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The Central Dogma of Molecular Biology

Topic 7 in the IB Biology Syllabus
by

Angela De Jong

on 4 May 2012

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Transcript of The Central Dogma of Molecular Biology

DNA is a nucleic acid.
d
eoxyribo
n
ucleic
a
cid
Nucleic acids are polymers of complex subunits called nucleotides.
A nucleotide is composed of a pentose sugar (deoxyribose, in DNA), inorganic phosphate, and a variable organic component called a base.
The Central Dogma of Molecular Biology
DNA
RNA
protein
DNA Structure
http://commons.wikimedia.org/wiki/File:Nucleotides.png
http://commons.wikimedia.org/wiki/File:DNA_Double_Helix.png
DNA Double Helix
Replication
Transcription
Translation
DNA replication is semi-conservative. Each daughter strand formed by replication is 50% new DNA and 50% original DNA. This was proven by Meselson & Stahl using radioisotopes, including N-15.
DNA Replication
http://commons.wikimedia.org/wiki/File:Meselson-stahl_experiment_diagram_en.svg
DNA Replication requires several enzymes:
Helicase
- breaks hydrogen bonds between base pairs & catalyzes the opening of the double helix
Gyrase
- breaks and rejoins the DNA double helix to relieve twisting forced by the opening of the helix
RNA Primase
- catalyzes the synthesis of the RNA primer
DNA Polymerase I
- removes RNA primer & replaces it with DNA.
DNA Polymerase III
- extends leading & lagging strands by attaching DNA nucleotides to 3' end of primer
DNA Ligase
- Forms (covalent) phosphodiester bonds between Okazaki fragments, making a continuous strand of DNA
Nucleotide Structure
P
Deoxyribose
Base
- - - -
- - - -
DNA consists of two anti-parallel polynucleotide chains in a double helix, held together by hydrogen bonds.
The "backbone" is made of alternating deoxyribose and phosphate molecules.
Phosphate attaches to the 5' carbon of deoxyribose and the 3' carbon of the next deoxyribose in the chain.
The base (adenine, thymine, guanine or cytosine) is attached to the 1' carbon of deoxyribose. Hydrogen bonds connect the base to its complement on the other strand (A to T, G to C).
DNA is read and assembled in the 5' to 3' direction.
hydrogen bonds
http://commons.wikimedia.org/wiki/File:DNA_replication_en.svg
Gyrase is a type of topoisomerase. It relieves tension caused by unwinding the double helix.
A portion of the DNA double helix is unwound by helicase.
DNA Primase forms a short segment of RNA (primer) on each strand.
DNA polymerase binds to one strand of the DNA molecule. This is the leading strand because it follows helicase.
Moving in a 3’ -> 5’ direction, it uses the DNA strand as a template, matching free nucleotides according to base-pairing rules.
Free nucleotides are in the form of deoxynucleoside triphosphates: dATP, dTTP, dGTP and dCTP. The 2nd & 3rd phosphates are removed, supplying energy to the process.
Once the fork opens, a second DNA polymerase attaches.
Discontinuous strands called Okazaki fragments are formed as replication proceeds on the lagging strand.
DNA ligase joins Okazaki fragments.
SSBP's, single strand binding proteins, help to stabilize the single stranded portions of DNA during replication. DNA is most stable as a double stranded molecule.
DNA synthesis on the leading strand is continuous, as DNA polymerase follows helicase. Due to the anti-parallel nature of DNA, synthesis on the lagging strand is discontinuous, as it must go opposite to the movement of helicase.
RNA is a nucleic acid.
r
ibo
n
ucleic
a
cid
RNA has several forms:
mRNA is used to copy DNA
tRNA brings amino acids to ribosomes
ribosomes are made of rRNA
RNA Structure
http://commons.wikimedia.org
mRNA Polynucleotide
DNA
RNA
pentose
bases
ribose
adenine
thymine
cytosine guanine
Compare & Contrast: DNA vs RNA
deoxyribose
structure
adenine
uracil
cytosine guanine
single stranded (structure varies)
double stranded (helix)
http://commons.wikimedia.org
tRNA Structure
inorganic phosphate
ribose
cytosine
guanine
adenine
uracil
http://commons.wikimedia.org/wiki/File:Genetic_code.svg
http://commons.wikimedia.org/wiki/File:Nucleotide.gif
DNA stores the instructions (code) for making proteins.
DNA remains in the nucleus during interphase.
Proteins are synthesized on ribosomes during interphase.
Ribosomes are made in the nucleus (nucleolus), but work in the cytoplasm.
The DNA code is copied into mRNA, which brings it to the ribosome, where the protein is finally assembled from amino acids.
Overview of Protein Synthesis
5'-ATG GCC TGG ACT TCA-3' = sense strand of DNA
3'-TAC CGG ACC TGA AGT-5' = antisense strand of DNA
transcription of antisense strand
5'-AUG GCC UGG ACU UCA-3' = mRNA
translation of mRNA
Met-Ala-Trp-Thr-Ser- = protein
mRNA takes the “message” from the DNA in the nucleus to the ribosomes in the cytoplasm.
It's like taking a photocopy of an article in the reference library, so you can take it home to write your EE.
Transcription
Transcription factors (50+) bind to the promoter region “upstream” (on the 5’ side) of the gene.
These are followed by other proteins, and RNA polymerase.
http://commons.wikimedia.org/wiki/File:DNA_transcription.svg
http://commons.wikimedia.org/wiki/File:Simple_transcription_initiation1.svg
The transcription factors and RNA polymerase work together to open the DNA molecule. This requires breaking of hydrogen bonds.
RNA polymerase “reads” the DNA molecule, moving in its 3’ to 5’ direction.
mRNA is assembled from nucleoside triphosphates (ATP, UTP, GTP & CTP) in the 5’ to 3’ direction, according to complementary base pairing rules.
http://commons.wikimedia.org/wiki/File:Simple_transcription_elongation1.svg
As each nucleoside triphosphate is brought in to add to the 3’ end of the growing mRNA strand, the two terminal phosphates are removed.
Transcription ends when RNA polymerase reaches a terminator sequence, and the mRNA and RNA polymerase are released from the DNA molecule.
commons.wikimedia.org/wiki/File:Simple_transcription_termination1.svg
mRNA Processing:
A cap of 7-methylguanosine is added to the 5' end shortly after initiation. This increases the molecule's stability.
A tail of 20-250 adenine molecules is added to the 3’ end (a poly-A tail).
http://vcell.ndsu.edu/animations/transcription/movie-flash.htm
Introns are excised (and subsequently hydrolysed & recycled) and exons are spliced together:
http://vcell.ndsu.edu/animations/mrnaprocessing/movie-flash.htm
http://commons.wikimedia.org/wiki/File:MRNA_structure.png
http://commons.wikimedia.org/wiki/File:DNA_exons_introns.gif
http://vcell.ndsu.edu/animations/mrnasplicing/movie-flash.htm
http://commons.wikimedia.org/wiki/File:Pre-mRNA_to_mRNA.png
Translation occurs in the cytoplasm.
Translation requires mRNA, produced by transcription of DNA, tRNA, amino acids, and ribosomes.
Ribosomes attached to the rough endoplasmic reticulum make proteins that are used in lysosomes or exported from the cell, while free ribosomes make proteins for use within the cell.
Translation
tRNA has a clover-leaf shape, with loops of single-stranded RNA at the end of regions of double-stranded helix.
AA binding site
Amino Acid Activation
Amino acids are attached to the appropriate tRNA molecules by activating enzymes called aminoacyl tRNA synthetases.
Activation is a two-step process:
aa + ATP aminoacyl AMP + PPi
aminoacyl AMP + tRNA aminoacyl tRNA + AMP
http://commons.wikimedia.org/wiki/File:Charge_tRNA.png
Ribosomes are comprised of two subunits made of rRNA:
http://commons.wikimedia.org/wiki/File:TRNA_ribosomes_diagram_en.svg
http://commons.wikimedia.org/wiki/File:Ribosome_mRNA_translation_en.svg
http://commons.wikimedia.org/wiki/File:Ribosome_structure_fixed.png
Translation
The ribosome attaches to the mRNA and begins translation of the mRNA codons from the start codon (AUG).
The ribosome provides a location for the complementary anticodon of the tRNA to base pair with the codon of the mRNA.
As the ribosome base pairs the appropriate codons (mRNA) with the tRNA anticodon a peptide bond is formed between the two adjacent amino acids.
Aminoacyl tRNA molecules enter the ribosome’s A-site. Once the peptide bond forms, the ribosome moves, which shifts the tRNA to the P-site.
When the ribosome moves again, the tRNA portion of the first amino acid moves the E-site, where it falls off and returns to the tRNA pool to become activated with another amino acid, and the process continues.
http://vcell.ndsu.edu/animations/translation/movie-flash.htm
E site
When a stop codon is reached, release factors bind to the mRNA. A water molecule is added and the polypeptide is released.
Eukaryotic chromosomes are composed of chromatin, which is about half DNA and half protein.
Nucleosomes are sub-units of chromatin. They consist of 8 histones (protein) that act as a spool for the threadlike DNA. Another histone locks it into place.
Eukaryotic Chromosomes
http://commons.wikimedia.org/wiki/File:Nucleosome.jpg
http://commons.wikimedia.org/wiki/File:Chromosome.gif
Full transcript