Chapter 2: Biological Molecules (Nucleic Acids & Proteins) Flashcards
an atom is chemically reactive when ()
the shell is not full
an atom is most stable and chemically unreactive when ()
the outermost shell is filled
sharing of electrons forms ()
covalent bonds
when a double bond forms, rotation of atoms around the bond is (1), so other bonds are (2)
- restricted
- in a single plane
covalent bond that forms between 2 amino acids
peptide bonds
both the C-O and C-N bonds in peptide bonds have () character
partial double bond
radius of an imaginary hard sphere representing the distance of the closest approach for another atom
van der Waals radius
unequal sharing of electrons within a covalent bond
polar covalent bond
() bonds do not have any charge separation
non-polar bonds
separation of charge in polar bonds is called a ()
dipole
tendency of non-polar groups to associate with one another, driven by (), is a big contributor to the behavior of biomolecules, including protein structure
hydrophobic interactions
attraction between fully charged atoms
ionic interactions
ion product of water
10^-14 M
molecules that release H+ into solution are (1), those that accept H+ are (2)
- acids
- bases
weaker () can be formed and broken, allowing flexibility and dynamics in biomolecular structure
non-covalent bonds
non-covalent ionic interactions between charged atoms
salt bridges
non-covalent interactions between polar atoms with partial charges
hydrogen bonds
weak covalent interactions between atoms at a certain distance
van der Waals interactions
in salt bridges, the attraction between charged atoms is a function of the () only
distance between them
salt bridges in proteins are bonds between oppositely charged amino acid residues that are ()
sufficiently close to each other
the salt bridge most often arises from the anionic carboxylate of either (1) and the cationic ammonium from (2) or the guanidinium of (3)
- aspartic acid or glutamic acid
- lysine
- arginine
distance between the amino acid residues participating in the salt bridge should be less than ()
4 angstrom
hydrogen bond interactions are due to the ()
partial charge resulting from a polar covalent bond
hydrogen bonding results from the attractive force between a (1) and (2)
- hydrogen atom covalently bonded to a very electronegative atom (e.g. F, O, N)
- another very electronegative atom
the energy of a hydrogen bond is greatest when the 3 atoms involved are (
in a straight line
strength of a hydrogen bond interaction weakens with ()
increasing angles
the dependence of hydrogen bond strength on angle ensures () between hydrogen bond donor and acceptor
specificity
how do hydrogen bonds impose a high degree of specificity on the interactions between 2 binding partners
hydrogen bond donors and acceptors must line up at the binding interface s.t. the hydrogen bonds that form have the appropriate geometry and distance from one another
the van der Waals interaction arises when the close approach of 2 atoms causes each atom to induce ()
transient dipoles
() around atoms constantly create transient dipoles
electron movements
the aqueous environment affects:
- strength of the interactions
- types of interactions that occur
hydrophobic interactions drive ()
molecular folding
attractive energy of salt bridges is () by surrounding water molecules
reduced
ionic bonds are weakened by the () which interact with the charges
polar water molecules
preferential binding between certain molecules relative to others is directed by (1), a concept generally referred to as (2)
- relative binding strength
- specificity
strength of molecular interactions comes from the () formed between them
non-covalent interactions
it’s not the strength of a specific interaction, but rather the () that governs specificity
comparative strength of binding to the correct binding partner vs the incorrect partner
nucleotides comprise:
- base
- sugar
- phosphate
examples of additional biological functions of nucleotides
energy storage (in the form of ATP) and molecular transport
present in ribose but absent in deoxyribose
ribose has an additional 2’ oxygen atom
2 types of bases in RNA and DNA
- purines (adenine and guanine)
- pyrimidines (thymine, uracil, cytosine)
in simple terms, pKa is a number that shows how () an acid is
weak or strong
in DNA/RNA: base + sugar = ()
nucleoside
in nucleosides, each base is joined to a sugar by a ()
glycosidic bond
glycosidic bonds form between:
- C1’ of the sugar
- N1 of pyrimidine
- N9 of purine
in RNA/DNA: nucleoside + () = nucleotide
phosphate
phosphate groups are linked to the 3’ or 5’-OH of the sugar by ()
phosphate ester linkage
nucleotides are joined by ()
phosphodiester bonds
phosphodiester bonds form between the (1) of one sugar and the (2) of the next sugar
- 3’-OH
- phosphate attached to the 5’-OH
nucleic acid strands are directional and have distinct ends:
5’ end = 5’ phosphate
3’ end = 3’ hydroxyl
by convention, nucleic acid sequences are written in the () direction
5’ to 3’
in nucleic acids, the sugars and phosphates form a repeating unit called the ()
sugar-phosphate backbone
molecules in which a proton has migrated to a different place
tautomer
examples of tautomer pairs
- amino-imino tautomer
- keto-enol tautomer
the capacity to form (1) is a frequent source of errors during DNA replication, and can provide (2)
- alternative tautomers
- genetic variation
examples of nucleotide derivatives and their important role in cellular functions: carrier of chemical groups
SAM (s-adenosyl methionine)
examples of nucleotide derivatives and their important role in cellular functions: enzyme cofactors
NAD, FAD
examples of nucleotide derivatives and their important role in cellular functions: signal transduction
cAMP
in complementary base pairing, A pairs with T via (1), while C pairs with G via (2)
- 2 H-bonds
- 3 H-bonds
in DNA, the two strands are ()
antiparallel