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Biochemistry I > Biochemistry Midterm 2.1 - DNA > Flashcards

Biochemistry Midterm 2.1 - DNA Flashcards

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:

A

guanine and adenosine

25
Q

pyrimidine bases:

A

cytosine and thymine and uracil

26
Q

Friedrich Miescher

A

isolated “nuclein” from cell nuclei
hydrolyzed reveal phosphate, pentose and nitrogenous base
discovered phosphodiester bonds and pentose as a ribofuranoside

27
Q

Franklin and Wilkins discovered

A

cross indicates helix structure
diamonds represent phosphate-sugar backbone on the outside

28
Q

Watson and Crick discovered

A

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
Q

major and minor groove length

A

major - 22 Å
minor - 12 Å

30
Q

forces that stabilize DNA helix

A

hydrogen bonds between complementary base pairs
van der waals interactions between adjacent base pairs

31
Q

other forms of DNA structure

A

Beta form predominates in cells
A form (compressed) and Z form (squiggly)

32
Q

semi conservative DNA replication

A

each strand serves as template for replication 5’ to 3’
new DNA has one daughter strand and one parent strand

33
Q

mRNA produced from
mRNA can code
advantage of different base

A

genetic template
for more than 1 protein
differentiates between the genetic coding functions

34
Q

why is RNA unstable compared to DNA?

A

ribose instead of deoxyribose is less stable
unstable un alkaline conditions or catalyzed by RNase
hydroxyl group acts as nucleophile

35
Q

function of palindromic sequences

A

used as recognition sites
can form hairpins and cruciforms

36
Q

RNA pairing

A

complex, unpredictable, many non-watson-crick pairs via H bonds
very folded to minimize energy

37
Q

anneal

A

reforming of structure (DNA after replication)

38
Q

why does UV absorption increase with DNA denaturation?

A

because base stacking is lost and aromatic bases are revealed

39
Q

why is more heat/energy required to denature guanine/cytosine H bonds?

A

because G-C has 3 H bonds and A-T/U has only 2

40
Q

Tm

A

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
Q

deamination

A

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
Q

depurination

A

type of spontaneous mutagenesis
removal of purine group involving breaking glycosidic bond
10000 per day!

43
Q

Effect of UV light on pyrimidines
Effect of ionizing radiation (x rays)

A

pyrimidine dimers (stick together)
ring opening and strand breaking

44
Q

NTP

A

nucleotide triphosphate
hydrolysis of these provides energy for enzymatic catalysis

45
Q

nucleotide coenzymes

A

adenosine containing
coenzyme A, FAD (active form B2 riboflavin)

46
Q

RNA and DNA pentose forms in solution and in nucleotides/nucleosides

A

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
Q

depurination of the N-glycosidic bond is often due to
frequency

A

hydrolysis under acidic conditions
10000 purines lost per day

48
Q

A form DNA

A

right handed, 26 Å diameter
more condensed
anti glycosidic conformation
favors low hydration conditions

49
Q

B form DNA

A

right handed, 20 Å diameter
less condensed than A form
anti glycosidic conformation
predominates in cells

50
Q

Z form DNA

A

left handed, 18 Å diameter
least condensed DNA
anti for pyrimidines, syn for purines
predominates in high salt conditions

51
Q

ATP is a

A

ribonucleoside triphosphate

52
Q

What are nucleosides?

A

Nucleosides are important biological molecules that function as signaling molecules and as precursors to nucleotides needed for DNA and RNA synthesis.

53
Q

groups participating in H bonds between A-T

A

A: N and NH
T: NH and =O (with another =O that doesn’t participate)

54
Q

groups participating in H bonds between G-C

A

G: NH, NH and =O
C: =O, N, NH

55
Q

difference between thymine and uracil?

A

thymine is methylated

56
Q

what is 5-methylcytosine

A

minor nucleotide in eukaryotes and bacteria
can be spontaneous deaminated into thymine

57
Q

what is xanthine and hypoxanthine?

A

xanthine - product of spontaneous deamination of guanine
hypoxanthine - product of spontaneous deamination of adenine

58
Q

spontaneous deamination of cytosine forms

A

uracil

Biochemistry I (12 decks)

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