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Biochemistry > 9. Nucleic Acids > Flashcards

9. Nucleic Acids Flashcards

1
Q

functions of nucleic acids

A

vitamins, coenzymes, energy carriers, second messengers, catalysts, genetic transmitting and storage materials

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2
Q

what are the two families of nitrogenous bases?

A
  1. Pyrimidine
  2. Purine
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3
Q

pyrimidine

A

single, planar ring structures
-includes thymine, cytosine, and uracil

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4
Q

purines

A

double, puckered ring structures (twisted, not planar)
-includes adenine, guanine, and hypoxanthine (intermediate)

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5
Q

minor bases

A

derivatives of the major nitrogenous bases that have undergone chemical changes
-most common are methylated bases
-ex: 7-methyl-G

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6
Q

properties of nitrogenous bases

A
  1. the free based are hydrophobic and have low water solubility at pH 7
  2. the exocyclic NH2 (not in the ring) are NON-IONIZABLE over pH 0-14 (just like NH2 in Asn and Gln)
    -at low and high pH, the endocyclic (WITHIN the ring) nitrogens ionize and the bases become more soluble
  3. exist as resonance structures (electron delocalization) so that each bond has a double bond character
  4. absorb uv light with a maximum near 260 nm
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7
Q

nucleosides

A

riboses with a 1’ nitrogenous base
-DO NOT have phosphate groups
-the sugars exist only in the ring forms (never become linear; hemiacetal)
-pentose carbon numbers are given a prime (‘) to distinguish them from the base numbers (which also have numbered carbons)

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8
Q

nucleoside naming

A

ribose + adenine = adenosine
ribose + guanine = guanosine
ribose + cytosine = cytidine
ribose + uracil = uridine
ribose + hypoxanthine = inosine

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9
Q

adenosine

A

a nucleoside that acts as a local hormone and neuromodulator
-other nucleosides mainly function as a component of nucleotides (not as versatile)

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10
Q

nucleotides , structure

A

nucleosides + phosphate

structure + Ribose-5’-phosphate + nitrogenous base

-the phosphate oxygens have pKas of about 1.0 and 6.0, and therefore are ionized at pH 7

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11
Q

what is the difference between a nitrogenous base, nucleoside, and nucleotide?

A

nitrogenous base: base ONLY (A,T,G,C,U)

nucleoside: sugar + nitrogenous base

nucleotide: sugar + nitrogenous base + phosphate group

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12
Q

what allows a phosphate group to attach?

A

OH groups
-cyclic molesules are attached at the 3’ and 5’ ends

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13
Q

cAMP and cGMP

A

second messengers important in intracellular “signal transduction”
(ex: used in fight or flight response)

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14
Q

ATP

A

Adenosine-5’-Triphosphate
-most common energy carrier
-CTP, GTP, and UTP are also used (act as energy carriers when they are TRI phosphates)

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15
Q

nucleic acids

A

linear polymers of nucleotides
-ex: DNA, RNA

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16
Q

DNA

A

Deoxyribonucleic Acid
-functions in the storage of genetic information of most cells
-contains 2’deoxy-D-Ribose and the bases adenine, thymine, cytosine, and guanine

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17
Q

what type of bonds link the 3’OH to 5’OH between the phosphate molecule

A

phosphodiester bonds
(linked with an oxygen in two areas)

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18
Q

structure of nucleic acids

A

backbone: repeating units of sugar-phosphate
side chains: nitrogenous bases

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19
Q

how are nucleotide sequences written?

A

5’ to 3’, left to right

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20
Q

oligonucleotide

A

fewer than 50 repeating units

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21
Q

polynucleotide = nucleic acid

A

greater than 50 repeating units

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22
Q

what was known about DNA in 1953?

A
  1. DNA is the component of chromosomes that carries genetic information
  2. the number of thymines equals the number of adenines, same for C and G
    -watson and crick determines the 3D structure of B-DNA in 1953
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23
Q

what is the largest contribution to the stability of the double helix?

A

base stacking
-stacking the bases on top of one another allows them to interact via van der waal and dipole:dipole interactions
-increases water entropy
(although they are weak bonds, there are MANY to increase stability)

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24
Q

what is now known about DNA ?

A
  1. two DNA strands coil around the same axis to form a right-handed, anti-parallel double helix
  2. the sugar-phosphates face the water (polar components; outside of the ring)
  3. the hydrophobic bases stack on top of one another to form a hydrophobic interior
  4. the bases are hydrogen bonded
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25
Q

hypochromic effect

A

base stacking reduces the UV absorption of nitrogenous bases at 260 nm
-free base pairs absorb uv easier than stacked pairs

26
Q

how are nitrogenous bases paired?

A

hydrogen bonds

27
Q

how many H bonds between A and T? G and C? A and U? G and C?

A

A-T: two hydrogen bonds

G-C: three hydrogen bonds

A-U: two hydrogen bonds

-this means that the two different strands have different but COMPLEMENTARY sequences

28
Q

how far apart are the bases in DNA?

A

0.33 nm apart

29
Q

how high does the double helix of DNA rise in one turn? how many bases are in a turn?

A

rises 3.4 nm
one turn has 10.5 bases

30
Q

major and minor grooves

A

seen in DNA, access points for enzymes
-allows for protein binding (for DNA replication/transcription, etc)

31
Q

what are the different forms of DNA? what is the most common?

A
  1. B form
  2. A form
  3. Z form

B form is the most common (most stable) but others are possible because of the many flexible bonds in the sugar-phosphate backbone

32
Q

A-DNA

A

formed in the absence of water
-the double helix is right-handed, complementary, and antiparallel (same as B-DNA)

33
Q

Z-DNA

A

named after zig-zag
-forms a LEFT-HANDED, complementary, double helix

34
Q

what does the self complementarity within DNA strands allow for?

A

allows for the formation of hairpins and cruciforms
(higher level of folding within a molecule)

35
Q

RNA structure

A

usually single-stranded, right-handed helix
-base stacking maintains the structure (same as DNA)
-A forms are most common

36
Q

what is the most common type of base stacking? what can it do?

A

Purine-Purine stacking is the strongest
-can disrupt regular stacking

37
Q

what else can disrupt RNA structure?

A

self-complementary sequences
-via watson-crick hydrogen bonds (ex: G-U; atypical)

38
Q

what happens before a cell divides?

A

the double helix unfolds and each strand serves as a template for the replication of a new complementary strand
-results in one double helix for each new cell

39
Q

central dogma

A

DNA —> RNA (transcription) —-> protein (translation)

40
Q

what are the types of RNA?

A
  1. messenger RNA
  2. transfer RNA
  3. ribosomal RNA
  4. micro RNA
41
Q

messenger RNA

A

carries the genetic information from the nucleus to the cytoplasm, where it is translated into protein

-makes up 5% of the total cellular RNA
-short lived (seconds to minutes)
-the length depends on the gene that it encodes (usually 100s-1000s of nucleotides)

42
Q

monocistronic RNA

A

RNA that encodes 1 polypeptide

43
Q

polycistronic

A

RNA that encodes two or more polypeptides
-more common in prokaryotes (simpler; allows DNA to be shorter)

44
Q

transfer RNA

A

carries the amino acids to the messenger RNA for protein assembly

-15% of cellular RNA
-the “translator” (pairs the RNA codon with the appropriate amino acid)

45
Q

structure of tRNA

A

usually about 100 nucleotides in length
-forms a “clover leaf” structure (NOT LINEAR)

-the amino acid is always carried on the 3’ end

46
Q

ribosomal RNA

A

the catalytic component of the ribosome (catalyzes the formation of peptide bonds)
-a machine for assembling protiens
-about 80% of cellular RNA
-typically made of molecules from 100-5000 nucleotides in length

47
Q

micro RNA (miRNA)

A

regulate the expression of mRNA (bind to mRNA to prevent translation; allows for control)
-about 22 base pairs of double stranded RNA
-show potential as new types of drugs (can prevent over-expression of genes)

48
Q

what happens to DNA at high temperatures?

A

at 70-90 degrees C, the double helix denatures
-H bonds are broken, bases unstack, and the strands separate
-note: if the temperature is lowered, the strands will re-anneal (come back together)
-extreme pH can also unfold DNA

49
Q

steps of DNA renaturation

A
  1. complementary base pairs align (slow step)
  2. double helix forms “zips up” (fast step)
50
Q

how is denaturation detected? renaturation?

A

denaturation: by an increase in the uv absorption of the single strands (hyperchromicity; single stranded, so higher absorbance)

renaturation: decrease in the uv absorption (hypochromicity; double stranded, so higher absorbance)

51
Q

does DNA denature at a higher temperature when it has a high G:C content or A:T content?

A

G:C (three hydrogen bonds instead of two)

52
Q

rank the duplexes from most to least stable: DNA:RNA, DNA:DNA, RNA:RNA

A

most: RNA:RNA > DNA:RNA > DNA:DNA (least stable, but most abundant)

53
Q

explain the temperature vs absorption graph for naturally occurring DNA, AT pairs, and GC pairs

A

bottom: 100% duplex (double stranded)

middle: TM (melting temperature; mid point of transition where strands are 50% melted and 50% duplex)

top: 100% melted (denatured; single stranded)

as you increase temperature, the strands will denature and the absorbance of UV increases
-AT has lower TM point because it is less stable
-GC has stronger TM point because it is more stable

54
Q

types of mutations (6)

A
  1. deamination of C –> U
  2. depuration
  3. UV light
  4. X-RAYS/radiation
  5. oxidative damage
  6. chemicals
55
Q

deamination of C–> U

A

removing an amino group from a C and replaces it with a carbonyl group (FORMS A URACIL INSTEAD)
-occurs in 1/10^7 of cytosines per 24 hours (happens quite frequently)
-have repair enzymes that recognize uracil and fixes it
-other deaminations occur in 1/10^9 bases per 24 hours (less frequent)

56
Q

depurination

A

release of the base (purine), which allows the formation of the linear aldehyde ribose
-can also be repaired
-occurs in 1/10^5 purines per 24 hour (much more frequent)

57
Q

UV light mutation

A

UV light induces the formation of a cyclobutane thymine dimer or 6-4 photoproduct if two T’s are stacked
-causes kinking in DNA
-very rigid “immobile”, which changes the structure

58
Q

x-ray radiation mutation

A

can also damage DNA
-ex: potassium 40: a long-lived, naturally occurring radioactive isotopes that is present at about 0.01%
-its half life is 1.2 billion years

59
Q

oxidative damage mutation

A

oxidative damage by H2O2 and free radicals (OH, O)
(can be found together or alone)

60
Q

chemical mutation

A

by nitrous acid, alkylating agents, and base analogs (looks like a base)
-base analogs can be used to treat HIV

61
Q

mutations

A

changes in the DNA structure that lead to changes in the genetic information carried by the cell
-important in aging and cancer
-a single mutation can lead to the death of a cell or organism

62
Q

RNA

A

functions in the storage of genetic information for SOME viruses (ex: influenza and HIV)
-primarily a carrier of genetic information and is involved in some catalysis (intermediate between DNA and protein)
-contains D-ribose and uracil instead of thymine

Biochemistry (18 decks)

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