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