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Biology Ch 4 & 5

Terms

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Mechanism
Scientific view that all natural phenomena are governed by both physical & chemical laws
Cellulose
Structural polysaccharide that is a major component of the tough walls enclosing plant cells; most abundant organic compound on earth; similar to starch in that it's a polymer of glucose but is a beta (β) glucose ring structure & lays straight & never branches
Tetramer
Protein with four polypeptide chains
Catalysts
Chemical agents that selectively speed up chemical rxns in cell w/o being consumed by rxn
Ester linkage
Bond btwn hydroxyl and carboxyl grp, joining glycerol and fatty acids together → dehydration rxn
Ribonucleic acid (RNA)
Genetic material that transcribes genetic information in DNA and translates it into proteins; acts as a messenger
Nuclear magnetic resonance spectroscopy
A method used to track the folding of a protein without using crystallization;
Alcohols
Name of the hydroxyl compounds
CO(NH2)2
Chemical composition of the organic compound found in urine (urea)
Amines
Name of amino compounds
Sulfhydryl group
(-SH); two of these grps can interact to help stabilize protein structure
Hydrophobic interaction
Interaction commonly occurring in tertiary structure where the nonpolar ends of the protein cluster together in the core of the protein, away from the water (allowing protein to be reshaped)
Lipids
The one class of large biological molecules not consisting on polymers; they have little/no affinity for water & consist mostly of hydrocarbons
Adipose cells
Cells that humans and other mammal stock their long-term food reserves (fats); also serve as cushioning and, when found in subcutaneous layer, as insulation
Deoxyribonucleic acid (DNA)
The genetic material that organisms inherit from their parents; contained in each chromosome
Monosaccharide
Simplest carbohydrates; known as simple sugars; chemical formula is usually some multiple of CH2O; carbon skeleton is usually 3-7
Adenosine triphosphate
Primary energy-transferring molecule in the cell; consisting of an organic molecule (adenosine) attached to a string of 3 phosphate grps
Carbohydrates, lipids, proteins, and nucleic acids
Four main classes of large biological molecules
Defensive proteins
Proteins serving as protection against disease
Berzelius
Swedish chemist who made the distinction between organic & inorganic compounds
Condensation reaction
How monomers are connected; rxn by which 2 molecules are covalently bonding through loss of a water molecule
Asymmetric carbon
The middle carbon in an enantiomer; what the four atom (groups) are arranged around
Hydroxyl group
(-OH); is polar as a result of the electronegative oxygen atom drawing e- towards itself; attracts water molecules helping dissolve organic compounds, e.g. sugars
Beta (β) glucose ring structure
Glucose ring structure where hydroxyl grp is above the plane
Structural isomers
Isomers differing in te covalent arrangements of their atoms
Tetravalence
A molecule branching off in four directions; carbon is an example of this, a quality allowing it to be extremely versatile
Ketose
Name of polysaccharide when carbonyl compound is within the C-skeleton; fructose is an ex.
Amino acids
(-NH2); acts as a base, can pick up a proton from the surrounding soln; ionized w/ a charge of 1+ under cellular conditions
Phospholipids
Similar to a fat but has only 2 fatty acids attached to a glycerol rather than three; third hydroxyl grp of glycerol is joined to a phosphate grp (w/ a negative electrical charge, polar) which in turn can be linked to other small molecules
Trimer
Protein with three polypeptide chains
Monomers
The repeating units that serve as the building blocks of a polymer
Acetone
C2H6CO; simplest ketone
Nucleoside
Portion of a nucleotide without a phosphate grp
Polynucleotides
Polymers that compose nucleic acids
Conformation
The shape that a protein assumes, determines the biological activity of the protein
Urea
Organic compound present in the urine of animals
N-terminus
The amino end of a polypeptide chain
Triacylglycerol
Aka fat molecule, three fatty acids linked to one glycerol molecule (by means of an ester linkage)
Hexoses
Sugars with six carbons
Thiols
Name of sulfhydryl compounds
Side chain
Another term for R-group; variable grp of an amino acid that differs w/ each and determines the unique characteristics of a particular amino acid
Lactose
Milk sugar; glucose and galactose monomers joined by a glycosidic linkage
Carboxylic acids
Name of carboxyl compounds; organic acids
Structural polysaccharides
Sugars used as building materials for structures that protect the cell/whole organism
Secondary structure
The coiling and folds of a peptide chain, contributes to the protein's overall conformation
Steroids
Lipids characterized by a carbon skeleton consisting of four fused rings
Alpha (α) glucose ring structure
Glucose ring structure where hydroxyl grp is below the plane
Antiparallel
The structure of how the two sugar-phosphate backbones run in a nucleotide (on the outside) w/ the nitrogenous bases paired off in the middle (Adenine pairs with Thymine & Guanine pairs with Cytosine - they are complimentary)
Proteins
Accounting for more than 50% of the dry mass of most cells; instrumental in almost everythin organisms do → speed up chemical rxns or play a role in structural support, storage, transport, etc. etc.
Aldehydes
Name carbonyl compound when it is at the end of a C-skeleton
Nucleotides
Monomers that compose polynucleotides; composed of a nitrogenous base, a pentose (5-C sugar) and a phosphate grp
Propanal
C2H6CO; an aldehyde version
Hydrocarbons
Organic molecules consisting of only carbon and hydrogen; can undergo reactions that release lg. amnt of energy; a major component of petroleum
Starch
Storage polysaccharide of plants, a polymer consisting entirely of glucose monomers (joined by 1-4 carbon linkages) & has bond angles that make the polymer helical
Fatty acids
Long carbon skeleton, at the end of which is a carboxyl grp; the rest of which is a long hydrocarbon chain (nonpolar) which is the reason why fats are hydrophobic
Dimer
Protein with two polypeptide chains
CO2
Substance that is the source of carbon for all organic molecules found in organisms even though it itself may not be organic
Cellular respiration
Process by which cells extract the energy stored in glucose molecules
Hydrolysis
The process that is reverse of the dehydration rxn: between monomers are broken by the addn of water molecules (attaching one monomer to H and another to a hydroxyl grp
Denaturation
Process by which added heat, for ex, can unravel a protein and make it lose its native conformation, making it biologically inactive.
Plastids
Cellular structure in plants where starch granules are stored → can be withdrawn by hydrolysis, which breaks bonds btwn glucose monomers
Insoluble fiber
Oftentimes refers to cellulose; though we cannot digest this, it aids our smooth passage of **** through intestines
Nucleic acids
Class of compounds that store information specifying the primary structure of proteins; consist of long polymers of repeated subunits called nucleotides
Aldose
Name of polysaccharide when carbonyl compound is at the end of a C-skeleton; glucose is an ex.
Bilayers
When phosopholipids are added to water, they form these double-layered aggregates (one end of the phospholipids is polar, the other non-polar) that shield their hydrophobic portions from water
Trans fat molecules
Partially hydrogenated unsaturated fats; not found in nature; can promote heart disease, etc.
Disaccharide
Double sugars; two monosaccharides joined by a condensation rxn; joined together by a glycosidic linkage
Chitin
Important structural polysaccharide used by arthropods (insects, crustaceans) to build their exoskeletons; similar to cellulose except the glucose monomer has a nitrogen-containing appendage
Functional groups
Components of organic molecules that are most commonly involved in chemical rxns; behaves consistently from one organic molecule to another
Structural proteins
Proteins serving as support
Carbonyl group
(>CO); C atom joined to an O atom w/ double bond ketone/aldehyde may be structural isomers w/ different properties
Disulphide bridges
In tertiary structure, the conformation of a protein owing to 2 cysteine monomers are brought close together & a S-S bond forms, riveting part of the protein together
C-terminus
The carboxyl grp end of a polypeptide chain
"cis" isomer
Type of geometric isomer where the two Xs on the same side relative to the double bond
Organic chemistry
Branch of chemistry specializing in carbon compounds
Macromolecule
Giant molecules consisting of a mass in excess of hundreds of thousands of Daltons
Peptide bond
Bond joining amino acids; the carboxyl grp of one is adjacent to the amino grp of another, an enzyme can conjoin them w/ a dehydration rxn known as this
Glycosidic linkage
Covalent bond formed between two monosaccharides in a dehydration rxn
Polypeptides
Polymers of amino acids (proteins consists of one or more of these folded and coiled into specific conformations)
Ketones
Name of carbonyl compound when it is within the C-skeleton
Chaperonins
Protein molecules that assist the proper folding of other proteins; they work by keeping the new polypeptide segregated from bad influences in the cytoplasmic environment while it folds spontaneously
"trans" isomer
Geometric isomer where two Xs are on opposing sides
Hydrogenation
Process by which unsaturated fats have been synthetically converted to saturated fats by adding H
Ethanol
C2H5OH; alcohol present in alcoholic beverages
Quaternary structure
A type of protein structure strictly for proteins w/ multiple polypeptide chains; the overall structure that results from these polypeptide chains being held together
Microfibrils
Main architectural unit of the plant cell wall formed by parallel cellulose molecules
Alpha (α) helix
In a protein's secondary structure, 3.6 amino acids occupy each turn of the helix and the helical structure is maintained by the formation of H-bonds between amino acids in successive turns; bond between the N of one amino acid & the O of the third one beyond it
Fibrous proteins
Type of proteins that generally have an alpha helix secondary structure
Vitalism
Belief in a life force outside the jurisdiction of physical & chemical laws; eventually crumbled after lab synthesis of complex organic molecules
x-ray crystallography
An important method used to determine a protein's three-dimensional structure (and thus track its folding behavior) by aiming an x-ray at a crystallized protein, diffracting the x-rays
Dehydration reaction
Another term for condensation reaction; specifically addresses the loss of the water molecule
Gene
A unit of inheritance upon which the primary structure of a protein is programmed
Tertiary structure
Protein structure resulting from common interaction with water; folding of the alpha helix upon itself creating spherical/globular shapes
Beta (β) pleated sheet
In a protein's secondary structure, two or more regions of the polypeptide chain lying side by side are connected by H-bonds between parts of the two parallel polypeptide chains
Wöhler
German chemist who, in 1828 chipped away at vitalism by mixing ammonium & cyanate ions & producing urea
Isomers
Variation in the architecture of organic molecules; compounds that have same # of atoms & same elements but different structures & thus different properties
Polysaccharides
Macromolecule carbohydrates that are polymers composed of many sugar building blocks
Carbohydrates
Include both sugars and the polymers of sugars
Tetrahedral
Four single bonds creating this molecular shape; 109.5 degree bond angles
Carboxyl group
(-COOH); O atom 2x-bonded to C atom bonded to a hydroxyl grp; has acidic properties because it's a source of H+; covalent bond between O & H is so polar that H+ tend to dissociate reversibly
Phosphate group
(-OPO32-); One of the O atoms is bonded to C-skeleton; two Os carry a negative charge; this grp is an ionized form of phosphoric acid grp (-OPO3H2); makes the molecule of which it's a part of an anion; can transfer energy between organic molecules
Geometric isomers
Isomers w/ same covalent partnerships but differ in their spatial arrangements; arise from the inflexibility of double bonds (which don't allow atoms they join to rotate)
Polymers
Long molecule consisting of many similar/identical building bocks linked by covalent bonds
Primary structure
The unique sequence of amino acids that determines the unique features of the polypeptide
Shape
The determining factor in how a functional protein functions; allows us to "mimic" endorphins (to create morphine - YAY!)
Glycogen
Polysaccharide that animals store (similar to amylopectin but more extensively branched); mainly stored in liver and muscle cells & released by hydrolysis
Globular proteins
Type of proteins that generally have a beta pleated sheet secondary structure
Ribbon model
Protein model showing how the single polypeptide chain folds and coils to form the functional protein
Glycerol
An alcohol with three carbons attached to three hydroxyl grps; a component of lipids
Enzymatic proteins
Proteins serving as a selective accelerator of chemical rxns
Storage proteins
Proteins serving to help store amino acids
Contractile and motor proteins
Proteins pivotal in movement
Carboxylate group
What (-COOH) is called when found in cells in ionic form
Pentoses
Five-carbon sugars
Enzymes
Most important type of protein; regulates metabolism by acting as catalysts
Adenosine diphosphate
When ATP loses a phosphate grp it becomes this
Transport proteins
Proteins that serve to transport other substances
Pentose
Five-carbon sugar that is one of three subunits composing nucleotides; is either ribose (found in RNA) or dioxyribose (found in DNA - has 1 less O than ribose)
Fats
Large molecules constructed from glycerol and fatty acids joined together by dehydration rxns; main function of which is energy storage (Can store 2x as much energy as polysaccharides)
Hormonal proteins
Proteins that serve as the coordination of an organisms activities
Receptor proteins
Proteins that serve as the response of cell to chemical stimuli
Glycine
Both an amine and carboxylic acid; compounds w/ both grps are called amino acids
Space-filling model
Protein model showing the globular shape seen in many proteins
Cholesterol
Steroid that serves as the common component of animal cell membranes & is precursor from which other steroids are synthesized (into hormones, for ex.)
Glucose
C6H12O6; the most common monosaccharide; composed of a carbonyl grp (>C=O) and multiple hydroxyl grps (-OH)
Sucrose
Table sugar w/ two monomers, glucose and fructose, joined by a glycosidic linkage
Rhodopsin
Chemical compound in the eye affected by the light-induced change from cis-isomer to trans-isomer.
Pyrimidine
One family of nitrogenous base (one of the three units that compose a nucleotide) that has a six-membered ring of carbon; members include cytosine (found in both RNA and DNA), thymine (found only in DNA), and uracil (found only in RNA)
Purine
One family of nitrogenous base (one of three subunits that compose a nucleotide) has a six-membered ring fused to a five-membered ring; members include adenine and guanine (found in both RNA and DNA
Storage polysaccharides
Sugars kept and hydrolyzed as needed to provide energy for cells
Trioses
Three-carbon sugars
Carbon chains
What form the skeletons of most organic molecules, varying in length, shape, and number
Enantiomers
Molecules that are mirror images of each other; one may not be biologically active (e.g. L-dopa is active but D-dopa suxcore)

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