Welcome toMolecular Biology Through Discovery

Tuesday, 15 October 2013Translation

Information+

Self-assembly

Structure+

Function

DNA

CGACCATCGCCTTAGTAC

Protein

SQ6: How do you respond to. . .

AlexanderDounce

. . . infinite regress

SQ6: How does protein synthesis avoid infinite regress?

SQ6: How does protein synthesis avoid infinite regress?

SQ6: How does protein synthesis avoid infinite regress?

What ideas underlie this scheme?

AlexanderDounce

SQ6: How does protein synthesis avoid infinite regress?

SQ5: Evidence that proteins are linear?

Sanger and Tuppy (1951)

SQ6: What are the S-S links mentioned by Crick?

Evidence that DNA is linear?

SQ6: How does protein synthesis avoid infinite regress?

I don't fully understand the different kinds of genetic code. How would the ribosome know what is overlapping and what is not?

Mechanism?

Types of Codes

Study Question 1:

Study Question 2:

Study Question 3:

Study Question 4:

. . .

7 students in class

1456

36

247

34

How to keep track of which student wants what questions?

Study Question 1:

Study Question 2:

Study Question 3:

Study Question 4:

. . .

19 students in class

4612

How to keep track of which student wants what questions?

4 6 1 2?

4 6 12?

Types of Codes

Study Question 1:

Study Question 2:

Study Question 3:

Study Question 4:

. . .

19 students in class

4,6,12

How to keep track of which student wants what questions?

Variable length code with commas

Types of Codes

Study Question 1:

Study Question 2:

Study Question 3:

Study Question 4:

. . .

19 students in class

040612

How to keep track of which student wants what questions?

Fixed length, 2-digit code

Types of Codes

Study Question 1:

Study Question 2:

Study Question 3:

Study Question 4:

. . .

200 students in class

How to keep track of which student wants what questions?

Fixed length, 3-digit code

004106128 201

Degenerate or nondegenerate?

What kind of code?

Types of Codes

Length?

Degenerate or nondegenerate?

What kind of code?

Types of Codes

SQ18. The Morse Code uses only two symbols (short, long), yet it can specify each of the 26 letters of the English alphabet. How many symbols do you predict must be used to represent one letter?

CodonsAAAAACAAGAAUACAACCACG. . .

UUAUUCUUGUUU

Amino acidsalaninearginine

asparagineaspartatecysteine

glutamateglutamine

glycinehistidine

isoleucineleucine

. . .

ACCGUACACUUAGGGCGAU

mRNA

64 codons 20 amino acids

Fixed-length?Variable-length?

Degenerate?Non-degenerate?

Types of Codes

CodonsAAAAACAAGAAUACAACCACG. . .

UUAUUCUUGUUU

Amino acidsalaninearginine

asparagineaspartatecysteine

glutamateglutamine

glycinehistidine

isoleucineleucine

. . .

64 codons 20 amino acids

Types of Codes

Types of CodesOverlapping or not?

Types of CodesOverlapping or not?

Types of CodesOverlapping or not?

Types of CodesOverlapping or not?

Types of CodesOverlapping or not?

Types of CodesOverlapping or not?

Types of CodesOverlapping or not?

Types of CodesOverlapping or not?

Types of CodesOverlapping or not?

Types of CodesOverlapping or not?

Possible?SQ23. Consider the codon AGC in an overlapping triplet code. How many possible codons can follow it? If AGC encoded proline, how many amino acids could follow proline?

Types of CodesOverlapping or not?

How would the ribosome know what is overlapping

and what is not?

Types of Codes

SQ22. How to modify the genetic code so that it is not degenerate?

How would the ribosome know what is overlapping

and what is not?

ACCGUACACUUAGGGCGAU

mRNA

GUGAAU

UGA

Types of Codes

SQ22. How to modify the genetic code so that it is not degenerate?

How would the ribosome know what is overlapping

and what is not?

ACCGUACACUUAGGGCGAU

mRNA

GUG

UGA

Comma-less code

Comma-less Code

SQ28. If AGA is a legal codon, then what two codons become illegal?

Can AAA be part of a comma-less code?

. . .

Me

Problem Set 7 #1

Problem Set 7 #5

Problem Set 7 #6

Translation

Take your pick

Shahroze Mandi Shaun

Bobby Supriya Tayab

Kaleigh Jonathan Michael Colleen

AbdulCailin Sue Kristen

Abdallah Celeste Neda Yordanos

Me

1. Sample summaries #1 & #22. Problem Set 7 #5 (VA ID)3. Problem Set 7 #6 (overlap)

Central Dogma: DNA to RNA to Protein

Replication

Processing /Translocation

DNA

I was wondering what was the distinction between an overlapping

and partially overlapping triplet nucleotide codon was

SQ22: Interpret T-E-A-T-E-N-D as triplets that are: {overlapping, partially overlapping, non-overlapping}

Study Question 11Degeneracy and frequency of amino acids

CodonsAAAAACAAGAAUACAACCACG. . .

UUAUUCUUGUUU

Amino acidsalaninearginine

asparagineaspartatecysteine

glutamateglutamine

glycinehistidine

isoleucineleucine

. . .

ACCGUACACUUAGGGCGAU

mRNA

64 codons 20 amino acids

Fixed-length?Variable-length?

Degenerate?Non-degenerate?

Study Question 11Degeneracy and frequency of amino acids

CodonsAAAAACAAGAAUACAACCACG. . .

UUAUUCUUGUUU

Amino acidsalaninearginine

asparagineaspartatecysteine

glutamateglutamine

glycinehistidine

isoleucineleucine

. . .

ACCGUACACUUAGGGCGAU

mRNA

64 codons 20 amino acids

GUG

Study Question 11Degeneracy and frequency of amino acids

CodonsAAAAACAAGAAUACAACCACG. . .

UUAUUCUUGUUU

Amino acidsalaninearginine

asparagineaspartatecysteine

glutamateglutamine

glycinehistidine

isoleucineleucine

. . .

ACCGUAAACUUAGGGCGAU

mRNA

64 codons 20 amino acids

GUG

Study Question 11Degeneracy and frequency of amino acids

CodonsAAAAACAAGAAUACAACCACG. . .

UUAUUCUUGUUU

Amino acidsalaninearginine

asparagineaspartatecysteine

glutamateglutamine

glycinehistidine

isoleucineleucine

. . .

ACCGUAAACUUAGGGCGAU

mRNA

64 codons 20 amino acids

UUG

Study Question 11Degeneracy and frequency of amino acids

CodonsAAAAACAAGAAUACAACCACG. . .

UUAUUCUUGUUU

Amino acidsalaninearginine

asparagineaspartatecysteine

glutamateglutamine

glycinehistidine

isoleucineleucine

. . .

ACCGUAAAUUUAGGGCGAU

mRNA

UUG

64 codons 20 amino acids

I was wondering what was the distinction between an overlapping

and partially overlapping triplet nucleotide codon was

SQ22: Interpret T-E-A-T-E-N-D as triplets that are: {overlapping, partially overlapping, non-overlapping}