BSC2010 - EXAM 1

organism

an individual living entity that grows and reproduces as an independent unit

All living organisms:

• are composed of cells

• depend on interactions among structurally complex parts to maintain the living state

• have genetic information that uses a nearly universal code

• convert molecules obtained from their environment into new biological molecules

• extract energy from the environment and use it for life functions

• replicate their genetic information and use it for life functions

• replicate their genetic information in the same manner when reproducing

• have a fundamental set of genes that share structural similarities

• evolve through gradual changes in genetic information

scientific investigations are based on…

quantitative observation, experimentation, and reasoning

Observation:

• enhanced by technology (e.g., microscopes, imaging)

• must be quantified by measurement and mathematical and statistical calculations

• lead to questions and often additional ones

What are the two broad methods of scientific inquiry?

1. discovery-based research

2. hypothesis-driven research

discovery-based research

methodology that emphasizes the analysis of data to find new patterns and develop new hypotheses and theories

hypothesis-driven research

methodology that emphasizes the formulation and testing of new hypotheses based on observations

What are the steps involved in hypothesis-driven research?

1. Make observations

2. Ask a question

3. Formulate possible answers to the hypothesis (construct a hypothesis)

4. Make predictions—usually in the form of an “if…,then…“ statement (Think: What will be true if my prediction is correct?)

5. Design and conduct an experiment

element

a substance that consists of only one kind of atom

What are the most abundant elements found in living systems?

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

An atom consists of three fundamental particles:

1. protons: positively-charged particles found in the nucleus

2. neutrons: uncharged particles found in the nucleus

3. electrons: negatively-charged particles found moving outside the nucleus in electron shells

What is the unit for atomic mass?

Dalton (Da)

An element is identified by its…

atomic number

atomic number

number of protons found in one element

Electrons in the same column (group) have the same number of…

electrons in their outermost (valence) shell. This results in having similar chemical properties.

mass number

the sum of the total number of protons and total number of neutrons found in an element

True or False: The behavior of electrons determines whether a chemical bond will form and what shape the bond will have.

True

atomic orbital

defined area in an atom where electrons in each electron shell move

What are the two ways an atom with unfilled outer shells can attain stability (fill their electron shells)?

1. by sharing electrons

   1. by gaining or losing electrons

octet rule

atoms with at least two electron shells form stable molecules so they have eight electrons in their outermost shells

electronegativity

an atom’s tendency to attract electrons from another atom; this increases as you go from bottom left to top right on the Periodic Table

electronegativity is dependent on…

• number of electrons in the outermost shell (it increases as the number of electrons increases)

• the atomic size of the element (the closer the electrons are to the nucleus, the greater it is)

ionic bond

a type of chemical bond in which a highly electronegative atom pulls one or more electrons away from an atom with low electronegativity; results from the electrical attraction between ions with opposing charges, with resulting molecules called salts.

This type of bond occurs between a nonmental which becomes an anion, and a metal which becomes a cation.

covalent bond

type of chemical bonding that occurs when two atoms share one or more pairs of electrons to attain stable electron configuration in their outermost shells; in this type of bonding, each atom contributes one member of the electron pair.

For this type of bonding to occur, atoms involved cannot have too dissimilar electronegativities.

Properties of molecules are influenced by characteristics of covalent bonds:

• orientation: length, angle, and direction of bonds between any two elements are always the same

• strength and stability: covalent bonds are very strong—it takes a lot of energy to break them. Differences in bond strengths are crucial in determining whether chemical reactions will occur.

• unequal sharing of electrons: when two atoms are different elements, the sharing of electrons may not be equal due to differences in electronegativity

  • nonpolar bond: electrons are shared equally

  • polar bond: electrons are pulled closer to the nucleus of the more electronegative atom

    • the more electronegative atom will have a negative dipole moment, and the other will have a slightly positive one

dipole

separation of opposite electric charges, such as in a polar covalent bond

dipole-dipole interactions

slightly charged atoms can interact with other atoms; this type of interactions is weak

hydrogen bonding

a type of chemical bonding that occurs between a slightly positively charged covalently-bonded hydrogen and a slightly negatively charged covalently-bonded nitrogen or oxygen

van der Waals (London dispersion) interactions

movement of electrons results in temporary dipoles; this type of chemical bonding is a result of the attraction between these temporary dipoles.

They are very weak, but many of these interactions often amount to significant force (like in polar molecules)

energy

the capacity to produce a change

kinetic energy

energy of movement; includes thermal, sound, and electromagnetic energy

potential energy

stored energy; includes gravitational, elastic, chemical, and nuclear energy

laws of thermodynamics

1. Energy cannot be created or destroyed.

2. When an energy transformation occurs, there is an increase in entropy.

entropy

a measure of disorder, or how spread out energy is, or how much is unusable (after each energy transformation, some of the energy in the system becomes unavailable to do work)

True or False: The 2nd law of thermodynamics tells us that a change that would decrease energy will not happen simultaneously but rather only occur if energy is added to the system.

True

chemical reaction

when atoms combine or change their bonding partners

hydrolysis

complex molecule + H2O → simpler molecules

What two things in a reaction will determine if the Gibbs free energy, G, or the total energy change, of a reaction is positive or negative?

1. the differences in bond energy

2. the change in entropy

If G is negative, the reaction ______ energy

releases (the reaction is exergonic, or exothermic)

If G is positive, the reaction ______ energy

requires (the reaction endergonic, or endothermic)

What reaction is the reverse of hydrolysis?

condensation reaction, an endergonic reaction which therefore has a positive G

glucose + fructose → sucrose + H2O

activation energy (Ea)

chemical transformations that require additional energy to initiate the reaction; required in both exergonic and endergonic reactions

functional groups

small groups of atoms with specific chemical properties; the number and location of these largely determines the chemistry of organic molecules

the alkyl functional group

identified by CH3; nonpolar and hydrophobic

the hydroxyl functional group

identified by their OH; polar and hydrophilic

the sulfhydryl functional group

identified by their SH; polar and hydrophilic

the aldehyde functional group

identified by a hydrogen single-bonded to a carbon and a double bond of oxygen; polar and hydrophilic

the keto functional group

identified by their O=C bond; polar and hydrophilic

the carboxyl functional group

identified by their O=C-OH bond; polar, hydrophilic, and charged

the amino functional group

identified by their H-N-H bond; polar, hydrophilic, and charged

the phosphate functional group

identified by their polar phosphate bond (usually three single (one O, two OH) bonds and one O double-bond); polar, hydrophilic, and charged

macromolecules

large polymeric molecules formed by covalent linkages of smaller molecules

What are the four types of macromolecules found in living organisms?

1. proteins

2. carbohydrates

3. nucleic acids

4. lipids

polymers

a large molecule made up of similar or identical subunits called monomers (which are often referred to as residues); they are created by the covalent linkages of monomers and are formed and broken apart in reactions involved water

condensation reaction

a type of reaction in which the removal of water creates a covalent bond between monomers

hydrolysis reaction

a type of reaction in which the addition of water breaks a covalent bond between monomers

lipids

• nonpolar, hydrophobic molecules that include fats, oils, waxes, steroids, and the phospholipids that make up biological membranes

• a structurally and functionally diverse group of compounds defined by their insolubility in water

• hydrocarbons (composed of C and H atoms) comprised of many nonpolar covalent bonds (hence their insolubility in water)

  • weak but additive van der Waals forces hold them together

• play a structural roll in cell membranes

lipids contain mostly what type of bonds?

C-C and C-H nonpolar bonds; this is where they store energy

triglyceride

• a simple lipid in which three fatty acids are combined with one molecule of glycerol

• have very little polarity and are extremely hydrophobic (e.g., fats and oils)

• its synthesis involves a three condensation reaction

fatty acids

• a nonpolar molecule made up of a long hydrocarbon chain attached to a polar carboxyl functional group (-COOH)

• amphipathic - they have a hydrophilic end and a hydrophobic tail

glycerol

a three-carbon alcohol with three hydroxyl groups (-OH); a component of triglycerides

saturated fatty acids

fatty acids in which all the bonds between carbon atoms are single—saturated with hydrogens

unsaturated fatty acids

fatty acids in which hydrocarbon chains contain one more double bonds; cause kinks in the chain and prevent molecules from packing together tightly

phospholipid

• a lipid containing a phosphate group; an important constituent of cellular membranes

• form a bilayer in an aqueous environment; the hydrophilic “heads” face outward to interact with water while the hydrophobic fatty acid “tails“ pack together

What are the biological roles of carbohydrates?

• source of stored energy

• transport stored energy within complex organisms

• structural molecules that give many organisms their shapes

• recognition or signaling molecules that can trigger specific biological responses

carbohydrates

organic compounds containing carbon, hydrogen, and oxygen in the ratio 1:2:1, with general formula Cm(H2O)n

Examples: sugars, starch, cellulose

the carbohydrates that are small are called…

simple sugars

monosaccharide

• the simplest carbohydrates, a simple sugar

disaccharide

• a carbohydrate composed of two monosaccharides joined in a condensation reaction

  • the monosaccharides are bonded by a link called the glycosidic bond/linkage

• the other simple sugar

oligosaccharide

• a polymer composed of three to ten monosaccharides joined by glycosidic bonds

• often bonded to proteins and lipids on cell surfaces, where they serve as recognition signals

  • many have additional functional proteins

polysaccharide

a macromolecule composed of many monosaccharides (simple sugars) that are connected by glycosidic bonds

Examples: cellulose and starch

starches

• a family of polysaccharides of glucose; a polymer of glucose

• used by plants to store energy

glycogen

a highly-branched polymer of glucose; main energy storage molecule in mammals

cellulose

• the most abundant carbon-containing (organic) biological compound on Earth; stale and good structural material

• an unbranched polymer of glucose with B-1, 4 glycosidic bonds that are chemically very stable

nucleic acids

polymers that store, transmit, and express genetic (hereditary) information

What are the two types of nucleic acids?

1. DNA

2. RNA

deoxyribonucleic acid (DNA)

• the fundamental hereditary material of all living organisms

• stored primarily in the cell nucleus in eukaryotic organisms

• a nucleic acid using deoxyribose rather than ribose

  • identified by -H

ribonucleic acid (RNA)

• an often single-stranded nucleic acid whose nucleotides use ribose rather than deoxyribose

  • utilizes uracil rather than thymine

  • identified by -OH—it has one more oxygen that deoxyribose

• serves as the genome for some viruses

nucleotide

• a nucleoside containing a pentose (5-carbon) sugar, a nitrogenous base, a phosphate group

• the building blocks of nucleic acids and important co-enzymes, especially ATP

In the absence of phosphate groups, the base and monosaccharide (the ribose or deoxyribose) make…

nucleoside

nucleoside

a nucleotide without the phosphate group; a nitrogenous base attached to a sugar

What are the two chemical forms the bases of nucleic acids can take on?

1. pyrimidine

2. purine

pyrimidine

• one of two types of single-ring nitrogenous bases in nucleic acids

• the nitrogenous bases cytosine, thymine, and uracil

• pairs with a specific purine

purine

• one of two types of double-ring nitrogenous bases in nucleic acids

• the nitrogenous bases adenine and guanine

• pairs with a specific pyrimidine

True or False: Nucleotides usually contain three phosphates when they are monomers; but in nucleic acids, they contain just one.

True

What are the differences between DNA and RNA?

• the monosaccharide in DNA is deoxyribose, whereas that of RNA is ribose

• DNA is composed of nucleotides with nitrogenous bases cytosine, thymine, adenine, and guanine. RNA, on the other hand, replaces thymine with uracil

• RNA is usually single-stranded, while DNA is usually double-stranded; the two strands of DNA are held by complementary base pairing using H bonds

In what direction do nucleic acids grow?

5’ to 3’ direction

oligonucleotide

nucleic acid made up of 20 or fewer monomers, and include small RNA molecules important for DNA replication and gene expression

polynucleotides

a nucleic acid strand consisting of more than 20 nucleotides; include the longest polymers in the living world—DNA and RNA

What are the pairings of the complementary nitrogenous bases that form hydrogen bonds?

In DNA:

• adenine with thymine (A-T)

• cytosine with guanine (C-G)

In RNA:

• adenine with uracil (A-U)

The two strands in DNA are antiparallel. Explain what this means.

They run in opposite directions, with their 5’ ends at opposite ends of the molecule. The two strands are able to form a “ladder“ that twists into a double helix.

In DNA, thymine forms how many hydrogen bonds with adenine?

two

In DNA, cytosine forms how many hydrogen bonds with guanine?

three

Explain the structure of RNA.

• usually single-stranded molecule, though it often folds back on itself to form short double-stranded regions that are stabilized by complementary base pairing (i.e., A-U, C-G)

  • its structure is thus determined by the particular order of bases in the RNA molecule

• the stabilized double-stranded regions give the molecule a distinctive 3D shape that affects how it interacts with other molecules

• the regions that exhibit base pairing are also antiparallel

Where is DNA’s information encoded?

in the sequence of bases

DNA replication

• the creation of a new strand of DNA in which DNA polymerase catalyzes the exact reproduction of an existing (template) strand of RNA

• DNA is copied into a new, identical DNA molecule that can be transmitted to daughter cells and offspring

What are the steps involved in DNA replication?

Replication occurs in three major steps: the opening of the double helix and separation of the DNA strands, the priming of the template strand, and the assembly of the new DNA segment. During separation, the two strands of the DNA double helix uncoil at a specific location called the origin. The entire DNA molecule is copied during DNA replication—since DNA holds essential information, it must be replicated completely so that each new cell or new offspring receives a complete set from its parent.

What are the steps involved in the synthesis of proteins using DNA information?

There are two steps involved in this process: transcription and translation.

1. Transcription: the synthesis of RNA using one strand of DNA as a template

2. Translation: the synthesis of a protein (polypeptide); takes place on ribosomes, using the information encoded in the messenger RNA. Information in the RNA base sequences is used to synthesize proteins.

Summarize the differences among DNA replication, transcription, and translation.

Replication copies DNA. Transcription makes a complementary RNA copy of one strand of DNA. Translation synthesizes protein using RNA sequence information.

genome

a completely set of DNA in a living organism