unit 6 part 2 (6.3-6.7) Flashcards
RNA transcription
process that copies a DNA template sequence into a new RNA sequence with RNA polymerase
RNA polymerase
enzyme that pries the DNA strands apart and synthesizes a new complementary RNA strand (mRNA)
Initiation (transcription)
promoter region has sequences where transcription factors bind, the TF proteins allow polymerase to attach
Elongation (transcription)
RNA Polymerase opens up transcription bubble and allows new RNA nucleotides to form hydrogen bonds with the DNA template. RNA polymerase adds bases to 3’ end of growing mRNA transcript///// one or many RNA polymerase can contribute in a convoy onto growing stand
Termination (transcription)
mRNA separates from the transcription complex after reaching terminator region
hairpin
tertiary structure formed by nucleotides that help separate DNA and RNA
mRNA
stores nucleotide sequence that is translated into protein sequences, carries info outside of the nucleus to ribosomes
tRNA
translates nucleic acid sequence into sequence of amino acids which are readily available in cytoplasm. anticodon base pairs with complimentary codons in mRNA which signals what amino acid is needed
rRNA
forms quartenary structure with other proteins to create functional ribosome, P site holds tRNA carrying the growing polypeptide chain, A site holds the tRNA holding the next amino acid to be added, E site is where the tRNAs leave
introns
noncoding sequences within genes
splicing
removal of introns from RNA sequence, remaining exons are reassembled to make mature mRNA
GTP
modified guanine cap on 5’ end of mature mRNA, stabilizes molecule and blocks any random chemical reactions from taking place in cytosol
Poly-A Tail
chain of adenine nucleotides that stablizes 3’ side and protects mRNA and helps ribosomes attach
poly a tail adding mechanism
proteins recognize specific sequences within mRNA and recruit poly-a polymerase to complete polyadenilation
alternative splicing
extra variation created in mature mRNA depending on which codons are considered introns
splicisome
structure made of five small RNA molecules and their proteins joined to a complex, binds to each INTRON and removes it, binds the remaining exons
translation
mRNA is read and generated into polypeptides (mRNA –> amino acids)
prokaryotic ribosomes
only has cytosolic ribosomes
eukaryotic ribosomes
has cytosolic ribosomes and ones bound to the endoplasmic reticulum
translation in prokaryotes occur…
while mRNA is being transcribed
initiation (translation)
rRNA interacts with the mRNA at the start codon (AUG) at A Site
elongation (translation)
amino acids are being added to growing polypeptide at P Sit, tRNA binds to exposed codon and new amino acid attaches to growing polypeptide
termination
where process stops (stop codon is read), newly synthesized polypeptide is released, rRNA subunites disassemble
retrovirus translation
when a viral RNA invades host cell, the reverse transcriptase copies viral RNA into viral DNA which is integrated into host cell’s genome and then transcribed and translation, resulting in new viruses
common ancestory and translation
translation is similar in all organisms, the same nucleotides are used and chemical compatibility
codons
nucleotide triplets that code for specific amino acids 5’ to 3’
mRNA editing is only in
EUKARYOTES
wobble
changing the 3rd base does not always change the amino acid
promoter
attachment and initiation point for RNA polymerase, marks the beginning of a gene
transcription unit
stretch of DNA that is transcribed into an RNA molecule
transcription factors
proteins that mediate binding of RNA polymerase and the initiation of transcription
transcription initiation complex
complex of transcription factors and RNA Polymerase bound to promoter
termination (transcription) in prokaryotes
in bacteria transcription proceeds through DNA terminator and it is transcribed as the terminator signal causing polymerase to dettach
termination (transcription) in eukaryotes
RNA polymerase transcribes a sequence on DNA for poludenylation and the proteins (transcription factors) cut free from polymerase
regulation of gene expression
process by which instructions in the DNA are selectively transcribed and translation into functional proteins, accounts for phenotypic differences between organisms
regulatory sequences
stretches of DNA that can be used to promote or inhibit protein synthesis based on code
regulatory proteins
used to assist the promotion or inhibition of protein synthesis, the interactions of regulatory sequences with regulatory proteins controls transcription and determines products
epigenetic changes
reversible changes in DNA or histones depending on the environmental factors
histones
proteins used to wrap DNA around, if the packing is tight or loose it can regulate the gene expression
tissues
groups of cells that have the same function, presence of specific proteins within the tissue’s cells give the tissue it’s function, phenotype depends on gene expression
cell differentiation
refers to cells within the same organism having different phenotypes (functions)
transcription factors
proteins that promote or inhibit the transcription of a gene, presence determines how cells differentiate
reg proteins vs transcription factors
RP: assist promotion/inhibition by interacting with reg. sequence
TF: presence promotes or inhibits transcription
phenotype depends on…
combination of genes expressed
metabolic control of bacteria on two levels
1) short term- cells adjust activity of enzymes that are already present through feedback inhibition
2) long term- cells adjust production level of certain enzymes by regulating gene expression at transcription level
coordinately controlled
PRO ONLY. because all similar functioning genes are clustered together, one “on and off switch” (operator) can control them all
operator
PRO ONLY. segment of DNA that is the “on and off switch), positioned within the promoter region or between the promoter and enzyme coding gene, controls access of RNA Polymerase.
operon
PRO ONLY includes operator and promoter and the genes they control, and entire stretch of DNA required for the enzyme production
represser
PRO ONLY turns off the operon, a protein that binds to the operator and blocks the attachment of RNA polymerase (specific to the operator), usually removed when gene is needed
regulatory protein PROKARYOTES
produces the repressers, has it’s own promoter and is expressed continuously
trp represser
allosteric protein
corepresser
PRO ONLY. small molecule that binds to and activates a represser protein to switch an operon off, reduces the rate of transcription
repressible operon
PRO ONLY. transcription is USUALLY ON but it can be INHIBITED by a small molecule (corepresser) that binds allosterically to a regulatory protein
inducable operon
PRO ONLY. transcription is USUALLY OFF bit it can be stimulated with a small molecule (inducer) interacts with a regulatory protein (EX: LAC OPERON)
inducer
PRO ONLY binds to and inactivates the represser to turn on transcription (ex: allolactase)
inducible enzyme
PRO ONLY function in catabolic pathways, synthesis is induced by a chemical signal when enzyme is needed to breakdown stuff
repressible enzyme
PRO ONLY function in anabolic pathways, suspends production of an end product when there’s enough in quantity already
activator
transcription factors that binds to DNA and stimulates transcription of a gene, the on and off for VOLUME
chromatin structure in EUK
tightly coiled is less likely to be transcribed, the location of the promoter relative to the nucleosome can affect whether or not it’s transcribed
histone acetylation
promotes transcription by opening chromatin structure, which allows enzymes to get in and turn genes on
DNA methylation
condenses DNA, making it impossible for enzymes to enter, turns genes off and can be inherited
control elements
segments of noncoding DNA having a particular nucleotide sequence that serves as the binding site for transcription factors
general transcription factors
are essential for transcription of all protein-coding genes (primarily bind proteins), low initiation rate
specific transcription factors
high level of transcription of particular genes at appropriate time and place, depend on the interactions of control elements and specific transcription factors
enhancers
distal control elements (genes have many)
proximal control elements
closer to promoter
2 common structural elements of activators
1) DNA binding domain
2) one or more activation domains (binds to ref proteins or components of transcription machinery facilitating interactions)
negative regulatory molecules
INHIBIT gene expression and influences gene products/function
RNAi
interference RNA, natural protection of cells against viruses that destroys suspicious recipes
mutation
changes in the genome of an organism, whether it is beneficial, detrimental, or neutral depends on environmental context, primary source of genetic variation
neutral mutation
change encodes the intended protein
positive mutation
change encodes a new protein that benefits the cell/organism
negative mutation
change encodes a new protein that harms the cell/organism
triploidy
having 3 copies of a particular chromosome, extra chromosome in trisomy 21
polyploidy
having multiple sets of homologous chromosomes
horizontal transfer
exchange of genetic info between two different genomes or unrelated organisms
transformation
IN PRO, uptake of naked DNA (not protected by proteins or other molecules, comes from the external environment)
transduction
transmission of foreign DNA into a cell, when a viral genome integrates with host genome
conjugation
IN PRO, cell to cell transfer, external cell extension connects cells and allows transfer
transposition
movement of DNA segments within or between DNA molecules (inversion, translocation, deletion, duplication)
reproductive processes that increase variation
sexual reproduction and combination of random gametes, independent assortment of homologous pairs, crossing over during meiosis
substitution mutations
replacement of one nucleotide and its partner with another pair of nucleotides (usually missense)
silent mutation
changes that have no observable effect on phenotype
missense mutation
change in one amino acid to another, might have little effect on protein becuase many have similar properties
nonsense mutation
a nucleotide changes a codon into a STOP, translation is ended prematurely and leads to nonfunctional protein
insertions and deletions
additions or losses of nucleotide pairs in a gene, usually have disastorous effects
frameshift mutation
when a number of nucleotides inserted/deleted is not a multiple of 3, nucleotides become improperly grouped into codons
mutagens
physical or chemical agents that cause mutations
