BCH - Samuelson lec 8/13 part 1 Flashcards
1
Q
Nucleic acids relevance to life - function?
A
organism maintenance
2
Q
What are nucleic acids
A
molecules of information
3
Q
what are the 2 types of nucleic acids
A
RNA (ribonucleic acid) and DNA (deoxyribonucleic acid)
4
Q
What do nucleic acids contain
A
- pentose sugar (ribose, 2’-deoxyribose)
- phosphate (mono, di or tri)
- Base (purine or pyrimidine)
5
Q
Nomenclature wise, what is a nucleotide
A
Sugar + base + phosphate
6
Q
Nomenclature wise, what is a nucleoside
A
sugar + base
7
Q
How are bases numbered
A
with numbers
8
Q
how is sugar numbered
A
primed numbers (3’)
9
Q
how are phosphates numbered
A
alpha, beta, gamma
10
Q
What are the 2 types of sugar backbones (DNA/RNA)
A
- Nucleotides in DNA/RNA
- Phosphates (mono, di, tri)
11
Q
What are the 2 types of sugars in nucleotides
A
Ribose (RNA) and 2’-deoxyribose (DNA)
12
Q
What are the 2 types of bases in DNA and RNA
A
Purines and Pyrimidines
13
Q
The purines?
A
A and G
pure As Gold
14
Q
The pyrimidines?
A
C, U, T
Cut the PY
15
Q
Where is Adenine found
A
DNA and RNA
16
Q
Where is Guanine found
A
DNA and RNA
17
Q
Where is Cytosine found
A
DNA and RNA
18
Q
Where is Uracil found
A
RNA
19
Q
Where is Thymine found
A
DNA
20
Q
Phosphodiester bonds link nucleotides to form
A
nucleic acids
21
Q
Nucleic acids - strong acids, example?
A
Phosphate group pKa of ~1
Gives a negative charge
22
Q
Nucleic acids are polymers of
A
nucleotides
23
Q
DNA is a polymer of
A
deoxyribionucleotides
24
Q
RNA is a polymer of
A
ribonucleotides
25
DNA is most often used as the genetic material, explain how
Stability - double helix
Copying mechanisms (exception: RNA viruses)
26
DNA Structure - polarity
nucleotides are joined by a 5'-3' phosphodiester linkage
27
What direction is DNA and RNA written
5' --> 3'
28
The backbone of the nucleic acid strands are alternating
pentose and phosphates
29
Explain DNA being double stranded
Two polymer strands running anti-parallel and are COMPLEMENTARY
30
Most common form of DNA
B form (right)
31
Chargraff's rule?
amount of purines (AG) = pyrimidines (CT) and A = T and G = C
32
Double helix is held together by?
hydrogen bonds between complementary base pairs
33
Force stabilizing nucleic acid structures?
G-C: 3 hydrogen bonds
A-T: 2 hydrogen bonds
34
Physical properties of DNA - explain melting
DNA can melt/denature which means it becomes single stranded
This happens when the temperature is increased
35
Physical properties of DNA - explain anneal / hybridize
The double stranded form is energetically more favorable under mild conditions, so double helix forms SPONTANEOUSLY
Complementary strands reanneal
36
Base composition and DNA - what is it?
It affects melting temperature
Tm = the temperature at which half the DNA is denatured to a single stranded state
37
Hyperchromic effect
striking absorbance increases as DNA denatures or melts
38
Biological Consequences and Biotechnial Utility of DNA Structural Properties - name the 3
1. each strand is template for other strand - DNA replication and DNA repair
2. DNA is used to store, disseminate, and pass on information
3. Nucleic acid sequences can be determined
39
How is DNA packaged inside a nucleus
by wrapping DNA around a protein core
this base unit is a nucleosome
40
Discuss the details of DNA being packaged inside a nucleus
Chromatin = DNA and protein core
Protein core made up of histones
- core histones: H2A, H2B, H3, H4
-linker histone: H1
Histones are highly basic (positively charged) mainly because high amount of Lysine
41
Chromatin Structure
Supercoiling of Chromosomal DNA starts with nucleosome, but there are increasing levels of supercoiling to produce chromatin
42
Nucleotide Synthesis - nucleotides are the monomers of
nucleic acids
43
What are the 2 metabolic sources of nucleotides
De novo biosynthesis
Salvage
44
Explain de novo biosynthesis
Almost ALL organisms synthesize nucleotides
Purines: amino acids, bicarbonate, tetrahydrofolate, energy
Pyrimidines: amino acids, bicarbonate, energy
45
Explain salvage
Turnover or recycling of cellular nucleic acids
Digestion of ingested nucleic acids
46
What is PRPP synthetase
enzyme responsible for the synthesis of activated ribose which is necessary for de novo synthesis of purine and pyrimidine nucleotides
47
PRPP is required for
synthesis of both purines and pyrimidines and nucleotide salvage
48
Purine Biosynthesis - what do amino acids provide
the "Ns"
Glutamine 2N
Aspartate 1N
Glycine 1N, 2C
49
Purine Biosynthesis - committed step?
Glutamine-PRPP amidotransferase
50
Purine Biosynthesis - first nucleotide?
Inosinate or Inosine monophosphate (IMP)
51
What is IMP converted to
A and G
52
What do IMP, AMP, and GMP depend on
GTP
53
How is purine nucleotide biosynthesis regulated
IMP pathway control points and Branch point control
54
Explain IMP pathway control points
- feedback inhibition
---ADP and GDP
- Feedforward activation
---allosteric activation by PRPP
55
Explain branch point control
Rates of AMP and GMP are coordinated
AMP and GMP are competitive inhibitors of IMP
56
Key points of purine ribonucleotide synthesis
1. purines are synthesized by assembling a purine base on PRPP, a molecule produced from R5P and ATP
2. IMP is the first purine nucleotide synthesized
3. PRPP, amino acids, folate, and ATP are used to synthesis purines
4. AMP and GMP are synthesized from IMP. The biosynthesis of ATP and GTP are reciprocally regulated by the concentration of the other
5. Kinases convert AMP and GMP to ATP and GTP
6. Purine synthesis is regulated by feedback inhibition and feedforward activation to maintain a concentration of purines. Branchpoint control regulation is used to maintain a balance of each purine
57
Pyrimidine Biosynthesis - 6 steps to UMP, what are they?
Carbamoyl phosphate, carbamoyl aspartate, dihydroorotate, orotate, OMP, UMP
58
When is PRPP added in pyrimidine biosynthesis
with Orotate
59
What gets added to PRPP in pyrimidine biosynthesis
OMP
60
De novo Biosynthesis ingredient list
Glutamine, aspartate, HCO3- (bicarbonate), energy (ATP), PRPP - activated sugar
61
Pyrimidine biosynthesis steps
HCO3- + glutamine + 2 ATP --> carbamoyl phosphate + 2 ADP + Pi + glutamate
62
Pyrimidine Biosynthesis (U and C) - 1st pyrimidine?
Orotate
63
Steps of pyrimidine biosynthesis (U and C)
Orotate (add PRPP) --> OMP --> UMP --> --> UTP (glutamine and ATP added) --> CTP
64
Remember we get CTP from
UMP
65
Animal pyrimidine biosynthesis - explain
Feedback inhibition to prevent energy use
66
Animal pyrimidine biosynthesis - what is PRPP doing
feedback activation
67
Convergence of Purine and Pyrimidine Nucleotide Biosynthesis to make dNTPs - know how to draw!!!!
What does RR stand for?
RR = ribonucleotide reductase: 1 enzyme produces 2'-deoxy (d) ribonucleoside diphosphate: dADP, dGDP, dCDP, and dUDP
68
Synthesis of 2'-deoxy-ribonucleotides for DNA
a. catalyzed by ribonucleotide reductase (RR)
b. NDP is reduced (2' position) to form the dNDP
c. NADPH provides reducing power, via a protein intermediate, thioredoxin (glutaredoxin can be used in place of thioredoxin)
69
Regulation of dNTP synthesis - goal of RR enzyme regulation?
to produce correct ratios of the 4 dNDPs
70
Regulation of dNTP synthesis doesn't make what
dTTP
71
Ribonucleotide Reductase
regulation of overall activity (reaction velocity)
regulation of substrate specificity (which substrate binds) --> look at picture it is slide 50
72
Thymidylate synthase and thymidine kinase make what together from dUMP
dTTP
73
Production of Deoxythymidine - for DNA only
a. Add methyl group to dUMP!
b. methyl donated by N5, N10
c. no ribothymidylate so dTMP, dTDP, dTTP used, always deoxy, which are often written as TMP, TDP, and TTP!
74
Folate derivative acts as 1 carbon donor -->
N5, N10 - methylene-tetrahydrofolate must be regenerated by
Dihydrofolate reductase, a key enzyme in the biosynthetic production of dTMP
75
Nucleotide salvage and degradation summed up
Nucleotide salvage = reuse of bases
Nucleotide degradation = catabolize bases
76
Nucleotide Metabolism - nucleotides and phosphates yield
nucleosides
77
Nucleosides are absorbed through
the intestine or further degraded by nucleosidases and nucleoside phosphorylases
78
Nucleotide Degradation
Purines are broken down to uric acid
Pyrimidines are converted to CoA derivatives for catabolism
79
Nucleotide degradation and salvage - purine degradation (end product Uric acid)
Degradation proceeds by removing base from
nucleotides, then sugars.
Deficiency of adenosine deaminase causes SCIDs
(bubble boy, gene therapy)
80
Nucleotide degradation and salvage - purine salvage (recycling of bases)
Bases added to PRPP by HGPRT (HPRT)
Deficiency of HGPRT (HPRT) causes Lesch-Nyhan
syndrome, lethal disease.
-Uric acid crystals
-feedback inhibition PRPP synthase causing deficiency in all nucleotides
81
Purine Salvage - free purines are reconverted to
corresponding nucleotides
82
Explain gout
Gout is the excess of uric acid
purines are broken down to uric acid
Allopurinol treats gout by irreversibly inhibiting xanthine oxidase which inhibits hypoxanthine from producing uric acid
83
Chemotherapy - cytotoxic
kills dividing cells
84
Antimetabolite Drugs: not just for cancer therapy, list the 4 drugs
6-mercaptopurine
Allopurinol
Fluorouracil
Methotrexate
85
Antimetabolite Drug: 6-mercaptopurine use?
acute lymphocytic leukemia (ALL)
86
Antimetabolite Drug: Allopurinol
Gout
87
Antimetabolite Drug: Fluorouracil
Anticancer
88
Antimetabolite Drug: Methotrexate
Anticancer autoimmune
89
Chemical structure of methotrexate
folate analog
90
chemical structure of 6-mercaptopurine
purine analog
91
What is 5-Fluorouracil used for
it is an antimetabolite used to treat cancer
92
Drug administration of 5 fluorouracil
Drug administered must be converted to 5F-dUMP to be efficacious
93
5 FU and methotrexate inhibit synthesis of
dTMP
94
List the 4 multi-drug cocktails that are used to treat cancer
ABVD, CHOP, FOLFOX, TIP
95
DNA damage response
apoptosis - programmed cell death
96
Chemotherapeutic drugs - DNA damaging agents
bleomycin, cyclophosphamide, dacarbazine, melphalan, chlorambucil, carboplatin/cisplatin, temozolomide
97
What is the therapeutic index
Drug selectivity, which leads to therapeutic indices larger than 1, implies that cancer cells are hypersensitive to a therapeutic agent
Lack of selectivity and the absence of a significant therapeutic index simply imply that cancer cells are as sensitive to an agent as are cells in normal tissues
98
Chemoresistance Mechanism?
Increased DNA repair
99
DNA repair pathways, common damaging agents? (2)
Alkylating agents and Ionizing Radiation
100
Ionizing Radiation DNA Damage - Xrays
Low LET (linear energy transfer)
single-strand breaks caused by X-rays for example
101
Double stand DNA damange
A non-damaged chromosome can be used to repair its double-strand DNA damaged homologous chromosome
102
Homology directed repair (HDR) of double-strand DNA damage - inherited mutations
Inherited mutations in BRCA1 or BRCA2 greatly increase lifetime risk of developing breast and ovarian cancer
103
Homology directed repair (HDR) of double-strand DNA damage - uses recombination ?
Uses recombination between DNA of the
undamaged and damaged homologous chromosomes to repair the damaged chromosome
104
IMP + GTP = ?
AMP (adenosine monophosphate)
105
IMP + ATP = ?
GMP (guanosine monophosphate)
106
The genetic code is used to
translate information stored in DNA into proteins
107
the genetic code is
evolutionary conserved
