzyme acts
diffusion
net drift of molecules in the direction of lower concentration due to random thermal movement
coupled reaction
linked pair of che ical reactions in which the free energy released by one of the reactions serves to drive the other
equilibrium
state at which there is no net change in a system; in a chemical reaction, this state is reached when the forward and reverse rates are equal
free energy (G)
the energy that can be extracted from a system to drive reactions; takes into account changes in both energy and entropy
citric acid cycle
central metabolic pathway found in aerobic organisms, which oxidizes acetyl groups derived from food molecules to CO2 to H2O; in eukaryotic cells, it occurs in the mitochondria
fat
energy-storage lipids in cells that are composed of triacylglycerols, which are fatty acids esterified with glycerol
glycogen
polysaccaride composed exclusively of glucose units used to store energy in animal cells; granules of it are especially abundant in liver and muscle cells
oxidative phosphorylation
process in bacteria and mitochondria in which ATP formation is driven by the transfer of electrons from food molecules to molecular oxygen
Electron-transport chain
series of electron carrier molecules along which electrons move from a higher to lower energy level to a final acceptor molecule, with the associated production of ATP
Glycolysis
ubiquitour metabolic pathway in the cytosol in which sugars are partially metabolized to produce ATP
quaternary structure
3-D relationship of the different polypeptide chains in a multisubunit protein or protein complex
alpha helix
common folding patter in proteins in which a linear sequence of amino acids folds into a right-handed coil stabilized by internal hydrogen-bonding between backbone atoms
primary structure
the amino acid sequence of a protein
binding site
a region on the surface of a protein that can interact with another molecule through noncovalent bonding
amyloid fibril
self-propagating, stable aggregate made up of identical polypeptide chains layered into a continuous stack of beta sheets
polypeptide backbone
the chain of repeating the carbon and nitrogen atoms, linked by peptide bonds in a protein
beta sheet
common structural motif in proteins in which differenct sections of the polypeptide chain run alongside each other and are joined together by hydrogen-bonding between atoms of the polypeptide backbone
protein domain
portion of a protein that has a tertiary structure of its own
secondary structure
regular local folding patters in a protein, including alpha helix and beta sheet
scaffold protein
a protein that serves both to link together a set of interacting proteins and to position them at a specific location in a cell
feedback inhibition
type of metabolic reulation in which the activity of an enzyme acting near the beginning of a reaction pathway is reduced by a product of the pathway
antibody
protein produced by the immune system in response to a foreign molecule or invading microorganism
active site
region of an enzyme surface to which a substrate molecule binds in order to undergo a catalyzed reaction
ubiquitin
the first example of a special family of small proteins whose members are covalently attached to other proteins to influence their activity or fate
linkage
mutual effect of the binding of one ligand on the binding of another that is a central feature of the behavior of all allosteric proteins
protein kinase
enzyme that transfers the terminal phosphate group of ATP to a specific amino acid in a target protein
transition state
rate-limiting structure that forms transiently in the course of a chemical reaction and has the highest free energy of any reaction intermediate
allosteric protein
protein that changes its conformation (and often activity) when it binds a regulatory molecule or when it is covalently modified
proteomics
a term often used to describe research focused on the simultaneous analysis of large numbers of proteins
coenzyme
small molecule that is tightly associated with a protein catalyst and participates in the chemical reaction, often by forming a covalent bond to the substrate
double helix
the 3-D structure of DNA, in which two DNA chains held together by hydrogen bonds between the bases are coiled around one another
antiparallel
describes the relative orientation of the two strands in a DNA helix; the polarity of one strand is oriented in the opposite direction to that of the other
base pair
two nucleotides in an RNA or DNA molecule that are held together by hydrogen bonds
karyotype
full set of chromosomes of a cell arranged with respect to size, shape, and number
centromere
constricted region of a mitotic chromosome that holds sister chromatids together
histone
any one of a group of small abundant proteins, rich in arginine and lysine, that form the primary level of chromatin organization
chromosome
structure composed of a very long DNA molecule and associated proteins that carries part (or all) of the hereditary information of an organism
cell cycle
the orderly sequence of events by which a cell duplicates its contents and divides into two
chromatin
complex of DNA, histones, and the non-histone proteins found in the nucleus of a eukaryotic cell
nucleosome
beadlike structure in eukaryotic chromatin, composed of a short length of DNA wrapped around a core of histone proteins
euchromatin
less condensed region of an interphase chromosome that stains diffusely
epigenetic inheritance
form of transmission of information from cell to cell, or from parent to progeny, that is not encoded in DNA
position effect variegation
difference in gene expression that depends on the location of the gene on the chromosome
psuedogene
a copy of a functional gene that has become irreversibly inactivated by multiple mutations
copy number variation (CNV)
long blocks of DNA sequence that differ in the number of times they are present in the genomes of different individuals in a population
purifying selection
evolutionary process that eliminates individuals carrying mutations that interfere with important genetic functions
single-nucleotide polymorphism (SNP)
variation between individuals at a certain nucleotide position in the genome
polytene chromosome
giant chromosome in which the DNA has undergone repeated replication without separation into new chromosomes
lampbrush chromosome
paired chromosomes in meiosis in immature amphibian eggs, in which the chromatin forms large stiff loops extending out from the linear axis of the chromosome
mitotic chromosome
highly condensed, duplicated chromosome with the two new chromosomes still held together at the centromere as sister chromatids
mutation
a randomly produced heritable change in the nucleotide sequence of a chromosome
germ cell
cell type in a diploid organism that carries only one set of chromosomes and is specialized for sexual reproduction; a sperm or an egg
somatic cell
any cell of a plant or animal other than a germ cell or germ-line precursor
RNA Primer
Short length of RNA synthesized on the lagging strand during DNA replication and subsequently removed
DNA ligase
enzyme that joins two adjacent DNA strands together
strand-directed mismatch repair
dna repari process that replaces incorrect nucleotides inserted during DNA replication
DNA helicase
enzyme that opens the DNA helix by separating the single strands
sliding clamp
a protein complex that encircles the DNA double helix and binds to DNA polymerase, keeping it firmly bound to the DNA while it is moving
DNA topoisomerase
Enzyme that binds to DNA and reversibly breaks a phosphodiester bond in one or both strands, allowing the DNA to rotate at that point
replication fork
Y-shaped region of a replicating DNA molecule at which the two daughter strands are formed
lagging strand
the newly made strand of DNA found at a replication fork that is made in discontinuous segments, which are later joined covalently
S phase
period during a eukaryotic cell cycle in which DNA is synthesized
origin recognition complex
large multimeric protein structure that is bound to the DNA at origins of replication in eukaryotic chromosomes throughout the cell cycle
telomerase
enzyme that elongates telomeres, the repetitive nucleotide sequences found at the ends of eukaryotic chromosomes
nonhomologous end joining
a means for repairing double-strand DNA breaks that links two ends with little regard for sequence homology
DNA repair
collective term for the enzymatic process that correct deleterious changes affecting the continuity or sequence of a DNA molecule
allele
one of a set of alternative forms of a gene; in a diploid cell, each gene will have two of these, each occupying the same position (locus) on homologous chromosomes
gene conversion
process by which DNA sequence information can be transferred from one DNA helix (which remains unchanged) to another DNA helix whose sequence is altered
hybridization
experimental process in which two complementary nucleic acid strands form a double helix; a powerful technique for detecting specific nucleotide sequences
Holliday junction
X-shaped structure observed in DNA undergoing recombination, in which the two DNA molecules are held together at the site of crossing-over, also called a cross-strand exchange
DNA-only transposon
length of DNA that moves from a donor site to a target site either by cut-and-paste transposition or by replicative transposition
reverse transcriptase
enzyme that makes a double-strand DNA copy from a single-strand RNA template molecule
conservative site-specific recombination
rearrangement of DNA that depends on the breakage and rejoining of two DNA helices at specific sequences on each DNA molecule
general transcription factor
helps to position RNA polymerase correctly at the promoter, to aid in pulling apart the two strands of DNA to allow transcription to begin
snRNA (small nuclear RNA)
small RNA molecules that are complexed with proteins to form the ribo-nucleoprotein particles involved in RNA splicing
promoter
nucleotide sequence in DNA to which RNA polymerase binds to begin transcription
exosome
a large protein complex containing multiple 3'-to-5' RNA exonucleases that degrade improperly processed mRNAs, introns, and other RNA debris retained in the nucleus
RNA polymerase
enzyme that carries out transcription
RNA splicing
process in which intron sequences are excised from RNA transcripts in the nucleus during the formation of messenger and other RNAs
Terminator
signal in bacterial DNA that halts transcription
Exon
segment of a eukaryotic gene consisting of a sequence of nucleotides that will be represented in mRNA or other functional RNAs
Nuclear Pore Complex
large muliprotein structure forming a channel through the nuclear envelope that allows selected molecules to move between nucleus and cytoplasm