Biochemistry Flashcards
Orbitals
a region around the nucleus of an atom with a high probability of containing an electron. The position of electrons can only be described by these probability distributions.
Cation
A positively charged ion
Anion
A negatively charged ion
Isotopes
Different forms of the same element with the same number of protons but different numbers of neutrons
Radioactive Isotopes
An isotope that is unstable and undergoes radioactive decay, releasing energy
Energy levels
A discrete level, or quantum, of energy that an electron in an atom possesses. To change energy levels, an electron must ABSORB or RELEASE energy
Oxidation
Loss of an electron by an atom or molecule; in metabolism often associated with a gain of oxygen or a loss of hydrogen.
Valence Electrons
An electron in the outermost energy level of an atom
Octet Rule
Rule to describe patterns of chemical bonding in main group elements that require a total of eight electrons to complete their outer electron shell.
Why is the molecule formed by two hydrogen atoms stable?
- It has no net charge (meaning the molecule formed with the covalent bonding isn’t charged because it still contains two protons and two electrons)
- The octet rule is satisfied (two orbiting electrons in its outer shell)
- It has no unpaired electrons
Electronegativity
A property of atomic nuclei that refers to the affinity of the nuclei for valence electrons; a nucleus that is more electronegative has a greater pull on electrons than one that is less electronegative.
Nonpolar
Said of a covalent bond that involves equal sharing of electrons. Can also refer to a compound held together by non polar covalent bonds.
Polar covalent bonds
A covalent bond in which electrons are shared unequally due to differences in electronegativity of the atoms involved. One atoms has a partial negative and the other partial positive charge, even though the molecule is electrically neutral overall.
What are the three factors which influence chemical reactions? and why?
- Temperature (heat increases rate of reaction)
- Concentration of reactants and products (reactions act quicker when more reactants are available)
- Catalysts (they naturally speed up chemical reactions)
Hydrogen bonds
A weak association formed with hydrogen in polar covalent bonds. The partially positive hydrogen is attracted to partially negative atoms in polar covalent bonds. In water, oxygen and hydrogen in different water molecules from hydrogen bonds.
Surface Tension
A tautness f the surface of a liquid, caused by the cohesion of the molecules of liquid. Water has an extremely high surface tension.
Hydrophobic
Literally translates as “water-fearing”and describes non polar substances that are not soluble in water. Non polar molecules in water associate with each other and form droplets
Hydrophilic
Literally translates to “water-loving” and describes substances that are soluble in water. These must be either polar or charged (ions).
Hydrophobic exclusion
The tendency of non polar molecules to aggregate together when placed in water, Exclusion refers to the action of water in forcing these molecules together.
mole
the weight of substance in grams that corresponds to the atomic masses of all the component atoms in a molecule of that substance. One mole of a compound always contains 6.02 x 10^23 molecules.
mole concentration
concentration expressed as moles of a substance in 1 L of pure water.
acid
any substance that dissociates in water to increase the hydrogen ion (H+) concentration and thus lower the pH.
base
any substance that dissociates in water to absorb and therefore decrease the hydrogen ion (H+) concentration and thus raise the pH
buffer
A substance that resists changes in pH. It releases hydrogen ions (H+) when a base is added and absorbs H+ when an acid is added.
functional group
A molecular attached to a hydrocarbon that confers chemical properties or reactivities. Examples include hydroxyl (OH), carboxylic acid (COOH) and amino groups (NH2)
Isomers
One of a group of molecules identical in atomic composition but differing in structural arrangement; for example glucose and fructose
polymer
A molecule composed of many similar or identical molecular subunits; starch is a polymer of glucose
monomer
The smallest chemical subunit of a polymer. The monosaccharide of alpha glucose is the monomer found in plant starch, a polysaccharide.
dehydration reaction
A type of chemical reaction in which two molecules join to form one larger molecule, simultaneously splitting out a molecule of water; one molecule is stripped of a hydrogen atom, and another is stripped of a hydroxyl group, resulting in t he joining of the two molecules, while the H and the OH real eased may combine to form a water molecule.
hydrolysis
A reaction that breaks a bond by the addition of water. This is the reverse of dehydration, a reaction that joins molecules with the loss of water.
monosaccharides
A simple sugar that cannot be decomposed into smaller sugar molecules
disaccharide
A carbohydrate formed of two simple sugar molecules bonded covalently.
cellulose
The chief constituent of the cell wall in all green plants, somoe algae, and a few other organisms; an insoluble complex carbohydrate formed of microfibrils of glucose molecules.
polysaccharides
a carbohydrate composed of many monosaccharide sugar subunits linked together in a long chain; examples are glycogen, starch and cellulose
starch
An insoluble polymer of glucose; the chief food storage substance of plants
glycogen
animal starch; a complex branched polysaccharide that serves as a food reserve in animals bacteria and fungi
chitin
A tough, resistant, nitrogen-containing polysaccharide that forms the cell walls of certain funny, the exoskeleton of arthropods, and the epidermal cuticle of other surface structures of certain other invertebrates.
DNA
The genetic material of all organisms; composed of two complementary chains of nucleotides wound in a double helix.
RNA
a class of nucleic acids characterized by the presence of the sugar ribose and the pyrimidine uracil; includes mRNA, tRNA, and rRNA
Dissociation
In proteins, the reversible separation of protein subunits from a quaternary structure without altering their tertiary structure. Also refers to the dissolving of ionic compounds.
Lipids
a non polar hydrophobic organic molecule that is insoluble in water (which is polar) but dissolves readily in non polar organic solvents; includes fats, oils, waxes, steroids, phospholipids, and carotenoids.
Triglyceride
and individual fat molecule, composed of a glycerol and three fatty acids
Saturated fat
a fat composed of fatty acids in which all the internal carbon atoms contain the maximum possible number of hydrogen
Unsaturated fat
a fat molecule in which one or more of the fatty acids contain fewer than the maximum number of hydrogens attached to their carbons
Polyunsaturated fat
a fat molecule having at least two double bonds between adjacent carbons in one or more of the fatty acid chains.
Phospholipids
similar in structure to a fat, but having only two fatty acids attached to the glycerol backbone, with the third space lined to a phosphorylated molecule; contains a polar hydrophilic “head” end (phosphate group) and a non polar hydrophobic “tail” end (fatty acids).
Phospholipid bilayer
the main component of cell membranes; phospholipids naturally associate in a bilayer with hydrophobic fatty acids oriented to the inside and hydrophilic phosphate groups facing outward on both sides.
Glycoproteins
protein molecule modified within the golgi complex by having a short sugar chain (polysaccharide) attached.
Glyclolipids
lipid molecule modified within the Golgi complex by having a short sugar chain (polysaccharide) attached
Enzymes
a protein that is capable of speeding up specific chemical reactions by lowering the require activation energy.
Diffusion
the net movement of dissolved molecules or other particles from a region where they are more concentrated to a region where they are less concentrated
Carrier proteins
A membrane protein that binds to a specific molecule that cannot cross the membrane and allows passage through the membrane.
Channel proteins
a transmembrane protein with a hydrophilic interior that provides an aqueous channel allowing diffusion of species that cannot cross the membrane. Usually allows passage of specific ions such as K+, Na+, or Ca 2+ across the membrane.
Facilitated diffusion
carrier-assisted diffusion of molecules across a cellular membrane through specific channels from a region of higher concentration to one lower concentration; the process is driven by the concentration gradient and does not require cellular energy from ATP
Osmosis
the diffusion of water across a selectively permeable membrane (a membrane that permits the free passage of a solute); in the absence of differences in pressure or volume, the net movement of water is from the side containing a lower concentration of solute to the side containing a higher concentration
Osmotic concentration
the property of a solution that takes into account all dissolved solutes in the solution; if two solutions with different osmotic concentrations are separated by a water-permeable membrane, water will move from the solution with lower osmotic concentration to the solution with higher osmotic concentration
Hypertonic
A solution with a lower concentration of solutes than the cell. A cell in a hypotonic solution tends to take in water by osmosis.
Hypotonic
A solution with a lower concentration of solutes than the cell. A cell in a hypotonic solution tends to take in water by osmosis.
Isotonic
A solution having the same concentration of solutes as the cell. A cell in an isotonic solution takes in and loses the same amount of water.
Turgor pressure
the internal pressure inside a plant cell, resulting from osmotic intake of water, that presses its cell membrane tightly against the cell wall, making the cell rigid. Also known as hydrostatic pressure
uniporter
a carrier protein in a cell’s membrane that transports only a single type of molecule or ion
symporter
a carrier protein in a cell’s membrane that transports two molecules or ions in the same direction across the membrane
antiporter
a carrier protein in a cell’s membrane that transports two molecules in opposite directions across the membrane
sodium-potassium pump
transmembrane channels engaged in the active (ATP-driven) transport of Na+, exchanging them for K+, where both ions are being moved against their respective concentration gradients; maintains the resting membrane potential of neurone and oner cells
phagocytosis
Endocytosis of a solid particle; the plasma membrane fold inward around the particle (which may be another cell) and engulfs it to form a vacuole
pinocytosis
the processor fluid uptake by endocytosis in a cell
receptor-mediated endocytosis
process by which specific macromolecules are transported into eukaryotic cells at clathrin-coated pits, after binding to specific cell-surface receptors.
exocytosis
A type of bulk transport out of cells in which a vacuole fuses with the plasma membrane, discharging the vacuole’s contents to the outside.
Peptide bond
the type of bond that links amino acids together in proteins through a dehydration reaction
polypeptides
a molecule consisting of many joined amino acids; not usually as complex as a protein
tertiary structure
the folded shape of a protein, produced by hydrophobic interactions with water, ionic and covalent bonding between side chains of different amino acids, and van der Waal’s forces; may be changed by denaturation so that the protein becomes inactive.
secondary structure
In a protein, hydrogen-bonding interactions between -CO and -NH groups of the primary structure
alpha helix
A form of secondary structure in proteins where the polypeptide chain is wound into a spiral due to interactions between amino and carboxyl groups in the peptide backbone.
beta sheet
a form of secondary structure in proteins where the polypeptide folds back on itself one or more times to form a planar structure stabilized by hydrogen bonding between amino and carboxyl groups in the peptide backbone. Also known as a beta pleated sheet
domains
a distinct modular region of a preteen that serves a particular function in the action of the protein, such as a regulatory domain or a DNA-binding domain
motifs
a substructure in proteins that confers function and cabe found in multiple proteins. One example is the helix-turn-helix motif found in a number of preens that is used to bind to DNA
denaturation
the loss of the native configuration of a protein or nucleic acid as a result of excessive heat, extremes of pH, chemical modification, or changes in solvent ionic strength or polarity that disrupt hydrophobic interactions; usually accompanied by loss of biological activity
nucleic acid
a nucleotide polymer; chief types are deoxyribonucleic acid (DNA), which is double stranded, and ribonucleic acid (RNA), which is typically single-stranded
double helix
the structure of DNA, in which two complementary polynucleotide strands coil around a common helical axis.
complementary
describes genetic information in which each nucleotide base has a complementary partner with which it forms a base-pair.
ATP
a nucleotide consisting of adenine, ribose sugar, and three phosphate groups; ATP is the energy currency of cellular metabolism in all organisms
Inorganic phosphate
a phosphate molecule that is not a part of an organic molecule; inorganic phosphate groups are added and removed in the formation and breakdown of ATP and in many other cellular reactions
substrates
a molecule on which an enzyme acts
active sites
the region of an enzyme surface to which a specific set of substrates binds, lowering the activation energy require for a particular chemical reactions and so facilitating it .
enzyme-substrate complex
the complex formed when an enzyme binds with its substrate. This complex often has an altered configuration compared with the non bound enzyme
multienzyme complexes
an assembly consisting of several enzymes catalyzing different steps in a sequence of reactions. Close proximity of those related enzymes speeds the overall process, making it more efficient
competitive inhibitors
an inhibitor that binds to the same active site as an enzyme’s substrate, thereby competing with the substrate.
noncompetitive inhibitors
an inhibitor that binds to a location other than the active site of an enzyme, changing the enzyme’s shape so that it cannot bind the substrate
allosteric site
a part of an enzyme, away from its active site, that serves as an on/off switch for the function of the enzyme.
allosteric inhibitor
a noncompetitive inhibitor that binds to an enzyme’s allosteric site and prevents the enzyme from changing to its active configuration
coenzyme
A nonprotein organic molecule such as NAD that plays an accessory role in enzyme catalyzed processes, often by acting as a donor or acceptor of electrons.
biochemical pathways
a sequence of chemical reactions in which the product of one faction becomes the substrate of the next reaction. The Krebs cycle is a biochemical pathway.
feedback inhibition
control mechanism whereby an increase in the concentration of some molecules inhibits the synthesis of that molecule
Condensation synthesis
Monomers bonded together. The Hydrogen is removed from one and combined with the OH from the other to form a molecule of water (H2O). “So you get the bonded thing + the water”
Waxes
a long chain of alcohol bonded to a fatty acid
