BIO 1140 Lecture Notes - Small Nuclear Rna, Regulatory Sequence, Transposable Element

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Transcription
-DNA is organized into functional DNA and non-functional DNA (genic and non-genic)
Functional Unit- describes what is going to be transcribed from DNA to RNA
-transcription involves nucleoside triphosphates instead of deoxynucleoside triphosphates
(as found in replication)
-transcription can start de novo
-RNA polymerases do not need a primer as long as there is some regulatory
system to tell it where to start
-the first nucleotide that is added will have a triphosphate on it
-the other nucleotides will have monophosphate
Genes
-a gene is described as something the codes for proteins that is less than 100 aa long
(according to genomics)
-originally, its definition was genetic and reflected the lack of understanding of DNA or
RNA
-e.g.: a gene is a unit associated with an inherited trait
-e.g.: genes are the units of heredity in living organisms
-e.g.: genes are the biological or basic unit of heredity found in all cells
-later, a gene was defined with molecular information
-e.g.: a gene is a unit of information on a chromosome
-e.g.: a gene is a basic unit of heredity; a section of DNA coding for a particular
trait
-in order to make a sense strand, you need to synthesize from the anti-sense strand
-the genetic code is redundant
-mutations can be made and may not affect some things
-amino acids are coded for by more than 1 codon
-genes have introns; if mutations occur in introns, it is removed during
splicing
Modern View of a Gene and Chromosome
-made up of exon, intron, exon, intron (which is removed), a TATA box (an A-T rich
sequence; the point at which RNA polymerase binds to start transcription), promoter
(proximal; sequences that regulate and is close and upstream to where RNA polymerase
binds), and promoters that are further away known as enhancers (distal promoters) found
on either side
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-sequences that bind proteins needed fro transcriptional control and RNA synthesis are
cis-acting
-refers to usually a regulatory sequence that usually bind proteins
-these proteins are said to be trans-acting
-a cis-regulatory element or cis-element is a region of DNA or RNA that regulates the
expression of genes located on that same molecule of DNA (often a chromosome)
-these cis-regulatory elements are often binding sites for one or more trans-acting
factors
-a gene can be described as a basic unit of hereditary material
-it is an ordered sequence of nucleotide bases that encodes a product
-the gene includes regions preceding and following coding regions as well as
intervening sequences (i.e.: introns) between individual coding segments (i.e.:
exons)
-the simplified idea of "one gene - one protein - one structure - one function" cannot take
into account proteins that have multiple functions depending on context
-most of the genome in higher eukaryotes consists of repeated sequences and mobile
elements called transposons or retrotransposons (retroposons)
-only a few % code for genes; the protein coding regions are only ~1.5% of the
total
-transposable elements involve elements that can make a copy of themselves,
independent of the genome replication, and then insert somewhere else
Genomics
-refers to activities at the DNA level (i.e.: sequences)
-includes cloning and functional analysis
-functional genomics describes what the genes do
Epigenomics
-looks at DNA modifications that are heritable and can influence the phenotype (i.e.: 5
Methyl-C)
Transcriptomics
-looks at the transcriptomes via the RNA by converting it to DNA and sequencing
-is simple
Proteomics
-looks at all the proteins
-can only look at ~1000 at a time and is very time consuming
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Transcription
-in prokaryotes, there is no compartmentalization for transcription, replication, or
translation
-in eukaryotes, the message that is made is not the final sequence that is translated
-general characteristics of RNA:
-usually single-stranded (one polynucleotide) but with double stranded regions
-complimentary to part of a DNA polynucleotide
-has ribose instead of deoxyribose
-has uracil instead of theymine
-may contain modified bases
-made by RNA polymerases instead of DNA polymerases
-1 type of RNA polymerase in prokaryotes
-is a multi-enzyme complex
-changing sigma-factors allows for recognition of different classes
of enzymes
-3 or more types of RNA polymerase in eukaryotes (3 in the nucleus and 1
or more in the mitochondria)
-allows for specialization of the polymerase
-the cis-acting sites that are recognized by the polymerase are
different for each type of polymerase
-different RNA polymerases transcribe different sets of genes
-RNA polymerase must recognize different signals in the DNA to
recognize the correct gene to transcribe
-RNA polymerase I transcribes rRNA in the nucleolus (part of the
nucleus)
-RNA polymerase II transcribes mRNA (encodes proteins) and most
snRNAs (small nuclear RNA)
-RNA polymerase III transcribes tRNA, 5S rRNA, some snRNAs amd
scRNAs (small cytoplasmic RNA)
-RNA polymerase starts at the 5' end and the regulatory sequences
are adjacent; the promoter is at the 5' end
-promoters are in the middle of the gene for some tRNA and 5S
rRNA
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Document Summary

Dna is organized into functional dna and non-functional dna (genic and non-genic) Functional unit- describes what is going to be transcribed from dna to rna. Transcription involves nucleoside triphosphates instead of deoxynucleoside triphosphates (as found in replication) Rna polymerases do not need a primer as long as there is some regulatory system to tell it where to start. The first nucleotide that is added will have a triphosphate on it. A gene is described as something the codes for proteins that is less than 100 aa long (according to genomics) Originally, its definition was genetic and reflected the lack of understanding of dna or. E. g. : a gene is a unit associated with an inherited trait. E. g. : genes are the units of heredity in living organisms. E. g. : genes are the biological or basic unit of heredity found in all cells. Later, a gene was defined with molecular information.

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