8

8: Describe DNA-Replication as a kind of Enzyme-Catalysis

Shaken formulation:

Describe a DNA-Replication as a kind of Enzyme-Catalysis ?

Answer

result

a DNA-Double-Strand

object

a Macromolecule

instrument

a DNA-Polymerase-Replication-Enzyme

Question in KM

Template

Describe <instance> as a kind of <class>?

Parameters

INSTANCE

CLASS Enzyme-Catalysis

INSTANCE
CLASS	Enzyme-Catalysis

Code

	 ("p6b: "Describe <instance> as a kind of <class>"
 (defun answer-p6b-data (instance class)
  (setq instance (okbc:coerce-to-frame instance  :kb *base-kb*))
  (setq class (okbc:coerce-to-frame class  :kb *base-kb*))
  `(answer
    (question-type p6b)
    (instance ,instance)
    (class ,class)
    (slot-values ,@(loop for slot in (question-slot-options class)
		  when (okbc:get-slot-values instance slot
					     :kb *base-kb* :inference-level :all-inferable)
		  collect (cons slot 
				(okbc:get-slot-values instance slot
					     :kb *base-kb* :inference-level :all-inferable))))))

)

Raw Answer

((question-type p6b) (instance _dna-replication1056)
 (class enzyme-catalysis)
 (slot-values (result _dna-double-strand1058)
  (object _macromolecule1059)
  (instrument _dna-polymerase-replication-enzyme1057))
 (explanations
  ((_dna-replication1056 result _dna-double-strand1058
    ((a tangible-entity)
     (a dna-double-strand with
      (has-part
       (((the polydeoxyribonucleotide has-part of
          (the dna-double-strand object of
           _dna-replication1056))
         called the template strand
         (@ dna-replication result dna-double-strand
          has-part))
        (a polydeoxyribonucleotide called daughter strand
         (@ dna-replication result dna-double-strand
          has-part))))
      (@ dna-replication result))))
   (_dna-replication1056 object _macromolecule1059
    ((a tangible-entity)
     (a macromolecule with
      (instance-of
       ((possible-values polydeoxyribonucleotide
         dna-double-strand
         (@ dna-replication object macromolecule
          instance-of))))
      (@ dna-replication object))))
   (_dna-replication1056 instrument
    _dna-polymerase-replication-enzyme1057
    ((a dna-polymerase-replication-enzyme
      (@ dna-replication instrument)))))))

Explanation

The DNA-Double-Strand is result of the DNA-Replication

KB rule (English):

The following rule was asserted for Concept

The result of a is: a Tangible-Entity

Concept DNA-Replication is a subconcept of concept

KB rule (KM):
```
( (a tangible-entity))
```
KB rule (English):

The following rule was asserted for Concept DNA-Replication

The result of a DNA-Replication is: a DNA-Double-Strand with the following-properties:
- Its parts are
  - the Polydeoxyribonucleotide part of the DNA-Double-Strand object of the DNA-Replication called the template strand the Polydeoxyribonucleotide part of the DNA-Double-Strand object of the DNA-Replication called the template strand
  - a Polydeoxyribonucleotide with the following-properties:
    - It is called daughter strand
    a Polydeoxyribonucleotide with the following-properties:
    - It is called daughter strand
KB rule (KM):
```
(every dna-replication has
 (result
  ((a dna-double-strand with
    (has-part
     (((the polydeoxyribonucleotide has-part of
        (the dna-double-strand object of
         _dna-replication1056))
       called the template strand)
      (a polydeoxyribonucleotide called
       daughter strand)))))))
```

The Macromolecule is object of the DNA-Replication

KB rule (English):

The following rule was asserted for Concept

The object of a is: a Tangible-Entity

Concept DNA-Replication is a subconcept of concept

KB rule (KM):
```
( (a tangible-entity))
```
KB rule (English):

The following rule was asserted for Concept DNA-Replication

The object of a DNA-Replication is: a Macromolecule with the following-properties:
- Its instance-of is possible-values Polydeoxyribonucleotide DNA-Double-Strand
KB rule (KM):
```
(every dna-replication has
 (object
  ((a macromolecule with
    (instance-of
     ((possible-values polydeoxyribonucleotide
       dna-double-strand)))))))
```

The DNA-Polymerase-Replication-Enzyme is instrument of the DNA-Replication

KB rule (English):

The following rule was asserted for Concept DNA-Replication

The instrument of a DNA-Replication is: a DNA-Polymerase-Replication-Enzyme

KB rule (KM):
```
(every dna-replication has
 (instrument ((a dna-polymerase-replication-enzyme))))
```

Terms

Terms		Definitions
the DNA-Double-Strand		An instance of DNA-Double-Strand
the DNA-Polymerase-Replication-Enzyme		An instance of DNA-Polymerase-Replication-Enzyme
the DNA-Replication		An instance of DNA-Replication
the Macromolecule		An instance of Macromolecule
DNA-Double-Strand		Two strands of DNA held together by hydrogen bonds. Examples: DNA double helix and replicon. Souther.
DNA-Polymerase-Replication-Enzyme		Enzyme that catalyzes the synthesis of a DNA molecule on a DNA template from nucleoside triphosphate precursors. Alberts: ECB:G-16.
DNA-Replication		A process by which a copy of all or part of a DNA molecule or DNA strand is made. Includes the replication of the replicon subunits of DNA and repair of damaged strands. Souther.
Enzyme-Catalysis		A chemical reaction whose rate is facilitated by the presence of an enzyme which is not altered by the reaction. Souther.
Macromolecule		Polymer molecule, such as a protein, nucleic acid, or polysaccharide, with a molecular mass greater than a few thousand daltons. Alberts:ECB:G-11
Polydeoxyribonucleotide		A molecular chain of deoxyribonucleotides chemically bonded by a series of phosphodiester linkages. Alberts:ECB:G-14.
Tangible-Entity		an Entity with physical extent
called		No Textual Definition
has-part		the parts that comprise a whole.
instance-of		No Textual Definition
instrument		the entity that is used (by the agent if there is one) to perform an event.
object		the entity that is acted upon by an Event. The main passive participant in the Event.
result		the entity that comes into existence as a result of an action.