The Central Dogma- The “Stuff of Life” Graphic http://effyeahimmunology.tumblr.com/ The pink cell is a T cell and the blue cell is an antigen presenting cell, more specifically a dendritic cell.

Proteins Proteins are the “workhorse” molecule found in organisms. The blue print for proteins is coded in the DNA of the organism. DNA contains genes that determine the phenotype of an organism or "what we look like". DNA codes for the synthesis of proteins. Proteins are responsible for the phenotype. Humans can make over 200,000 proteins actually much more than that if the immune system is taken into consideration. Made of polypeptide chains. Proteins have primary, secondary, tertiary and quaternary structure. There are 20 different amino acids and the average polypeptide chain is 400 amino acids long. The part of the DNA that codes for a particular polypeptide chain is known as a gene. 2 2

Uses of Proteins Uses of proteins Enzymes (catalase) Structure (silk, hair, nails) Antibodies Movement(muscle, flagella) Hormones (insulin) Carry gases (hemoglobin) Storage of amino acids (albumin)

History In 1909, British physician Archibald Gerrod first suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactions. He thought symptoms of an inherited disease reflect an inability to synthesize a certain enzyme. Linking genes to enzymes required understanding that cells synthesize and degrade molecules in a series of steps, a metabolic pathway. Archibald Garrod was the first to connect a human disorder with Mendel's laws of inheritance. He also proposed the idea that diseases came about through a metabolic route leading to the molecular basis of inheritance. Garrod was studying the human disorder alkaptonuria. He collected family history information (as well as urine) from his patients. Based on discussions with Mendel advocate William Bateson, Garrod deduced that alkaptonuria is a recessive disorder. In 1902, Garrod published a book called The Incidence of Alkaptonuria: a Study in Chemical Individuality. This is the first published account of a case of recessive inheritance in humans. 1909 Archibald Gerrod suggested that genes determine phenotype through defective enzymes controlling biochemical pathways.

Overview of Protein Synthesis DNA is located in the nucleus Proteins are made in the cytoplasm RNA is the intermediate between the DNA code and the actual synthesis of a protein The DNA that codes for the proteins is located in the nucleus but proteins are actually made in the cytoplasm. There must be an intermediate that can take the code (instructions) out to the cytoplasm so that the protein can be made. RNA is the intermediate that takes the code out to the ribosome so that the protein can be made. Protein synthesis has two major parts. Transcription-DNA nucleotides found in a gene are used as a template to make a molecule of RNA Translation- RNA template or mRNA is used in conjunction with ribosomes, tRNA with attached amino acids to produce a polypeptide chain.

Structure of RNA versus DNA RNA vs. DNA RNA DNA Single stranded Double stranded Ribose Deoxyribose U instead T T instead of U Nucleus and cytoplasm Restricted to nucleus & organelles Multiple uses Used as template for RNA synthesis and proteins

Three Main Types of RNA There are different types of RNA mRNA-carries the information from the DNA gene to the cytoplasm. Determines the sequence of amino acids for a protein tRNA-brings the correct amino acid to the ribosome and mRNA in translation rRNA-found on ribosomes and used to "connect" the tRNA to the mRNA snRNA-found on spliceosomes. Used to remove introns. SRP RNA-part of the signal recognition particle used to bring a translating ribosome to the E.R. and threads the emerging polypeptide chain into the lumen of the E.R.

Differences in Protein Synthesis between Prokaryotes and Eukaryotes Prokaryotes do not have introns like eukaryotes. RNA in prokaryotes does not have to be processed like eukaryotes. Transcription and translation can be simultaneous in prokaryotes. The major difference between prokaryotic and eukaryotic protein synthesis is prokaryotes do not have a nucleus so transcription and translation can be simultaneous. Also, the mRNA is not processed like eukaryotic RNA. Both types of cells use the same genetic code.

Genetic Code Amino acids are coded for by a triplet of DNA nucleotides called a codon. Notes on codons- 1. There 64 codons- 61 code for amino acids. There is "redundancy" in the code; more than one codon codes for the same amino acid. 2. Three codons code for stop. 3. One codes for start and also for methionine. Since DNA code is transcribed into mRNA, the genetic code in books is described in terms of mRNA codons.

Genetic Code The code has redundancy (GGU, GGC, GGA, and GGG); all code for the amino acid glycine. Each codon only codes for one amino acid. The code is a universal code meaning almost all cells use the same code. A eukaryotic gene can be expressed in a prokaryotic cell. It is called the universal genetic code BUT there are several exceptions where UAA and UAG represent glutamine instead of stop in a species of paramecia. Animal mitochondria use AUA for methionine instead of isoleucine and vertebrate mitochondria use AGA and AGG as stop codons.

Specifying or Coding for a Polypeptide This gene designates that the following peptide chain be made with the amino acids in this particular order.

Transcription Overview Transcription-RNA synthesis from a DNA template Initiation Elongation Termination RNA processing

Initiation Initiation-There is a region prior to beginning of a gene where the RNA polymerase attaches called the promoter region. The promoter region determines which side of the gene will be transcribed. In a prokaryotic cell, the RNA polymerase attaches directly to the region, but in a eukaryotic cell there are transcription factors (proteins) which help facilitate the attachment of the RNA polymerase. Within the promoter region, there is a sequence of TATA nucleotides, called the TATA box, that helps identify where the RNA polymerase should bind. Once the RNA polymerase attaches, there are even more transcription factors that attach. Now the RNA polymerase unwinds the DNA at the start point of the gene. In prokaryotes there is only one type of RNA polymerase, but in eukaryotes there are three types of RNA polymerase.

Elongation B. Elongation- RNA polymerase unwinds the DNA and base pairs RNA nucleotides to the DNA gene. RNA is made 5’ → 3’ so the DNA gene is 3’ →5’. The base pairing for RNA is adenine with uracil and guanine with cytosine. The approximate rate of base paring by RNA polymerase is about 60 RNA nucleotides/minute. The RNA molecule will peel off of the DNA gene and DNA molecule will reform. The average mRNA is 8000 base pairs long. A gene can be simultaneously transcribed by a number of transcription factors. This is important when many copies of the same protein are needed, such as albumin in an egg, or hemoglobin in a red blood cell. Do the math, if the average protein is 400 amino acids long then the number of nucleotides absolutely necessary to code for an average protein is 1200 nucleotides. However the average mRNA is 8000 base pairs long. There seems to be some extra nucleotides. Elongation- RNA polymerase unwinds the DNA and base pairs RNA nucleotides to the DNA gene. RNA is made 5′ → 3′ so the DNA gene is 3′ → 5′.

Termination Animation RNA synthesis proceeds until the RNA polymerase encounters a sequence that triggers its dissociation. This process is not well understood in eukaryotes. In eukaryotic cells, the RNA polymerase actually passes the termination point before the RNA molecule is released. C. Termination --there are two different methods for prokaryotic cells Intrinsic termination -- RNA transcription stops when the newly synthesized RNA molecule forms a G-C-rich hairpin loop followed by a run of U’s. When the hairpin forms, the mechanical stress breaks the weak rU-dA bonds. This pulls the poly-U transcript out of the active site of the RNA polymerase, in effect, terminating transcription. Extrinsic termination -- a protein factor called rho destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex.

RNA Processing Eukaryotic RNA processing 5' cap is added. At the 3' end 30-200 adenine nucleotides are added (poly-A-tail). Introns are removed http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120077/bio30.swf::How%20Spliceosomes%20Process%20RNA D. RNA processing- In eukaryotic cells the RNA is processed. 5' cap with a modified guanine nucleotide is added. At the 3' end 30-200 adenine nucleotides are added (poly-A-tail). These modifications prevent the mRNA from being degraded Signal the ribosome where to attach. The poly-A-tail also determines how many times the mRNA can be translated before it is destroyed. The average immature RNA is 8000 nucleotides long but the mature mRNA is 1200 nucleotides long. There are noncoding regions (introns) that are removed in eukaryotic cells. The remaining regions (exons) are joined together to form the cistron.

Guanosine5’ Cap mRNA

Removing Introns A spliceosome removes the introns. Spliceosomes are composed of smaller particles called snRNP The spliceosome will splice the intron at a specific RNA sequence releasing a "lariat" RNA.

RNA Processing http://www.dnalc.org/view/16940-Alternative-RNA-Splicing.html Graphic http://en.wikipedia.org/wiki/File:Splicing_overview.jpg Different exons are recombined in different ways for certain mRNAs. This increases the number of different proteins.

Exon Shuffling and Different Proteins Proteins often have a modular architecture consisting of discrete regions called domains In many cases, different exons code for the different domains in a protein Exon shuffling may result in the evolution of new proteins.

Ready for Translation This mRNA has been processed and is called mature mRNA. It is ready to go to the cytoplasm for translation.