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Test 1

Matter

anything that takes up space and has mass

element

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

compound

is a substance consisting of two or more different elements

Essential Elements of Life

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

Make up 96% of living matter

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

Trace elements

are required by an organism in only minute quantities

atomic number

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

Mass Number

sum of protons and nuetrons in the nucleus of an atom

atomic mass

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

isotopes

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

radioactive isotope

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

Energy

the capacity to cause change

potential energy

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

Valence Electrons

Electrons in the outermost shell

valence shell

the outermost electron shell

orbital

the 3D space where an electron is found.

Covalent bond

sharing of a pair of valence elctrons by two atoms

Single bond

a pair of shared electrons

double bond

the sharing of two pairs of valence electrons

Electronegativity

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

Nonpolar covalent bond

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

polar covalent bond

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

ion

a charged atom or molecule

ionic bond

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

strongest chemical bonds

covalent bonds

Hydrogen bond

noncovalent attraction between a hydrogen and an electronegative atom

van der Waals interaction

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

Polar covalent bonds

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

Cohesion

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

adhesion

the clinging of one substance to another

surface tension

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

hydrophilic

any substance that has an affinity for water

colloid

A stable suspension of fine particles in a liquid

hydrophobic

substances that seem to repel water.

Acid

a substance that increases the hydrogen ion concentration of a solution

base

a substance that reduces the hydrogen ion concentration of a solution

pH

the negative log of the hydrogen ion concentration

buffer

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

hydrocarbons

organic molecules consisting of only carbon and hydrogen

isomers

variations in the architecture of organic molecules

structural isomers

differ in the covalent arrangements of their atoms.

cis-trans isomers

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

enantiomers

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

Hydroxyl group

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.

Carbonyl

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

Carboxyl

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.

Amino

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+

Sulfhydryl

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.

Phosphate

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

methyl

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

Adenosine triphosphate (ATP)

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

How do isomers differ from one another?

isomers differ in the arrangement or bonding of atoms.

Which property of water allows a paper towel to pick up a puddle of water?

adhesion of water molecules to other kinds of molecules

How many molecules of water are needed to completely hydrolyze a polymer that is 11 monomers long?

10

Molecules with which functional groups may form polymers via dehydration reactions?

either hydroxyl or carboxyl groups

Which of the following are qualities of any good scientific hypothesis?
I. It is testable.
II. It is falsifiable.
III. It produces quantitative data.
IV. It produces results that can be replicated.

I and II

What is the structural feature that allows DNA to replicate?

complementary pairing of the nitrogenous bases

Which of the following is true of both starch and cellulose?

They are both polymers of glucose.

The Ionization of Water

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+).

What maintains the secondary structure of a protein?

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

No amino acid molecule by itself can speed up or catalyze reactions between other molecules; however, when amino acids are joined together to make a protein with catalytic properties, the new structure (enzymatic protein) can speed up the rate of a specific chemical reaction. What does this illustrate?

emergent properties

The tertiary structure of a protein is the

unique three-dimensional shape of the fully folded polypeptide.

The main source of energy for producers in an ecosystem is

light energy.

Which of the following statements best distinguishes hypotheses from theories in science?

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

Which of the following is an example of qualitative data?

The fish swam in a zigzag motion.

Which of the following statements is true for the class of biological molecules known as lipids?

They are insoluble in water.

One of the primary functions of RNA molecules is to

function in the synthesis of proteins

Which statement about isomers is correct?

Enantiomers differ in biological activity.

Prokaryotes are classified as belonging to two different domains. What are the domains?

Bacteria and Archaea

Which of the following statements concerning saturated fats is not true?

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

How will brief heating (to 95°C) affect macromolecular structures in aqueous solution?

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

The enzyme amylase can break glycosidic linkages between glucose monomers only if the monomers are the α form. Which of the following could amylase break down?

Starch

Which statement about weak bonds is correct?

Weak bonds are transient and easily reversible.

Which molecule is a nucleotide?

ATP

What is a nucleotide?

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.

Which level of protein structure is characteristic of some, but not all, proteins?

Quaternary level of protein structure

Why are human sex hormones considered to be lipids?

They are not soluble in water.

These figures show primary, secondary, tertiary, and quaternary protein structure. Which level(s) of protein structure may be stabilized by covalent bonds?

Primary and tertiary levels of protein structure

What is the primary structure of a protein?

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.

What structural difference accounts for the functional differences between starch and cellulose?

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.

Which statement about a methyl functional group is correct?

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

There are 20 different amino acids. What makes one amino acid different from another?

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

Which of these molecules is not formed by dehydration reactions?

fatty acids

Which of these is an example of inductive reasoning?

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

The difference between the sugar in DNA and the sugar in RNA is that the sugar in DNA

contains one less oxygen atom.

Which of the following statements best summarizes the differences between DNA and RNA?

DNA nucleotides contain a different sugar than RNA nucleotides.

Identify the functional groups.

Amino and carboxyl are functional groups.

Which statement about relative potential energy of electrons is correct?

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

Which of the following bonds can form between atoms of equal electronegativity?

Van der Waals interactions

Polymer

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.

monomers

are the building blocks of polymers and are smaller molecules.

enzymes

specialized macromolecules that speed up chemical reactions.

dehydration reaction

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

hydrolysis

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.

monosaccharides

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

disaccharide

consists of two monosaccharides joined by a glycosidic linkage

glycosidic linkage

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

Polysaccharides

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

starch

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

glycogen

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

cellulose

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

chitin

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

fat

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

fatty acid

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

triaglycerol

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.

saturated fatty acid

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.

unsaturated fatty acid

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

trans fats

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.

phospholipids

are essential for cells because they make up cell membranes.

cholesterol

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.

Steroids

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

polypeptides

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

protein

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

Amino Acid

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

peptide bond

covalent bond formed between amino acids

primary structure of a protein

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

secondary structure of a protein

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

helix

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

pleated sheet

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.

tertiary structure

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

hydrophobic interaction.

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.

disulfide bridges

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.

Quaternary structure

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

sickle cell disease

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.

denaturation

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.

chaperonins

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

X-ray crystallography

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

Nucleic acids

are polymers made of monomers called nucleotides.

deoxyribonucleic acid (DNA)

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

Ribonucleic Acid (RNA)

Controls Protein Synthesis

polynucleotides

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

nucleotides

each polynucleotide consists of monomers called...

pyrimidine

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

Purines

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

Deoxyribose

sugar in DNA, lacks an oxygen

ribose

sugar in RNA

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