DNA, RNA, and Protein Conventions

Question 1

Equivalent and Antiparallel

Answer 1

• Equivalent - no logical way to distinguish the two strands based on physical properties
• Antiparallel - the strands have an antiparallel arrangement
  
  • 5’ - 3’ - strand on top
  • 3’ - 5’

Question 2

Both Strands Can Contain Genes

Answer 2

• both strands can contain “genes” and be transcribed but in different directions.
• The top strand is the coding strand for gene 1. The bottom strand is the coding strand for gene 2.
• Often, when genome sequences are concerned, the sequence of only one strand is given.

Question 3

The Two-Strand Convention

Answer 3

• The coding strand 5’-3’ on the top

- the template strand 3’-5’ on the bottom.

Question 4

coding strand

Answer 4

• has the same “sense” (direction and sequence) as the mRNA that it codes for.
  
  • exception of U in RNA and deoxyT in DNA
• it is called the sense strand or the gene.

Question 5

template strand

Answer 5

• the strand that basepairs with the incoming nucleotides that are connected by phosphodiester linkage to form RNA in the process of transcription.
• it is complementary to the mRNA
• It is also code the non-coding strand, or the anti-sense strand or non-sense strand.

Question 6

Transcription/RNA polymerase

Answer 6

• template is read 3’-5’.
• mRNA is synthesized 5’-3’.
• Therefore has the same “sense” as the gene or coding strand.

Question 7

Translation/Ribosomes

Answer 7

• mRNA read 5’-3’
• protein synthesized N-terminal - C-terminal
• using these conventions, gene, mRNA, and protein all have the same “sense”

Question 8

Go from coding strand to mRNA

Answer 8

• without flipping

- just switch T’s to U’s

Question 9

nucleic acids versus proteins

Answer 9

• nucleic acids have 5’ to 3’ ends

- proteins have amino and carboxy termini

Question 10

The way usually seen

Answer 10

5’ gene or coding strand 3’
3’ template strand 5’
I
transcription V

5’ mRNA 3’
I
V
+H3N Protein COO-

Question 11

Making cDNA

Answer 11

• sequence of the cDNA same as gene.
• ALWAYS TALKS ABOUT SEQUENCE OF SECOND STRAND
• most time cDNA made double stranded so we can easily clone and sequence them
• reverse transcriptase requires polyDT as a primer
• RNA sensitive to high pH so remove and degrade with NaOH
• remove loop with single-stranded nucleotides

Question 12

capital blue

Answer 12

exons translated

Question 13

capital black

Answer 13

exons untranslated

Question 14

lowercase blue

Answer 14

introns.