1. Science, Computing and Society Week 7 Chapter 5
Computer Science 129
Science, Computing and Society
Week 7
Chapter 5

2. GRE/GMAT WORDS Equivocal – ambiguous, questionable
Erudite – learned, deep and broad familiarity with subjects
Fervid – vehement, impassioned, very hot
Lucid – easily understood, clear, rational

3. Chapter 5 THE COMPUTATIONAL CELL
Many Biological processes process information similarly to computers
Consider DNA inside a cell

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5. Chapter 5
Inside a cell’s nucleus we find DNA

6. Chapter 5 DNA is a Nucleic Acid Nucleic Acids are made up of 3 things
Sugar
Phosphate
And Bases

7. Chapter 5
If the sugar of a Nucleic Acid is Deoxyribose, then it is DNA
DNA = Deoxyribonucleic Acid
There are 4 Different types of bases in a DNA molecule

8. Chapter 5
DNA Bases:
Adenine
Cytosine
Guanine
Thymine

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Watson and Crick discovered the double helix structure of DNA
Also discovered:
A always pairs with T
C always pairs with G

10. DNA replication is gene copying
Chapter 5
DNA replication is gene copying
Each strand of the double helix contains the information necessary to make its complementary strand

11. REPLICATION When the DNA is ready to multiply, its 2 strands pull
Apart and a
structure
Reads the
Strands (RNA)

12. REPLICATION
Along each
strand, RNA writes the corresponding base

13. REPLICATION
This creates 2 copies of the original

14. REPLICATION
Once replicated, the 2 copies are untangled to allow cell division to take place

15. Chapter 5
A structure or “device moved along a strand of symbols, reading and then writing a new symbol depending on what was just read”
DNA is “Biology’s version of a Turing Machine”

16. TRANSCRIPTION & TRANSLATION
Go to the above website and follow the instructions on the next slides
**This information is a very large portion of the midterm exam**

17. TRANSCRIPTION & TRANSLATION
The first thing that happens in transcription is DNA splits apart
Then RNA polymerase comes and reads the DNA one nucleotide at a time. It will lay down the RNA but not connect it to itself

18. TRANSCRIPTION & TRANSLATION
Transcription is DNA making RNA – all of this happens in the nucleus and DNA is read one nucleotide at a time
First thing to do is to type in the corresponding base pair
In DNA A-T and C-G, but since we begin by DNA making RNA, the base pairs will be A-Uracil and C-G. RNA does not have thymine, it has Uracil instead

19. TRANSCRIPTION & TRANSLATION
DNA will then zip up and go away and you are left with a half strand of RNA.
The RNA then moves out of the nucleus into the cytoplasm and a ribosome will come along and read the RNA three nucleotides at a time. This triplet is called a Codon.
Codons code for an amino acid.

20. TRANSCRIPTION & TRANSLATION
Position the pointer over the start codon (AUG) and click. Then click and drag the correct amino acid on the right over to the ribosome area on the left. Keep doing this until you get to the stop codon. Drag that one as well and that is the end of transcription.

21. TRANSCRIPTION & TRANSLATION
There are 4 different bases and the combination of codons is calculated as:
4x4x4=64
There are 64 different combinations of Codons (AAA, UUU, GGG, CCC, AAU etc)
But there are only 20 different amino acids for which the codons code.
This means that more than one codon will code for an amino acid

22. TRANSCRIPTION & TRANSLATION
The chain of amino acids is the protein.
Enzymes are a type of protein and are created the same way.
All enzymes are proteins, not all proteins are enzymes.

23. TRANSCRIPTION & TRANSLATION
There is a start codon (AUG) and three different stop codons
The ribosome will start at a start codon and lay down amino acids until it gets to a stop codon, then it will cleave it off and send it out to do work.

24. TRANSCRIPTION & TRANSLATION

25. Chapter 5
JUST AS BEFORE,
A structure or “device moved along a strand of symbols, reading and then writing a new symbol depending on what was just read”
DNA is “Biology’s version of a Turing Machine”

26. Chapter 5 For every three DNA bases (codon), we have an amino acid
Many amino acids hooked together are called proteins
ENZYMES ARE A TYPE OF PROTEIN

27. Chapter 5 Crick discovered basic dogma: DNA makes RNA
RNA makes proteins
Proteins do their own type of computing

28. Chapter 5 A large portion of proteins are Enzymes
Enzymes are proteins that take apart or put together other molecules
Enzymes have particular shapes that will specifically affect a chemical process

29. Chapter 5 Enzymes drive ALL chemical reactions in the body
If the enzyme is misshapen, it will not work, or it will “turn off” the process
If the enzyme is correctly shaped, it will work, or it will “turn on” the process
(Similar to 0’s and 1’s)

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35. Chapter 5
Consider:
If the enzyme is correctly shaped, it represents a 1, the enzyme is active, the reaction goes
If the enzyme is misshapen, it represents a 0, the enzyme is inactive, the reaction stops

36. Chapter 5
“Enzymes thus provide a cell with the basic computing language to process information”
G-proteins work similarly to enzymes only are much more complicated – they act like logic gates (AND OR NOT)

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They are located on the inside of a cell and are “turned on” by a specific receptor cell
Without the presence of the proper enzyme to activate the receptor cell, the process is “turned off”

39. Chapter 5
Some processes require two G-proteins to be present and active (AND)
Some processes require two G-proteins, one of them on and one of them off (OR)
Some processes require a specific one on and a specific one off (NOT)

40. What You Should Know
Know all GRE/GMAT words

41. What You Should Know WHAT IS DNA MADE UP OF? 1.
WHAT ARE NUCLEIC ACIDS MADE UP OF? 2. 3.

42. What You Should Know
NAME THE 4 BASES IN DNA: 1. 2. 3. 4.

43. What You Should Know
HOW DO THE BASES IN DNA PAIR UP:

44. What You Should Know LIST THREE THINGS AN ENZYME IS RESPONSIBLE FOR:1. 2. 3.
LIST THREE THINGS AN ENZYME IS RESPONSIBLE FOR:
Enzymes are proteins that take apart or put together a molecule.
Each enzyme has a specific shape that will turn it “on” or “off”
Enzymes Drive ALL chemical reactions

45. What You Should Know Name three differences between DNA and RNA 1. 2.3.

46. What You Should Know HOW DO G-PROTEINS ACT LIKE LOGIC GATES? AND =
OR =
NOT =

47. What You Should Know SHORT ESSAY:
EXPLAIN DNA REPLICATION AND HOW IT’S PROCESS IS SIMILAR TO A TURING MACHINE

48. What You Should Know SHORT ESSAY:
EXPLAIN DNA TRANSCRIPTION AND TRANSLATION AND HOW IT’S PROCESS IS SIMILAR TO A TURING MACHINE

49. What You Should Know SHORT ESSAY:
EXPLAIN THE PROCESS OF ENZYMES AND HOW IT RELATES TO INFORMATION PROCESSING

50. What You Should Know SHORT ESSAY:
EXPLAIN THE PROCESS OF G-PROTIENS AND HOW IT RELATES TO LOGIC GATES.