The Molecule of Life

Rosalind Franklin & Maurice Wilkins Important Scientists in the Discovery Of DNA Rosalind Franklin & Maurice Wilkins X-ray crystallographic images of DNA Photo 51 James Watson, Francis Crick Used x-ray crystallography images & models to figure out double helix structure

Basic Structure Chains of nucleotides, phosphodiester bonds Dehydration reaction

Basic Structure Double helix, 2 strands of anti-parallel DNA nucleotides Ladder-like Sugar,P on outside (sides of ladder) Bases on inside (rungs of ladder) Base pairing- Always A/T, G/C (purine/pyrimidine) H bonds between bases Entire molecule twisted in helix shape

3’ 5’ 3’ 5’

DNA replication is semi-conservative The instructions For making each new strand Are contained in the old, Parent strand!!! http://www.lewport.wnyric.org/JWANAMAKER/animations/DNA%20Replication%20-%20long%20.html

The Players Helicase-enzyme which “unzips” the helix by breaking hydrogen bonds Begins at origin of replication, creates “Y” replication fork DNA Polymerase-enzyme which builds the new strands of DNA “reads” base on parent strand, adds complementary base to new strand Only moves in one direction!!!!-moves 3’(OH) to 5’(P) Leading strand-built continuously, in one piece, toward the replication fork Lagging strand-built in pieces called Okazaki fragments, away from the fork DNA ligase-puts Okazaki fragments together

Origin of replication-where DNA synthesis starts Helicase first binds here

Steps in DNA synthesis…. Helicase unzips helix at origin of rep., forming replication fork DNA polymerase reads bases on leading strand, places complementary nucleotides in place as it moves toward rep. Fork On lagging strand, DNA polymerase builds new strand in Okazaki fragments-DNA ligase joins them together This continues until the ends of the parent strands are reached

Why can’t the lagging strand be built continuously? The replication fork continues to grow and…. DNA polymerase can’t go “backwards”

DNA repair                                                                           DNA polymerase proofreads its work as it goes along & fixes most mistakes!!!!

Transcription DNA to RNA

DNA vs.RNA: differences DNA (deoxyribose nucleic acid) and RNA (ribose nucleic acid) are both nucleotide polymers. These molecules are very similar but there are some distinct differences between them. Both molecules are helical: DNA is a double helix RNA is a single helix. DNA bases: Adenine (A), Thymine (T), Cytosine (C) & Guanine (G) RNA bases: A, G and C but T is replaced with Uracil (U) DNA has one less oxygen on the 5 carbon sugar than RNA; thus the difference in their names. Deoxyribose simply refers to a ribose sugar lacking an oxygen molecule.

DNA vs. RNA molecular difference The lack of one oxygen molecule on the DNA 5 carbon sugar

RNA types 1. Ribosomal RNA (rRNA): make up ribosomes 2. Transfer RNA (tRNA): transport amino acids to ribosomes 3. Messenger RNA (mRNA): copied from DNA, conveys information from chromosomes to ribosomes

DNA vs. RNA: Similarities Both essential in protein synthesis. Transcription: DNA is transcribed into Messenger RNA (mRNA). Translation: mRNA is translated into a polypeptide chain with the aid of Ribosomal RNA (rRNA) and Transfer RNA (tRNA).

Transcription Essentials Transcription occurs in nucleus. Transcription: production of mRNA copy of the DNA gene. Think of DNA as instructions to build hardware (proteins), unfortunately, these instructions are in another language and incomprehensible to the workers that will eventually assemble the hardware. This is where mRNA will come into the picture - to provide new instructions that will be used by the workers.

Steps of Transcription Initiation: DNA is unzipped and the enzyme RNA polymerase runs along the template strand of the DNA. The template strand of DNA can be identified by finding the promoter region: nucleotide sequence T A C at the 3’ end (If the strand is written backwards it may look like C A T at the 3’ end). This identifies that strand as the template and the other strand, the information strand, will not be used in this transcription (this does not mean, however, that it may not be used in future transcription processes).

Steps of Transcription Elongation: As the RNA polymerase runs along the DNA template strand it will add the complementary RNA nucleotides to the DNA nucleotides. This means that G will be paired with C, and visa versa, and A (DNA) will be paired with U (RNA - rather than T in DNA replication) and T (DNA) paired with A (RNA). 

Steps of Transcription Termination: Transcription continues until RNA polymerase reaches a DNA region called the termination signal: nucleotide sequence that marks the end of a gene. When the single helix mRNA strand is complete, RNA polymerase releases the DNA andnew RNA molecule. The DNA will re-zip into the double helix.

The Process of Transcription

Diagrams of Transcription

Processing the Products of Transcription In eukaryotes, once the mRNA is transcribed it will then be processed. A cap and tail will be added to the ends of the mRNA strand. The strand will be spliced. The introns (non-coding regions) will be removed The exons (coding regions) will be spliced together The completed mRNA strand has groups of three nucleotides known as codons (for example, A U G is the codon in mRNA that was transcribed from T A C). These groups of three will code for a particular amino acid in translation (A U G will code for the start amino acid, methionine, in translation).

Translation From RNA to Protein

The Process of Translation Protein Synthesis: Translation

Translation Translation occurs when the mRNA strand moves out of the nucleus and into the cytoplasm to a ribosome. At this point mRNA, rRNA and tRNA all come together. The rRNA consists of two parts, the large ribosomal unit and the small ribosomal unit. On the large ribosomal unit are two sites- the A site and the P site. These will be the sites of polypeptide synthesis and elongation. The rRNA is like the factory of translation and tRNA is the worker.

Terminology for Translation The tRNA molecules have an amino acid attachment site and carries an anticodon. Anticodon: the 3 nucleotide sequence on t-RNA which the ribosome must fit against m-RNA to ensure that the correct amino acid is placed in the growing protein during translation. The tRNA will pick up the appropriate amino acid in the cytoplasm that is coded for by the mRNA codon that its anticodon matches. A lock and key process.

General Steps of Translation Initiation: tRNA is bonded to mRNA, rRNA polymerase binds to mRNA strand. Elongation: Ribosome reads mRNA chain in three nucleotide groups (codon) & inserts another tRNA. tRNA anti-codon (with amino acid) binds to mRNA codon. Translocation: the ribosomal unit physically moves (translocates) 3 bases (a new codon: AUG) along the mRNA in the 5' ---> 3' direction. Termination: tRNA recognizes release factors of nonsense codon. Newly completed polypeptide is released from ribosome.

Specifics of Initiation The large (top) and small (bottom) ribosomal units must be bound together to the strand of mRNA with the help of rRNA polymerase. The ribosomes position themselves so that the "start" codon sequence AUG on the mRNA is exposed. A tRNA unit with the anticodon sequence UAC bonds to the exposed "start" codon. This first tRNA only carries the amino acid methionine (met) which is now set in place.

Specifics of Elongation tRNA and its associated amino acids bond to the complementary codon on mRNA to elongate the polypeptide chain. As the large ribosomal unit sets in place, a second codon on mRNA is exposed (in this case, the codon is CAU) (A site). Elongation factors assists the 2nd tRNA to bond to this newly exposed codon. The newly arrived amino acid (his) is lined up next to the 1st amino acid (met). An enzyme binds both amino acids via dehydration synthesis (loss of water) bonding.

Amino Acid Chart

Intermediate Step 3. When the 1st two amino acids are bonded, the first tRNA leaves the mRNA/ ribosomal complex.

Specifics of Translocation Ribosomal unit physically moves (translocates) 3 bases (a new codon: AUG) along the mRNA in the 5' ---> 3' direction. When the new codon is exposed, another elongation protein assists the new tRNA and its associated amino acid (Ser) bind to the codon. After this occurs, an enyme binds the amino acids His and Ser via dehydration synthesis.

Specifics of Termination The diagram to the right illustrates the ribosomal complex after it has been translocated down the mRNA many codon sequences. The ribosome has constantly read the mRNA in the 5' ---> 3' direction. The result is a growing chain of amino acids, all bonded together to make a polypeptide chain. When a codon with the nonsense sequence UAA, UAG (seen here), or UGA is exposed, that is a signal that translocation is to stop. The stop codon is not bonded to a complementary anticodon sequence on a tRNA. Rather, a protein known as a release factor binds at the A site. The release factor ultimately will help release the finished polypeptide chain in the next step.

Release 6. The release factor prevents further reading of the mRNA message. The polypeptide molecule is released from the ribosomal units. The mRNA and the large and small ribosomal units are thus free to begin the translation process again.

Protein Synthesis

RNA – ribonucleic acid RNA nucleotides are composed of a sugar, a phosphate group, and a nitrogen base Ribose is the sugar

Nitrogen Bases Cytosine Adenine Guanine T nope Uracil

Single strand RNA is single stranded not double stranded like DNA

3 types of RNA mRna messenger – single long chain that carries the message from DNA in the nucleus to the ribosomes in the cytoplasm (Transcription)

mRNA Codon Nucleotides are arranged into groups of three. Also called triplets – 3 nitrogen bases

Amino acids Each codon represents one of the 20 different amino acids AUG CGA UGA

3 types of RNA tRNA transfer – hair pin chain that carries amino acids to help build proteins tRNA contains an anti-codon on one end and an amino acid on the other

3 types of RNA rRNA ribosomal – rRNA and protein make the ribosome

Problem DNA is in the nucleus…… Proteins are made on the ribosomes in the cytoplasm…… How does the information get from the DNA in the nucleus to the ribosomes in the cytoplasm?

Transcription The process where genetic information from DNA is “downloaded” to messenger RNA

This happens in the nucleus only! The DNA never leaves the nucleus!

Transcription Works just like DNA replication, but produces only one strand of mRNA The DNA is unzipped by the enzyme “Helicase” RNA Polymerase reads the DNA and pairs complimentary RNA nucleotides to the RNA strand The mRNA leaves the nucleus DNA zips back up

Transcription cont. The strand of mRNA is complimentary because it is constructed from the DNA nucleotide sequence! Remember: Uracil replaces Thymine in the mRNA sequence

Translation The process of making a protein from the mRNA code…….. The mRNA leaves the nucleus and goes to the ribosome The mRNA goes through the ribosome and is read by the ribosome The ribosome recognizes a codon and send a message to the tRNA

Translation tRNA carries an amino acid that is floating in the cytoplasm over to the ribosome The tRNA anti-codon binds to the mRNA codon while linking the amino acids together………. Thus creating a polypeptide, amino acid chain (protein)

Make a protein At the ribosomes, the tRNA gives the amino acid away to build protein Then goes back into the cytoplasm to look for a free amino acid and repeats The ribosome keeps reading the mRNA taking the amino acids from tRNA and sticking them together to make a protein chain This all happens very quickly!