DNA & RNA structure

  1. Mutation
    a change within the original DNA sequence
  2. A ______ may change one or more amino acids coded by a _____, depending on the _____ it may cause a mild, moderate or severe change in function of the coded ______.
    • mutation 
    • gene 
    • mutation
    • protein
  3. Hemoglobin
    the protein in blood that carries oxygen and is responsible for the red color of blood. It has 4 polypeptide chains (2 beta and 2 alpha chains)
  4. A mutation in the ____ _____ gene causes sickle cell anemia.
    beta globin gene(specifically the β-globinWT turned into β-globinS)
  5. In the sickle cell mutation, the 6th amino acid on beta globin has been modified in the sense that _____ ____ has been changed into ______. How do they differ?
    • glutamic acid 
    • valine
    • They are very different from one another, valine is hydrophobic or non-polar amino acid, while glutamic acid is very polar.
  6. When the glutamic acid to valine mutation occurs, if the person is in  an area with _____ _______ pressure they will be fine. However, if they go to an area of _____ _____ pressure _____ becomes unstable, it ______ and its shape is modified into something resembling a sickle.
    • high oxygen pressure
    • low oxgegn pressure
    • hemoglobin
    • polymerizes
  7. The original shape of hemoglobin is very _____, so it can easily move through capillaries in the body, in contrast, the sickle mutation is very ____ and does not move freely through capillaries which leads to ____ and ____ ____ in red blood cells
    • flexible
    • rigid 
    • clogs 
    • permanent ruptures
  8. chromosome
    a genetic structure made of long DNA molecules and the proteins associated with the DNA.
  9. Human cells have ___ chromosomes (___ pairs of somatic chromosomes and XX or XY). Human chromosome 1 contains _______ nucleotides
    • 46 chromosomes
    • 22 pairs
    • 260 million
  10. Chromosomes are made of ____ with some _____ associated.
    • DNA 
    • proteins 
    • (basically a very long strand of DNA)
  11. Proteins are the product of ______
    RNA not the genes themselves
  12. DNA doesn't have _____ they are strictly strands that vary in ______
    • branches 
    • length
  13. Majority (____) of DNA doesn't code for anything while the remaining ____ codes for _____
    • 97.5%
    • 2.5%
    • proteins
  14. Genes
    parts of the DNA molecule of each chromosome
  15. The order of the _______ in a gene will code for a particular protein or function
  16. Genome
    The entire genetic complement of a living organism that contains the biological information needed to construct and maintain a living example of that organism.
  17. Genome (3 characteristics)
    • Made of DNA in most organisms.
    • Made of RNA in some viruses.
    • Offspring inherit entire genomes, not half
  18. Why was chromosome 22 the 1st to be sequenced after years and billions of dollars spent as opposed to chromosome 1.
    Out of the 22 pairs, chromosome 22 is the shortest and chromosome 1 is the longest
  19. The general structure of DNA is the same in  different organisms and genes. The main difference is in the order of ________
  20. Some specific sequences of nucleotides may affect the general  structure of DNA to some extent. Some viruses have ______ _____ ___ as their genome and there are also some organisms with _____ DNA as opposed to linear.
    • single strand DNA
    • circular
  21. List the 3 parts of DNA
    • a sugar (deoxyribose)
    • a base aka nucleotide
    • phosphate
  22. 2 characteristics of DNA's sugar
    • deoxyribose is a 5 carbon sugar
    • carbons are numbered 1' to 5'
  23. Why are deoxyribose's carbons designated '
    to differentiate them from the numbering of carbons in the base
  24. List what all 5 carbons do in DNA's deoxyribose
    • carbon 1' because the base is attached to it via glycosidic bond
    • carbon2' is important because it differentiates it from RNA by having two hydrogens as opposed to one hydrogen and a hydroxyl
    • carbon 3' because that is where the phosphate of the next nucleotide binds to it via phosphodiester bond
    • carbon 4' just carries carbon 5'
    • carbon 5' is important because the phosphate is attached to it
  25. Each base is attached to the carbon 1' of deoxyribose by a ______ bond while deoxyribose and phosphate are linked by _____ bonds.
    • glycosidic bond
    • ester bonds
  26. There are two groups of bases ______ & ______
    • pyrimidines: cytosine and thymine, both made of a single heterocyclic ring
    • purines: adenine and guanine, both made of a double heterocyclic ring
  27. _______ bind to deoxyribose by their N9, while purines bind to deoxyribose by their N1
    • purines 
    • pyrimidines
  28. Caffeine is classified as a _______ though not part of the DNA structure
  29. Tautomers are a structure of _______ that are in ______ with each other
    • isomers
    • equilibrium
  30. In nucleotides, bases can occur as either form of two alternative _____.
  31. The equilibrium of tautomers is biased very much toward the _____ and _____ forms but sometimes _____ or _____ versions occur
    • keto and amino
    • enol or imino
  32. Base + sugar = _______
    • Base + sugar + phosphate (1, 2 or 3) = _______
    • What happens as more phosphates are attached?
    • nucleoside
    • nucleotide
    • More energy available in the nucleotide
  33. DNA is a _______ of nucleotides
  34. In DNA, two strands of _____ _____ are twisted around each other in the form of a _____ ____ (like a twisted ladder). The backbone of DNA (the poles of the ladder) is made of alternates of _______ & ______.
    • nucleotide polymers 
    • double helix
    • deoxyribose & phosphate
  35. DNA has a negative charge because of _______ and the steps of the "ladder" are made of ______.
    • phosphates
    • bases
  36. Nucleotides are linked by ______ bonds connecting the ___ of the sugar of one nucleotide to the ___ of the next nucleotide's sugar. There is a ______ in the structure of each strand, starting at ___ ______ and ending with the ___ ___ on the other end
    • phosphodiester bonds 
    • 3' 
    • 5'
    • polarity 
    • 5' phosphate
    • 3'-OH
  37. In one strand of DNA, nucleotides can be arranged in _____ order. Additionally, the two strands are said to be _______ in orientation
    • any order
    • antiparallel (in opposite direction from 3' to 5' on one end and 5' to 3' on the other)
  38. The two strands are held together by ______ ______. This uses ______ bonds between ______ bases. The two strands have _______ sequences.
    • base pairing 
    • hydrogen
    • complementary bases
    • complementary sequences
  39. State the complementary base pairs and their expected bonds
    • A:T, two hydrogen bonds
    • G:C, three hydrogen bonds
  40. Hydrogen bonds
    Hydrogen bonds are not a form of covalent bond, they are a weak bond between two molecules resulting from an electrostatic attraction between a proton in one molecule and an electronegative atom in the other.
  41. Hydrogen bonds are powerful in numbers, state a viable example. 
    • **Bonus: how would you break a hydrogen bond
    • for example the reason water is liquid on earth is because all the molecules of water are pulled to each other through hydrogen bonds
    • **increasing the temperature
  42. The distance between A and T is ______ to the distance between C and G. DNA is a _______ structure
    • equal
    • symmetrical
  43. Why are there dominant tautomers or specific bases pairs
    DNA is very stable, and mismatch bases causes steric hindrance
  44. What two things stabilize the structure of DNA?
    • base pairing (hydrogen bonds)
    • bases being stacked on top of each other
  45. Bases are almost ______ with the axis of helix, they are flat and not very h2O _____. As a result, stacking of the bases almost excludes ______ molecules. How does this help stabilize DNA?
    • perpendicular
    • soluble
    • water
    • It causes hyrdophobic and Van der waals interactions between the stacks of bases
  46. Bases can be flipped out of the double helix one by one. This phenomena seems to be implemented by some enzymes that are involved in (4):
    • Methylation of bases
    • removing damaged bases
    • DNA repair
    • homologous recombination
  47. DNA is a ____ handed double helix, for instance, if you were walking up a helical staircase, the rail would be on the ____ side. You would be going up in _____ ______ direction. Each base pair would be twisted approx _____ and it would take almost ___ _____ to make a full turn on the helix.
    • right
    • right
    • counter-clockwise 
    • 36°
    • 10 bases
  48. Gel electrophoresis
    Gel electrophoresis is the process of separating different sizes of DNA from each other
  49. Experimental proof of the number of bases in one turn of DNA (story)
    • DNA molecules were linked to a surface (mica, a volcanic glass-like rock) on their sides.
    • Only one side of DNA is available the other side is attached to mica.
    • These DNA molecules were partially digested by DNase.
    • The digested DNA fragments were detached from the surface and separated by gel electrophoresis.
    • The DNA bands on the gel had sizes with increments of 10
  50. In a base pair of DNA, the glycosidic bonds between the sugar and bases are not in _____ ____, there is angling involved. On one side of each glycosidic bond, the less open angle is _____ and the other side is ______. These angles in glycosidic bonds generates _____ & ____ of DNA
    • straight line
    • ~120°
    • ~240°
    • major and minor grooves
  51. Why are major grooves more important that minor
    more room for interaction of proteins with DNA
  52. A=
    • D=
    • M=
    • H=
    • A = hydrogen bond acceptor
    • D = hydrogen bond donor
    • M = Methyl group (hydrophobic)
    • H = Non-polar hydrogen
  53. Major grooves are _____ in chemical info. State the chemical codes for their base pairs
    The chemical codes of major groves: G:C = AADH, C:G = HDAA A:T = ADAM, T:A = MADA
  54. Two reasons why chemical codes are important
    • help us differentiate base pairs
    • help proteins read the sequence of DNA and without separating the strands, attach to the correct sequence
  55. Chemical codes for minor groves
    The chemical codes of minor groves: G:C = ADA, C:G = ADA A:T = AHA, T:A = AHA
  56. Though minor grooves are not as important as major grooves, they are still used by proteins for _____ ______
    sequence recognition
  57. B-form (double helix)
    • A-form (double helix)
    • B-form: the average conformation seen in physiological conditions
    • A-form: sometimes occur in DNA protein interactions. A-form is more similar to RNA if it makes double strand structure.
  58. The B form may change to some extent, affecting major and minor grooves. This is dependent on?
    the sequence of DNA
  59. B-DNA
    • High humidity
    • Right handed
    • 11 base pairs/turn
    • Best approximation
  60. A-DNA
    • Low humidity
    • Right handed
    • 11 base pairs/turn
    • Broad/short alternance
  61. Z DNA
    Z DNA is a left handed helix with a zigzag structure (Z DNA). High concentration of + charged ions
  62. Z DNA occurs when the ______ is made of ______ & _____ alternates in a solution with ____ concentration of charged ions (___).
    • sequence 
    • purine & pyrimidine 
    • high 
    • Na+
  63. Glycosidic bonds can assume syn or anti positions explain

    In B-DNA, the position is always in the _____ conformation, while in purine and pyrimidine alternates, the pyrimidine is in the _____ and the purine in the ______ conformation
    • syn: same direction of base and sugar
    • anti: opposite direction of base and sugar
    • anti conformation
    • anti conformation
    • syn conformation
  64. Syn vs anti-syn alternates
    • syn conformation: left hand helix
    • anti-syn alternates: zigzag appearance
  65. The info of DNA comes from ______, and there are molecules that bind to it and read its info. Without DNA, nothing would direct ____ ______ and the formation of DNA would be rendered useless
    • nucleotides
    • RNA polymerase
  66. Denaturation:
    Separating the two strands of DNA from each other. Denaturation can happen by breaking hydrogen bonds via high temperature or high pH.
  67. How do we reattach denatured DNA strands?
    • What is the process called?
    • Reducing Temp or pH
    • hybridization or annealing
  68. DNA can absorb _____ at 260 nm (not the same as using this spectrum to damage DNA)
    UV light
  69. In double strand DNA, the manner in which bases are _______makes them less available to UV light so the absorption is less in comparison to _______ _____
    • stacked
    • denatured DNA
  70. A double strand absorbs ____ less UV than a denatured one. We increase absorption by increasing ______. This helps us determine the _____ point of DNA
    • 40%
    • temp.
    • melting point
  71. Melting point of DNA
    a temp at which 50% of the DNA is hybridized and the other 50% is not, if the temp is increased, DNA becomes denatured and if it is decreased, DNA anneals
  72. 3 factors that affect the melting point (Tm) of DNA
    • the size of DNA (number of bases): short DNA fragments have lower Tms.
    • GC content: higher G:C content leads to more hydrogen bonds which leads to a higher melting point. 
    • Ionic strengths: Higher salt concentration leads to higher Tm because we have more cations and high levels of positively charged ions surround the negatively charged phosphates in DNA backbone, therefore its is easier for both strands to not repel each other.
Card Set
DNA & RNA structure
Week 1 pt 3