Glossary of Bio 181: Eukaryotic Gene Expression

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In terms of genetics and related processes, what makes eukaryotic cells different from prokaryotic cells?
-Genomes are larger
-Genomes have more regulatory sequences
-Much of eukaryotic DNA is noncoding
-Multiple chromosomes
-Multiple copies for many eukaryotic genes; large amount of non-essential DNA
-Genes are interrupted by non-coding DNA, which is transcribed
-Eukaryotic genes in nucleus. Translation in cytoplasm
-Polycistronic mRNAs rare
-In multicellular organisms, gene expression is development and tissue specific
Where is pre-mRNA processed to mature mRNA? and where does it go after that?
It is processed in the nucleus and then transported to the cytoplasm.
What compound translates mRNA into proteins? Where does this occur?
What characteristics describe Satellite DNA?
5-50 bp in length and repeated 105 to 106 times. Usually present at the centromere.
What characteristics describe Minisatellites?
12-100 bp in length; repeated a variable number of times; used for DNA fingerprinting during the 1990's.
What characteristics describe Microsatellites?
1-5 bp repeated sequences; present in 10-50 copies; very useful genetic markers; Used in modern DNA fingerprinting.
What are the names for three highly repetitive DNA sequences, present in large copy number?
-Satellite DNA
What do Telomeres do?
Maintain the length and integrity of the chromosomes.
What two types of RNA account for 75% or more of stable DNA in a cell?
rRNA and tRNA
Where is it thought that tandem array of genes arise from?
gene duplication during evolution
During active cell division, a massive amount of _____ is transcribed from the _____ region of the genome.
What are the four different types of transposons in eukaryotic cells?
-SINEs (short interspersed elements)
-LINEs (long interspersed elements)
-DNA transposons
Describe SINEs.
short interspersed elements up to 500 bp in length
Describe LINEs.
long interspersed elements up to 7000 bp in length which may code for protein
Describe Retrotransposons.
May encode the enzymes required for their movement. Movement involves an RNA copy. The 300 bp Alu element accounts for 11% of the human genome, with a million scattred copies.
Describe DNA transposons.
move to a new spot without replicating and without an RNA intermediate
What are some of the consequences of transposons?
-When a transpon moves into a functional gene, mutation can result.
-When in the germ line, the mutation can be inherited. When in a somatic cell, cancer might result.
-Transposition contributes to genetic variation and evolution.
What's the significance of promoters and terminators?
-Promoters occur before genes (on DNA) to signal the start site for transcription.
-Terminators at the opposite end of the gene are stop sites for RNA synthesis.
What's the difference between exons and introns on DNA?
-Exons are stretches of DNA whose transcripts are present in mature mRNA.
-Introns are stretches of DNA whose transcripts are absent from mature mRNA product, yet they are present on pre-mRNA
What are mRNA's first transcripted as?
larger precursor mRNA's (pre-mRNA)
What is an important research technique for gene isolation and intron discovery? Describe it.
-Hybridization of DNA and RNA
-mRNA can form a hybrid with a DNA template strand by complementary base pairing.
The extra DNA in genes was first identified by _________ of DNA-mRNA hybrids.
electron microscopy
What is an "R-loop"?
Hybridization of spliced mRNA with double stranded DNA.
What method, other than the "R-loop," can be used to find the introns within a gene?
Hibridization of spliced mRNA with the coding strand of DNA (single-stranded DNA).
Name some of the places where introns occur (or may not occur).
-mRNA, tRNA, rRNA genes of eukaryotic nucleus
-chloroplast and mitochondrial DNA
-rare in prokaryote and archebacterial genes
Non-identical genes for mRNA form multigene famiilies. Name some of the places where such families are present.
-Hemoglobin subunit genes are a multigene family in mammalian cells.
-Mutations may accumulate in duplicated genes.
-Active genes encode globin subunits specific for different stages of mammalian development: i.e. embryo, young, and adult organisms.
-Human Chromosome 16: alpha globin genes
-Human Chromosome 11: beta globin genes
Different ______ are expressed at different times during human development, and in different cell types.
Define Heterogeneous Nuclear RNA.
They are Primary Precursor mRNA transcripts, termed hnRNA.
What does are the processing events that hnRNA goes through to become mature and translatabe mRNA? Where does this occur?
1. a 5'-cap is added
2. a 3'-poly [A] tail is added
3. splicing

-This occurs in the nucleus of a cell
During processing, what is attached to the 5' end of hnRNA? how is it attached?
-a modified GTP
-It attaches covalently
What are some of the functions of a 5' cap?
It's involved in ribosome binding and mRNA stability.
What is attached to the 3' end of hnRNA during processing?
A poly [A] tail of 100-200 adenine nucleotides.
Are poly [A] tails coded for in DNA?
Are poly [A] tails and G-caps present on all RNAs?
What occurs during the splicing of hnRNA?
Removal of introns and joining of exons.
Where to most mature mRNA's go after processing?
the cytoplasm
What is a spliceosome?
A spliceosome is a large, nuclear-located RNA-protein complex that catalyzes RNA SPLICING.
________ participate directly in splicing reactions via RNA-RNA interactions.
snRNPs are formed when...
snRNAs complex with proteins.
Spliceosomes are formed when...
6 major snRNPs assemble on pre-mRNA.
Describe the two-step splicing reaction for hnRNAs.
Step 1: Cleavage of 5'exon-intron boundary and formation of intron-lariat; 1st phosphodiester transfer reaction

Step 2: Joining of 5' and 3' exons, and release of intron as lariat; 2nd phosphodiester transfer reaction
Describe alternate splicing?
How does it work?
-The process by which different mRNAs and proteins can form from a single gene.
-usually, certain exons are left out of the mature mRNA, depending on what tissue or developmental stage it is specified for.
Is alternate splicing regulated? If so, what's an example?
-Splicing of a precursor mRNA can vary by tissue or developmental stage.
How is transcription controlled in eukaryotes?
Transcription factors bind DNA.
Eukaryotic promoter sequences are more ________ than in prokaryotes.
A transcription complex positions RNA polymerase at the beginning of a eukaryotic gene. The complex contains four kinds of proteins. What are they, and what do they do?
1. Basal factorts, i.e. TATA-binding proteins
2. Coactivators, linking basal factors to activators
3. Activators, which bind at distant enhancer sites on DNA
4. Repressors, binding to silencer sites on DNA preventing activator binding
What do enhancers and silencers do, and where are they in relation to the promoter?
-Enhancers and silencers are DNA sequence elements located at a distance from the promoter, up to 20,000 bp.
-They stimulate specific promoters.
-They bind transcriptional activator proteins.
Negative regulatory elements are called ________. They turn off transcription by binding proteins termed _________.
Specifically, what are activators?
Activators are proteins with surfaces for DNA binding, and one or more surfaces for binding other transcription proteins.
Activators have motifs to bind in the ________. What are the five main motifs, and what do they do?
-major groove

1. helix-turn-helix
-These proteins regulate genes involved in development.

2. homeodomain

3. luecine zipper
-These proteins regulate cell division genes.

4. zinc finger
-These proteins are steroid hormone receptors.

5. helix-loop-helix
-These proteins regulate immune system genes.
Draw simple diagrams for the supposed shapes of these activators (if known).
*check in book
How can a protein recognize a specific DNA sequence?
-The edges of the DNA base pairs protrude into the Major Groove of DNA

-Each base pair has unique recognition elements.
What are the four recognition elements unique to each base pair?
1. Hydrogen bond donors
2. Hydrogen bond acceptors
3. Hydrophobic methyl groups
4. Hydrogen: non-hydrogen bonding
What is Coordinate Regulation of gene expression?
Coordinate Regulation involves a coordinate, or location on the DNA that transcribes signal proteins that are used in turning on expression of multiple genes.
In what ways is coordinate regulation used for multiple genes?
-Genes may be on different chromosomes.

-Coordinately expressed genes may have the same regulatory sequences which bind the same regulatory protein.

-A single signal may cause the synthesis of a transcriptional regulator for many genes.
How are different combinations of activators and enhancers used?
-Activators often bind to different genes in different combinations to activate those genes.

-Activators can help to activate one gene in one cell and a different gene in a different cell.
RNAs that catalyze BIOLOGICAL REACTIONS, such as self-splicing introns, are known as:
-A ribozyme is an RNA molecule that can catalyze a biochemical reaction.
Polycistronic mRNAs are very common in ___________, but are rare in ____________.
What is reverse transcription?
Reverse transcription is the enzymatic synthesis of DNA from an RNA template by the enzyme reverse transcriptase.

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