Biochemistry Unit IV – Transcription

Basic 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

Transcription – Informational “Transfer”Word/Construct Wall – Unit IV

Transcription Nitrogenous Base

Pentose Sugar

Ribose Sugar

Deoxyribose Sugar

Phosphate Group

Phosphodiester Bond

[5’ 3’ Parallel “Template” Side [3’ 5’ Anti-

parallel “Coding” SideCodons Pyrimidine Purine

Adenine (A) Cytosine (C) Thymine (T) Guanine (G)

Uracil (U) Phosphorylation Carbon “prime” sites 5-4-3-2-1

“Hydrogen-Bonding” Site(s)

Enzyme Gene

NucleotideSigma factor

Promoter Sequence

RNA Polymerase

Promoter

DNA’s Structural “Backbone”

DNA’s structure is made up of three different types of molecules or compounds that form a “unit” – identify the cmpds & “unit”.

Review of our “scaffold”

Transcription – Informational “Transfer”DNA: Structure, Form, Function, & Information

Deoxyribose Sugar Phosphate

Group

Nucleotide

Nitrogenous Base

CodonsRibose Sugar

DNA’s Structural “Backbone”

DNA’s structure is made up of three different types of molecules or compounds that form a “unit” – identify the cmpds & “unit”.

Review of our “scaffold”

Transcription – Informational “Transfer”DNA: Structure, Form, Function, & Information

Deoxyribose Sugar Phosphate

Group

Nitrogenous Base

CodonsRibose SugarNucleotide

Nitrogenous Base Nucleotide

Phosphate Group

Deoxyribose Sugar

DNA: Structure, Form, Function, & Informational Transfer

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.

Review of our “scaffold”DNA’s Structural “Backbone”

DNA: Structure, Form, Function, & Informational Transfer

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).

Review of our “scaffold”DNA’s Structural “Backbone”

DNA: Structure, Form, Function, & Informational Transfer

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”.

Review of our “scaffold”DNA’s Structural “Backbone”

DNA: Structure, Form, Function, & Informational Transfer

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).

Review of our “scaffold”DNA’s Structural “Backbone”

DNA: Structure, Form, Function, & Informational Transfer

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.

Review of our “scaffold”DNA’s Structural “Backbone”

DNA: Structure, Form, Function, & Informational Transfer

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.

Review of our “scaffold”DNA’s Structural “Backbone”

DNA: Structure, Form, Function, & Informational Transfer

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.

Review of our “scaffold”DNA’s Structural “Backbone”

• 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)

• 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.)

DNA: Structure, Form, Function, & Informational Transfer

DNA: Structure, Form, Function, & Informational Transfer

The other basic function of the nucleotide’s three components [is] providing “anchor-sites” of nitrogenous bases [in order to] create “codons” (three successive nitrogenous bases)…

Review of our “scaffold”DNA’s Structural “Backbone”

DNA: Structure, Form, Function, & Informational Transfer

Three successive nitrogenous bases on the 5’ 3’ parallel side is called?

Review of our “scaffold”DNA’s Structural “Backbone”

Codons

DNA: Structure, Form, Function, & Informational Transfer

Unwinding of the DNA Helix by RNA polymerase (an “enzyme”)

1. The RNA polymerase (a protein enzyme) and the sigma factor(another protein) join together and begin to look for the “promoter” sequence on the DNA strand;

1. Once the RNA polymerase/sigma factor complex recognizes the correct “promoter”…,

Review of our “scaffold”

DNA: Structure, Form, Function, & Informational Transfer

Unwinding of the DNA Helix by RNA polymerase (an “enzyme”)

1. Once the RNA polymerase/sigma factor complex recognizes the correct “promoter”,

2. The sigma factor dissociates from the RNA polymerase;

Review of our “scaffold”

DNA: Structure, Form, Function, & Informational Transfer

Unwinding of the DNA Helix by RNA polymerase (an “enzyme”)

1. Once the RNA polymerase/sigma factor complex recognizes the correct “promoter”,

2. The sigma factor dissociates from the RNA polymerase;

3. There are a few steps here we will cover later – but for now… the DNA strands start to “pry” apart (come apart):

Real time video of transcriptionhttp://www.dnalc.org/resources/3d/TranscriptionBasic_withFX.html

Real time video of entire Protein Synthesis process.http://teachertube.com/viewVideo.php?video_id=162889

DNA: Structure, Form, Function, & Informational Transfer

Unwinding of the DNA Helix by RNA polymerase (an “enzyme”)

1. Once the RNA polymerase/sigma factor complex recognizes the correct “promoter”,

2. The sigma factor dissociates from the RNA polymerase;

3. There are a few steps here we will cover later – but for now… the DNA strands start to “pry” apart (come apart):

Review of our “scaffold”

DNA: Structure, Form, Function, & Informational Transfer

Let’s take a moment for a “word bank”

DNARNATemplate StrandCoding StrandEnzymeRNA PolymerasePromoter (Promoter Sequence)Gene

Word Bank

DNA: Structure, Form, Function, & Informational Transfer

Let’s take a moment for a “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 );

RNATemplate StrandCoding StrandEnzymeRNA PolymerasePromoter (Promoter Sequence)Gene

Word Bank

DNA: Structure, Form, Function, & Informational Transfer

Let’s take a moment for a “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 StrandCoding StrandEnzymeRNA PolymerasePromoter (Promoter Sequence)Gene

Word Bank

DNA: Structure, Form, Function, & Informational Transfer

Let’s take a moment for a “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 StrandEnzymeRNA PolymerasePromoter (Promoter Sequence)Gene

Word Bank

DNA: Structure, Form, Function, & Informational Transfer

Let’s take a moment for a “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.

EnzymeRNA PolymerasePromoter (Promoter Sequence)Gene

Word Bank

DNA: Structure, Form, Function, & Informational Transfer

Let’s take a moment for a “word bank”

DNA RNA Template Strand Coding Strand Enzyme - protein catalysts that regulate all body functions. RNA PolymerasePromoter (Promoter Sequence)Gene

Word Bank

DNA: Structure, Form, Function, & Informational Transfer

Let’s take a moment for a “word bank”

DNA RNA Template Strand Coding Strand EnzymeRNA Polymerase - an enzyme which reads DNA and makes a complementary

messenger RNA strand (mRNA) during transcription.

Promoter (Promoter Sequence)Gene

Word Bank

DNA: Structure, Form, Function, & Informational Transfer

Let’s take a moment for a “word bank”

DNA RNA Template Strand Coding Strand EnzymeRNA 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

Word Bank

DNA: Structure, Form, Function, & Informational Transfer

Let’s take a moment for a “word bank”

DNA RNA Template Strand Coding Strand EnzymeRNA Polymerase Promoter (Promoter Sequence)Gene - area of DNA which codes mRNA

Word Bank

DNA: Structure, Form, Function, & Informational Transfer

Putting the 1st Steps to Transcription altogetherAs 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.

ATP = adensosine TRIphosphate

ADP = adenosine DIphosphate

AMP=adenosine MONOphosphate

Notice – these nucleotides are called “deoxyribonucleotides because it’s on the DNA strand.

DNA: Structure, Form, Function, & Informational Transfer

Putting the 1st Steps to Transcription altogether

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”