The Central Dogma of                                                                                                                                        Molecular Biology

The Central Dogma of Molecular Biology Describes the flow of genetic information from DNA to RNA to Proteins DNA Replication Transcription Translation

“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” -Watson and Crick

Copying DNA Page 286-287 in your text…..additional information is in this power point

Replication Definition All gene duplication The DNA base sequence is precisely copied Produces two copies that each contains one of the original strands and one entirely new strand DNA must be copied before a cell divides (S phase of interphase). New cells have identical DNA strands

DNA Replication DNA Replication is semi-conservative                                                                                                    DNA Replication is semi-conservative Each newly synthesized molecule contains 1 “parent template” strand and 1 new “daughter” strand

DNA Replication Step 1: Initiation Enzyme named Helicase unwinds DNA by breaking hydrogen bonds forming a “replication fork” Multiple replication forks along a DNA molecule create many replication bubbles New strands grow at the forks (bubbles)

Replication Fork

DNA Replication Step 2: Elongation---Adding New Nucleotides Enzyme Topoisomerase attaches to the 2 forks of the bubble to relieve stress on the DNA molecule as it separates

Step 2 cont…… RNA Primase adds a complimentary RNA primer to each template strand as a starting point for replication DNA Polymerase reads the template strand (3’ to 5’) and adds new complimentary nucleotides (5’ to 3’) DNA synthesized in the direction of the replication fork is called the leading strand

DNA Replication DNA polymerase can only add new nucleotides in the 5’ to 3’ direction Because of the antiparallel nature of DNA, replication occurs in two directions An RNA primer is laid down on the other strand, and new nucleotides are added 5’ to 3’ moving away from the replication fork. This is the lagging strand and the segment of DNA produced is called an Okazaki fragment

DNA Replication The DNA unwinds some more and the leading strand is extended by DNA polymerase adding more DNA nucleotides. Thus, the leading strand is synthesized continuously.

DNA Replication On the top template strand, a new RNA primer is synthesized by primase near the replication fork DNA polymerase adds new DNA . This produces the second Okazaki fragment. Thus, the lagging strand is synthesized discontinously

DNA Replication Step 3: Termination A different type of DNA polymerase removes the RNA primer and replaces it with DNA DNA ligase joins the two Okazaki fragments with phosphodiester bonds to produce a continuous chain Each new DNA molecule is rewound by helicase. Each molecule is identical

DNA Replication Summary and Other Facts: Leading Strand: 1 primer, 5’ to 3’ continuous Lagging Strand: multiple primers, 5’ to 3’ discontinuous In humans, DNA polymerase adds 50 nucleotides/second DNA polymerase can proofread its own work and does excision repair 1 in 10,000 bases are in error After proofreading, rate of mutation is 1 in 10,000,000

Summary of events: Helicase-unzips Topoisomerase- Primase- adds RNA primers Polymerase- adds DNA 5’ to 3’ Okazaki fragments formed between bubbles Ligase-connects bubbles

Replication Animations http://www.youtube.com/watch?v=teV62zrm2P0 http://www.youtube.com/watch?v=z685FFqmrpo http://www.youtube.com/watch?v=zdDkiRw1PdU

Section Assessment Page 287 1-6 Replication quiz tomorrow

What is a genome? A genome is an organism’s complete set of DNA. Genomes vary widely in size; the smallest known genome is for a bacterium and contains 600,000 DNA base pairs. Humans have 3 billion base pairs Except for mature red blood cells, all human cells contain a complete genome “Human Genome Project” completed in 2003- mapped every gene in the genome of humans

Map of the Human Genome

Interesting facts about DNA The human genome contains 3164.7 million chemical nucleotide bases (A, C, T, G) The average gene consists of 3000 bases The largest human gene is 2.4 million bases (dystrophin)- deficiency causes muscular dystrophy The total number of genes is estimated at 30,000 Almost all (99.9%) nucleotide bases are exactly the same in all people The functions are unknown for over 50% of discovered genes DNA contains repeated sequences that do not code for proteins. This is called “junk DNA” (INTRONS) and it makes up 50% of the genome (EXONS=code) Our genome is predominantly composed of the bases G and C Chromosome 1 has the most genes and chromosome “Y” has the fewest Although genes get a lot of attention, it’s the proteins that perform most life functions and even make up the majority of cellular structures

Proteins…… Proteins are large, complex molecules made of smaller subunits called amino acids. Amino acids build polypeptide chains to create PROTEINS Chemical properties that distinguish the 20 different amino acids cause the protein chains to fold up into specific 3-D structures that define their particular functions in the cell A protein’s chemistry and behavior are specified by the gene sequence and by the number and identities of other proteins made in the same cell at the same time and with which it associates and reacts

Ssooooooo………

Section 11.2 in your text Genes and proteins RNA Transcription RNA processing The genetic code translation

text Read page 288 “genes and proteins”

PROTEIN SYNTHESIS Transcription- pages 290-292 Translation pages 293-295

RNA Synthesis: Transcription RNA is an important type of nucleic acid that plays several roles in the production of protein RNA is necessary to carry the instructions of the DNA out of the nucleus and to the ribosomes where proteins are built from amino acids

How is RNA different from DNA RNA is single stranded RNA sugar is ribose RNA does not contain THYMINE but rather URACIL

RNA Synthesis: Transcription The genome of any organism contains all the information for making that organism. The information is encoded in various types of genes that are transcribed into 3 types of RNA: mRNA - Messenger RNA: Encodes amino acid sequence of a polypeptide. Carries instructions from DNA to cytoplasm. Involved in TRANSCIPTION rRNA - Ribosomal RNA: With ribosomal proteins, makes up the ribosomes, the organelles that translate the mRNA. “reads the instructions and builds proteins” tRNA - Transfer RNA: Brings amino acids to ribosomes during translation

Messenger RNA Involved in TRANSCRIPTION “Genetic Messenger” Do you know why???? Contains nucleotide sequences which code for amino acids Code of mRNA is called a CODON Leaves the nucleus with only EXONS

RNA Synthesis: Transcription Messenger RNA carries the actual code that specifies the amino acid sequence in a polypeptide chain (protein) Making mRNA starts with a protein encoding gene on a template strand of DNA

RNA Synthesis: Transcription Step 1: Initiation- RNA Polymerase binds to DNA RNA Polymerase binds to a promoter which is a region of bases that signals the beginning of a gene RNA Polymerase is bound to the TATA box (5’TATAAA3’) of the promoter by transcription factors which are proteins that recruit RNA polymerase

RNA Synthesis: Transcription Step 2: Elongation Transcription factors unwind the DNA and allow RNA polymerase to transcribe DNA into mRNA RNA Polymerase moves along the protein encoding gene adding new RNA nucleotides (ribonucleotides) in the 5’ to 3’ direction and complimentary to the DNA template Transcribes in “RNA language” so C=G and A=U Works at up to 60 nucleotides/second

RNA Synthesis: Transcription Step 3: Termination RNA Polymerase reaches the terminator region of the protein encoding gene mRNA will then detach from the DNA The product of these 3 steps is called immature or pre-mRNA

RNA Processing Most eukaryotic protein encoding genes contain non-coding segments called introns, which break up the amino acid coding sequence into segments called exons RNA Processing includes modification and splicing. Mature mRNA after introns removed from the sequence.

RNA Synthesis: Transcription Check out these animations and reviews: http://www.youtube.com/watch?v=5MfSYnItYvg&feature=related http://www.youtube.com/watch?v=AGzsgTMgSog&feature=related

What’s Next???? Now that a copy of the DNA has been made (transcribed into the language of RNA), it can leave the nucleus and go out into the cytoplasm to a ribosome to make PROTEIN. That process is called translation. ***Pg 293 “the process of converting the information in a sequence of nitrogenous bases in mRNA into a sequence of amino acids in protein”***** Translation takes place in the ribosome

Protein Synthesis: Translation The language of nucleic acids in translated into the language of proteins Nucleic acids have a 4 letter language Proteins have a 20 letter language (20 different amino acids). 11 made by body, 9 from the foods you eat

Protein Synthesis: Translation The Genetic Code If 3 RNA bases code for 1 amino acid, RNA could code for 43 = 64 amino acids. More than enough coding capacity for 20 amino acids

Protein Synthesis: Translation The “Players” Messenger RNA (mRNA) Ribosomes Transfer RNA (tRNA) Amino Acids Ribosomal RNA (rRNA)

Protein Synthesis: Translation Messenger RNA (mRNA) goes to ribosome Synthesized in Transcription Composed of Codons Codons are 3-base sequences of mRNA Some codons do not code for amino acids; they provide instructions for making the protein AUG is a START codon and for the amino acid METHIONINE

Start and Stop Codons of mRNA Start: AUG………amino acid methionine Stop: UAA, UAG, UGA…..no amino acid associated with these

Protein Synthesis: Translation Ribosomes Made of rRNA and protein 2 subunits (large and small) form a 3D groove 2 major sites: P site---holds the growing polypeptide A site---new amino acids enter here

Ribosome…..

tRNA- also on page 293

mRNA goes to ribosome Enters ribosome at mRNA binding site tRNA anticodon, which has an attached amino acid, will match with mRNA codon on the “P site” of the ribosome This places the amino acid in the correct position for forming a peptide bond with the next amino acid Always starts with START codon AUG and amino acid METHIONINE Both codon and anticodon move to “A site” where the polypeptide chain will form The ribosome will slide down the mRNA chain to the next codon and a new tRNA brings another amino acid Stops at the STOP codon (UAA or UGA or UAG)

Protein Synthesis: Translation Transfer RNA (tRNA) Carries amino acids to the ribosome During tRNA charging each tRNA picks up an amino acid from the cytoplasm 3 base anitcodon pairs with the mRNA codon

Protein Synthesis: Translation Amino Acids There are 20 amino acids, each with a basic structure Amino acids are held together by peptide bonds

Protein Synthesis: Translation 3 Steps: Initiation Elongation Termination

Protein Synthesis: Translation Step 1: Initiation 5’ G-cap of mRNA binds to ribosome Start codon AUG and anticodon with Methionine bind a P site A site is open and ready to receive new tRNAs

Protein Synthesis: Translation Step 2: Elongation Adding New Amino Acids Codon recognition Peptide bond formation Translocation: ribosome moves along mRNA, aminoacyl tRNA shifts from A site to P site

Protein Synthesis: Translation Step 3: Termination A stop codon is reached UAA UAG UGA All parts release

Amino acid chains become proteins when they are freed from the ribosome and twist and curl into complex 3-D shapes. These proteins become enzymes and cell structures

This pathway of information from DNA to mRNA to a protein is called Protein synthesis or CENTRAL DOGMA It is found in all organisms from the simplest bacteria to the most complex plant and animal This produces the diverse living world

Protein Synthesis: Translation Animations: http://www.youtube.com/watch?v=5bLEDd-PSTQ http://www.youtube.com/watch?v=TfYf_rPWUdY&feature=related

Activities Mini lab 11.1 page 293 Section Assessment page 295 1-6

Bozeman Biology http://www.youtube.com/watch?v=yLQe138HY3s

Activities Making a model of protein synthesis- in class Homework- making a “say it with DNA” project