a biology primer part iii: transcription, translation, and regulation vasileios hatzivassiloglou...
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A Biology PrimerPart III: Transcription, Translation,
and Regulation
Vasileios Hatzivassiloglou
University of Texas at Dallas
We have covered so far
• Biological classification
• Organisms, tissues, cells and organelles
• Cell, protein, DNA, RNA function, structure, and form
• DNA replication
• (In part) The mechanisms of reproduction
Mitosis
Distribution of chromatids
• Applies to diploid eukaryotic cells
Errors during mitosis
• Chromosome does not separate (non-disjunction), 3:1 imbalance in genes
• Deletion of part of a chromosome
• Attachment to non-homologous chromosome (translocation)
• Reversal of orientation (inversal)
Meiosis
• Two phases:
• Meiosis I separates homologous chromosomes, but with a twist – genes are exchanged between non-sister chromatids (from the two different parents)
• Meiosis II separates the sister chromatids in each chromosome
Meiosis vs Mitosis
• Cell has two chromosomes, 1 and 2; homologues come from F or M
• Cell: F1M1+F2M2
• Replication: F1F1+M1M1+F2F2+M2M2
• Meiosis I: 2 x (F1M1+F2M2)
• Meiosis II: random distribution of the four chromosome pairs, e.g., F1F1+M2M2 with transformations, then randomly F1+M2
Meiosis graphically
Gene expression
• DNA encodes proteins in genes• Two stages: Transcription (from DNA to
mRNA) and translation (from mRNA to proteins via tRNA)
• Somewhat simpler in prokaryotic organisms because there is no nucleus, everything happens directly in the cytoplasm
Transcription
• Similar to replication, DNA is “unzipped” with an RNA polymerase (another enzyme protein)
• One strand of the DNA is copied onto messenger RNA via the correspondence– C to G– G to C– T to A– A to U (replaces T in RNA)
Where to start and stop?
• Special DNA sequences tell the RNA polymerase where to start (transcription start site) and where to end (transcription end site)
• Additional control sections of DNA specify when the process will be initiated
• These are usually close to the gene
Transcription process
Translation
• mRNA now contains all the information from the gene
• Another RNA molecule attaches to mRNA – this is transfer RNA
• There are many kinds of transfer RNA, each capable of recognizing the code for a single amino acid (or for the stop signal)
Coding for amino acids
• DNA and RNA have four letters
• We need at least 21 specifications (20 amino acids plus a stop code)
• Two-base combinations not enough (42 = 16)
• Three-base combinations (codons) sufficient (43 = 64), introduces redundancy (synonymous codons)
The genetic code
Translation process
• Actual translation takes place in the ribosomes, made up of proteins and rRNA
• Yet another RNA type (ribosomal RNA)
• tRNA for each codon attaches to the mRNA on one side (via anti-codon) and attracts the appropriate amino acid on the other side
Translation
Complications in eukaryotes
• DNA is in the nucleus; ribosomes are in the cytoplasm
• mRNA has to be transported outside the nucleus
• Also, eukaryotic DNA contains mysterious regions that do not code (introns) in addition to the useful regions (exons)
• Average length of introns 10,000 bp, of exons 200 bp
Transcription in eukaryotes
• Normal transcription process in the nucleus produces pre-mRNA which still contains all the introns
• Splicing eliminates the introns and results in mature mRNA
• This travels outside the cell for translation
Intron elimination and splicing
Alternative splicing
• Allows for much variation in the end product of transcription
• Some introns behave like exons in different tissue, e.g., liver vs. brain
• This results in many more proteins than genes
• In humans, about 32,000 genes code for 1,000,000 proteins
Other complications
• Cannot translate in parallel with transcription
• Regulatory regions can be further upstream or downstream, even within the introns
• Genes much harder to identify (computational implications)
Protein diversity
• Two major mechanisms:– Alternative splicing; depends on variable
function of introns in different cells within the same organism
– Post-translational modification; changes to the protein after gene expression
Post-translational modifications
• Many proteins undergo further change after translation
• Removal of one or more amino acids
• Cutting the protein in two parts (e.g., insulin)
• Addition of non amino acid groups, in particular phosphates (phosphorylation)– Controls when a protein can bind to something– Controls where the protein goes (cytosol / membrane)
Expression regulation
• Promoters: Short DNA sequences that attract the RNA polymerase to bind to them and start the transcription
• In prokaryotes, typically like
<-- upstream 5’-XXXXXPPPPPXXXXXXPPPPPPXXXXGGGG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
GGGGGGGGGGGXXXX-3' downstream -->
• In eukaryotes, promoters are more diverse and further away
How expression is regulated
• RNA polymerase can bind to promoters, but it doesn’t always do so
• Proteins can activate or suppress expression
• Activator proteins enhance the promoter’s tendency to bind with RNA polymerase
• Repressor proteins bind with the promoter and make it unavailable for RNA polymerase
Examples of regulation
• Positive feedback / activation– When heat increases, a protein in E. Coli
binds with its RNA polymerase and alters its properties so it can bind with promoters for heat-response proteins
• Negative feedback / repression– The protein lac repressor can bind either to
lactose (if there is any) or to the promoters that produce enzymes that digest lactose
Ubiquitylation
• Ubiquitin is a small protein that occurs in all eukaryotic cells
• Human sequence: (76 amino acids) MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
• Yeast sequence 96% similar
• Function: Attach to other proteins to mark them for destruction at the proteasome