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
most energetically favorable formation of double-stranded DNA
right-handed double helix
the () arrangement is very energetically favorable, and in important for the stability of DNA
base-stacking
predominant configuration of cellular DNA
B-DNA
grooves in DNA arise from the ()
asymmetrical attachment of bases to the backbone sugars
the structural features of the DNA helix, in particular, the () govern the way in which proteins can interact with DNA
atoms of the bases that are exposed in the grooves
other conformations of DNA
- A-DNA
- Z-DNA
regions rich in A-T pairing tend to be more ()
bendable
DNA that is under torsional strain and thus twists in on itself to alleviate the strain
supercoiled DNA
linear DNA can also be supercoiled if ()
the ends are immobilized and not free to rotate to release superhelical tension
number of times one strand of DNA wraps around the other
linking number (Lk)
Lk cannot change in (1) or (2)
- closed circular DNA
- constrained DNA
the only way to change Lk is to introduce a ()
DNA strand break
number of turns in a given fragment of DNA
Twist (Tw)
if Tw > 0, DNA is a () helix
right-handed
if Tw < 0, DNA is a () helix
left-handed
number of superhelical turns
Writhe (Wr)
if Wr > 0, supercoiled DNA is ()
positively coiled (left-handed turns)
if Wr < 0, supercoiled DNA is ()
negatively coiled (right-handed turns)
to maintain the Lk value, any change in Tw must be ()
balanced by an opposite change in the value of Wr
negative supercoiling can occur when
right-handed DNA is underwound
positive supercoiling can occur when:
right-handed DNA is overwound
supercoiling can adopt either of 2 forms
- toroidal
- interwound
why is negative supercoiling important in DNA
negative supercoiling balances the torsional strain of the DNA while it is being unwound for cellular processes
introduce or remove supercoils from DNA in an energy-requiring process by temporarily breaking DNA and twisting it
topoisomerases
(1) and (2) allow RNA to adopt diverse structures
- 2’ OH (hydroxyl) on ribose
- distinct chemical structure of uracil
many RNA molecules (especially directly functional RNA rather than mRNA) require () to become fully functional
chemical modification after synthesis
the position and nature of () in particular RNA are often conserved among species reflecting their crucial functional roles
nucleotide modifications
chemical modifications of RNA are usually (1) and are (2)
- irreversible
- not regulatory
the 2’ OH in RNA facilitates are reaction that ()
breaks phosphodiester bonds
the 2’ OH in RNA means that RNA favors the () conformation
A-type helix
the sugar part of nucleic acid molecules has buckled conformations, known as ()
sugar pucker
in ribose, a formation called () is found, and favors the A-type helix
C3’ endo
in deoxyribose, a formation called () is found, and favors the B-type helix
C2’ endo
the C2’ OH also allows RNA to form () more extensively than DNA
hydrogen bonds
structure of RNA: the RNA sequence, in 5’ to 3’ direction
primary structure
structure of RNA: short double-helical regions
secondary structure
structure of RNA: arrangement of the double helices and single-stranded regions in the final configuration of the RNA
tertiary structure
the fundamental structural unit of folded RNA is the ()
RNA double helix
if complementary sequences are close in primary RNA sequence, a () forms
hairpin structure
in an RNA hairpin structure, the double-stranded part is the (1), and the unpaired section is the (2)
- stem
- loop
what happens when complementary sequences are far in primary RNA sequence
RNA can still form double-helical structures, but lack hairpin structure
the non-Watson-Crick base pairs in RNA molecules often feature ()
chemically modified bases (e.g. methylation)
base pairing with modified bases in RNA can introduce ()
structural distortion
() RNA structure is formed when short double-stranded helices interact with each other and with single-stranded regions
tertiary
general features of tertiary RNA structure
- coaxial stacking
- hydrogen bonding interactions (particularly involving the 2’ OH)
two Watson-Crick bases interacting with a third via an additional H-bond
base triple interaction
() often stabilize a folded RNA structure
hydrogen bonding interactions
an adenosine inserts into the minor groove of a double-helical region, and is stabilized by H-bonds (H bonds with 1 or 2 2’ OH groups and the bases)
A-minor motif
main barrier to the folding of RNA into a compact 3D structure
electrostatic repulsion due to the high density of negative charge with the phosphodiester backbone
RNA strategy to overcome barrier to folding into 3D structure
RNA molecules bind large numbers of cations to counteract electrostatic repulsion
() is the comparison of characteristics among species
phylogenetic analysis
phylogenetic analysis helps identify () as these are more likely to be conserved during evolution
true pairing regions
differences that occur among species, yet conserve interactions, are known as (); sequences may change but base-pairing is conserved
covariations
modern-day evidence to putative “RNA world”
- RNAs play diverse roles
- composition of many enzyme factors
- ability of RNA to fold in vitro and discovery of RNA switches
() groups on cysteine can form covalent bonds with one another to make disulfide bridges
sulfhydryl (-SH) groups
stereoisomer configuration often found in naturally occurring proteins
L-amino acids
the pKa of () is close to the neutral pH of a cell, so it can act as H+ donor or acceptor during biological interactions
histidine
bond between 2 amino acids
peptide bond
a peptide bond between 2 amino acids results from a () between the carboxyl group of one amino acid and the amino group of another amino acid
condensation reaction
distinct ends of proteins
- N-terminus
- C-terminus
in proteins, a repeating series of C and N atoms forms the () with side chains protruding
peptide backbone
peptide bonds are planar due to ()
resonance
the () in peptide bonds prevents free rotation about the bonds, locking the atoms into a planar conformation
delocalization of electrons (between O, C, and N atoms)
other parts of the polypeptide that can still rotate
- N-Calpha bond (rotation angle: phi)
- C-Calpha bond (rotation angle: psi)
some angle combinations of phi and psi do not occur because ()
they cause collisions of side chains or the polypeptide backbone
a () depicts the allowable combinations of phi and psi angles; depends on the amino acid residues of the polypeptide
Ramachandran plot
due to the () side chain being small, it can tolerate many more angle combinations
glycine
protein folding is driven by () of the atoms in the polypeptide
non-covalent interactions
protein structure: sequence of amino acids in a protein chain
primary
protein structure: regular and spatial organization of neighboring segments
secondary
secondary protein structure is stabilized by ()
hydrogen bonds
protein structure: final overall 3D shape of a protein molecule
tertiary
tertiary protein structure depends on the interactions of amino side chains that are ()
far apart along the same backbone
protein structure: overall structure of proteins composed of more than 1 polypeptide chain
quaternary
common secondary protein structures are:
- alpha helices
- beta sheets
protein folding forms structures that have cores filled with non-polar side chains that form ()
van der Waals interactions
while protein folding occurs spontaneously in an aqueous environment, some proteins require the assistance of ()
chaperones
comparing amino acid sequences: proteins with () the same amino acids are likely to have almost identical structures
50%
() is a strong indicator of genes that have similar functions
conservation of important amino acids
the arrangement of secondary structural elements in a protein
protein fold
two proteins may have identical folds (even if they don’t appear to have identical structures) if they have essentially the same ()
secondary structural elements
changes in the amino acid sequence that do not () may be tolerated
alter the protein’s fold
pro of protein mutations: as a protein collects more mutations (also insertions or deletions), the protein may ()
evolve a new, useful function
happens when proteins of different functions derive from a single ancestral protein
divergent evolution
happens when proteins with similar functions evolve separately, from different ancestors
convergent evolution
structurally distinct regions in polypeptides; is able to fold on its own
domains
polypeptide domains can be thought of as “()”
that make up the whole protein
modules
the pattern of functional groups exposed in the (1) of DNA is unique, while that of the (2) is less variable
- major groove
- minor groove
DNA binding proteins recognize a specific base pair sequence by forming a () with the exposed groups of the DNA’s major group
chemically complementary set of non-covalent interactions
to allow DNA-binding proteins to interact with the highly negatively charged sugar-phosphate backbone, residues facing the DNA helix are often:
- positively charged (e.g. lysine and arginine)
- have hydrogen bond donors, -OH groups (e.g. serine and tyrosine)
proteins also interact extensively with RNAs via ()
specific RNA-binding domains
