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Module 9 Flashcards

1
Q
  • are the monomeric units that make up the nucleic acids DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid)
A

Nucleotides

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2
Q
  • are responsible for the storage and passage of the information needed for the production of proteins
A

Nucleic acids

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3
Q

Each nucleotide consists of __

A

a pentose sugar, a nitrogenous base, and a phosphate group

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4
Q

Result from linking one or more phosphates with a nucleoside onto the 5’ end of the molecule through esterification

A

Nucleotides

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5
Q

A __ is a 5-carbon sugar in a pentose ring form

A

pentose sugar

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6
Q

__ contains ribose, which has a hydroxyl group in both the 2’ and 3’ positions (prime refers to the carbon of the sugar)

A

RNA

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7
Q

__ has only a single hydroxyl group in the 3’ position

A

DNA

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8
Q

A __ is attached by a glycosidic bond to the 1’ carbon of the nucleotide’s sugar

A

nitrogenous base

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9
Q

__ consist of linked 5-membered and 6-membered rings (Adenine and Guanine, A and G) which can be found in DNA or RNA

A

Purines

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10
Q

__ consist of 6-membered rings Cytosine, Thymine, and Uracil (C, T, and U)

A

Pyrimidines

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11
Q

(pyrimidines)

__ is found in DNA or RNA, T is found in DNA, while U is found in RNA

A

Cytosine

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12
Q
  • Planar, aromatic, and heterocyclic
  • Derived from purine or pyrimidine
  • Numbering of bases is “unprimed”
A

Nitrogenous Bases

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13
Q

The sugar derivatives

__ participate in sugar interconversions and in the biosynthesis of starch and glycogen

A

UDP-glucose and UDP-galactose

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14
Q

nucleoside-lipid derivatives such as __ are intermediates in lipid biosynthesis.

A

CDP-acylglycerol

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15
Q

The __ serve
as the second messengers in hormonally regulated events, and GTP and GDP play key roles in the cascade of events that characterize signal transduction pathways.

A

cyclic nucleotides cAMP and cGMP

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16
Q

__ are nitrogen-containing heterocycles, cyclic structures that contain, in addition to carbon, other (hetero) atoms such as nitrogen.

A

Purines and pyrimidines

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17
Q

Pyrimidine vs Purine

A

Note that the SMALLER
PYRIMIDINE MOLECULE has the longer name and the LARGER PURINE MOLECULE the shorter name, and that their six-atom rings are numbered in opposite directions.

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18
Q

__ are weak bases (pKa values 3-4), although the proton present at low pH is associated, not as one might expect with the exocyclic amino group, but with a ring nitrogen, typically N1 of adenine, N7 of guanine, and N3 of cytosine.

A

Purines or pyrimidines with an ´NH2 group

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19
Q

The sugar in ribonucleosides is D-ribose, and in deoxyribonucleosides is
2-deoxy-D-ribose. Both sugars are linked to the heterocycle by a __, almost always to the N-1 of a pyrimidine
or to N-9 of a purine

A

B-N-glycosidic bond

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20
Q

__ are nucleosides with a phosphoryl group esterified to a hydroxyl group of the sugar.

A

Mononucleotides

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21
Q

Additional phosphoryl groups, ligated by __ to the phosphoryl group of a mononucleotide, form nucleoside diphosphates and triphosphates.

A

acid anhydride bonds

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22
Q

Steric hindrance by the heterocycle dictates that there is no freedom
of rotation about the β-N-glycosidic bond of nucleosides or nucleotides. Both therefore exist as noninterconvertible __. While both syn and anti
conformers occur in nature, the anti conformers predominate.

A

syn or anti conformers

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23
Q

The conjugated double bonds of __ absorb ultraviolet light.

A

purine and pyrimidine derivatives

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24
Q

__ serves as an allosteric regulator and as an

energy source for protein synthesis.

A

GTP

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25
Q

__ serves as a second messenger in response to nitric oxide (NO)
during relaxation of smooth muscle

A

cGMP

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26
Q

__ forms the urinary glucuronide conjugates of bilirubin and of many drugs, including aspirin.

A

UDP-glucuronic acid

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27
Q

__ participates

in biosynthesis of phosphoglycerides, sphingomyelin, and other substituted sphingosines

A

CTP

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28
Q

__ have two acid anhydride bonds and one ester bond.

A

Nucleotide triphosphates

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29
Q

The purine analog __, used in treatment of hyperuricemia and gout, inhibits purine biosynthesis and xanthine oxidase activity.

A

allopurinol

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30
Q

__ is used in chemotherapy of cancer

A

Cytarabine

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31
Q

__ which is catabolized to 6-mercaptopurine, is employed during organ transplantation to suppress immunologic
rejection

A

azathioprine

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32
Q

The 5′-phosphoryl group of a mononucleotide can esterify a second hydroxyl group, forming a __. Most commonly, this second hydroxyl group is the 3′-OH of the pentose of a second nucleotide.

A

phosphodiester

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33
Q

This forms a __ in which the pentose moieties are linked by a 3′,5′-phosphodiester bond to form the “backbone” of RNA and DNA.

A

dinucleotide

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34
Q

Posttranslational modification of preformed polynucleotides can generate additional structures such as __, a nucleoside in which D-ribose is linked to C-5 of uracil by a carbon-to-carbon bond rather than by the usual β-Nglycosidic
bond.

A

pseudouridine

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35
Q
  • contains a single phosphate group, which is a strong acid
  • can be attached through the oxygen of a hydroxyl at either the 5’ or 3’ position of the sugar
  • It is more commonly attached to the 5’ position.
A

phosphate

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36
Q

A __ is the term for a sugar and a base

A

nucleoside

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37
Q

From __ can be attached to nucleosides to from nucleoside mono, di, or triphosphates

A

1 to 3 phosphates

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38
Q

A __ can also be called a nucleotide

A

nucleoside monophosphate

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39
Q

(Naming Conventions)

Nucleosides

A

Purine nucleosides end in “-sine”
- Adenosine, Guanosine

Pyrimidine nucleosides end in “-dine”
- Thymidine, Cytidine, Uridine

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40
Q

(Naming Conventions)

Nucleotides

A

Start with the nucleoside name from above and add “mono-”, “di-”, or “triphosphate”
- Adenosine Monophosphate, Cytidine Triphosphate, Deoxythymidine Diphosphate

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41
Q

__ are linked together by phosphodiester bonds between the 3’ hydroxyl on the sugar of one nucleotide through a phosphate molecule to the 5’ hydroxyl on the sugar of another nucleotide

A

Nucleotides

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42
Q

Nucleotide bonds are broken by __

A

phophodiesterases

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43
Q

Adenine nucleotides are components of 3 major coenzymes:

A

NAD+, FAD, COENZYME A

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44
Q

__ are activated precursors in nucleic acid synthesis.

A

Nucleoside triphosphates

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45
Q

(PURINE NUCLEOTIDE SYNTHESIS)

First purine derivative formed is __

A

Inosine Mono-phosphate (IMP)

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46
Q

SOURCES OF ATOMS IN PURINE BIOSYNTHESIS

A 
N1 - Aspartate
C2, C8 - 10-Formyl-THF
N3, N9 - Glutamine
C6 - CO2
C4, C5, N7 - Glycine
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47
Q

The activated sugar used is __

  • is generated by the action of PRPP synthetase and requires energy in the form of ATP
  • This reaction releases AMP. Therefore, 2 high energy phosphate equivalents are consumed during the reaction.
  • First committed step of purine synthesis (Regulated)
A

5-phosphoribosyl-1-pyrophosphate, PRPP

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48
Q

5-phosphoribosyl-1-pyrophosphate, PRPP is inhibited by __

A

ADP and GDP

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49
Q

The major site of purine synthesis is in the __.

A

liver

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50
Q

Synthesis of the purine nucleotides begins with PRPP and leads to the first fully formed nucleotide, __.

A

inosine 5’-monophosphate (IMP)

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51
Q

The synthesis of IMP requires __

A

five moles of ATP, two moles of glutamine, one mole of glycine, one mole of CO2, one mole of aspartate and two moles of formate

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52
Q

The formyl moieties are carried on tetrahydrofolate (THF) in the form of __.

A

N5,N10-methenyl-THF and N10-formyl-THF

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53
Q

(SYNTHESIS OF AMP OR GMP)
__ represents a branch point for purine biosynthesis, because it can be converted into either AMP or GMP through two distinct reaction pathways.

A

IMP

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54
Q

The pathway leading to AMP requires energy in the form of GTP; that leading to GMP requires energy in the form of __

A

ATP

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55
Q

The accumulation of excess __ will lead to accelerated AMP synthesis from IMP instead, at the expense of GMP synthesis.

A

GTP

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56
Q

the conversion of IMP to GMP requires ATP, the accumulation of excess __ leads to accelerated synthesis of GMP over that of AMP.

A

ATP

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57
Q

The synthesis of PRPP by PRPP synthetase is feed-back inhibited by __ (predominantly AMP and GMP).

A

purine-5’-nucleotides

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58
Q

The amidotransferase reaction (2nd step) catalyzed by __ is also feed-back inhibited allosterically by binding ATP, ADP and AMP at one inhibitory site and GTP, GDP and GMP at another.

A

PRPP glutamyl amidotransferase

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59
Q

__ is regulated in the branch pathways from IMP to AMP and GMP. The accumulation of excess AMP leads to accelerated synthesis of GMP, and excess GMP leads to accelerated synthesis of AMP.

A

purine biosynthesis

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60
Q

Catabolism of the purine nucleotides leads ultimately to the production of __ which is insoluble and is excreted in the urine as sodium urate crystals.

A

uric acid

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61
Q

The synthesis of nucleotides from the purine bases and purine nucleosides takes place in a series of steps known as the __.

A

salvage pathways

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62
Q

The free purine bases, adenine, guanine, and hypoxanthine, can be reconverted to their corresponding nucleotides by __.

A

phosphoribosylation

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63
Q

Two key transferase enzymes are involved in the salvage of purines:

A
  1. adenosine phosphoribosyltransferase (APRT)

2. hypoxanthine-guanine phosphoribosyltransferase (HGPRT)

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64
Q

A critically important enzyme of purine salvage in rapidly dividing cells is __ which catalyzes the deamination of adenosine to inosine.

A

adenosine deaminase (ADA)

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65
Q

Deficiency in adenosine deaminase (ADA) results in the disorder called __

A

severe combined immunodeficiency, SCID

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66
Q

__ can also contribute to the salvage of the bases through a reversal of the catabolism pathways. However, this pathway is less significant than those catalyzed by the phosphoribosyltransferases.

A

Purine nucleotide phosphorylases (PNPs)

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67
Q
  • separate kinase for each nucleotide
A

Nucleoside Monophosphate kinases

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68
Q
  • single enzyme with broad specificity
A

Nucleoside Diphosphate kinases

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69
Q

One genetic disorder of pyrimidine catabolism,

__, is due to total or partial deficiency of the enzyme dihydropyrimidine dehydrogenase.

A

β-hydroxybutyric aciduria

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70
Q

This disorder
of pyrimidine catabolism, also known as __, is also a disorder of β-amino acid biosynthesis, since the formation of β-alanine and of β-aminoisobutyrate is
impaired.

A

combined uraciluria-

thyminuria

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71
Q

The three processes that contribute to purine nucleotide biosynthesis are, in order of decreasing importance.

A
  1. Synthesis from amphibolic intermediates (synthesis de novo).
  2. Phosphoribosylation of purines.
  3. Phosphorylation of purine nucleosides.
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72
Q

__ has a low level of PRPP glutamyl amidotransferase, and hence depends in
part on exogenous purines.

A

Human brain tissue

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73
Q

__ cannot synthesize 5-phosphoribosylamine
and, therefore, also utilize exogenous
purines to form nucleotides.

A

Erythrocytes and polymorphonuclear

leukocytes

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74
Q

The rate of PRPP
synthesis depends on the availability of ribose 5-phosphate and on the activity of __, an enzyme whose activity is feedback inhibited
by AMP, ADP, GMP, and GDP

A

PRPP synthase

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75
Q

__ also inhibit hypoxanthine-guanine phosphoribosyltransferase,
which converts hypoxanthine and guanine to IMP and GMP, and GMP feedback inhibits PRPP glutamyl amidotransferase

A

AMP and GMP

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76
Q

Reduction of the 2′-hydroxyl of purine and pyrimidine ribonucleotides,
catalyzed by the complex that includes __, provides the deoxyribonucleoside diphosphates (dNDPs) needed for both the synthesis and repair of DNA

A

ribonucleotide

reductase

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77
Q

Five of the first six enzyme activities of pyrimidine biosynthesis
reside on __.

A

multifunctional polypeptides

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78
Q

For further pyrimidine synthesis to occur, dihydrofolate must be reduced
back to tetrahydrofolate. This reduction, catalyzed by dihydrofolate
reductase, is inhibited by __

A

methotrexate

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79
Q
  • are alternate substrates for orotate phosphoribosyltransferase.
    Both drugs are phosphoribosylated, and allopurinol is converted
    to a nucleotide in which the ribosyl phosphate is
    attached to N1 of the pyrimidine ring.
A

Allopurinol and 5-fluorouracil

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80
Q

Humans convert adenosine and guanosine to __. Adenosine is first converted to inosine by adenosine
deaminase.

A

uric acid

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81
Q

In mammals other than higher primates, __,converts uric acid to the watersoluble
product allantoin. However, since humans lack __, the end product of purine catabolism in humans is uric acid.

A

uricase

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82
Q

__ is a condition that results from the precipitation of urate (uric acid) as monosodium urate (MSU) or calcium pyrophosphate dihydrate (CPPD) crystals in the synovial fluid of the joints, leading to severe inflammation and arthritis.

A

Gout

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83
Q

Most forms of gout are the result of excess purine production or to a partial deficiency in the salvage enzyme, __

A

Hypoxanthine-guanine phosphorybosyl transferase (HGPRT)

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84
Q

increased activity of PRPP synthetase leads to excess PRPP leading to increased purine nucleotide production that can increase the rate of purine degradation and subsequently increase __

A

uric acid synthesis

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85
Q

Responsible for re-forming IMP and GMP from hypoxanthine and guanine

A

Hypoxanthine-guanine phosphorybosyl transferase (HGPRT) and the Salvage Pathway

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86
Q

Most forms of gout can be treated by administering the antimetabolite __ .
This compound is a structural analog of hypoxanthine that strongly inhibits xanthine oxidase.

A

allopurinol

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87
Q
  • results from the loss of a functional HGPRT gene.
  • is inherited as a sex-linked trait, with the HGPRT gene on the X chromosome (Xq26-q27.2).
  • Patients with this defect exhibit not only severe symptoms of gout but also a severe malfunction of the nervous system.
  • In the most serious cases, patients resort to self-mutilation.
A

Lesch-Nyhan syndrome

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88
Q
  • is most often (90%) caused by a deficiency in the enzyme adenosine deaminase (ADA).
  • This is the enzyme responsible for converting adenosine to inosine in the catabolism of the purines
A

SCID (Severe Combined Immunodeficiency Disease)

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89
Q
  • selectively leads to a destruction of B and T lymphocytes, the cells that mount immune responses.
  • deoxyadenosine is phosphorylated to yield levels of dATP that are 50-fold higher than normal
A

ADA deficiency

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90
Q

A less severe immunodeficiency results when there is a lack of __, another purine-degradative enzyme.

A

purine nucleoside phosphorylase (PNP)

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91
Q
  • One of the many glycogen storage diseases __ also leads to excessive uric acid production.
  • results from a deficiency in glucose 6-phosphatase activity.
  • The increased availability of glucose-6-phosphate increases the rate of flux through the pentose phosphate pathway, yielding an elevation in the level of ribose-5-phosphate and consequently PRPP
  • The increases in PRPP then result in excess purine biosynthesis.
A

von Gierke disease

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92
Q

3 different enzyme defects can lead to gout:

A
  • PRPP synthetas elevated
  • HGPRT deficiency
  • glucose-6-phosphatase deficiency
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93
Q

APRT lacking

A

Renal lithiasis

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94
Q

PNP lacking

A

Immunodeficiency

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95
Q

Xanthine oxidase absent

A

Xanthinuria

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96
Q

(Pyrimidine Nucleotide Biosynthesis)

The first completed base is derived from __

A

1 mole of glutamine, one mole of ATP and one mole of CO2 (which form carbamoyl phosphate) and one mole of aspartate.

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97
Q

The carbamoyl phosphate used for pyrimidine nucleotide synthesis is derived from __, within the cytosol

A

glutamine and bicarbonate

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98
Q

Carbamoyl phosphate is then condensed with aspartate in a reaction catalyzed by the rate limiting enzyme of pyrimidine nucleotide biosynthesis, __.

A

aspartate transcarbamoylase (ATCase)

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99
Q

UMP Synthesis Overview

A
  • 2 ATPs needed: both used in first step
  • One transfers phosphate, the other is hydrolyzed to ADP and Pi
  • 2 condensation reactions: form carbamoyl aspartate and OMP
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100
Q

Pyrimidine ring is synthesized from __

A

Carbamoyl phosphate and Aspartate

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101
Q

Carbamoyl-P for pyrimidine synthesis:

A

a. Formed in cytosol
b. Formed by a cytosolic form of the carbamoyl-P-synthetase II
c. Uses Glutamine as N-donor
d. Pyrimidine are attached to PRPP after synthesis

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102
Q

(DIFFERENCES IN PURINE AND PYRIMIDINE BIOSYNTHESIS) 1

A
  1. The ring structure is assembled as a free base, not built upon PRPP.
    * PRPP is added to the first fully formed pyrimidine base (orotic acid), forming orotate monophosphate (OMP), which is subsequently decarboxylated to UMP.
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103
Q

(DIFFERENCES IN PURINE AND PYRIMIDINE BIOSYNTHESIS) 2

A
  1. There is no branch in the pyrimidine synthesis pathway. UMP is phosphorylated twice to yield UTP (ATP is the phosphate donor).
    * The first phosphorylation is catalyzed by uridylate kinase and the second by ubiquitous nucleoside diphosphate kinase.
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104
Q

(DIFFERENCES IN PURINE AND PYRIMIDINE BIOSYNTHESIS) 3

A
  1. UTP is aminated by the action of CTP synthase, generating CTP.
    * The thymine nucleotides are in turn derived by de novo synthesis from dUMP or by salvage pathways from deoxyuridine or deoxythymidine.
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105
Q
  • is a multifunctional enzyme that contains redox-active thiol groups for the transfer of electrons during the reduction reactions.
A

Ribonucleotide reductase (RR)

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106
Q
  • is reduced in turn, by either thioredoxin or glutaredoxin.
  • The ultimate source of the electrons is NADPH.
  • The electrons are shuttled through a complex series of steps involving enzymes that regenerate the reduced forms of thioredoxin or glutaredoxin.
A

Ribonucleotide reductase (RR)

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107
Q

ATP ACTIVATES REDUCTION OF

A
  • CDP

- UDP

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108
Q
  • induces GDP reduction

- inhibits reduction of CDP. UDP

A

dTTP

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109
Q
  • inhibits reduction of all nucleotides
A

dATP

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110
Q
  • stimulates ADP reduction

- inhibits CDP,UDP,GDP reduction

A

dGTP

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111
Q

(Synthesis of the Thymine Nucleotides)

The de novo pathway to __ first requires the use of dUMP from the metabolism of either UDP or CDP.

A

dTTP synthesis

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112
Q

(Synthesis of the Thymine Nucleotides)

The dUMP is converted to dTMP by the action of __.

A

thymidylate synthase

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113
Q

(Synthesis of dTMP from dUMP)
The unique property of the action of __ is that the THF is converted to dihydrofolate (DHF), the only such reaction yielding DHF from THF.

A

thymidylate synthase

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114
Q

(Synthesis of dTMP from dUMP)
In order for the thymidylate synthase reaction to continue, THF must be regenerated from DHF. This is accomplished through the action of __.

A

dihydrofolate reductase (DHFR)

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115
Q

(Synthesis of dTMP from dUMP)

THF is then converted to N5,N10-THF via the action of __.

A

serine hydroxymethyl transferase

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116
Q

__, unlike mammals, cannot use exogenous folate but must synthesize it from PABA. This pathway is thus essential for production of purines and nucleic acid synthesis in bacteria

A

Sulfonamide-susceptible organisms

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117
Q

__ is also useful as an antibacterial; it does not affect mammalian cells because it is about 50,000 times less efficient in inhibition of mammalian dihydrofolate reductase

A

Trimethoprim

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118
Q

The activity of __ (one of the various deoxyribonucleotide kinases) is unique in that it fluctuates with the cell cycle, rising to peak activity during the phase of DNA synthesis; it is inhibited by dTTP.

A

thymidine kinase

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119
Q

The regulation of pyrimidine synthesis occurs mainly at the first step which is catalyzed by __.

A

aspartate transcarbamoylase, ATCase

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120
Q

__ is inhibited by CTP, UDP, UTP, and dUTP; it is activated by ATP

A

ATCase

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121
Q

The role of glycine in ATCase regulation is to act as a competitive inhibitor of the __ binding site.

A

glutamine

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122
Q

Catabolism of the __ leads ultimately to β-alanine (when CMP and UMP are degraded) or β-aminoisobutyrate (when dTMP is degraded) and NH3 and CO2.

A

pyrimidine nucleotides

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123
Q

These deficiencies result in __ that causes retarded growth, and severe anemia caused by hypochromic erythrocytes and megaloblastic bone marrow.
- Leukopenia is also common in __

A

orotic aciduria

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124
Q

Orotic aciduria can be treated with __, which leads to increased UMP production via the action of nucleoside kinases.

A

uridine and/or cytidine

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125
Q

__ can also cause orotic aciduria because it can act as an alternate substrate and compete with orotic acid for degradation

A

Allopurinol

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126
Q
  • Storage, transmission, and expression of genetic information
A

Nuclei Acids

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127
Q
  • Lack nucleus
  • Single chromosome
  • Plasmids (nonchromosomal DNA)
A

Prokaryotes

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128
Q
  • Nucleus
  • Mitochodrion
  • chloroplasts
A

Eukaryotes

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129
Q

The DNA Structure

A
  • Deoxyribonucleoside monophosphate polymer
  • 3’ → 5’ covalent phosphodiester bond
  • Cleaved chemically (ONLY RNA cleaved by alkali)
  • Enzymatically: deoxyribonucleases (DNAse) and ribonucleases (RNAse)
  • Occur as double stranded (exception ssDNA viruses)
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130
Q

The DNA Structure (Prokaryotes vs Eukaryotes)

A

Prokaryotes: associated with nucleoid

Eukaryotes: nucleoproteins

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131
Q
  • 2 chains coiled around the axis of symmetry
  • Antiparallel chains/strands
  • Deoxyribose-phosphate backbone: hydroPHILIC
  • Base pairs: hydroPHOBIC
  • “Twisted ladder”
  • Proposed structure: 1953 by Watson and Crick
A

DNA

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132
Q

provide spatial access to DNA-binding proteins

A

Minor (narrow) and major (wide) grooves

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133
Q

__ intercalates into the minor groove

A

Dactinomycin (actinomycinD)

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134
Q
  • In a dsDNA, amount of A is equal to T, amount of G is equal to C, amount of purines A and G = pyrimidines T and C
A

Chargaff Rule

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135
Q

Base Pairs are Complementary (1)

A
  • The base of one strand is paired to the other
  • Base pairs are perpendicular (900 ) to axis of symmetry
  • A to a T (U), G to a C
  • A to T (2 hydrogen bonds)
  • G to C (3 hydrogen bonds)
  • Strand separation: pH ionization and heat
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136
Q

Base Pairs are Complementary (2)

A
  • NOTE: Phosphodiester bonds not broken down by pH and heat
  • Denaturation: loss of helical DNA
  • Measured at 260 nm absorbance
  • ssDNA has higher relative absorbance
  • Tm : melting temperature where there is loss of half of the DNA helical structure
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137
Q

AT DNA will have a higher peak of relative absorbance. __ will form at a lower temperature compared to high GC containing DNA

A

More single stranded DNA

138
Q

The Structural Variants of the DS DNA

A
  1. B Form
  2. A Form
  3. Z Form
139
Q
  • Right-handed helix with 10.4 nucleotide residues per 3600 turn
  • most common, cross like
  • Base planes perpendicular to axis
  • Chromosomal DNA
140
Q
  • Formed by moderately dehydrating the B
  • Right-handed helix
  • 11 base pairs per turn
  • Base pair plane are 20 away from perpendicularity to helical axis
  • DNA-RNA hybrids and ds RNA
141
Q
  • Left handed
  • 12 base pairs per turn
  • Found in DNA with alternating purine and pyrimidine a poly GC
  • B and Z helical transitions play a role in regulating gene expression
142
Q

Linear and Circular DNA

A
  • Eukaryotic mitochondrial and chloroplastic DNA are closed and circular chromosomes
  • Prokaryotes have single, ds, supercoiled, circular chromosome
143
Q
  • small, circular, extrachromosomal DNA molecules that undergo replication but may or may not be synchronized to chromosomal division. *Carry antibiotic resistance
144
Q

DNA Replication

A
  • Semiconservative
  • Each parental strand incorporated into the duplex
  • DNA replication is well-studied in Escherichia coli
  • Eukaryotic DNA replication is complex
145
Q
  • parent strand will divide into two. One each will go to the daughter strands
A

Semiconservative

146
Q

Prokaryotic DNA Replication (1)

A
  • DNA replication starts at one origin of replication (a single, unique nucleotide sequence noted to be consensus)
  • Exclusively at AT pairs (It will start at AT because it is where the hydrogen bonds are the weakest.)
  • Eukaryotes have multiple origins of replication
  • DNA polymerases use single strand DNA therefore the parental strands are melted
  • Parental strand is unwound and separated
147
Q

Prokaryotic DNA Replication (2)

A
  • 2 replication forks are produced
  • BIDIRECTIONAL movement forming a replication BUBBLE
  • DNA strand-separation proteins (prepriming complex)
148
Q

[DNA strand-separation proteins (prepriming complex)]

- binds to the specific nucleotides at the origin of replication and melts AT-rich regions; ATP-dependent

A

Dna A protein

149
Q

[DNA strand-separation proteins (prepriming complex)]

  • bind to ssDNA near the replication fork; move into the neighboring double-stranded region and force strands apart; ATP-dependent NOTE: DnaB is E.coli’s principal helicase; must bind to DnaC
150
Q

[DNA strand-separation proteins (prepriming complex)]

  • bind to the ssDNA brought about by the helicase; NOT ENZYMES; protect DNA from nucleases
151
Q

A replication fork consists of four components that form in the following sequence:

A

(1) the DNA helicase unwinds a short segment of the parental duplex DNA;
(2) a primase initiates synthesis of an RNA molecule that is essential for priming DNA synthesis;
(3) the DNA polymerase initiates nascent, daughter-strand synthesis; and
(4) SSBs bind to ssDNA and prevent premature reannealing of ssDNA to dsDNA.

152
Q
  • acts on the lagging strand to unwind dsDNA in a 5′ to 3′ direction.
  • associates with the primase to afford the latter proper access to the template.
153
Q
  • Positive supercoil or “super twists” interfere with unwinding
  • Negative supercoil
  • Topoisomerase – used to release the stress or tension brought about by the helicase
A

SUPERCOILING PROBLEM

154
Q

– Nuclease and ligase properties
– Reuses energy stored from cleaving the phosphodiester bond to resealing the strand
– The intact DNA is passed through the break before it is resealed
– Relaxes negative supercoils in E.coli and both supercoils in eukaryotes
– energy efficient

A

Type I DNA topoisomerase: single strand break

155
Q

– Causes a second stretch of DNA double helix to pass through the break
– ATP-requiring
– Needed for separation of interlocked DNA molecules following chromosomal replication
– DNA gyrase: unusual property to introduce negative supercoils into a relaxed circular DNA; neutralizes the positive supercoils during double helix opening

A

Type II DNA topoisomerase: double strand break

156
Q

Etoposide, teniposide, and doxurubicin (anticancer agents) targets __.

A

human toposiomerase II

157
Q

__ target DNA gyrase.

A

Quinolones

158
Q

– Copied in the direction of the advancing replication fork
– 3’→ 5’
– Synthesize continuously

A

Leading strand

159
Q
  • Copied in the direction away from the replication fork
  • Synthesize discontinuously
  • Okazaki fragments (short fragments)
  • 3’→ 5’
A

Lagging strand

160
Q

DNA polymerase

A
  • Read 3’→ 5’

- Synthesize 5’ → 3’

161
Q

RNA Primer Initiates Chain Elongation

A
  • DNA pol cannot initiate synthesis of complementary strands on a ss template
  • Require an RNA primer (short, double-stranded region of RNA-DNA hybrid)
  • Hydroxyl group of RNA primer serves as first acceptor of a deoxynucleotide
  • Primase (DnaG or RNA pol): synthesize short RNA sequences (10 nucleotides)
  • Leading strand:1
  • Lagging strand: multiple
162
Q

RNA Primer Initiates Chain Elongation (2)

A
  • Requires 5’ – ribonucleotide triphosphates
  • Added via 3’ to 5’ phosphodiester bond
  • Primosome: addition of primase to prepriming complex
163
Q

__ is the initiator complex plus the helicase and the Single stranded binding protein (plus the primase = PRIMOSOME)

A

3’ complex

164
Q

The mobile complex between helicase and primase has been called a __.

165
Q

HOW THE SLIDING CLAMP FITS

A

The sliding clamp will be loaded by the clamp loader → magbubukas siya, you will need ATP → pag napasok na niya yung ssDNA, magfoform na siya ng dsDNA → irerelease niya yung ATP
→ hydrolyze the phosphate group
→ magbibind na ngayon yung clamp tapos dun na magbibind yung polymerase

166
Q
  • A number of different DNA polymerase molecules engage in DNA replication. These share three important properties: (1) chain elongation, (2) processivity, and (3) proofreading.
A

DNA POLYMERIZATION

167
Q

DNA POLYMERIZATION

A
  • DNA pol III uses the 3’ –OH of RNA primer as first acceptor
  • Highly processive enzyme
  • Remains bound to template and does not diffuse away
  • Its β subunit forms a ring that encircles the template DNA thus serving as a sliding DNA clamp
  • New strand grows from 5’ to 3’, antiparallel to parent
  • 5-deoxynucleoside triphosphates as substrates
168
Q

DNA POLYMERIZATION 2

A
  • PPi is released when each new deoxynucleoside monophosphate is added to the growing chain
  • DNA synthesis stops if a nucleotide is depleted
  • DNA pol III has 3’ to 5’ proofreading (exonuclease)
  • Checks to make certain the added nucleotide is complementary to base template
169
Q

RNA Primer Excision and DNA Replacement

A
  • DNA pol I has a 5’ to 3’ exonuclease activity besides 3’ to 5’ exonuclease and 5’ to 3’ polymerase activity
  • DNA pol I locates the space or nick between the 3’-end of newly-synthesized DNA and 5’-end of adjacent RNA primer
170
Q

RNA Primer Excision and DNA Replacement (2)

A
  • Removes RNA primer via 5’ to 3’ exonuclease and puts deoxyribonucleotides via 5’ to 3’ direction and proofreads via 3’ to 5’
  • 5’ to 3’ exonuclease activity removes one nucleotide that is properly base-paired and 1-10 nucleotides if mutated
171
Q
  • mediates the formation of the final phosphodiester bond between the 5’-phosphate group on the DNA chain synthesized by DNA pol III and the 3’-OH group on the chain made by DNA pol I
A

DNA ligase

172
Q

High-Fidelity DNA Synthesis

A

High fidelity = konting error lang ang pwede niyang magawa

173
Q
  • Closely follows prokaryotic DNA synthesis
  • Contains multiple origins of replication
  • RNA primers removed by Rnase H and FEN1 rather than DNA pol I
A

Eukaryotic DNA Replication

174
Q

• Contains primase
• Initiates DNA
synthesis
• Proofreading (-)

A

Pol α (alpha)

175
Q
  • Repair

* Proofreading (-)

A

Pol β (beta)

176
Q

• Replicates
mitochondrial DNA
• Proofreading (+)
• Location: mitochondria

A

Pol γ (gamma)

177
Q

• Thought to elongate
Okazaki fragments
of the lagging strand
• Proofreading (+)

A

Pol δ (delta)

178
Q

• Thought to elongate
the leading strand
• Proofreading (+)

A

Pol ε (epsilon)

179
Q
  • Complexes of noncoding DNA plus proteins located at the linear chromosomal ends
  • Maintain the structural integrity
  • Prevent nuclease attack
  • Allow repair systems to distinguish a true end from a dsDNA break
180
Q

Telomeres

A
  • In humans, telomeric DNA contains several thousand tandem repeats of noncoding hexameric , AG3T2, base-paired to complementary region of Cs and As
  • GT-rich strand is longer than its CA complement leaving ssDNA a few hundred nucleotides in length at 3’ end
  • Single stranded region is thought to fold back on itself – forming a loop
181
Q
  • Following removal of RNA primer from the extreme 5’ end of the lagging strand, there is no way to fill in the remaining gap with DNA
  • Telomeres shorten with each successive cell division
  • Once telomeres shorten beyond some critical length, the cell is no longer able to divide
A

Telomere shortening

182
Q
  • Cancer cells, stem cells and germ cells, telomeres do not shorten and cells do not age
  • This is due to the presence of the ribonucleoprotein telomerase
A

Telomere shortening

183
Q

This complex contains a protein that acts as a
reverse transcriptase, and a short piece of RNA that acts as a
template. The CA-rich RNA template base-pairs with the GT-rich,
single-stranded 3’-end of telomeric DNA

A

Telomerase

184
Q
  • Translocates to the newly synthesized end
  • GT-rich strand has been lengthened
  • Add TTAGGG
  • Primase can use it as a template to synthesize an RNA primer
  • The RNA primer is extended by DNA pol and the primer removed
  • Viewed as mitotic clocks
  • Their length is inversely related to the number of times the cells have divided
  • Aging and cancer
A

Telomerase

185
Q
  • Results from endogenous and exogenous causes
  • Most DNA damage is repaired before DNA is replicated
  • Mutagens are most effective in causing damage during the S phase when new DNA is being synthesized
A

DNA Damage

186
Q
  • Rate of mutations occurring from endogenous (internal cellular)
  • Absence of environmental mutagens
  • Caused by errors during DNA replication
  • Spontaneous tautomeric shifts
  • Spend very little time in their less stable forms so mutation from tautomeric shift is rare
A

Basal Mutation Rate

187
Q

– there are changes in the base pair. It’s still the same molecule but may isang double bond na nareplace sa isang position pero pag binilang mo siya same lang. Shift in the double bonds can have an effect on the fidelity of the DNA, mutation may happen.

A

Tautomeric shift

188
Q

– Outside influences: ionizing radiation (X-ray and radioactive radiation), UV radiation, hydrocarbons and oxidative free radicals

A

Exogenous Agents

189
Q

DNA Repair Mechanisms

A
  • Necessary because cells are continuously bombarded by environmental mutagens and basal mutations
  • Most cases, cells use the undamaged strand of the DNA as template to correct the mutations
  • When both strands are damaged, the cell resorts to use the sister chromatid or to an error-prone recovery mechanism
190
Q

DNA Repair Mechanisms: General Scheme

A

recognition, removal, repair and religation

191
Q

DNA Repair Mechanisms

A
  1. Direct Repair
  2. Mismatch Repair
  3. Base Excision Repair
  4. Nucleotide Excision Repair
  5. Homologous Recombination
  6. Nonhomologous End Joining
192
Q
  • Removes alkyl groups by a direct transfer to MGMT in a one-time reaction
  • Repairs only one type of lesion
  • NOT an enzyme
  • May be the most efficient of all repair paths
  • Cells must be able to continually manufacture more MGMT to perform the function
A

Direct Repair

193
Q
  • Deals with correcting the mismatches of normal bases that fail to maintain normal Watson-Crick base pairing
  • Due to DNA pol mistakes during replication
  • In eukaryotes, mismatch is accomplished by MSH2, MLH1, MSH6, PMS1, and PMS2 gebes
  • Hereditary nonpolyposis colon cancer (HNPCC) at young age
A

Mismatch Repair

194
Q
  • Required to correct spontaneous depurination and deamination
  • 10,000 purine bases lost per cell per day
  • Spontaneous deamination of cytosine results in uracil
  • Involves recognition of nucleotides that have lost the bases or have been modified
A

Base-Excision Repair

195
Q
  • Remove UV light-induced DNA damage
  • UV light is nonionizing and cannot penetrate beyond the outer layer of the skin
  • Form pyrimidine-pyrimidine dimers (cytosine and guanine)
  • Necessary to recognize chemically induced bulky additions to DNA that distort the shape if DNA double helix and cause mutations
A

Nucleotide Excision Repair

196
Q
  • Carcinogens like benzopyrene in cigarette smoke

- Xeroderma pigmentosum

A

Nucleotide Excision Repair

197
Q
  • Takes advantage of sequence information available from unaffected homologous chromosome
  • BRCA1 and 2 proteins
  • Breast CA, Fanconi’s anemia
A

Homologous Recombination

198
Q
  • Permits joining ends even if there is no sequence similarity between them
  • Error-prone
    Introduce mutations during repair
  • Is important before the cell has replicated its DNA because there is no template available for repair by HR
A

Nonhomologous End Joining

199
Q

Eukaryotic DNA Organization

A
  • 46 linear chromosomes
  • Paternal and maternal origins
  • 20000 to 25000 genes
  • MtDNA has 37 genes (all maternal)
200
Q

Eukaryotic DNA Organization (2)

A
  • DNA + proteins = chromatin
  • Human haploid genome (23 chromosomes) = 3 x108 base pairs
  • Total uncoiled DNA in a cell: 1 meter
  • Uncoiled individual chromosome: 1.7 -8.5 cm in length
201
Q

– loosely packaged and transcriptionally active

A

Euchromatin

202
Q

__ is always condensed – essentially inactive. It is found in the regions near the chromosomal centromere and at chromosomal ends (telomeres).

A

Constitutive heterochromatin

203
Q

__ is at times condensed, but at other times it is actively transcribed – uncondensed and appears as euchromatin

A

Facultative heterochromatin

204
Q

Genomic Organization

A
  • Organized into unique and repetitive sequences
  • Repeat Sequences: satellites and LINES and SINES
  • Alpha satellite: 171 bp extending several million base pairs
  • Minisatellite: 20-70 bp, few thousand base pairs
  • Microsatellite: 2,3,4 bp anf few hundred in length
  • Trinucleotide repeats: microsatellite sequences when expanded associated with a disease
205
Q
  • Less than 106 copies
  • Short interspersed elements (SINES): 90-500 bp (100,000 copies)
  • Long interspersed elements (LINES): 7,000 bp (20-50,000 copies)
  • Wala siyang ineencode na any protein but sobra siyang nag repeat in a single sequence
A

SINES AND LINES

206
Q
  • Done for trisomy 21, to see the problems in the genes, translocations, deletions, mutations
  • Giemsa stain is used. Fluorescent microscope is used to see the fluorescent antibodies binding to different chromosomes
A

Spectral Karyotyping

207
Q

CLASSES OF RNA

A
  1. Protein coding RNA – mRNA
  2. Non-protein coding RNA
    * Large – rRNA and lncRNA(long non-coding)
    * Small – tRNA, snRNA, miRNA and siRNA
208
Q

Types: ≥10^5 Different species
Abundance: 2%-5% of total
Stability: Unstable to very stable

A

Messenger (mRNA)

209
Q

Types: 28S, 18S, 5.8S, 5S
Abundance: 80% of total Stability: Very stable

A

Ribosomal (rRNA)

210
Q

SIMILARITIES BETWEEN DNA SYNTHESIS AND RNA SYNTHESIS

A
  1. General steps of initiation, elongation, and termination with 5’ to 3’ polarity
  2. Involves large, multi-component initiation complexes
  3. Adherence to Watson-Crick base pairing rules
211
Q

DIFFERENCE BETWEEN DNA SYNTHESIS AND RNA SYNTHESIS

A
  1. Ribonucleotides are used in RNA synthesis rather than deoxyribonucleotides
  2. U replaces T as the complementary base pair for A in RNA
  3. Primer is not involved in RNA synthesis
  4. Only a portion of the genome is transcribed or copied into RNA, whereas the entire genome must be copied during DNA replication
  5. No proofreading function during RNA transcription.
212
Q

Exons vs Introns

A

Exons - one that codes for protein

Introns - one that is a noncoding proteins

213
Q

RNA is synthesized from a DNA template by an RNA polymerase

A

TRANSCRIPTION

214
Q

Template Strand vs Coding Strand

A

Template strand – strand that is transcribed into an RNA molecule

Coding strand – the other DNA strand; sequence corresponds to the primary transcript which encodes the protein

215
Q

Information on template strand is read out in __

A

3’ to 5’ direction

216
Q
  • specific site to which the RNA polymerase attaches; always located upstream from the transcription start site
  • upstream nucleotide has a negative number
217
Q
  • region of DNA that extends between the promoter and terminator; always located downstream from transcription start site
A

Transcription Unit

218
Q
  • Responsible for the polymerization of ribonucleotides into a sequence complementary to the template strand of the gene
A

DNA-DEPENDENT RNA POLYMERASE (RNAP)

219
Q
  • Exist as 400 kDa core complex consisting of:
  • Two identical alpha subunits
  • Similar but not identical B and B’ subunits
  • omega subunit
  • sigma subunit
  • B subunit binds Mg++ ions

(Core enzyme: omega, 2 alpha, B and B’ subunits)

A

DNA-DEPENDENT RNA POLYMERASE (E coli)

220
Q

[DNA-DEPENDENT RNA POLYMERASE (E coli)]

__ enables the core enzyme to recognize and bind the promoter region to form the preinitiation complex (PIC)

A

Sigma factor/Sigma subunit

221
Q
  • Binding of RNAP holoenzyme (core + sigma factor) to template at promoter site
A

TEMPLATE BINDING

222
Q

RNA Synthesis

A
  1. Initiation
  2. Elongation
  3. Termination
223
Q

(RNA Synthesis)

  • First nucleotide (usually a purine) associates with initiation site on B subunit of enzyme
  • RNAP catalyzes the coupling of the nucleotide to the second nucleotide
  • RNAP undergoes a conformational change after RNA chain length reaches 10-20 and then able to move away from the promoter
A

INITIATION

224
Q

(RNA Synthesis)

  • Successive residues are added to 3’ terminus with sequence dictated by base pairing rules
  • DNA unwinding must occur to provide access for appropriate base pairing; unwinding about 17 bp / polymerase molecule
A

ELONGATION

225
Q

(RNA Synthesis)

  • Termination signal recognized by rho factor (an ATP-dependent RNA-DNA helicase)
  • RNA chain release; core enzyme separates from DNA template
A

TERMINATION

226
Q

RNA POLYMERASE

A
  • More than one RNA polymerase may transcribed the same template strand of a gene simultaneously
227
Q

RNA polymerase continues to incorporate nucleotides +3 to ~+10, at which point the polymerase undergoes another conformational change and moves away from the promoter;
this reaction is termed __

A

promoter clearance

228
Q

RECOGNITION OF INITIATION SITE (E coli)

A
  • RNAP scans DNA sequence at rate of 103 bp/sec until it recognizes specific regions of DNA to which it binds with higher affinity (promoter)
229
Q

The __ contains regions of highly conserved nucleotide sequence – located 35 and 10 bp upstream from the start site of transcription

230
Q
  • A T rich sequence
  • Low melting temperature (lack G C)
  • Eases dissociation between coding and non-coding strands so RNAP can have access to nucleotide sequence of immediately downstream coding strand
A

TATA BOX (PRIBNOW BOX)

231
Q
  • 40 nucleotide pairs in length
  • Contains hyphenated or interrupted inverted repeat, followed by a series of AT base pairs *forms hairpin structure
  • With aid of rho factor [an ATP-dependent RNA-stimulated helicase], RNAP stops and dissociates from DNA template and releases RNA transcript
A

TERMINATION SIGNAL in E coli

232
Q

(Classification of RNA Polymerase)

major products: rRNA
sensitivity to alpha-amanitin: insensitive

A

RNA polymerase I

233
Q

(Classification of RNA Polymerase)

major products: mRNA, miRNA
sensitivity to alpha-amanitin: high sensitivity

A

RNA polymerase II

234
Q

(Classification of RNA Polymerase)

major products: tRNA, 5s RNA, snRNA
sensitivity to alpha-amanitin: intermediate sensitivity

A

RNA polymerase III

235
Q
  • Present in genes that lack TATA box; requires same transcription factors
A

INITIATOR (Inr) SEQUENCE/ DOWNSTREAM PROMOTER ELEMENT (DPE)

236
Q

CLASS II GENE IN EUKARYOTES Requires:

A

RNA polymerase II, transcription factors A, B, D, E, F, H

237
Q
  • Binds to TATA box
  • Only one of the factors capable of binding to specific sequences of DNA
  • Originally considered to be a single protein
  • Consist of TBP (TATA binding protein) and 8 TAFs (TBP associated factors)
238
Q
  • Similar to bacterial sigma factor
239
Q
  • Has kinase activity
240
Q
  • Increases kinase activity of TF IIH
241
Q

STEPS IN THE ASSEMBLY OF PREINITIATION COMPLEX

A
  1. TBP binds to TATA box in the minor groove of DNA and causes an approximately 100 degree bend of DNA helix which facilitates interaction of TAFs
  2. Binding of TFIIA, then TFIIB binds to TFIID/promoter complex
  3. Pol II/TFIIF complex binds to the ternary complex of TFIIA/TFIIB/TFIID to the promoter
  4. Complex attracts Pol II-TFIIF to promoter
  5. Addition of TFIIE and TFIIH&raquo_space; assembly of PREINITIATION COMPLEX (PIC)
242
Q
  • Sequences upstream from start site which determines frequency of transcription
  • Binds protein factors, Sp1 and CTF
A

GC and CAAT boxes

243
Q
  • Increase or decrease rate of transcription initiation
  • Can exert their effect when located hundreds or thousands of bases away from transcription units located on same chromosome
A

Enhancers /Silencers

244
Q
  • For steroids, T3, TRH, cAMP, prolactin, etc.

- Acts as or in conjunction with enhancers or silencers

A

Hormone response element (HRE)

245
Q
  • Consists of 12 subunits
  • Has a carboxy terminal repeat domain (CTD)
  • Activated when phosphorylated on the Ser and Thr residues; inactive when dephosphorylated
A

EUKARYOTIC POLYMERASE II

246
Q
  • Contains a heptad repeat of Tyr-Ser-Pro-Thr-Ser-Pro-Ser
  • Substrate for several kinases
  • Binding site for proteins known as Srb (suppressor for Polymerase B) or mediator protein
A

carboxy terminal repeat domain (CTD)

247
Q

THREE CLASSES OF TRANSCRIPTION FACTORS INVOLVED IN mRNA GENE TRANSCRIPTION

A
  1. Basal Components
  2. Coregulator
  3. Activators
248
Q
  • RNA polymerase II, TBP, TFIIA, B, D, E, F, H
A

Basal components

249
Q
  • Bridging factor that communicate between the upstream activators, proteins associated with Pol II or the other components of TFIID
  • TAFs, Mediator, Chromatin modifiers, Chromatin remodelers
A

Coregulators

250
Q
  • Binds to DNA and stimulate PIC formation or PIC function

* SP1, ATF, CTF, AP1

A

Activators

251
Q

TWO MODELS FOR THE ASSEMBLY OF THE PREINITIATION COMPLEX

A
  1. Stepwise assembly

2. Recruitment

252
Q

Sequential addition of components; takes place in DNA template

A

Stepwise assembly

253
Q

Role of activators and coactivators may be solely to recruit preformed PIC to the promoter

A

Recruitment

254
Q
  • Transcribes tRNA and 5SRNA

- Recognizes a promoter internal to the gene to be express (intragenic promoter)

A

RNA POLYMERASE III

255
Q
  • mRNA subjected to little modification and processing

- Serve as translation templates even before their transcription has been completed

A

RNA PROCESSING (PROKARYOTES)

256
Q
  • Primary transcript undergoes extensive processing within the nucleus
  • Capping
  • Nucleolytic and ligation reactions
  • Terminal addition
  • Nucleoside modification
A

RNA PROCESSING (EUKARYOTES)

257
Q

(PROCESSING OF mRNA)

Primary transcript which is processed to generate mRNA

A

hn RNA (heterogenous nuclear RNA)

258
Q

(PROCESSING OF mRNA)

Sequence that represent the amino acid-coding portion

259
Q

(PROCESSING OF mRNA)

Intervening sequences between the exons that are excised

260
Q

PROCESSING OF mRNA

A
  • Introns sequences are cleaved out and exons are spliced together
  • Addition of 5’ cap and poly(A) tail at 3’ terminus
261
Q
  • Structure involved in converting the primary transcript to mRNA
  • Consists of primary transcript and snRNAs– U1, U2, U4/U6, U5
A

SPLICEOSOME

262
Q

(PROCESSING OF mRNA)

  • 5’end of the intervening sequence is joined via 2’ – 5’ phosphodiester linkage to an __ 28-37 nucleotide upstream from the 3’ end of the intervening sequence
A

adenylate residue

263
Q

Alternative RNA Processing

A
  1. Use of alternative transcription start site
  2. Use of alternative polyadenylation sites
  3. Use of alternative splicing and processing
264
Q
  • Precursor tRNA reduced in size by a specific class of ribonucleases which recognize molecules capable of folding into functionally competent products
    Modification of standard bases
  • Attachment of CCA terminus at 3’end in the cytoplasm
A

PROCESSING OF tRNA

265
Q
  • Eukaryotic ribosome made up of:
    60S subunit – 5S, 5.8S, 28S
    40S subunit – 18S
  • Transcribed from a single large precursor molecule (45S) which encodes an 18S, 5.8S and 28S rRNA
  • Processed in nucleolus; undergoes methylation
A

PROCESSING OF rRNA

266
Q

Inhibits gene expression by decreasing specific protein production

267
Q

(miRNA PROCESSING)

Primary transcript termed __; transcription unit either located independently in the genome or within intronic DNA of other genes

268
Q

(miRNA PROCESSING)

Processed by __ maintaining its hairpin structure

A

Drosha-DGCR8 nuclease

269
Q

(miRNA PROCESSING)

Transported through nuclear pore via action of __

A

exportin 5

270
Q
  • Once in the cytoplasm, further processed by Dicer nuclease-TRBP complex
  • One of two strands loaded to RISC (RNA-induced silencing complex) composed of Argonaute proteins (Arg 1»4)
  • RISC complex promote mRNA degradation or inhibit translation
A

miRNA PROCESSING

271
Q
  • RNA molecules as with catalytic activity
  • Generally involves transesterification reactions, splicing and endoribonuclease activities
  • Plays central role in peptide bond formation
272
Q
  • From the poisonous mushroom, Amanita phalloides

- Forms a tight complex with RNA polymerase II and a looser one with RNAP III

A

alpha-Amanitin

273
Q
  • Inhibits transcription by binding to  subunit of prokaryotic RNA polymerase
A

Rifamycin B and Rifampicin

274
Q
  • Intercalating agent

- Tightly binds to duplex DNA, strongly inhibiting both transcription and replication

A

Actinomycin D

275
Q
  • Important in the understanding of protein synthesis and mutation
  • Refers to the collection of codons that specifies amino acids
A

GENETIC CODE

276
Q

– sequence of 3 nucleotides that codes for a specific amino acid

277
Q

Occurs in the ribosome where the various classes of RNA interact

A

PROTEIN SYNTHESIS

278
Q

– synthesize proteins that remains within the cell

A

Free ribosome

279
Q

– membrane-bound polyribosome; synthesize integral membrane proteins and proteins to be exported

A

Rough Endoplasmic Reticulum

280
Q

PROTEIN SYNTHESIS

Requires the participation of the different RNAs

281
Q

contains the nucleotide sequence that translate to amino acid sequence of the protein

282
Q

recognizes specific nucleotide sequence as well as specific amino acids

283
Q

forms the structure of the ribosome where protein synthesis takes place

284
Q
  • Specifies each of the 20 amino acids
  • 4 different nucleotides (A, T, C, G)
  • 3 nucleotides in a codon
  • therefore, 43 = 64 possible combinations
  • 64 specific codons
  • 3 nonsense codons
  • 61 amino acid codons
285
Q

(BASIC CHARACTERISTICS OF THE GENETIC CODE)

– multiple codons must code for the same amino acids

A

Degenerate

286
Q

(BASIC CHARACTERISTICS OF THE GENETIC CODE)

– for a given codon, only a single amino acid is indicated

A

Unambiguous

287
Q

(BASIC CHARACTERISTICS OF THE GENETIC CODE)

  • Reading of the genetic code during the process of protein synthesis does not involve any overlap of codons
A

Non-overlapping

288
Q

(BASIC CHARACTERISTICS OF THE GENETIC CODE)

  • Read in a continuing sequence of nucleotide triplets until a nonsense codon is reached
A

No punctuations

289
Q

(BASIC CHARACTERISTICS OF THE GENETIC CODE)

  • Same for all organisms
  • Exception: 4 codons reads differently in the mitochondria and cytoplasm within the same cell (AUA, UGA, AGA, AGG)
290
Q

At least one __ exist for each of the 20 amino acids

291
Q

(tRNA)

– site of attachment of specific amino acid

A

Acceptor arm

292
Q

(tRNA)

– involved in binding of aminoacyl tRNA to ribosomal surface at site of protein synthesis

293
Q

(tRNA)

– for proper recognition of a given tRNA species by its proper aminoacyl-tRNA synthetase

294
Q

(tRNA)

– recognize codon in mRNA

A

Anticodon region

295
Q
  • Enzyme that attaches the amino acids to their specific tRNAs
  • Capable of recognizing specific tRNA and specific amino acids
A

AMINOACYL tRNA SYNTHETASE

296
Q

STEPS IN THE RECOGNITION AND ATTACHMENT OF AA TO tRNA

A
  1. Aminoacyl tRNA synthetase binds to a specific amino acid forming an activated intermediate of aminoacyl-AMP-enzyme complex
  2. Complex recognizes a specific tRNA to which it attaches the aminoacyl moiety at 3’OH adenosine terminus
297
Q
  • Base pairing between last nucleotide of codon and corresponding nucleotide of anticodon is not strict
  • occurs allowing formation of hydrogen bonds on bases other than the standard ones
  • E.g., 3 codons for glycine (GGU, GGC, GGA) can form base pair from one anticodon, CCI
298
Q

Change in the nucleotide sequence

299
Q

(MUTATION: Single Base Substitution)

  • Pyrimidine changed to another pyrimidine or purine changed to another purine
  • Eg. A—>G; C—>T
A

Transition

300
Q

(MUTATION: Single Base Substitution)

  • Purine changed to a pyrimidine or pyrimidine changed to a purine
  • Eg. A—>T, C—>G
A

Transversion

301
Q

(EFFECTS OF BASE SUBSTITUTION)

  • More likely if changed base in mRNA is the 3rd nucleotide of a codon
A

No detectable effect

302
Q

(EFFECTS OF BASE SUBSTITUTION)

  • Occurs when a different amino acid is incorporated at the corresponding site in protein molecule
  • Might be acceptable, partially acceptable, or unacceptable depending on location of the amino acid in the specific protein
A

Missense effect

303
Q

(EFFECTS OF BASE SUBSTITUTION)

  • Results in premature termination of amino acid incorporation into peptide chain &raquo_space; peptide fragment&raquo_space; non-functional
A

Nonsense Effect

304
Q
  • Results from deletion or insertion of nucleotide in the gene thus generation an altered reading frame in mRNA&raquo_space; results in garbled translation
A

FRAME SHIFT MUTATION

305
Q

(Effects of Frameshift mutation)

If 3 or multiple of 3 nucleotides are missing/added&raquo_space; on translation, protein will __

A

lack or have an added amino acid

306
Q

(Effects of Frameshift mutation)

Insertion/deletion of 1, 2 or non-multiple of 3&raquo_space; reading frame will be distorted

A

a. Garbled amino acid sequences
b. Generation of nonsense codon
c. Reading through normal termination codon

307
Q
  • mRNA sequence is translated into sequence of amino acids of specified protein
  • Message is read from 5’ to 3’ direction
A

PROTEIN SYNTHESIS

308
Q

PROTEIN SYNTHESIS (Prokaryotes vs Eukaryotes)

A

Prokaryotes: translation can begin even before transcription is completed

Eukaryotes: primary transcript must first be process to generate mature mRNA before translation can begin

309
Q

3 PHASES OF PROTEIN SYNTHESIS

A
  1. Initiation
  2. Elongation
  3. Termination
310
Q

PROTEIN SYNTHESIS: INITIATION

a. Ribosomal dissociation

A
  1. eIF-3 and eIF-1A binds to 40s subunit

2. Dissociation of the 80s ribosome to 40s and 60s

311
Q

PROTEIN SYNTHESIS: INITIATION

b. Formation of 43s preinitiation complex

A
  1. Binding of GTP by eIF-2
  2. Binary complex binds to met-tRNA (first codon to be translated is usually AUG)
  3. Ternary complex binds to 40s (with eIF-3 and eIF-1A) to form 43s preinitiation complex
312
Q

PROTEIN SYNTHESIS: INITIATION

c. Formation of 48s initiation complex

A
  1. eIF-4F binds to cap of mRNA
  2. eIF-4B binds to mRNA and reduces the secondary structure of 5’ end
  3. mRNA associates with 43s preinitiation complex with hydrolysis of ATP to form 48s initiation complex
  4. Complex scans mRNA for a suitable initiation codon (AUG)
313
Q

(Initiation in eukaryotic cells)

Precise initiation codon determined by __ that surrounds the AUG

A

Kozak consensus sequences

314
Q

(Initiation in E. coli)

  • A purine-rich sequence located 6-10 bases upstream of the AUG codon of the mRNA (5’-end)
  • Complementary to the sequence near the 3’-end of the 16s rRNA of the 30s subunit
  • Facilitates the binding and positioning of the mRNA on the 30s subunit
A

Shine-Dalgarno sequence

315
Q

(PROTEIN SYNTHESIS: INITIATION)

D. Formation of 80s initiation complex

A
  1. 60s binds to 48s initiation complex with hydrolysis of GTP (bound to eIF-2) by eIF-5
  2. Release of initiation factors
  3. Formation of 80s ribosome
316
Q
  • 2 sites in complete ribosome – A and P sites
  • After the formation of 80s ribosome:
  • met-tRNA at P site
  • A site is free
A

INITIATION

317
Q

– consist of  subunits alpha, B, gamma
- eIF-2 alpha when phosphorylated binds tightly to and inactivates the GTP-GDP recycling protein eIF-2B&raquo_space; prevents formation of 43s preinitiation complex&raquo_space; blocks protein synthesis

  • Kinases are activated when cell is under stress and energy expenditure is deleterious for the cell
318
Q

(POINTS OF REGULATION IN INITIATION:eIF-4E)

– made up of 4E and 4G-4A complex

  • 4E – binds to m7G cap at 5’ end (rate limiting step in translation)
  • 4G – scaffolding protein; binds to eIF-3, 4A and 4B
319
Q

– binds to m7G cap at 5’ end (rate limiting step in translation)

320
Q

(POINTS OF REGULATION IN INITIATION:eIF-4E)

– links 4F to 40s ribosomal subunit

321
Q

(POINTS OF REGULATION IN INITIATION:eIF-4E)

– ATPase and helicase complex; unwinds RNA

322
Q

LEVELS OF REGULATION OF 4E

A
  1. 4E when phosphorylated by insulin and mitogenic growth factors binds to cap more avidly
  2. 4E bound and inactivated by protein BP1, BP2 and BP3, preventing it from binding to 4G
    * BP1 dissociates from 4E when BP1 is phosphorylated by insulin or other growth factors
323
Q

Cyclic process on the ribosome in which one amino acid at a time is added to the nascent peptide chain

A

Elongation

324
Q

(PROTEIN SYNTHESIS: ELONGATION)

a. Binding of aminoacyl-tRNA to A site

A
  1. eEF-1A forms a complex with GTP and the entering aminoacyl-tRNA
  2. The complex with the aminoacyl tRNA enters A site
  3. GTP is hydrolyzed
  4. eEF-1A, GDP and PO4- is released which will then be recycled to eEF-1A•GTP
325
Q

(PROTEIN SYNTHESIS: ELONGATION)

b. Peptide bond formation

A
  1. alpha-Amino group of new aminoacyl-tRNA in A site carries out a nucleophilic attack on esterified carboxyl group of peptidyl-tRNA occupying P site catalyzed by peptidyltransferase
  2. Growing peptide chain is now attached to the tRNA in the A site
326
Q

__ is a component of the 28s RNA of the 60s ribosomal subunit

A

Peptidyltransferase activity

327
Q

(PROTEIN SYNTHESIS: ELONGATION)

c. Translocation

A
  1. Deacylated tRNA is attached by its anticodon to the P site at one end and by the open CCA tail to an E (exit) site
  2. eEF-2 binds to displace the peptidyl tRNA from the A site to the P site; deacylated tRNA is on the E site from which it leaves the ribosome
  3. eEF-2•GTP complex is hydrolyzed to eEF-2•GDP moving the mRNA forward by one codon and leaving the A site open for occupancy by another ternary complex of amino acyl tRNA-eEF1alpha•GTP and another cycle of elongation
328
Q
  • Energy requirement for the formation of one peptide bond = 4 high-energy phosphate bonds
  • 2 ATP for charging of tRNA with aminoacyl moiety
  • 1 GTP for entry of aminoacyl tRNA to A site
  • 1 GTP for the translocation of peptidyl tRNA from A site to P site
A

ELONGATION

329
Q
  1. After multiple cycles of elongation with polymerization of amino acids into protein molecule, termination codon of mRNA appears in A site
  2. Releasing factors recognize termination signal, with GTP and peptidyltransferase, they promote hydrolysis of bond between peptide and tRNA at the P site
  3. tRNA and protein molecule are released from P site
  4. 80s ribosome dissociates into 40s and 60s subunits
A

Protein Synthesis: TERMINATION

330
Q
  • Many ribosomes can translate the same mRNA molecule simultaneously – about 80 nucleotides apart
  • A single mammalian ribosome is capable of synthesizing about 400 peptide bonds per minute
A

PROTEIN SYNTHESIS

331
Q
  • Many proteins are synthesized from mRNA as precursor molecules which are then modified to the active protein
  • e.g. Insulin
A

POST-TRANSLATIONAL PROCESSING

332
Q
  • Structural analogue of tyrosyl-tRNA
  • Binds to A site&raquo_space; peptide chain formed between peptide and free NH2 group of puromycin&raquo_space; premature termination of chain growth
  • Unselective; inhibits both prokaryotic and eukaryotic protein synthesis
333
Q
  • Binds to 60s ribosomal subunit inhibiting peptidyltransferase activity
  • Blocks eukaryotic protein synthesis
A

CYCLOHEXIMIDE

334
Q
  • Catalytically inactivates eEf-2 by ADP-rybosylation
A

Diphtheria Toxin

335
Q
  • Poisonous plant protein that catalytically inactivates the eukaryotic large subunit
A

Ricin/Abrin

336
Q
  • inhibits the binding of aminoacyl tRNAs to the prokaryotic small subunit
A

Tetracycline

337
Q
  • Inhibits elongation in prokaryotes by binding to EFG•GDP in a way that prevents its dissociation from large subunits
A

Fusidic Acid

338
Q
  • Inhibits peptidyltransferase on the prokaryotic large subunit
A

Chlorampenicol

339
Q
  • Inhibits translocation by the prokaryotic large large subunit
A

Erythromycin

340
Q
  • Causes mRNA misreading and inhibits chain initiation in prokaryotes
A

Streptomycin

341
Q
  • block the bacterial translation by binding reversibly to the 30s subunit and distorting it in such a way that the anticodons of the charged tRNA cannot properly align with the codons of the mRNA
A

Tetracycline

342
Q
  • bind reversibly to the 50s subunit. they appear to inhibit elongation of the proteins by preventing peptidyltransferase from forming peptide bond between the amino acids
A

Macrolide (erythromycin, azithromycin, clarithromycin, dinithromycin)

Biochemistry (9 decks)

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