BIO230H1 Chapter Notes - Chapter All CHapters: Nucleotide, Noncoding Dna, Piwi

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10 Jun 2018
School
Department
Course
BIO 230
Tetook Readig THE CELL Reie Notes
General Summary
All cells use DNA for their hereditary code
All cells transcribe using RNA
RNA chains are flexible and can bend back on itself to connect segments giving each RNA
sequence a different shape. This allows it to recognize and selectively bind to other molecules or
catalyze chemical changes in molecules that are bound.
All cells use proteins as catalysts
64 codons (triplet of actg) and only 20 amino acids mean that some triplets encode for the same
amino acid
A gene is a segment of DNA sequence that is corresponding to a single protein or a set of
alternative protein variants
The rate of transcription and translation are adjusted according to need
Regulatory DNA are sections of non-coding DNA between coding DNA that control the rate of
transcription.
Genes can be expressed with different efficiencies
DNA polymerase
RNA polymerase
Catalyzes the linkage of deoxyribonucleotides
Catalyzes the linkage of ribonucleotides
Needs primer to begin transcription because it
needs to be more accurate (107 mistakes)
Does not need a primer because it does not need
to be as accurate (104 mistakes)
Makes segments that are later stitched together
Must begin and end the chain it is transcribing
Polymerases can back up on a chain if the incorrect nucleotide is attached and the activate site does a
reverse reaction with a water molecule instead of a pyrophosphate releasing a nucleoside
monophosphate.
Trasriptio is 5’ to ’
Type of RNA
Function
mRNA
Messenger RNAs, code for proteins
rRNA
Ribosomal RNAs,form the basic structure of the ribosome and catalyze protein synthesis
tRNA
Transfer RNAs central to protein synthesis s adaptors between mRNA and amino acids
snRNA
Small nuclear RNAs, function in a variety of nuclear processes, including the splicing of
pre-mRNA
snoRNA
Small nuclear RNAs, help to process and chemically modify rRNAs
miRNA
MicroRNAs, regulate gene expression by blocking translation of specific mRNAs and
cause their degradation
siRNA
Small interfering RNAs, turn off gene expression by directing the degradation of
selective mRNAs and the establishment of compact chromatin structures
piRNA
Piwi-interacting RNAs, bind to piwi proteins and protect the germ line from
transposable elements
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lncRNA
Long noncoding RNAs, many of which serve as scaffolds; they regulate diverse cell
processes, including x-chromosome inactivation
External signals can cause a cell to change the expression of its genes and every specialized cell type will
respond differently.
Gene expression can be controlled at all stages
1) When and how often a gene is transcribed (transcriptional control) MOST COMMON, prevents
cell from using resources for no reason
2) Splicing and processing of RNA transcripts (RNA processing control)
3) Choosing which mRNAs get exported and to where in the cytosol (RNA transport and localization
control
4) Which mRNA is translated by ribosome (translation control)
5) Destabilizing certain mRNA (mRNA degradation control)
6) Selective activation, inactivation, degrading, or localizing specific protein molecules after they
are made (protein activity control
Transcription regulators recognize cis-regulatory sequences and make up 10% of protein coding genes
The position, identity, and arrangement of cis-reg proteins determine when and where the gene is
transcribed
Bacteria gene regulates based on food source
In ecoli, 5 genes code enzymes that make tryptophan repressor, all 5 genes are in 1 line on the
chromosome, all are transcribed together by 1 promoter to create one long mRNA molecule
THIS IS AN OPERON- a cluster/line of genes, common in bacteria but rare in eukaryotes where genes are
usually transcribed individually
Trp conc. low operon transcribed enzymes that together make tryptophan from simpler molecules
Trp conc. high (like in a mammalian gut after a protein meal) trpcellshuts off production of enzymes
The trp operon has a promoter with a cis- regulatory sequence that is bound to by tryptophan repressor
blocking RNA polymerase from transcribing the sequence that encodes for the trp enzymes. The
repressor can bind to DNA only if it has bound with multiple molecules of tryptophan (meaning there is
a lot in the cell)
Trp repressor is allosteric trp binds at a point on the repressor that is NOT the active site and causes a
conformational change allowing it to bind to the operator and repress the gene
Trp repressor is always being transcribed at low levels so that when changes in trp conc. happen the
bacterium can respond quickly
In conclusion:
High trp conc. trp binds to repressor repressor changes shape binds to operon so RNA
polymerase cannot trp is no longer transcribed
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Low trp conc. trp falls off repressor repressor falls off operon RNA polymerase binds 5
enzymes transcribed enzymes make tryptophan
DNA bound activator proteins increase the rate of transcription initiation as much as 100 fold. Weak
noncovalent bonds help RNA polymerase bind to DNA but the activator protein must be bound to the cis
regulatory sequence next to the promoter.
Activators also have to bind to additional molecules to work.
Eg. CAP (activator protein) must bind to cAMP to be able to bind to DNA. This also means that
genes activated by CAP are transcribed in response to an increase intracellular conc. of cAMP. cAMP
conc. increases in a lack of glucose activating CAP to bind to DNA and drive the production of enzymes
that will digest sugars other than glucose.
The lac operon encode the proteins that allow for bacterium to import and digest lactose. It is activated
by CAP and inhibited by lac repressor. Lac repressor is bound until lactose is available if lactose is
available and glucose is not then the cAMP activates CAP which activates the lac operon RNA
polymerase.
Control of transcription regulators in eukaryotic cells
1. The protein is synthesized when needed and degrades immediately after
2. Its activated by ligand binding
3. Activation by covalent modification
4. Forming a complex by binding a DNA-binding subunit to a protein with a transcription-activating
subunit
5. Unmasking: phosphorylating an inhibitor (removing it) of the activation domain
6. The activation subunit enters the nucleus when the inhibitor cannot
7. Release from lipid-bilayer by proteolysis (protein degradation)
Cell memory- the patterns of gene expression responsible for maintaining cell identity through
subsequent generations
1. Parent cell + transient signal = gene A is transcribed
2. Gene A transcribes for transcription regulator A
3. Cell divides and TR A is in progeny cells (cell memory)
4. TR A promotes transcription of gene A = more TR A
5. TR A promotes transcription of cell specific genes (differentiation)
This is a positive feedback loop
Organisms use a combination of many network motifs (e.g. negative feedback loop, flip-flop device) to
cause cell differentiation
Post transcriptional controls
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BIO230H1 Full Course Notes
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Document Summary

All cells use dna for their hereditary code: all cells transcribe using rna, rna chains are flexible and can bend back on itself to connect segments giving each rna sequence a different shape. Needs primer to begin transcription because it needs to be more accurate (107 mistakes) Makes segments that are later stitched together must begin and end the chain it is transcribing. Polymerases can back up on a chain if the incorrect nucleotide is attached and the activate site does a reverse reaction with a water molecule instead of a pyrophosphate releasing a nucleoside monophosphate. Does not need a primer because it does not need to be as accurate (104 mistakes) Messenger rnas, code for proteins rrna trna snrna snorna mirna sirna pirna. Ribosomal rnas,form the basic structure of the ribosome and catalyze protein synthesis. Transfer rnas central to protein synthesis s adaptors between mrna and amino acids.

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