Ch. 1 - 4 Review Flashcards
List some of the characteristics that define “life”
- Common set of chemical components: carbohydrates, fats, nucleic acids, amino acids
- Cells enclosed by plasma membranes
- Convert molecules in environment to new molecules
- Extract energy from environment and use it to do biological work
- Contain genetic information with universal code to specify proteins
Identify general differences/similarities between prokaryotes and eukaryotes
Prokaryotes are unicellular organisms with a cellular membrane but no nucleus. Eukaryotes are made up of cells that have a cellular membrane, nucleus and organelles
What does it mean to have “differentiated” cells?
Cells that carry out specific functions
What is the definition of matter? An element? A compound?
Matter is anything that has mass and occupies space; element is the purest form of a substance; compound is a combination of elements in a fixed ratio
What are the 3 major atomic particles we discussed in class and what charges are associated w/ each?
Protons (positive), neutrons (neutral) and electrons (negative)
Where, within an atom, are the protons and neutrons located? Where are the electrons?
Protons and neutrons are located in the nucleus; electrons are located in orbitals surrounding the nucleus
How much does each proton or neutron “weigh?” (answer is 1 dalton or 1 atomic mass unit)
1 AMU = 1.7 x 10^-24 grams
What is the definition of atomic number? Mass number? Atomic weight?
Atomic number is the number of protons; mass number is the numer of protons and neutrons; atomic weight is the average mass of all isotopes for the element
Can the number of protons or neutrons for a given element vary? Explain.
Yes, the number of neutrons can vary depending on the number of isotopes. Protons cannot vary, because each element contains a unique number of protons
What is the definition of an isotope?
Variations of an element that contain a differing number of neutrons
What is an orbital? Which orbitals did we discuss in class?
An orbital is the region electrons spend 90% of the time; each orbital can hold up to 2 electrons; the descending order of orbitals are s-p-d
How many electrons can exist in one orbital?
2 electrons
What is an electron shell or energy level?
Series of orbitals filled in a specific sequence; the energy level becomes higher the further it is from the nucleus
What is the “octet rule?”
The rule that each valence shell seeks to fill the shell completely with 8 electrons to stabilize
What is an electron configuration? If I show you one and also give you a periodic table, could you tell me which kind of atom it represents?
It is a demonstration of the number of electrons that fill each electron shell to the maximum of 8 electrons
- What’s the difference between the terms “valence electrons” and “valence of?”
Valence electrons indicate the number of electrons in the valence electron shell; “valence of” indicates the number of bonds the atom can form to fill the valence shell
What is a covalent bond? How many electrons are shared in one covalent bond?
A covalent bond is the interaction of two elements that share at least one pair of electrons in both element’s valence shell; the strongest bond
How is a polar covalent bond different from a non-polar covalent bond?
A polar covalent bond is an unequal sharing of electron pairs in the outer shell that creates a partial positive and partial negative charge; a non polar covalent bond is an equal sharing of electron pairs in the valence shell
What is an ionic bond? How is it different from a covalent bond?
A complete transfer of valence electrons between atoms; it is a type of chemical bond that generates two oppositely charged ions
What is a hydrogen bond?
An electrostatic attraction between two polar groups that occurs when a hydrogen (H) atom covalently bound to a highly electronegative atom such as nitrogen (N), oxygen (O), or fluorine (F); weaker than most ionic attractions because of its partial charges
Describe the properties of one water molecule (describe the water molecule on a molecular level.)
H2O is polar covalently bonded and the electrons in the valence shell are unequally shared; the oxygen molecule is strongly electronegative and the hydrogen molecules are electropositive
What is meant by the statement that “water has polarity?”
Water has polarity means that the oxygen and hydrogen atoms unequally share their valence electrons and are considered polar molecules
Which “end” of a water molecule represents the partial positive charge? Partial negative charge?
The partial positive end is on the hydrogen atoms and the partial negative end is on the oxygen atom.
What is an anion? What is a cation?
An anion is an positively charged ion that has given up at least one electron. A cation is an negatively charged ion that has acquired at least one electron.
What do the following terms mean? Solvent? Solute? Aqueous solution? Solution?
Solute is a smaller concentration of a substance in a solution. A solvent is a the larger substance that dissolves a solute. A solution is the dissolved solute in the solvent. Aqueous solution is water that acts as a solvent.
What is the difference between hydrophobic and hydrophilic as it pertains to molecules?
Hydrophobic molecules are water-fearing molecules that are stable and not electrically charged. Hydrophilic molecules are water-loving molecules that are electrically charged and are attracted to water molecules.
What is the definition of a mole?
Amount of a substance that contains the same number of entities as there are atoms in exactly 12 g of Carbon-12
What is Avogadro’s number?
6.02 x 10^23 molecules per mole
How would you calculate the mass of 1 mole of substance? (what are the steps?)
Find the total relative atomic mass of all the atoms in the molecule.
What is the definition of molarity? How would you produce 1L of a 1M solution?
Molarity is equivalent to 1 mol/1L of solution, where 1 mol is the total relative atomic mass of the molecule
What is one definition of a base?
Base is an ionized solution with a larger concentration of —OH- ions and accept H+ to a solvent
What is one definition of an acid?
A solution that has a larger concentration of H+ ions that donate H+ ions to a solvent
If you are given the hydrogen ion concentration of an aqueous solution, could you tell me what the hydroxide ion concentration would be? How about the reverse of this?
Both the hydrogen ion concentration and hydroxide ion concentration need to equal to a 10^-14
In pure water under standard conditions, what is the [H+]? What is the [OH-]?
The [H+] is equivalent to the [OH-] concentration at 10^-7 ions or pH 7
If you are given the hydrogen ion concentration of an aqueous solution, could you tell me what the hydroxide ion concentration would be? How about the reverse of this?
Both the hydrogen ion concentration and hydroxide ion concentration need to equal to a 1 x 10^-14; each pH value up or down represents a 10 fold increase/decrease in hydrogen ion concentration
Which pH values constitute a “basic” solution? An “acidic” solution? A neutral solution?
A basic solution has a pH between 8-14, an acidic solution has a pH between 0-6, a neutral solution has a pH of 7
If given only one of these: pH or [H+] or [OH-], could you calculate the other values?
pH is equivalent to the [H+] concentration. The [OH-] concentration and the [H+] concentration equal 1 x 10^-14, so you can calculate the [OH-] concentration if given the [H+] concentration and vice versa.
What is the definition of an isomer?
An isomer are two chemically equivalent molecules that are arranged differently
What is the definition of an geometric (or cis/trans) isomer?
A geometric isomer are two structurally different isomers that orient around a C=C double bond
What is the definition of an enantiomer (or optical isomer)?
An enantiomer are two isomers that are mirror images of each other and are not superimposable; a carbon atom have 4 different groups attached and has an isomer that is a reflection of the carbon atom attached to 4 different groups
List the functional groups we discussed in class. Be able to recognize them on a molecule.
Hydroxyl group are also called alcohols, which has a —OH attached; an aldehyde group contain aldehydes with an (C=O-H) attached, an amino group or amide contains an NH2 attached, a carboxyl group or carboxylic acid contains a —C=O-OH attached, a keto group or ketone contains a C=C in between two groups, a sulfhydryl group or thiol has a —SH attached, and a phosphate group or organic phosphate has a PO4 2- attached
What do you call a group of molecules that contain a hydroxyl group?
Alcohols
What do you call a group of molecules that contain a –C=O group on the END of the molecule?
Either a carboxylic acid (C=O-OH) or an aldehyde (C=O-H)
What do you call a group of molecules that contain a –C=O internally within the molecule?
A ketone
What does a carboxyl group look like when it is ionized or un-ionized?
When ionized, it is C=O-O-, when un-ionized, it is C=O-OH
What does an amino group look like when it is ionized or un-ionized?
When ionized, it is NH3+, when un-ionized, it is NH2
What is a sulfhydryl group? What is a disulfide bridge?
A sulfhydryl group is a functional group with an attached —SH. A disulfide bridge are two cysteine molecules that covalently bond through their attached sulfhydryl groups
What is a thiol?
A thiol is the the class of compounds of a sulhydryl group
Be able to recognize a phosphate group in the ionized or non-ionized form.
A phosphate group in its ionized form is PO4 2-, and the non-ionized form is PO2OH2
What is a condensation reaction or dehydration reaction?
When two monomers bond together to form a polymer, the bond releases an H2O molecule
What does hydrolysis mean?
Hydrolysis utilizes H2O to break polymers up into monomers; requires an aqueous environment and releases energy
What is the definition of a carbohydrate?
A macromolecule composed of monosaccharides that are used to transport or store energy
What is a monosaccharide (or simple sugar)?
It is the monomer of a carbohydrate that build larger carbohydrates
What should you think when you see a molecule’s name with an –ose ending?
A carbohydrate or sugar
What should you think when you see a molecule’s name with an –ase ending?
An enzyme that breaks down macromolecules
What is a disaccharide? What is the specific name of the bond that links two monosaccharides together?
A disaccharide is a carbohydrate with two monosaccharides bonded together. The bond is called a glycosidic linkage. An example of a disaccharide is sucrose
How are starch and glycogen similar? How do they differ from each other?
Starch and glycogen are both large polysaccharides that are linked together by alpha glycosidic bonds. Starch is moderately branched while glycogen is heavily branched.
What are the two conformations that a ring structure of a monosaccharide can exist in? (Answer:
a and b conformations). Which is which?
Monosaccharides can conform in an alpha and beta formation. Alpha monosaccharides have —OH attached to the bottom of Carbon-1 and beta monosaccharides have —OH attached to the top of Carbon-1
How is starch similar to cellulose? How is it different from cellulose?
Starch and cellulose are both large polysaccharides. Cellulose is composed of monosaccharides linked by beta-glycosidic bonds that create a linear chain while starch is composed of monosaccharides bonded by alpha-glycosidic bonds and are moderately branched
What is chitin?
Chitin is a chemically modified carbohydrate made up of acetylglucosamine that is found in the exoskeleton of arthropods; plays a structural role
What is another name for a polypeptide?
Protein
What are the subunits of polypeptides called?
Amino acids
What is the basic structure of an amino acid?
A carbon attached to a carboxyl group, an amino group, a hydrogen atom and an r-group/side chain.
A chiral carbon is also referred to as an asymmetric carbon. Which ONE of the amino acids is the only one that does not have a chiral carbon?
Glyceine
What are the four levels of protein structure? What does each entail?
Primary structure consists of the polypeptide chain of amino acids; secondary structure consists of hydrogen bonding between the amino or carboxyl groups or backbone of the polypeptide to create an alpha helix or a beta-pleated sheet; tertiary structure bonds r-groups together through hydrogen bonds creating 3-D structures; quaternary structure occurs only when 2 or more polypeptide chains called subunits are linked and the subunits interact to form larger proteins
Which level of protein structure is the minimum level that must be present for the protein to be functional?
Tertiary structure
What are the two options for secondary structure, and how are these structures held in that shape?
Amino acids either form alpha helices or beta pleated sheets in the secondary structure. An alpha helix is a single polypeptide chain that links its carboxyl groups to amino groups via hydrogen bonds to create a coiled shape. A beta pleated sheet is composed of 2 or more polypeptide chains that form hydrogen bonds between the backbone of the chain and are almost completely aligned or extended to create “sheets”
What kinds of bonds hold a protein in its 3-dimensional conformation (tertiary structure)?
Hydrogen bonds, disulfide bridges, ionic attractions, hydrophobic side chains
What is the definition of quaternary structure? Do all proteins have this level of structure?
The quaternary structure of protein requires 2 or more polypeptide chains that create subunits. Quaternary structures form out of multiple subunits but not all proteins have multiple subunits or a quaternary structure
What kind of forces (environmental conditions) can alter a protein’s structure and why?
Increased temperature, change in pH and change in salt concentrations; these conditions can break the bonds of the secondary and tertiary structures of protein, causing denaturation
What are the definitions for denaturation, renaturation, and degradation of proteins?
Denaturation is the breakdown of bonds in the secondary and tertiary structures of protein; some proteins can reverse the denaturation and renature and reconstruct secondary and tertiary structure after the breakdown; degradation is the complete breakdown of the primary structure of protein that is irreversible
What is the definition of a chaperone protein?
A heat shock protein that protects the 3-D structure of other proteins; pulls in a polypeptide, causes it to fold into the correct shape and then releases it
What is another name for a polynucleotide?
Nucleic acid
What are the names of the four nitrogenous bases in DNA? In RNA?
DNA - adenine, thymine, cytosine, guanine; RNA - adenine, uracil, cytosine, guanine
One nucleotide is a monomeric unit of nucleic acids. What are the three main parts of a nucleotide?
A Phosphate group, pentose and nitrogenous base
What does the central dogma explain?
The central dogma describes the flow of information from DNA transcribed to RNA translated into a protein
When creating a polynucleotide chain, which part of the incoming nucleotide binds to which part of the existing chain?
The incoming nucleotide’s phosphate group attaches to the hydroxyl group on the 3’ end of a polynucleotide
Which nitrogenous bases are purines and which are pyrimidines? How can you tell the difference between purines and pyrimidines in terms of structure?
Pyrimidines include cytosine, uracil and thymine; purines include adenine and guanine; pyrimidines are single 6-ring structures and purines are a 6-ring and 5-ring structure
What are the sugar components of a nucleotide from DNA and RNA? How do these two sugars differ from each other in structure?
DNA consists of a deoxyribose sugar, a pentose with a hydrogen attached at Carbon-2; RNA consist of a ribose sugar with a hydroxyl group (—OH) attached to Carbon-2
When you look at a DNA double helix, what components of the nucleotides form the backbones of the molecules (the ‘sides’ of the ladder)? What components of the nucleotides form the ‘rungs’ of the ladder (i.e. they face toward each other within the helix).
The backbone of the DNA consists of the phosphate group and deoxyribose. The rungs of the ladder include the nitrogenous bases that bond to its complementary pair
What is the name of the covalent linkage between two adjacent nucleotides?
Phophodiester linkage
What is the name of the non-covalent linkages that hold together two complementary strands of DNA?
Hydrogen bond; two hydrogen bonds link A-T (or A-U) and three hydrogen bonds linked C-G
What are the complementary pairs of nitrogenous based in DNA and in RNA?
DNA pairs are A-T and C-G; RNA pairs are A-U and C-G
What is a lipid?
A lipid is non polar hydrocarbon; it is a glycerol molecule attached to 3 fatty acids; also known as triglyceride
What is a fatty acid?
A fatty acid is a long chains of hydrocarbons that are amphipathic, which is hydrophilic on the carboxyl group end and hydrophobic on the hydrocarbon end
What are the components of a triacylglyceride (same as triacylglycerol)?
The components of a triglyceride are a glycerol molecule bonded to three fatty acids via ester linkages
How can triglycerides differ from each other in structure?’
Triglycerides differ in the type of fatty acids linked to the glycerol; Unsaturated fatty acids contain at least one double bond in the chain and saturated fatty acids contain single bonds between the hydrocarbons
What’s the difference between a saturated and an unsaturated fat in terms of structure?
Saturated fatty acids contain single bonds in its hydrocarbon chain while unsaturated fatty acids contain at least one double bond in its hydrocarbon chain
What is the major function of lipids?
To store energy; phospholipids play a structural role in the cell membrane; steroids such as cholesterol help maintain membrane integrity
What is a phospholipid? What are the major parts of this molecule?
A phospholipid is a an amphipathic macromolecule that consists of a hydrophilic phosphate group, glycerol molecule and two hydrophobic fatty acid chains
Phospholipids self-assemble in aqueous solutions. In a phospholipid bilayer, where are the polar heads of the phospholipid molecules located and where are the hydrophobic tails of the phospholipid molecules located?
The polar heads are facing outward towards the water molecules while the hydrophobic tails face inward within the phospholipid bilayer
What does the basic structure of a sterol lipid look like?
Three six ring structures attached to one-five ring structure
What are the names of some sterol lipids that we talked about in class?
Cholesterol, an important steroid that plays a structural role in membranes; hormones (testosterone, estrogen)
How do those sterol lipids differ from each other?
Sterol lipids differ with the attached R-groups to the basic three 6-ring/one 5-ring structure
