Principles of Biochemistry Chapter 1 – Flashcards
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any molecule present in living organisms, including macromolecules, and small molecules such as primary and secondary metabolites and natural products
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biomolecules
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The chemistry of living organisms/matter: the scientific study of chemical substances, processes, and reactions that occur in living organisms
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Biochemistry
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An isolated collection of matter; all other matter in the universe apart from the _____ is called the surroundings
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system
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The system and its surroundings together
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universe
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When a system exchanges neither matter not energy with tis surroundings
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isolated
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A system that exchanges neither matter nor energy with the surroundings
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closed system
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A system that exchanges matter and energy with its surroundings
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open system
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A reaction in which electrons are transferred from a donor to an acceptor molecule; also called a redox reaction
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oxidation reduction reactions
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The extent of randomness or disorder in a system
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entropy (S)
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Is defined in terms of three quantities: Enthalpy, (H), reflecting the number and kinds of bonds; Entropy, S, and the absolute temperature, T (in Kelvin) G= H-TS
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free-energy content (G)
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The heat content of a system
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enthalpy (H)
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The exterior membrane surrounding the cytoplasm of a cell
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plasma membrane
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The portion of the cells contents outside the nucleus but within the plasma membrane; includes organelles such as mitochondria
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cytoplasm
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the continuous aqueous phase of the cytoplasm, with its dissolved solutes; excludes the organelles such as mitochondria
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cytosol
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The amount of free energy released (negative Delta G) or absorbed (positive Delta G) in a reaction at constant temperature and pressure
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free-energy change (Delta G)
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Supramolecular assembly of enzymatic complexes that function in the degradation of damaged or unneeded cellular proteins
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proteasomes
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The free-energy change for a reaction occurring under a set of standard conditions: temperature, 298 K; pressure, 1 atm or 101.3 kPa; and all solutes at 1 M concentration. Delta G' denotes the ___ ____ ____ at pH 7.0 in 55.5 M water
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standard free-energy change (Delta Gº)
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A biomolecule, either protein or RNA, that catalyzes a specific chemical reaction. It does not affect the equilibrium of the catalyzed reaction; it enhances the rate of the reaction by providing a reaction path with a lower activation energy
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enzymes
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An activated form of a molecule in which the molecule has undergone a partial chemical reaction; the highest point on the reaction coordinate
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transition state
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The amount of energy (in joules) required to convert all the molecules in 1 mol of a reacting substance from the ground state to the transition state
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activation energy (Delta G++)
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The thousands of enzyme-catalyzed chemical reactions in cells are functionally organized into many sequences of consecutive reactions
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pathways
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The phase of intermediary metabolism concerned with the energy-yielding degradation of nutrient molecules
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catabolism
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The phase of intermediary metabolism concerned with the energy-requiring biosynthesis of cell components from smaller precursors
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anabolism
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The entire set of enzyme-catalyzed transformations of organic molecules in living cells; the sum of anabolism and catabolism
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metabolism
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Inhibition of an allosteric enzyme at the beginning of a metabolic sequence by the end product of the sequence; also known as end-product inhibition
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feedback inhibition
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The study of complex biochemical systems, integrating the functions of several to all of the macromolecules in a cell (RNA, DNA, Proteins)
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systems biology
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A polynucleotide with a specific sequence of deoxyribonucleotide units covalently joined through 3',5'-phosphodiester bonds; serves as the carrier of genetic information
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deoxyribonucleic acid, DNA
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The biologically active conformation of a macromolecule
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native conformation
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An inheritable change in the nucleotide sequence of a chromosome
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mutation
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The normal (unmutated) genotype or phenotype
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wild-type
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The ability of pigments to capture energy of light from the sun, which could be used to reduce, or fix, CO2 to form more complex, organic compounds
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photosynthetic
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The symbiosis in which one organism lives inside of a partner organism and functions as one orrganism
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endosymbiotic
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Genes or proteins that possess a clear sequence and functional relationship to each other
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homologs
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Genes or proteins present in the same species that possess a clear sequence and functional relationship to each other
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paralogs
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Genes or proteins from different species that possess a clear sequence and functional relationship to each other
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orthologs
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a description of the likely function of each gene product, deduced from comparisons with other genomic sequences and established protein functions.
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annotated genome
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An organic cofactor required for the action of certain enzymes; often has a vitamin component
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coenzymes
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evolved from the same branch that gave rise to archaea, makes up the 3rd domain of life and includes all eukaryotic organisms
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Eukarya
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component of plant cells, store large quantities of organic acids, degrades and recycles macromolecules, and stores metabolites
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vacuoles
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An organism that can use the energy of light to synthesize its own fuels from simple molecules such as carbon dioxide, oxygen, and water; as distinct from a chemotroph
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Phototrophs
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A membrane-bounded organelle of eukaryotic cells; it contains many hydrolytic enzymes ans serves as a degrading and recycling center for unneeded components
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lysosomes
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An organism that obtains energy by metabolizing organic compounds derived from other organisms
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Chemotrophs
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A complex membranous organelle of eukaryotic cells; functions in the post-translational modification of proteins and their secretion from the cell incorporation into the plasma membrane or organellar membranes
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Golgi complexes
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Membrane-bounded organelle of eukaryotic cells; contains peroxide-forming and peroxide-destroying enzymes
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peroxisomes
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Membrane-bounded organelle of eukaryotic cells; contains the enzyme systems required for the citric acid cycle, fatty acid oxidation, electron transfer and oxidative phosphorylation
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mitochondria
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An extensive system of double membranes in the cytoplasm of eukaryotic cells; it encloses secretory channels ans is often studded with ribosomes (rough endoplasmic reticulum)
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endoplasmic reticulum
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constituted by the plasma membrane and layers outside of it
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cell envelope
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An extrachromosomal, independently replicating, small circular DNA molecule; commonly employed in genetic engineering
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plasmids
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An organism that can synthesize its own complex molecules from very simple carbon and nitrogen sources, such as carbon dioxide and ammonia
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autotrophs
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An organism that requires complex nutrient molecules, such as glucose, as a source of energy and carbon.
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heterotrophs
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Requiring or occurring in the presence of oxygen
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Aerobic
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Occurring in the absence of air or oxygen
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Anaerobic
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In bacteria, the nuclear zone that contains the chromosome but has no surrounding membrane
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Nucleiod
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One of the five kingdoms of living organisms; _______ have a plasma membrane but no internal organelles or nucleus
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Bacteria
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One of the five kingdoms of living organisms; includes many species that thrive in extreme environments of high ionic strength, high temperature, or low pH.
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Archaea
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A unicellular or multicellular organism with cells having a membrane bonded nucleus, multiple chromosomes and internal organelles
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eukaryotes
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A term used historically to refer to any species in the kingdoms Bacteria and Archaea. The differences between bacteria (formerly referred to as "eubacteria) and archaea are sufficiently great that the inclusive term is of marginal usefulness. A tendency to use "prokaryote" when referring only to bacteria is common and misleading; "prokaryote" also implies an ancestral relationship to eukaryotes, which is incorrect. In the text, "prokaryote" and "prokaryotic" are not used.
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prokaryotes
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All the genetic information encoded in a cell or virus
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genome
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A chemical intermediate in the enzyme-catalyzed reactions of metabolism.
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metabolites
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The state of a system in which no further net change is occurring; the free energy is at a minimum
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equilibrium
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A supramolecular complex of rRNAs and proteins, approximately 18 to 22 nm in diameter; the site of protein synthesis
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ribosomes
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A chemical reaction that proceeds with the release of free energy (that is, for which Delta G is negative).
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exergonic reaction
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The component of the total energy of a system that can do work at constant temperature and pressure
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free-energy (Delta G)
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A chemical reaction that consumes energy (that is, for which Delta G is positive)
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endergonic reaction
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Chlorophyll-containing photosynthetic organelle in some eukaryotic cells
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chloroplasts
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The filamentous network that provides structure and organization to the cytoplasm; includes actin filaments, microtubules, and intermediate filaments
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cytoskeleton
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Segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reactions occur.
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endomembrane system
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The fusion of an intracellular vesicle with the plasma membrane, releasing the vesicle contents to the extracellular space
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Exocytosis
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The uptake of extracellular material by its inclusion in a vesicle (endosome) formed by invagination of the plasma membrane
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Endocytosis
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small biomolecules, specific to certain types of cells or organisms which play roles specific to plant life
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Secondary metabolites
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The complete set of small molecule metabolites (metabolic intermediates, signals, secondary metabolites) present in a given cell or tissue under specific conditions
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metabolome
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The systematic characterization of the metabolome of a cell or tissue
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metabolomics
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A molecule having a molecular weight in the range of a few thousand to many millions
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macromolecules
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A short polymer, usually of amino acids, sugars, or nucleotides; the definition of "short" is somewhat arbitrary, but usually fewer than 50 subunits
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oligomers
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A macromolecule composed of one or more polypeptide chains, each with a characteristic sequence of amino acids linked by peptide bonds
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proteins
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The capacity of a substance to rotate the plane -polarized light
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optical activity
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Broadly, the study of the protein complement of a cell or organism
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proteomics
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Isomers related by rotation about a double bond; also called cis or trans isomers
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cis-trans isomers
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A linear or branched polymer of monosaccharide units linked by glycosidic bonds
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polysaccharides
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A science devoted broadly to the understanding of cellular and organism genomes
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genomics
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All the carbohydrate-containing molecules
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glycome
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An enquimolar mixture of the D and L stereoisomers of an optically active compound
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racemic mixture (racemate)
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Requiring specific configurations in the interacting molecules
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stereospecific
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The spatial arrangement of an organic molecule that is conferred by the presence of either (1) double bonds, about which there is no freedom of rotation, or (2) chiral centers, around which substituent groups are arranged in a specific sequence. Configurational isomers cannot be interconverted without breaking one or more covalent bonds
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configuration
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Compounds that have the same composition and the same order of atomic connections but different molecular arrangements
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stereoisomers
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Biomolecules containing information in the form of specific sequences of different monomers; for example, many proteins, lipids, polysaccharides, and nucleic acids
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informational macromolecules
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A small water-soluble biomolecule generally containing fatty acids, sterols, or isoprenoid compounds
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lipids
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The full complement of lipid containing molecules in a cell, organ, or tissue under a particular set of conditions
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lipidome
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Stereoisomers that are nonsuperposable mirror images of each other
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enantiomers
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Pair of stereoisomers that are not mirror images of each other
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diastereomers
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An atom with substituents arranged so that the molecule is not superposable on its mirror image
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chiral centers
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Biologicallyoccurring polynucleotides in which the nucleotide residues are linked in a specific sequence by phosphodiester bonds; DNA and RNA
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nucleic acids
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Any two molecules with the same molecular formula but a different arrangement of molecular groups
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isomers
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The full complement of proteins expressed in a five cell, or the complete complement of proteins that can be expressed by a given genome
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proteome
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In eukaryotes, a membrane-bonded organelle that contains chromosomes
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nucleus
