From RNA to protein
Overview of transcription and translation in prokaryotes vs. eukaryotes
Tracking a trait from gene to phenotype: The BAD2 gene determines fragrance in rice
RNA
A. Ribonucleic acid (RNA) is a key nucleic acid in transcription and translation. RNA is like DNA except that:
- it is usually single rather than double stranded
- it contains ribose rather than deoxyribose
- it contains the base uracil rather than thymine
A comprehensive comparison of deoxyribonucleotides and ribonucleotides
B. General classes of RNA: informational, functional, and regulatory
A. Overview: The process of transcription uses an intermediate - the messenger RNA (mRNA) - which can transmit the information in the DNA to the next step: translation. There are three steps in transcription: initiation, elongation, and termination. 2/20/09: Note: The figure accessed by the "Either strand" hyperlink in the next sentence is NOT CORRECT - The dark blue strand should be 5' left and 3' right and the complementary strand 3' left, 5' right. The mRNA transcripts are correct as shown in the Figure and the the concept is right ...Either strand of the DNA may be the template strand for RNA synthesis for a given gene. For any given gene, the template strand is also referred to as the antisense (or non-coding) strand and the non-template strand as the sense (or coding) strand. The same DNA strand is not necessarily transcribed throughout the entire length of the chromosome or throughout the life of the organism.
B. RNA polymerases: ______________________
C. The three steps in transcription
- Initiation: Transcription is initiated at the promoter. The promoter is a key feature for control of gene expression. Promoters have defined attributes, in terms of their sequence organization. Example: the HvBM5A promoter region.
Elongation: ______________________
Termination: ______________________
5' and 3' UTRs: ______________________
D. Processing the mRNA transcript. In prokaryotes the mRNA is sent on to the ribosome for translation. In eukaryotes, in contrast, the primary RNA transcript is processed into a mature mRNA before it is exported to the cytoplasm for translation (Figure). There are three components to processing:
- 5’ cap: ____________________
- 3’poly(A tail): ______________________
- Splicing to remove internal portions of the RNA transcript. Most, but not all, eukaryotic genes have shorter mature mRNAs than primary transcripts because introns are removed during processing. The coding regions, “exons”, are then rejoined.
E. Changes in intron sequence splicing can affect what the gene encodes
More reading on alternative splicing in plants: Chen et al. 2007. Plant Phys. 143: 1086-1095.
F: Expressed Sequence Tags (ESTs)
The genetic code
The sequence of a coding (sense, non-template) strand of DNA, read 5’ – 3’, specifies a sequence of amino acids (read N-terminus to C-terminus) via a triplet code. Each triplet is called a codon.
A. Reading the DNA code: There are 64 codons; 61 represent amino acid codes and 3 cause the termination of protein synthesis (stop codons).
B. Degeneracy: __________________________
Translation
A. Overview: The process of translation takes the information that has been transcribed from the DNA to the mRNA and, via some more intermediates (ribosomes and transfer RNA), give the sequence of amino acids that determine the polypeptide.
The translation process (animation - a; animation - b) involves initiation, elongation, and termination.
- Initiation: In addition to the mRNA, ribosomes, and tRNAs, initiation factors are required to start translation. The AUG codon specifies initiation, in the correct sequence context. It also specifies methionine (MET).
- Elongation: Much as initiation factors were important in the first step, now elongation factors come into play. The reactions also require additional components and enzymes.
- Termination: There are three "stop" codons.
VI. From DNA to amino acid sequence
The following data from GenBank (accession No.AY785841 ) illustrate several points made in the preceding sections on transcription, the DNA code, and translation.
1: AY785841. Hordeum vulgare s...[gi:60547428] |
LOCUS AY785841 772 bp DNA linear PLN 01-DEC-2005
DEFINITION Hordeum vulgare subsp. vulgare cultivar Dicktoo HvCBF2A (CBF2A)
gene, complete cds.
ACCESSION AY785841
VERSION AY785841.1 GI:60547428
KEYWORDS .
SOURCE Hordeum vulgare subsp. vulgare
ORGANISM Hordeum vulgare subsp. vulgare
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Pooideae; Triticeae; Hordeum.
REFERENCE 1 (bases 1 to 772)
AUTHORS Skinner,J.S., von Zitzewitz,J., Szucs,P., Marquez-Cedillo,L.,
Filichkin,T., Amundsen,K., Stockinger,E.J., Thomashow,M.F.,
Chen,T.H. and Hayes,P.M.
TITLE Structural, Functional, and Phylogenetic Characterization of a
Large CBF Gene Family in Barley
JOURNAL Plant Mol. Biol. 59 (4), 533-551 (2005)
PUBMED 16244905
REFERENCE 2 (bases 1 to 772)
AUTHORS Skinner,J.S., Szucs,P., von Zitzewitz,J., Marquez-Cedillo,L.,
Filichkin,T., Stockinger,E.J., Thomashow,M.F., Chen,T.H. and
Hayes,P.M.
TITLE Mapping of barley homologs to genes that regulate low temperature
tolerance in Arabidopsis
JOURNAL Theor. Appl. Genet. (2006) In press
REFERENCE 3 (bases 1 to 772)
AUTHORS Skinner,J.S., Chen,T.H.H. and Hayes,P.M.
TITLE Direct Submission
