Biology 2 - Unit 2 - VOCAB

Mutations

• Mutagen- things that cause errors in DNA; UV radiation, chemicals, viruses, reaction oxygen species (ROS)

• Transition mutation- a nucleotide mutation that turns a purine into another purine or a pyrimidine into another pyrimidine

• Transversion- a nucleotide mutation that turns a purine into a pyrimidine or the other way around

• Double mutation- 2 mutations occurring near each other

• Reversion mutation- a mutation that reverts a mutation to being unmutated, undoes a mutation

• Chromosomal inversion- a piece of a chromosome flips

• Chromosomal translocation- a piece of a chromosome joins a different chromosome

• Chromosomal deletion- a piece of a chromosome is deleted

• Chromosomal insertion- an extra piece of a chromosome is inserted

• De Novo mutation- a mutation that is not previously in a genome

• Multiple sequence alignment (MSA)- a way to look at protein sequences by looking at residues or amino acids, comparing different species, a way to look at evolution

• Silent mutation- a mutation with no phenotypic effect

• Loss of function mutation- a mutation that causes a protein to lose its function

• Gain of function mutation- a mutation that causes something new to happen, a new function, or overproduction

• Hot spots- locations with many mutations

DNA Replication Mutation and Repair

• All errors in DNA are mutations

• about 1 in every 100,000 bases are incorrectly added by DNA polymerase

• DNA polymerase has an exonuclease ability to remove incorrect nucleotides

  • considered exonuclease because it repairs at it builds

• DNA acts as its own repair manual

• 1 in 10,000 incorrectly added bases aren’t fixed

• Mismatch repair enzymes (MMR)- goes back through replicated DNA to find and fix mistakes

• MMR has an endonuclease function

• Mismatch pairs create bumps in DNA that are seen by repair enzymes

• DNA polymerase fills holes made by the MMR

• Ligase seals the gaps made from base removal and repair

• Excision repair- repair completed by endonucleases to fix damage from mutagens, also involves DNA polymerase and ligase

• DNA repair steps:

  • MMR or endonucleases remove incorrect or damaged bases

  • DNA polymerase fills in holes in DNA

  • Ligase seals gaps in the DNA

Translation

• Transcription and translation are specially separated by organelles

• RNA is single-stranded

• Pre-mRNA matures before leaving the nucleus

• Translation begins in the cytoplasm

• Proteins go through post-translational modification before they are complete and ready for function

• Translation has 3 main steps initiation, elongation, and termination

• The ribosome is the location of all modifications in translation

• Amino acids- protein building blocks, 20 of them, 21 in eukaryotic organisms

• Transcriptome- all the mRNA in a cell or organism at a certain time

• Proteogenic- the amino acids that are directly coded from the codon table

Initiation

• RNA polymerase is recruited to a particular gene to transcribe a specific gene or dsDNA

• Promoter- in every organism, specific dsDNA sequences, non mRNA coding, that indicate the beginning of genes

• Transcription factors- proteins that bind to both RNA polymerase and DNA to help the RNA polymerase bind

Elongation

• RNA polymerase has a helicase function in translation

• RNA polymerase unwinds the double helix in translation

• Synthesis always occurs 5’ to 3’

• The transcript- the newly made mRNA

• DNA template- the DNA strand that is read and built from, read 3’ to 5’

• Coding/ complementary strand- the strand that is the same as mRNA with Ts instead of Us

• DNA takes no energy to rewind

• 5’ and 3’ UTR- the untranslated region, the DNA between the transcription start site and the start codon

Termination

• Termination site- where translation stops

• Termination complex- a location on mRNA that ends translation

• Release factors- bind to the stop codon and remove everything from the mRNA

Genetic code

• Genetic code- the informational key by which a sequence of nucleotides corresponding to a gene is translated into the sequence of amino acids composing the protein expressed by that gene

• Codon- a group of 3 nucleotides which specify a particular amino acid

• Genetic code is redundant meaning more codons than there are amino acids

• Genetic code is universal and identical across multiple species

mRNA End Modification

• 3 primary end modifications include pre-mRNA capping, splicing, and pre-mRNA tailing

• The GTP cap can be added after the mRNA exits the RNA polymerase

• Splicing can begin as the 1st exon moves through the RNA polymerase

• Pre-mRNA tailing can be added after the last exon leaves the RNA polymerase

• GTP cap- a protective sequence that is added 5’ to 5’ to the mRNA

• The GTP cap protects mature mRNA from being degenerated by nucleases

• Ribosomes locate and bind to the GTP cap

• Proteins that assist or disable translation bind to the GTP cap

• LARP- a protein that binds to the GTP cap assisting or disabling translation

• Poly-adenyline (A) tail- a sequence of AAUAAA added to the end of a eukaryotic mRNA, contributes to the protection and stability of mRNA

• The poly-adenyline tail is added to the 3’ end of eukaryotic mRNA

• Poly-adenyline binding proteins- bind to the poly-A tail which can stimulate translation

Co-transcriptional RNA Splicing

• Intron- non-coding regions of mRNA

• Exon- the coding part of mRNA, end up spliced together

• Mature mRNA has UTRs, a start codon, exons, and a stop codon

• Not mature mRNA has a promoter, introns, and a terminator

• Splice sites- boundaries between introns and exons where introns are removed and exons are spliced together

• Endonucleases cut introns out of mRNA

• RNA splicing- the removal of introns from pre-mRNA resulting in much smaller mature mRNA

• Splicing uses a looping process

• Alternative splicing- the mix and matching of exons during splicing, can create multiple different mRNAs

• Isoforms- different proteins made from 1 gene, made by alternative splicing

• snRNPs- proteins that form loops in introns and splice exons

• snRNPs are small ribonucleic proteins

• snRNPs have RNA complementary to the splice site

• Riboenzymes- RNA with catalytic ability

Ribosomes

• Ribosomes are comprised of a small and a large subunit

• Ribosomes are mostly RNA

• Initiation complex- where the small ribosomal subunit binds, the large subunit binds opposite completing the complex

• A ribosome has 3 sites that are E, P, and A

• The large subunit has catalytic RNA

• The mRNA enters the ribosome A site

• The mRNA leaves the ribosome E site

• Polysome- multiple ribosomes bound to one mRNA

Shine Delgarno Sequence

• Shine Delgarno sequence- a ribosomal binding site in prokaryotes, helps the ribosome stabilize on the mRNA

• The Shine Delgarno sequence is located upstream of the start codon

Gene Expression and Regulation

• Every Eukaryotic cell has every gene

• Genome- all of the DNA in a cell or organism

• Proteome- all the proteins in a cell or organism at a certain time

• Gene expression- which cells turn on transcription and how much

• Gene regulation- the process of determining the amount and timing of RNA production and transcription

• Regulation- a dynamic process of modulating production, modification, and targeting of RNA and proteins

• Transcriptional regulation- the dynamic start and stop of transcription

• Protein regulation- modification of post-translational modifications, like protein folding

• Leaky expression- low level or rare expression of a not-needed gene

• Housekeeping genes- genes that are usually on, have high-affinity promoters, do not need activators

• Specialized genes- genes that are not always on, low-affinity promoters, usually need activators

Chromatin

• Chromatin- used to wind up genes that are not needed

• Chromatin winds genes around histones

• Nucleosomes- repeating subunits of chromatin in a nucleus, the fundamental unit of the human genome that helps package it into the nucleus of a cell

• Heterochromatin- tightly packed nucleosomes, cannot be transcribed

• Euchromatin- loosely packed nucleosomes, can easily be transcribed

• The presence of methyl or acetyl on a histone drives if a histone winds up or not

Gene Repression V. Activation

• Repressors- bind to segments of dsDNA near promoters to reduce transcription, negative regulation

• Repressors and activators vary transcription by changing access to the promoter

• Repressors bind to a site on or near the promoter

• Activators- bind to segments of dsDNA near promoters increasing transcription, positive regulation

Operons

• Operons are only located in prokaryotes

• Operons- functionally related genes, a group of genes turned on or off at once

• An operon has one promoter for the entire operon

• Corepreseed/ coactivated- all genes activated or repressed together

• The repressor comes from a regulatory gene adjacent to the lac gene

• Beta galactoside- the enzyme that breaks down lactose

• LCT gene- the eukaryotic gene to digest lactose

• Regulatory site- where regulatory proteins bind

• Intergenic region- the region between genes in an operon

• In normal lac conformation, the repressor is bound to the lac operator

• Conformation- the shape of the repressor enzyme

• Sigma factors- prokaryotic proteins that bind to RNA polymerase and direct it to different classes of promoters

• Allolactase- binds to the repressor limiting its ability to bind to the dsDNA, and comes from splitting lactose

• Leaky expression is needed for lactose to be split into allolactose which acts as a repressor inhibitor

• RNA polymerase can bind to the lac promoter when no repressor is bound to the operator

• CRP- the lac operon activator

• cAMP- binds to CRP allowing it to bind to the dsDNA

• When an activator is bound to the lac operon operator the RNA polymerase becomes very efficient

tRNA Sequence and Structure

• tRNA anticodon- allows amino acids to bind

• tRNA runs 5’ to 3’

• Initiator tRNA- used to start bacteria translation

• Each amino acid has its own specific tRNA

• tRNA has a tertiary structure

Post Translational Modification

• Methylation- the addition of a methyl group

• Demethylation- the removal of methyl group

• Cleavage- the cutting of a protein

• Cleavage often removes the starting methionine

• Proteolysis- the cutting up of a protein to add or change its function, many times reveals an active site

• Proteases- the proteins responsible for cutting proteins

• Kinases- add and remove phosphate groups from proteins

• Phosphorylation- the addition of a phosphate group, the most common modification

• Glycosylation- the addition of sugars to a protein

• Acetylation- the addition of an acetyl group to a protein

• Ubiquitination- the binding of ubiquitin to proteins, flags damaged proteins

• Proteasome- cuts up a polypeptide that has ubiquitin splicing