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50 Cards in this Set
- Front
- Back
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4 main types of macromolecules
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DNA and RNA, proteins, glycans
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DNA and RNA are polymers of _________
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nucleic acids
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proteins are polymers of _________
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amino acids
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glycans are polymers of _________
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sugars
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how are DNA, RNA and proteins different from glycans?
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DNA, RNA, and proteins are linear polymers (do not branch). Glycans branch.
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gene
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a segment of DNA that codes for functional RNA or protein molecules.
a segment of DNA that is transcribed into RNA. |
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informational molecules
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carry the instructions needed to make other polymers
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operational molecules
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form the molecular machines that carry out the functions required for life.
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DNA is an...(operational/informational polymer)
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informational molecule
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RNA is an...(operational/informational polymer)
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can be either operational or informational
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proteins are...(operational/informational)
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operational polymer
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the energy of interaction between two molecules can be calculated by...
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summing up the interaction energies btwn pair-wise combinations of atoms in the two molecules
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noncovalent interactions
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interactions btwn atoms that are not covalently bonded to each other. Can be attractive or repulsive. Arise from interactions btwn transient or stable charges on atoms.
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Compared with covalent interactions, noncovalent interactions...
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are weak and can form or break during molecular collisions and vibrations at room temperature
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covalent bonds
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electrons shared btwn atoms. So strong that atoms that are held together this way stay together through all of the fluctuations and collisions that occur when two molecules interact with each other at room temp.
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Electrostatic attractions can be broken by...
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collisions w/ water molecules
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induced dipole
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the result of a transient separation of charge in an atom that causes the atom to behave as if it were a dipole.
occur when an atom is subjected to an electric field that causes the redistribution of electrons in an asymmetric way. results in attraction btwn two neutral atoms as they approach each other closely. |
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London force/Van der Waals attraction
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When two neutral atoms approach each other, transient fluctuations in the electron clouds of each atom set up transient dipoles.
The transient dipoles mutually reinforce each other, leading to an attractive force btwn the atoms. Optimal at distances btwn 3-4 A. Of negligible strength beyond 5 A. |
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Van der Waals repulsion
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Caused by electron repulsion at short distances.
Prevents atoms from getting closer than 3 A. Causes atoms to behave like hard spheres when they approach each other very closely. Once two atoms are at the distance of minimum energy, further decreases in the interatomic distance cause the energy to rise very sharply. |
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Van der Waals radius
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Radius of "hard sphere" that approximates atom.
When two atoms approach each other, the energy is at a minimum (the atoms interact optimally) when the distance btwn the two atoms is equal to the sum of their Van der Waals radii. |
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Van der Waals contact
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describes two atoms that are separated by the sum of their Van der Waals radii.
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steric effects
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Repulsion btwn atoms at short distances.
Provide important constraints on the three-dimensional structures of biological macromolecules. Ex. Van der Waals repulsions prevent RNA from forming double-helix. |
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stabilization energy
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the amount by which the energy at the optimal distance is lower than when the atoms are far apart.
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thermal energy
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the amount of energy that is readily transferred btwn molecules by random collisions. Value depends on the temperature.
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Why are Van der Waals forces important in biological molecules?
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While they are weak, the additive effect of many interactions stabilizes protein + DNA conformation
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ion pair/salt bridge
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when two oppositely charged groups are close to each other.
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energy graph of ion pair vs. Van der Waals interaction
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Similar, but ion pair stabilization energy is greater + attractive force makes optimal distance smaller for an ion pair than for a Van der Waals interaction + electrostatic attraction falls off more slowly w/ increasing distance for ion pair.
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Why is interaction energy for opposite charges = -500 kJ/mol misleading in determining strength of electrostatic interactions?
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electrostatic effects are strongly modulated by the shielding provided by the medium in which the charged groups are dissolved (-500 kJ/mol is based on ions in vacuum).
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Effect of water and ions on electrostatic interactions:
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reduces their strength and the distance over which they operate
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Effect of electrostatic interactions in protein interior vs. surface:
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Environment w/in interior of protein closer to that of vacuum than water in terms of effect on electrostatic interaction.
Interaction energy barely reduced in interior of protein. |
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Why are fully charged groups rarely found in the interior of proteins?
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There is an energetic penalty associated w/ separating charged groups from strongly bound water molecules --> charged groups usually found on the surfaces of proteins.
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polarized
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Describes covalent bonds.
Means that one of the atoms participating in the bond withdraws electrons toward it --> generation of an electric dipole. |
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electronegativity
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a property of an atom that describes its tendency to attract electrons toward it when it is in a covalent bond.
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if two atoms that are covalently bonded have different electronegativities...
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the bond will be polarized --> electric dipole
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polar molecules/polar groups
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molecules or groups of atoms containing polarized covalent bonds
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nonpolar
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molecules or groups that do not contain stong polarized covalent bonds
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hydrogen bond
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when a partial positive hydrogen (covalently bound to electronegative atom) forms a favorable dipole-dipole interaction with another electronegative atom
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hydrogen-bond donor
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the atom bearing the hydrogen
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hydrogen-bond acceptor
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the atom that interacts closely w/ the hydrogen
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Hydrogen bonds are energetically favorable only when...
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only when the atoms are very close to one another and are oriented appropriately.
Dipole-dipole interaction falls off quickly w/ distance, interaction energy falls off if the angle btwn the dipoles is too far from linear. |
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Effect of water on hydrogen bonds
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just as for ion pairs, presence of H2O weakens the strength of hydrogen bonds.
In addition to electrostatic shielding, additional attenuation arises b/c water is a very polar molecule that forms strong hydrogen bonds w/ itself and w/ other polar molecules. When a polar group in a biological molecule forms hydrogen bonds w/ another polar group it gives up hydrogen bonds w/ water --> reduction in strength of H-bond. |
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effective strength of H-bond
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the difference in energy btwn the actual hydrogen bond and the H-bond that these groups form w/ water.
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hydrogen bonds w/ polar groups bearing full charges
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polar bearing full charges can form H-bonds, and these are stronger than those btwn groups that do not have an overall charge
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nucleotide
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consists of a 5-carbon sugar covalently bonded to a phosphate group and to a heterocyclic aromatic ring system
Phosphate attached to 5' carbon Nitrogenous base attached to 1' carbon |
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ribonucleotides
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The nucleotide building blocks of RNA.
C2'-OH present (not present in DNA) |
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The three phosphate groups, starting w/ the one attached to C5', are called...
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the α, β, and γ phosphates.
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nucleoside
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The combination of the sugar and a base, without the phosphate
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nitrogenous bases bound to ____ carbon in nucleotides
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1' carbon
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nitrogenous bases are...
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electron-pair donors --> Lewis bases
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Pyrimidine
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Has single six-member aromatic ring.
Cytosine + thymine + uracil (in RNA) |
