DNA: Structure, Form, &Function as they Relate Ultimately [to] Informational Transfer

1. Biochemistry Unit IV – TranscriptionBasic Introductory Terms & Concepts Mr. Gibson Lecture Hall: Rm 213/Labs: Rm 215 DNA: Structure, Form, &Function as they Relate Ultimately [to] Informational Transfer 1st Step in “Informational Transfer” Transcription

2. Transcription – Informational “Transfer”Word/Construct Wall – Unit IV Ribose Sugar Transcription Nitrogenous Base Pentose Sugar Deoxyribose Sugar Phosphate Group Phosphodiester Bond [5’  3’ Parallel “Template” Side [3’  5’ Anti-parallel “Coding” Side Codons Pyrimidine Purine Enzyme Gene Adenine (A) Cytosine (C) Thymine (T) Guanine (G) Uracil (U) Phosphorylation Carbon “prime” sites 5-4-3-2-1 “Hydrogen-Bonding” Site(s) Nucleotide Sigma factor Promoter Sequence RNA Polymerase Promoter

3. Transcription – Informational “Transfer”DNA: Structure, Form, Function, & Information DNA’s Structural “Backbone” Review of our “scaffold” DNA’s structure is made up of three different types of molecules or compounds that form a “unit” – identify the cmpds & “unit”. Deoxyribose Sugar Phosphate Group Nitrogenous Base Nucleotide Ribose Sugar Codons

4. Transcription – Informational “Transfer”DNA: Structure, Form, Function, & Information DNA’s Structural “Backbone” Review of our “scaffold” DNA’s structure is made up of three different types of molecules or compounds that form a “unit” – identify the cmpds & “unit”. Deoxyribose Sugar Phosphate Group Nitrogenous Base Deoxyribose Sugar Phosphate Group Nitrogenous Base Nucleotide Nucleotide Ribose Sugar Codons

5. DNA: Structure, Form, Function, & Informational Transfer DNA’s Structural “Backbone” Review of our “scaffold” The three components of a nucleotide have two basic functions: Function #1: Make A “Spine” The phosphate groups & pentose (5-sided) sugar rings link together via the C₅ and C₃ positions in order to form a “spine” or “backbone” structure.

6. DNA: Structure, Form, Function, & Informational Transfer DNA’s Structural “Backbone” Review of our “scaffold” In fact TWO such “spines” or “backbone” structures are formed AND linked together; which brings us to the second function of the nucleotide’s THIRD component... … the nitrogenous base(s).

7. DNA: Structure, Form, Function, & Informational Transfer DNA’s Structural “Backbone” Review of our “scaffold” The nucleotide’s Function #2: Covalently Bond to a Nitrogenous Base The nitrogenous base(s) will form a strong covalent bond (share a pair of electrons together) – binding the base to the “spine” or “backbone”.

8. DNA: Structure, Form, Function, & Informational Transfer DNA’s Structural “Backbone” Review of our “scaffold” The nucleotide’s three components have two basic functions: Function #2: Covalently Bond to a Nitrogenous Base That covalently bound nitrogenous base will – ultimately “hydrogen bond” (magnetic-like) to another n-base to make a same-sized “stair step”; linking the two “spines” or “backbones” together to form a “helix” (spiral staircase).

9. DNA: Structure, Form, Function, & Informational Transfer DNA’s Structural “Backbone” Review of our “scaffold” This “spiral” helix structure has two spines of backbones much like the handles on a spiral staircase. Each “step” or “rung” of the helix is always the same width due to the exclusive A-U (forming two) and C-G (forming three) hydrogen bonds.

10. DNA: Structure, Form, Function, & Informational Transfer DNA’s Structural “Backbone” Review of our “scaffold” The two “spines” are different! One spine (left side) is labeled as the 5’  3’ parallel “template” side of the spiral DNA helix “staircase” because that side; • begins @ the 5’ carbon position of the uppermost pentose sugar ring. • and it ends @ the lowest pentose sugar ring’s 3’ carbon position.

11. DNA: Structure, Form, Function, & Informational Transfer DNA’s Structural “Backbone” Review of our “scaffold” The other spine (right side) is labeled as the 3’  5’ anti-parallel “coding” side of the spiral DNA helix “staircase” because that side; • begins @ the 3’ carbon position of the uppermost pentose sugar ring. • and it ends @ the lowest pentose sugar ring’s 5’ carbon position.

12. DNA: Structure, Form, Function, & Informational Transfer • The 3’  5’ anti-parallel side is called the “coding” side because it is the source of informational code that allows for the protein templates to be created & copied for later construction (and other things as well – more on this later too.) • The 5’  3’ parallel side is called the “template” side because it is like a template for a model – the “template(s) information” stored on that side is mainly used to provide the template [to] make “proteins” (more on that later)

13. DNA: Structure, Form, Function, & Informational Transfer DNA’s Structural “Backbone” Review of our “scaffold” Theother basic function of the nucleotide’s three components [is] providing “anchor-sites” of nitrogenous bases [in order to] create “codons” (three successive nitrogenous bases)…

14. DNA: Structure, Form, Function, & Informational Transfer DNA’s Structural “Backbone” Review of our “scaffold” Three successive nitrogenous bases on the 5’ 3’ parallel side is called? Codons

15. DNA: Structure, Form, Function, & Informational Transfer Unwinding of the DNA Helix by RNA polymerase (an “enzyme”) Review of our “scaffold” • The RNA polymerase (a proteinenzyme) and the sigma factor(another protein) join together and begin to look for the “promoter” sequence on the DNA strand; • Once the RNA polymerase/sigma factor complex recognizes the correct “promoter”…,

16. DNA: Structure, Form, Function, & Informational Transfer Unwinding of the DNA Helix by RNA polymerase (an “enzyme”) Review of our “scaffold” • Once the RNA polymerase/sigma factor complex recognizes the correct “promoter”, • The sigma factor dissociates from the RNA polymerase;

17. DNA: Structure, Form, Function, & Informational Transfer Unwinding of the DNA Helix by RNA polymerase (an “enzyme”) Real time video of transcription http://www.dnalc.org/resources/3d/TranscriptionBasic_withFX.html Real time video of entire Protein Synthesis process. http://teachertube.com/viewVideo.php?video_id=162889 • Once the RNA polymerase/sigma factor complex recognizes the correct “promoter”, • The sigma factor dissociates from the RNA polymerase; • There are a few steps here we will cover later – but for now… the DNA strands start to “pry” apart (come apart):

18. DNA: Structure, Form, Function, & Informational Transfer Unwinding of the DNA Helix by RNA polymerase (an “enzyme”) Review of our “scaffold” • Once the RNA polymerase/sigma factor complex recognizes the correct “promoter”, • The sigma factor dissociates from the RNA polymerase; • There are a few steps here we will cover later – but for now… the DNA strands start to “pry” apart (come apart):

19. DNA: Structure, Form, Function, & Informational Transfer Let’s take a moment for a “word bank” Word Bank DNA RNA Template Strand Coding Strand Enzyme RNA Polymerase Promoter (Promoter Sequence) Gene

20. DNA: Structure, Form, Function, & Informational Transfer Let’s take a moment for a “word bank” Word Bank DNA -two strands, coding strand &template strand, that contain the instructional code for organisms entire living process made up of nucleotides possessing the phosphate group, pentose sugar (deoxy-ribose) and any one of the four nitrogenous bases (ATCG; A—T & C—G ); RNA Template Strand Coding Strand Enzyme RNA Polymerase Promoter (Promoter Sequence) Gene

21. DNA: Structure, Form, Function, & Informational Transfer Let’s take a moment for a “word bank” Word Bank DNA RNA - similar to DNA with a phosphate group, but is less stable because the pentose sugar – ribose – has an extra oxygen atom at its 2-prime position in the molecule making it more reactive). Four nitrogenous bases are (AUCG) – A=U(t), C=G. Template Strand Coding Strand Enzyme RNA Polymerase Promoter (Promoter Sequence) Gene

22. DNA: Structure, Form, Function, & Informational Transfer Let’s take a moment for a “word bank” Word Bank DNA RNA Template Strand -is the strand that is used as a template in the synthesis of mRNA (5’  3’ parallel side) Coding Strand Enzyme RNA Polymerase Promoter (Promoter Sequence) Gene

23. DNA: Structure, Form, Function, & Informational Transfer Let’s take a moment for a “word bank” Word Bank DNA RNA Template Strand Coding Strand - is the strand that is NOT used as a template in the synthesis of mRNA (3’ 5’ antiparallel side) but is identical in sequence to the mRNA except that all the U's are still T's at this point. Enzyme RNA Polymerase Promoter (Promoter Sequence) Gene

24. DNA: Structure, Form, Function, & Informational Transfer Let’s take a moment for a “word bank” Word Bank DNA RNA Template Strand Coding Strand Enzyme - protein catalysts that regulate all body functions. RNA Polymerase Promoter (Promoter Sequence) Gene

25. DNA: Structure, Form, Function, & Informational Transfer Let’s take a moment for a “word bank” Word Bank DNA RNA Template Strand Coding Strand Enzyme RNA Polymerase - an enzyme which reads DNA and makes a complementary messenger RNA strand (mRNA) during transcription. Promoter (Promoter Sequence) Gene

26. DNA: Structure, Form, Function, & Informational Transfer Let’s take a moment for a “word bank” Word Bank DNA RNA Template Strand Coding Strand Enzyme RNA Polymerase Promoter (Promoter Sequence) - Region of DNA where RNA polymerase attaches and initiates transcription. It is a specific sequence of codons that serve as a “Promoter”… (promotes attachment @ the beginning –and- promotes detachment @ the end of the gene it is after). Gene

27. DNA: Structure, Form, Function, & Informational Transfer Let’s take a moment for a “word bank” Word Bank DNA RNA Template Strand Coding Strand Enzyme RNA Polymerase Promoter (Promoter Sequence) Gene - area of DNA which codes mRNA

28. DNA: Structure, Form, Function, & Informational Transfer ATP = adensosine TRIphosphate Putting the 1st Steps to Transcription altogether As the “ribo-nucleotides are added… the ATP groups stay intact on the first base-pair bonding, but will cleave (cut off) two of the groups in the process: phosphorDIester bond formation. AMP=adenosine MONOphosphate ADP = adenosine DIphosphate Notice – these nucleotides are called “deoxyribonucleotides because it’s on the DNA strand.

29. DNA: Structure, Form, Function, & Informational Transfer Putting the 1st Steps to Transcription altogether

30. The DNA Backbone structur with Nucleotide replications. • http://www.umass.edu/microbio/chime/ C Click on the link on the right; On the lower left hand side of the 1st page click on the link: DNA Structure Jmol On the 2nd page opened (DNA Structure)– scroll down to option “3-C”