Bio 160

anything that takes up space and has mass

a substance that cannot be broken down to other substances by chemical reactions

is a substance consisting of two or more different elements

elements that an organism needs to live a healthy life and reproduce

Oxygen (O), Carbon (C), Hydrogen (H), and Nitrogen (N)

are required by an organism in only minute quantities

the number of protons and is written as a subscript to the left of the symbol for the element.

sum of protons and nuetrons in the nucleus of an atom

Total mass of the protons and neutrons in an atom, measured in atomic mass units

different atomic forms of the same element. (differs in number of electrons)

isotope in which the nucleus decays (breaks down) over time, giving off radiation in the form of matter and energy

the capacity to cause change

is the energy that matter possesses because of its location or structure.

Electrons in the outermost shell

the outermost electron shell

the 3D space where an electron is found.

sharing of a pair of valence elctrons by two atoms

a pair of shared electrons

the sharing of two pairs of valence electrons

the attraction of a particular atom for the electrons of a covalent bond

a bond between two atoms of the same element, the electrons are shared equally.

When one atom is bonded to a more electronegative atom, the electrons of the bond are not shared equally.

a charged atom or molecule

Because of their opposite charges, cations and anions attract each other.

covalent bonds

noncovalent attraction between a hydrogen and an electronegative atom

are individually weak and occur only when atoms and molecules are very close together.

Oxygen is more electronegative than hydrogen, so the electrons of the covalent bonds spend more time closer to oxygen than to hydrogen.

(physics) the intermolecular force that holds together the molecules in a solid or liquid

the clinging of one substance to another

a measure of how difficult it is to stretch or break the surface of a liquid.

any substance that has an affinity for water

A stable suspension of fine particles in a liquid

substances that seem to repel water.

a substance that increases the hydrogen ion concentration of a solution

a substance that reduces the hydrogen ion concentration of a solution

the negative log of the hydrogen ion concentration

is a substance that minimizes changes in the conentration of Hplus and OHminus

organic molecules consisting of only carbon and hydrogen

variations in the architecture of organic molecules

differ in the covalent arrangements of their atoms.

carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds.

are isomers that are mirror images of each other and that differ in shape due to the presence of an asymmetric carbon.

OH alcohols functional properties; Is polar as a result of the electrons spending more time near the electronegative oxygen atom. Can form hydrogen bonds with water molecules helping dissolve organic compounds such as sugars.

CO Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton.

COOH Carboxylic acids, or organic acids Ex: Acetic acid, which gives vinegar its sour taste. Acts as an acid; can donate an H because the covaelent bond between oxygen and hydrogen is so polar: Found in cells in the ionized form with a charge of 1- and called a carboxylate ion.

NH2 Amines glycine, a compound that is both an amine and a carboxylic acid because it has both an amino group and a carboxyl group; compounds with both groups are called amino acids. Acts as a Base; can pick up an H+ from the surrounding solution found in cells in the ionized form with a charge of 1+

SH Thiols cysteine, an important sulfur containing amino acid. two sulfhydryl groups can react, forming a covalent bond. This "cross linking' helps stabilize protein structures. cross linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be permanently curled by shaping it around curlers and them breaking and reforming the cross linking bonds.

OPO3 organic phosphates glycerol phosphate, which takes part in many important chemical reactions in cells; glycerol phosphate also provides the backbone for phospholipids, the most prevalent molecules in cell membranes

CH3 methylated compounds methyl cytidine a component of DNA that has been modified by addition of a methyl group.

consists of an organic molecule called adenosine atttached to a string of three phosphate groups, is an important source of energy for cellular processes.

isomers differ in the arrangement or bonding of atoms.

adhesion of water molecules to other kinds of molecules

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either hydroxyl or carboxyl groups

I and II

complementary pairing of the nitrogenous bases

They are both polymers of glucose.

Water ionizes to form hydroxide and hydronium ions. Occasionally, a proton participating in a hydrogen bond shifts from one molecule to the other, leaving its electron behind. The result is the formation of a hydronium (H3O+) and a hydoxide (OH-) ion. The hydronium ion is often represented by a proton (H+).

hydrogen bonds between the amino group of one peptide bond and the carboxyl group of another peptide bond

emergent properties

unique three-dimensional shape of the fully folded polypeptide.

light energy.

Hypotheses usually are relatively narrow in scope; theories have broad explanatory power.

The fish swam in a zigzag motion.

They are insoluble in water.

function in the synthesis of proteins

Enantiomers differ in biological activity.

Bacteria and Archaea

They have multiple double bonds in the carbon chains of their fatty acids.

DNA duplexes will unwind and separate, and proteins will unfold (denature).

Starch

Weak bonds are transient and easily reversible.

ATP

A nucleotide consists of three parts: a nitrogenous base, a pentose sugar, and one or more phosphate groups. ATP consists of a nitrogenous base (adenine), a pentose sugar, and three phosphate groups.

Quaternary level of protein structure

They are not soluble in water.

Primary and tertiary levels of protein structure

The primary structure of a protein is the specific linear sequence of amino acids forming the protein. The amino acids are joined by covalent peptide bonds. Tertiary structure, producing the unique structure of a protein, is stabilized by interactions among the R groups on each amino acid in the protein. Tertiary structure may be stabilized by covalent bonds, called disulfide bridges, that form between the sulfhydryl groups (SH) of two cysteine monomers. Tertiary structure may also be stabilized by weaker interactions, including hydrogen bonds between polar and/or charged areas, ionic bonds between charged R groups, and hydrophobic interactions and van der Waals interactions among hydrophobic R groups.

Starch and cellulose differ in the glycosidic linkages between their glucose monomers. Both starch and cellulose are glucose polymers, but the glycosidic linkages in these two polymers differ, as shown in Figure 5.7. Glucose can have two slightly different ring structures. When glucose forms a ring, the hydroxyl group attached to the number 1 carbon is positioned either below (alpha)or above (beta) the plane of the ring. In starch, all the glucose monomers are in the alpha configuration (Figure 5.7b). In cellulose, all the glucose monomers are in the beta configuration. As a result, every other glucose monomer is "upside down" with respect to its neighbors (Figure 5.7c). The differing glycosidic linkages in starch and cellulose give the two molecules distinct three-dimensional shapes, leading to key functional differences.

A methyl group consists of a carbon bonded to three hydrogen atoms.

different side chains (R groups) attached to an α carbon

fatty acids

Hundreds of individuals of a species have been observed and all are photosynthetic; therefore, the species is photosynthetic.

contains one less oxygen atom.

DNA nucleotides contain a different sugar than RNA nucleotides.

Amino and carboxyl are functional groups.

The lone electron of a hydrogen atom and an electron of a helium atom have equal potential energy.

Van der Waals interactions

is a long molecule consisting of many similar or identical building blocks linked by covalent bonds, much as a train consists of a chain of cars.

are the building blocks of polymers and are smaller molecules.

specialized macromolecules that speed up chemical reactions.

Monomers are connected by a reaction in which two molecules are covalently bonded to each other, with the loss of a water molecule.

a process that is essentially the reverse of the dehydration reaction. (to break using water) The bond between the monomers is broken by the addition of a water molecule, with the hydrogen from the water attaching to one monomer.

generally have molecular formulas that are some multiple of the unit CH2O. Glucose is the most common monosaccharide.

consists of two monosaccharides joined by a glycosidic linkage

a covalent bond formed between two monosaccharaides by a dehydration reaction.

are macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by a glycosidic linkages.

a polymer of glucose monomores, Plants store this as granules within cellular structures known as plastids.

a polymer of glucose that is like amylopectin. Animals store this polysaccharide.

is a major component of the tough walls that enclose plant cells. a strong material that organisms build.

another important structural polysaccharide. The carbohydrate used by arthropods to build their exoskeletons.

constructed from two kinds of smaller molecules; glycerol and fatty acids.

has a long carbon skeleton, usually 16 or 18 carbon atoms in length.

in making a fat, three fatty acid molecules are each joined to glycerol by an ester loinkage, a bond between a hydroxyl group and a carboxyl group.

if there are no double bonds between carbon atoms composing a chain, then as many hydrogen atoms as possible are bonded to the carbon skeleton.

has one or more double bonds, with one fewer hydrogen atom on each double bonded carbon

Recent studies have shown that the process of hydrogenating vegetable oils produces not only saturated fats but also unsaturated fats with trans double bonds. This type of fat may also contribute more to atherosclerosis.

are essential for cells because they make up cell membranes.

is a crucial molecule in animals. it is a common component of animal cell membranes and is also the precursor from which other steroids are synthesized.

are lipids characterized by a carbon skeleton consisting of four fused rings.

A polymer (chain) of many amino acids linked together by peptide bonds.

is a bioligically functional molecule that consists of one or more polypeptides, each folded and coiled into a specific 3D shape.

is an organic molecule possessing both an amino group and a carboxyl group

covalent bond formed between amino acids

is a linked series of amino acids with a unique sequence.

are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone.

A shape like a coiled spring, used to describe the structue of DNA molecules.

two or more strands of the polypeptide chain lying side by side are connected by hydrogen bonds between parts of the two parallel polypeptide backbones.

is the overall shape of a polypeptide resulting from interactions between the side chains of the various amino acids.

As a polypeptide folds into its functional shape, amino acids with hydrophobic side chains usually end up in clusters at the core of the protein, out of contact with water.

further reinforce the shape of a protein. They form where two cysteine monomores, which have sulfhydryl groups on their side chains, are brought close together by the folding of the protein. The sulfur of one cysteine bonds to the sulfur of the second, and the disulfide bridge rivets parts of the protein together.

is the overall protein structure that results from the aggregation of these polypeptide subunits.

an inherited blood disorder, is caused by the substitution of one amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin, the protein that carries oxygen in red blood cells.

For proteins, a process in which a protein unravels and loses its native conformation, thereby becoming biologically inactive. For DNA, the separation of the two strands of the double helix. Denaturation occurs under extreme conditions of pH, salt concentration, and temperature.

protein molecules that assist in the proper folding of other proteins.

used to determine the 3D structure of many other proteins.

are polymers made of monomers called nucleotides.

provides directions for its own replication. Also directs RNA synthesis and, through RNA, controls protein Synthesis.

Controls Protein Synthesis

Nucleic acids are macromolecules that exist of polymers called....

each polynucleotide consists of monomers called...

has one six-membered ring of carbon and nitrogen atoms. Cyotosine (C), thymine (T) and Uracil (U)

are larger, with a six-membered ring fused to a five-membered ring. Adenine (A) and guanine (G)

sugar in DNA, lacks an oxygen

sugar in RNA