nucleotide
each monomer in a single DNA strand which consists of two parts: a sugar (deoxyribose) with a phosphate group attached to it and a base- either A, G, C and T. DNA and RNA are polymers of this. linked together by strong covalent chemical bonds.
DNA replication
process by which a copy of DNA molecule is made. this process occurs at different rates, with different controls to start it or stop it, and different auxiliary molecules to help it along.
transcription
copying of one strand of DNA into a complementary RNA sequence by the enzyme RNA polymerase. RNA monomers are lined up and selected for polymerization on a template strand of DNA.
ribonucleic acid (RNA)
polymer formed from covalently linked ribonucleotide monomers.
translation
process by which the sequence of nucleotides in an mRNA molecule directs the incorporation of amino acids into protein.
messenger RNA (mRNA)
RNA molecule that specifies the amino acid sequence of a protein
protein
the major macromolecular constituent of cells. a linear polymer of amino acids linked together by polypeptide bonds in a specific sequence. they fill out most of the of the cell's mass.
peptide bond
a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). This is a dehydration synthesis reaction (also known as a condensation reaction),
amino acids
organic molecule containing both an amino group and a carboxyl group. those in which the amino and carboxyl groups are linked to the same carbon atom serve as the building blocks of proteins. monomers of protein with 20 different types.
polypeptide
protein molecules which are created by joining amino acids in a particular sequence folds into a precise three-dimensional form with reactive sites on its surface.
enzyme
protein that catalyzes a specific chemical reaction that make or break covalent bonds.
codon
triplet of nucleotides that codes for a single amino acid in a corresponding protein.
transfer RNAs (tRNAs)
set of small RNA molecules used in protein synthesis as an interface (adaptor) between mRNA and amino acids. Each molecule is covalently linked to a particular amino acid.
ribosomal RNAs (rRNA)
any one of a number of specific RNA molecules that form part of the structure of a ribosome and participate in the synthesis of proteins. often distinguished by their sedimentation coefficient.
gene
region of DNA that is transcribed as a single unit and carries information for a discrete hereditary characteristic, usually corresponding to (1) a single protein or (2) a single RNA
genome
the total genetic information carried by a cell or an organism (or the DNA molecules that carry this information)
plasma membrane
the selective barrier composed of a lipid bilayer and embedded proteins that surrounds a living cell.
bacteria
one of the three main branches of the tree of life. lacks a distinct nuclear compartment, and comprise the Procaryotes.
archaea
single-celled organism without a nucleus, superficially similar to bacteria. at a molecular level, more closely related to bacteria in metabolic machinery, but more similar to eucaryotes in genetic machinery and comprise the Procaryotes.
mutations
heritable change in the nucleotide sequence of a chromosome.
highly conserved genes
a gene that codes for a highly optimized essential protein or RNA molecule cannot alter so easily: when mistakes occur, the faulty cells are almost always eliminated.
intragenic mutation
an existing gene can be modified by changes in its DNA sequence, through various types of error that occur mainly in the process of DNA replication.
gene duplication
an existing gene can be duplicated so as to create a pair of initially identical genes within a single cell
segment shuffling
two or more existing genes can be broken and rejoined to make a hybrid gene consisting of DNA segments that originally belonged to separate genes.
horizontal (intercellular) transfer
a piece of DNA can be transferred from the genome of one cell to that of another-even to that of another species.
orthologs
genes or proteins from different species that are similar in sequence because they are descendants of the same gene in the last common ancestor of those species.
paralogs
genes or proteins that are similar in sequence because they are the results of a gene duplication event occurring in an ancestral organism.
homologs
one of two or more genes that are similar in sequence as a result of derivation from the same ancestral gene. the term covers both paralogs and orthologs.
viruses
particle consisting of nucleic acid (RNA or DNA) enclosed in a protein coat and capable of replicating within a host cell and spreading from cell to cell. non-living and act as vectors for gene transfer.
model organism
organism selected for intensive study as a representative of a large group of species.
polypeptide backbone
the chain of repeating carbon and nitrogen atoms, linked by peptide bonds, in a protein.
side chains
the part of an amino acid that differs between amino acid types. this structure gives each type of amino acid its unique physical and chemical properties.
conformation
the final folded structure of any polypeptide chain is generally the one that minimizes its free energy.
molecular chaperones
special proteins that assist in protein folding.
denature
treatment with certain solvents, which disrupt the noncovalent interactions holding the folded chain together, unfolding a protein.
protein domains
structural units that fold more or less independently of each other. portion of a protein that has a tertiary structure of its own. larger proteins are generally composed of several domains, each connect to the next by short flexible regions of polypeptid
alpha helix
common folding pattern in proteins in which a linear sequence of amino acids folds into a right-handed coil stabilized by internal hydrogen bonding between backbone atoms. a hydrogen bond forms between every fourth peptide bond, linking the C=O of one pep
beta helix
common structural motif in proteins in which different sections of the polypeptide chain run alongside each other and are joined together by hydrogen bonding between atoms of the polypeptide backbone.
coiled-coil
alpha helices wrap around each other to form a particularly stable structure. alpha helices have most of their nonpolar (hydrophobic) side chains on one side, so they can twist around each other with these chains facing inward.
primary structure
the amino acid sequence of a protein
secondary structure
regular local folding patterns in a protein, including alpha helix and beta sheet
tertiary structure
complex three-dimensional form of a folded protein
quaternary structure
three-dimensional relationship of the different polypeptide chains in a multisubunit protein or protein complex.
protein module
a subset of protein domains that have been especially mobile during evolution; they seem to have particularly versatile structures.
binding site
region on the surface of one molecule (usually a protein or nucleic acid) that can interact with another molecule through noncovalent bonding.
protein subunit
an individual protein that mediates the transport of another protein across a membrane.
hemoglobin
the protein that carries oxygen in red blood cells, contains two identical alpha-globin subunits and two identical beta-globin subunits, symmetrically arranged.
globular proteins
the polypeptide chain folds up into a compact shape like a ball with an irregular surface. ex. enzymes.
fibrous proteins
other proteins that have rolls in the cell that require each individual protein molecule to span a large distance. they have a relatively simple, elongated three-dimensional structure.
intermediate filaments
an important component of the cytoskeleton that creates the cell's internal structural framework.
ligand
any molecule that binds to a specific site on a protein or other molecule.
catalyst
substance that can lower the activation energy of a reaction (thus increasing its rate), without itself being consumed by the reaction.
lysozyme
enzyme that catalyzes the cutting of polysaccharide chains in the cell walls of bacteria. the active site is a long groove that holds six linked sugars at the same time.
allostery
change in a protein's conformation brought about by the binding of a regulatory ligand (at a site other than the protein's catalytic site), or by covalent modification. the change in conformation alters the activity of the protein and can form the basis o
active site
region of an enzyme surface to which a substrate molecule binds in order to undergo a catalyzed reaction. recognizes the substrates.
regulatory site
recognizes a regulatory molecule on an enzyme.
conformational change
in a protein- binding at one of the sites causes a shift from one folded shape to a slightly different folded shape.
chromosome
structure composed of a very long DNA molecule and associated proteins that carries part (or all) of the hereditary information of an organism.
deoxyribonucleic acid (DNA)
polynucleotide formed from covalently linked deoxyribonucleotides units. the store of hereditary information within a cell and the carrier of this information from generation to generation.
double helix
the three-dimensional structure of DNA, in which two anti-parallel DNA chains, held together by hydrogen bonding between the bases, are wound into this structure.
base pairs
two nucleotides in an RNA or DNa molecule that are held together by hydrogen bonds. A and T, G and C.
antiparallel
describes the relative orientation of the two strands in a DNA double helix or two paired regions of a polypeptide chain; the polarity of one strand is oriented in the opposite direction to that of the other.
complementary
of nucleic acid sequences: capable of forming a perfect base-paired duplex with each other.
gene expression
a cell converts the nucleotide sequence of a gene first into the nucleotide sequence of an RNA molecule, and then into the amino acid sequence of a protein.
template
single strand of DNA or RNA whose nucleotide sequence acts as a guide for the synthesis of a complementary strand.
chromatin
complex of DNA, histones and nonhistone proteins found in the nucleus of a eukaryotic cell. the material of which chromosomes are made.
homologous chromosomes
the maternal and paternal copies of a particular chromosome in a diploid cell.
karyotype
display of the full set of chromosomes of a cell, arranged with respect to size, shape and number.
exon
segment of eucaryotic gene that consists of a sequence of nucleotides that will be represented in mRNA or in the final transfer, ribosomal, or other mature RNA molecule. in protein-coding genes, these encode the amino acids in the protein. it is usually a
intron
noncoding region of a eucaryotic gene that is transcribed into an RNA molecule but is then excised by RNA splicing during production of the mRNA or other functional RNA.
cell cycle
reproductive cycle of a cell: the orderly sequence of events by which a cell duplicates its chromosomes, and, usually the other cell contents and divides into two.
replication origin
location on a DNA molecule at which duplication of the DNA begins.
centromere
centrally located organelle of animal cells that holds sister chromatids together. also the site on the DNA where the kinetochore forms that captures microtubules from the mitotic spindle.
telomere
end of chromosome, associated with a characteristic DNA sequence that is replicated in a special way. counteracts the tendency of the chromosome otherwise to shorten with each round of replication.
histone
one of a group of small abundant proteins, rich in arginine and lysine. they form the nucleosome cores around which DNA is wrapped in eucaryotic chromosome.
nucleosome
beadlike structure in eucaryotic chromatin, composed of a short length of DNA wrapped around an octameric core of histone proteins. the fundamental structural unit of chromatin.