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Biochemistry I > Biochemistry Midterm 2.1 - DNA > Flashcards

Biochemistry Midterm 2.1 - DNA Flashcards

(58 cards)

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1
Q

what is an irreversible inhibitor?
how does it affect Vmax and Km?

A

covalently link to enzyme to shut it off
ex. toxins, drugs (aspirin, penicillin
Vmax and Km decrease because of substrate competition and blocking enzyme itself

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2
Q

what is allosteric inhibition/regulation

A

small chemicals, non covalent modification of enzymes
can be up regulation or down regulation

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3
Q

covalent enzyme modifications

A

R groups that are often modified to become more or less reactive: serine threonine and histidine
phosphorylation by kinases can work like an allosteric regulator

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4
Q

what is a zymogen?

A

an inactive precursor molecule of an enzyme, which requires irreversible covalent modification to become active form

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5
Q

nucleic acids are (5)

A

polymers of nucleotides used in:
DNA - storage of genetic info
mRNA - transmission of genetic info
ribozymes - processing of genetic info
protein synthesis using tRNA and rRNA

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6
Q

nucleotide uses

A

ATP, cofactors (NAD+) and cAMP (signal transduction)

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7
Q

pyrimidine structure
purine structure

A

nitrogenous bases
pyrimidines are hexagonal, purines are bicyclic

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8
Q

nucleotide vs nucleoside structure and numbering

A

nucleotide: phosphate, pentose, nitrogenous base
nucleoside: nitrogenous base and pentose
pentose ring is numbered #’, nitrogenous base is just #

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9
Q

phosphate group in nucleotide

A

connected to 5’ end of the ribose (can be on other positions in other molecules)
PO4 is negatively charged at pH 7

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10
Q

phosphodiester bond between nucleotides

A

5’ phosphate and 3’ hydroxyl

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11
Q

what is beta furanose? which molecules have this structure?

A

beta furanose is a 5 ring with 1 oxygen, and 4 carbons
ribose and deoxyribose (H instead of OH on 2’) for RNA/DNA

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12
Q

nitrogenous base chemical structural properties

A

heteroaromatic, UV light absorbing (250 nm- 270nm), planar, good H acceptor and donor, neutral at pH 7

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13
Q

Nucleotide/nucleoside nomenclature

A

Adenine: Adenosine / Adenylate
Guanine: Guanosine / Guanylate
Cytosine: Cytidine / Cytidylate
Thymine: Thymidine / Thymidylate
Uracil: Uridine/Uridylate

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14
Q

phosphate group in nucleotide

A

connected to 5’ end of the pentose (can be on other positions in other molecules)
PO4 is negatively charged at pH 7

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15
Q

B-N-Glycosidic bond

A

bonds that connect nucleotides/nucleosides
1’ pentose connected to N1 on pyrimidines and N9 on purines
bond has rotation which allows helix to form
stable bond, especially in pyrimidines

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16
Q

conformations of N-glycosidic bond
number of bonds that affect nucleotide conformation
ring pucker

A

0° - syn conformation
180° - anti conformation (found in B DNA)
7 bonds
ring pucker (bond 4) limits torsion angle between nitrogenous base and pentose

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17
Q

nucleotide absorption measurement wavelength

A

260 nm

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18
Q

minor nucleosides that mark DNA to be transcribed

A

post synthesis modifications
in eukaryotes and bacteria: 5-methylcytosine
in bacteria: N^6-methyladenosine
used to mark one’s own DNA and genes to be transcribed

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19
Q

inosine

A

often in wobble position of anti-codon in tRNA
deaminated adenosine

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20
Q

wobble position

A

3rd nucleotide in a codon
allows for non-watson and crick pairing that is looser

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21
Q

pseudouridine

A

found in tRNA and rRNA
made from uridine (glycosylated uracil) after RNA synthesis
made stabilize tRNA and help folding rRNA

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22
Q

phosphodiester bonds in DNA/RNA

A

3’ carbon of pentose and the phosphate group 5’ carbon of deoxyribose/ribose
releases 1 water during formation
contributes to 5’ to 3’ orientation of DNA

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23
Q

Chargaff’s rule
base pairs bond via
ratio of base pairs in DNA

A

pyrimidines pair with purines (AT(U), GC)
hydrogen bonds
1:1 ratio of purines to pyrimidines

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24
Q

purines bases:

Study These Flashcards
A

guanine and adenosine

25
pyrimidine bases:
cytosine and thymine and uracil
26
Friedrich Miescher
isolated "nuclein" from cell nuclei hydrolyzed reveal phosphate, pentose and nitrogenous base discovered phosphodiester bonds and pentose as a ribofuranoside
27
Franklin and Wilkins discovered
cross indicates helix structure diamonds represent phosphate-sugar backbone on the outside
28
Watson and Crick discovered
missing layers indicate major and minor groove of helix and hydrogen pairing between bases beta-DNA model - 36 Å (10.5 bases) between per turn of helix 3.4 Å between adjacent bases 20 Å wide
29
major and minor groove length
major - 22 Å minor - 12 Å
30
forces that stabilize DNA helix
hydrogen bonds between complementary base pairs van der waals interactions between adjacent base pairs
31
other forms of DNA structure
Beta form predominates in cells A form (compressed) and Z form (squiggly)
32
semi conservative DNA replication
each strand serves as template for replication 5' to 3' new DNA has one daughter strand and one parent strand
33
mRNA produced from mRNA can code advantage of different base
genetic template for more than 1 protein differentiates between the genetic coding functions
34
why is RNA unstable compared to DNA?
ribose instead of deoxyribose is less stable unstable un alkaline conditions or catalyzed by RNase hydroxyl group acts as nucleophile
35
function of palindromic sequences
used as recognition sites can form hairpins and cruciforms
36
RNA pairing
complex, unpredictable, many non-watson-crick pairs via H bonds very folded to minimize energy
37
anneal
reforming of structure (DNA after replication)
38
why does UV absorption increase with DNA denaturation?
because base stacking is lost and aromatic bases are revealed
39
why is more heat/energy required to denature guanine/cytosine H bonds?
because G-C has 3 H bonds and A-T/U has only 2
40
Tm
higher C-G content in a sequence, the higher the midpoint of melting (Tm) Longer DNA sequence increases Tm pH and ionic strength affects Tm (salt increases Tm)
41
deamination
type of spontaneous mutagenesis slow reaction that affects a large number of residues C --> U (100 per day) 5-methylcytosine --> thymine adenine --> hypoxanthine G --> xanthine
42
depurination
type of spontaneous mutagenesis removal of purine group involving breaking glycosidic bond 10000 per day!
43
Effect of UV light on pyrimidines Effect of ionizing radiation (x rays)
pyrimidine dimers (stick together) ring opening and strand breaking
44
NTP
nucleotide triphosphate hydrolysis of these provides energy for enzymatic catalysis
45
nucleotide coenzymes
adenosine containing coenzyme A, FAD (active form B2 riboflavin)
46
RNA and DNA pentose forms in solution and in nucleotides/nucleosides
in solution exists in equilibrium between aldehyde form and beta furanose RNA exists as beta-d-ribofuranose DNA exists as beta-2'-deoxy-d-ribofuranose
47
depurination of the N-glycosidic bond is often due to frequency
hydrolysis under acidic conditions 10000 purines lost per day
48
A form DNA
right handed, 26 Å diameter more condensed anti glycosidic conformation favors low hydration conditions
49
B form DNA
right handed, 20 Å diameter less condensed than A form anti glycosidic conformation predominates in cells
50
Z form DNA
left handed, 18 Å diameter least condensed DNA anti for pyrimidines, syn for purines predominates in high salt conditions
51
ATP is a
ribonucleoside triphosphate
52
What are nucleosides?
Nucleosides are important biological molecules that function as signaling molecules and as precursors to nucleotides needed for DNA and RNA synthesis.
53
groups participating in H bonds between A-T
A: N and NH T: NH and =O (with another =O that doesn't participate)
54
groups participating in H bonds between G-C
G: NH, NH and =O C: =O, N, NH
55
difference between thymine and uracil?
thymine is methylated
56
what is 5-methylcytosine
minor nucleotide in eukaryotes and bacteria can be spontaneous deaminated into thymine
57
what is xanthine and hypoxanthine?
xanthine - product of spontaneous deamination of guanine hypoxanthine - product of spontaneous deamination of adenine
58
spontaneous deamination of cytosine forms
uracil

Biochemistry I (12 decks)

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