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Flashcards by Marissa Alvarez, updated more than 1 year ago
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Created by Marissa Alvarez
about 5 years ago
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| Question | Answer |
| Learning goals for Lecture 37 Need to know the following key points | • The building blocks of DNA and RNA • The primary structure of DNA Hydrogen bond donor and acceptor sites on bases • The DNA double helix and the forces that stabilize the helical structure • The antiparallel nature of double-stranded DNA • Primary structure of RNA • Secondary and tertiary structures of RNA |
| Figure 19.6 Hydrogen bonding sites of bases. While A has ___, T G, and C have ___ donor or acceptor sites each. C & T have __ donor and __ acceptors G has ___ donors and ___ acceptor A has __ donor and ___ acceptor | two three one two two one one one |
| Primary structure of DNA Nucleotides are joined by ___ phospho-diester linkages. The backbone of the polynucleotide chain consists of phosphoryl groups, 5' 4' and 3' carbon atoms, and 3' oxygen of the deoxyribose So backbone = ___ + ___ | 3'-5' phosphate + sugar |
| DNA double strand formation Two anti-parallel strands form the DNA double helix through ____ bonding between the bases of complementary strands. Note that the backbone of the two strands formed by the deoxyribose- phosphate phospho-diester linkages are ___-____ G-C = ___ H bonds A-T = ___ H bonds | hydrogen anti-parallel 3 (stronger) 2 |
| Complementary base pairing and stacking in double-stranded DNA Base pairing produces a regular structure in which one strand is complementary to the other. Base-pair ___ lead to the formation of a double helix with stacked base pairs. Weak interactions stabilize the double helix: 1. ___ bonds between bases in the double helix. 2. Stacking interactions: stacked bases form __ __ ___ interactions. 3. ____ effects: burying of bases in the interior of the double helix. | interactions Hydrogen van Der Waals Hydrophobic |
| Some terms used to describe double helix DNA Major and minor groove of the helix with unequal width induced by ___-___ mechanism. Diameter of the double helix (2.37 nm in B DNA) • Rise of the helix (0.33 nm in B DNA). Rise = distance b/w two neighboring DNA ___ ___ • Pitch of the helix (3.4 nm in B DNA, -10.4 bases). Pitch = one ____ of the helical structure | base-pairing base pairs rotation |
| A slide with a space-filling model of __ DNA, the most common form in cells. • bases (light shades) project ___ from the sugar-phosphate backbones (dark red and blue) of each strand • the major and minor grooves are lined by potential hydrogen bond donors and acceptors (yellow), which can interact with proteins and other molecules without ___ the helix. Note: electrostatic repulsion due to the negatively charged phosphate groups is a destabilizing force, but mitigated by cations such as ___ and positively charged proteins (e.g. ____). | B inward disrupting Mg2+ histones |
| Stacking interactions for the 10 possible combinations in double-stranded DNA The stacking energy of two base pairs depends on the nature of the base pair (G/C or A/T) and the orientation of each base pair. Within the hydrophobic core of the stacked double helix, the hydrogen bonds between the base pairs have -27 kJ/mol each. However, if the stacking interactions are ___, the hydrogen bonds in the base pairs become exposed to competition with water and the overall contribution to keeping the strands together diminishes greatly. Under physiological conditions, double-stranded DNA is thermodynamically much more ____ than separated strands and that is why the double-stranded form predominates in vivo. The complete separation of strands of a double helix DNA is called ____. The temperature at which half of the double-stranded DNA is separated is the ___ ___ | weakened stable denaturation melting point. |
| The _ form of the double helix is the most common form in cells. However, two other forms of the DNA double helix have been discovered. The _ DNA with tighter stacking but wider diameter that forms when DNA is dehydrated, and the _ DNA with left-handed helix. Z DNA is formed by __ rich regions with alternating purine and pyrimidine bases in the primary structure. B & A DNA = ___ handed Z DNA = ___ handed | B A Z GC Right Left |
| UV absorbance of DNA is maximum at ___ nm. Single-stranded DNA absorbs 12-40% ___ light than double-stranded DNA since the bases are more exposed in ssDNA than dsDNA. | 260 more |
| A plot of change in absorbance of a DNA solution versus temperature is called a ___ ___ Generally, absorbance increases sharply at the melting point and ____ occurs in a narrow range after that. The sigmoidal nature of the curve indicates ____ between base pairing and stacking. Note that GC-rich DNA has a ___ melting point due to the increased energy conferred by G-C base pairing. For instance, the melting point of poly-AT, poly-AT/GC and poly-GC in the figure below are 69°C, 88°C, and 109°C, respectively. | melting curve. denaturation cooperativity higher |
| Primary structure of RNA Like DNA, each RNA strand has the same basic structure composed of nitrogenous bases ___ bound to a sugar-phosphate backbone. However, unlike DNA, RNA is usually a ___-____ molecule. | covalently single-stranded |
| RNA molecules can form secondary and tertiary structures: Unlike DNA which exists primarily as a long double helix, most cellular RNAs are ___ stranded and exhibit a variety of conformations. Differences in size and conformations permit them carry out specific functions. a) Secondary structures: ___ : complementary sequences 5-10 ntds from each other. ___-___ : by complementary strands 10 to several hundred ntds from each other. b) Tertiary structure: combination of ___ and ___ | single Hairpin Stem-loop stems and loops |
| Cells contain several types of RNA 1. ___ ___ (__): Integral part of ribosomes and the most abundant RNA in cells. 2. ___ ___ (__): they carry activated amino acids to ribosomes for incorporation into proteins. 3. ___ ___ (__): carry the genetic information (encode the sequence of amino acids) for the synthesis of proteins by the ribosomes. 4. ___ ___ molecules (miRNA, IncRNAs, primer RNAs, etc) | Ribosomal RNA (rRNA) Transfer RNA (tRNA) Messenger RNA (mRNA) Small RNA |
| Alkaline hydrolysis of RNA: DNA is more stable than RNA and therefore a better carrier of genetic information. RNA is less stable because the _-___ group can act as a nucleophile and attack the phosphodiester bond and break the strand when activated by proton withdrawal. First, 2',3' cyclic monophosphate product is formed and then hydrolyzed to a mixture of 2' and 3' monophosphates. This can happen in 0.1 M NaOH at room temperature in which DNA is stable. RNA is a very UNSTABLE molecule due to the presence of the __ group on the 2' carbon on the sugar (ribose) and can be degraded very ___ | 2'-hydroxyl OH easily |
| Mechanism of RNA cleavage by RNase A. Three ionic residues in the active site of RNase A (His-12, Lys-41, and His-119) cooperate to ___ RNA. The process is similar to alkaline hydrolysis in that His-12 acts as a __ to abstract H from the 2'-hydroxyl group, leading to activation of the 2'-oxygen to act as a nucleophile. His-119 then acts as an __ and donates H to the 5'oxygen atom of the next nucleotide residue to produce an alcohol leaving group (Product 1 or PI). The end of the truncated RNA molecule now has a 2',3'-cyclic nucleoside, which is attached by an activated water molecule. Note this His-119 after donating H now acts as a __ to activate water. The role of Lys-41 is to ___ the transition state. Finally, His-12 which was converted to an acid donates H to produce P2 and ____the enzyme. | hydrolyze base acid base stabilize regenerate |
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