Unit 6: Gene Expression & Regulation Flashcards
nucleotide structure
nitrogenous base, five-carbon sugar, phosphate group
nitrogenous bases in DNA
adenine, guanine, cytosine, thymine
nitrogenous bases in RNA
adenine, guanine, cytosine, uracil
purines
adenine and guanine; consist of a two-ringed structure
pyrimidines
cytosine, thymine, and uracil; have a one-ringed structure
base pairing rules
adenine + thymine/uracil; guanine + cytosine
five-carbon sugars in DNA & RNA
DNA: deoxyribose with hydrogen atom attached to 2’ carbon, RNA: ribose with hydroxyl group attached to 2’ carbon; this difference makes DNA more stable than RNA
DNA structure
- double helix with two antiparallel strands;
- one strand is oriented with the 5’ phosphate group at the start of the strand, while the opposite strand has the 3’ hydroxyl group at the start of the strand
- a purine on one of the strands is always paired with a pyrimidine on the opposite strand, which keeps the width of the double helix consistent
RNA structure
typically single-stranded, but can fold to form 3D structures in rRNA’s in the ribosome and in tRNAs
purpose of DNA replication
to ensure the continuity of genetic information between generations
semiconservative replication
- each of the original two strands in the double helix serves as a template for a new strand
- each new double helix is composed of one strand from the original piece of DNA and one newly synthesized strand
helicase
- starts DNA replication by unwinding the two DNA strands in an area called the origin of replication (ori)
- as part of the double helix is unwound, other sections of the double helix become more tightly wound (supercoiling)
topoisomerase
make temporary nicks in the sugar-phosphate backbone of the DNA to relieve supercoiling from helicase unwinding, then reseal the nicks
RNA polymerase
synthesizes an RNA primer using complementary RNA nucleotides, which is where new DNA nucleotides can begin being added
DNA polymerase
adds new nucleotides the 3’ hydroxyl group at the end of the RNA primer in the 5’ to 3’ direction, always connecting the 5’ phosphate on the new nucleotide to the 3’ hydroxyl on the growing nucleotide strand
directionality
- two strands of the DNA double helix are antiparallel
- because DNA polymerase can only add new nucleotides in the 5’ to 3’ direction, and because the two strands of DNA are antiparallel, DNA must proceed slightly differently on the two strands
leading strand replication
on one strand, DNA polymerase reads the original strand in the 3’ to 5’ direction and can add new nucleotides continuously in the 5’ to 3’ direction
lagging strand replication
- the other strand of the double helix is oriented in the 5’ to 3’ direction, so DNA polymerase must proceed in the 3’ to 5’ direction to read the strand
- replication occurs discontinuously, producing short fragments called lagging strand (Okazaki) fragments
ligase
joins together Okazaki fragments produced by lagging strand replication
transcription
process in which genetic information in a sequence of DNA nucleotides is copied into newly synthesized RNA molecules
mRNA (messenger RNA)
- single-stranded
- carries information from DNA to the ribosome
- contains codons, which are complementary to the DNA base pair sequence
codons
three base pair sequences that specify specific amino acids during translation
tRNA (transfer RNA)
- folds into a 3D structure that acts as an adapter molecule during translation
- one end of the tRNA binds to a specific amino acid, while the other end contains an anticodon that pairs up with the appropriate mRNA codon at the ribosome during translation
rRNA (ribosomal RNA)
folds into a 3D structure; rRNA and proteins form the ribosomes that perform translation; 3D rRNA acts as a ribozyme to catalyze reactions needed in translation
promoter
noncoding DNA sequence that the RNA polymerase must bind to to start transcription
transcription factors
proteins that help RNA polymerase bind to the promoter sequence and begin transcription
during transcription
RNA polymerase adds new RNA nucleotides in the 5’ to 3’ direction
template strand
strand of DNA being transcribed by RNA polymerase, which the newly synthesized RNA must be antiparallel to
mRNA transcript
in prokaryotic cells, mRNA transcript is immediately ready for translation because they have no nucleus; in eukaryotic cells, the initial mRNA transcript (pre-mRNA) must be modified before it can leave the nucleus and be translated
mRNA modifications in eukaryotes
1) alternative splicing
2) addition of 5’ GTP cap
3) addition of 3’ poly-A tail
introns
noncoding RNA sequences found in eukaryotic pre-mRNAs that are interspersed between exons (coding sequences)
alternative splicing
when introns are removed from between exons by spliceosomes, the exons can be joined in different combinations to generate multiple RNA transcripts from the same gene, creating more variety
addition of 5’ GTP cap
- protects 5’ end of the pre-mRNA transcript from degradation before it can be translate
- recognized by nuclear pores so that mRNAs with the cap can exit the nucleus
- helps initiation of translation when RNA reaches ribosome
addition of 3’ poly-A tail
- added to 3’ end of pre-mRNA transcript by the poly-A polymerase
- prevents degradation of transcript
- mRNAs with longer poly-A tails have longer durations in the cytosol, which allows more copies of the protein to be generated
mature mRNA
mRNA after excision of introns and splicing of exons & additions of 5’ GTP cap and 3’ poly-A tail; ready for translation by the ribosome
translation
- three steps: initiation, elongation, and termination
- occurs at ribosomes; in eukaryotes, cytoplasmic ribosomes translate proteins for the inside of the cell, rough ER ribosomes translate proteins that will leave the cell
- prokaryotes: translation by multiple ribosomes can occur as transcription occurs because there is no nucleus
initiation
- when rRNA in ribosome pairs with the start codon (AUG)
- tRNA with the complementary anticodon bring the appropriate amino acid to the ribosome, and the anticodon on the tRNA pairs with the codon on the mRNA
elongation
- ribosome translocates to the next codon after the first amino acid is placed by the tRNA
- new tRNA with the appropriate anticodon and amino acid pairs with this codon, then the ribosome catalyzes the formation of a peptide bond between the amino acids brought to the ribosome by the first two tRNA’s forming the beginning of the polypeptide chain
- once the peptide bond is formed between the amino acids, the first tRNA releases its amino acid, and the first tRNa is released
- this process repeats until the stop codon is reached
termination
- stop codons do not code for any amino acid
- when the ribosome reaches a stop codon, proteins called release factors bind to the ribosome, causing it to disassemble and release the polypeptide chain
flow of information in eukaryotes
1) genetic info in DNA is transcribed into mRNA in the nucleus
2) ribosomes on the rough ER use the info in mRNA to translate proteins
3) after the protein is translated, a vesicle containing the protein will travel to the Golgi
4) at the Golgi, the protein will be modified and packaged into vesicles for export from the cell
5) these vesicles bud off from the Golgi and travel to the cell membrane, fusing with the cell membrane and releasing their contents from the cell
retrovirus
virus that contains RNA as its primary carrier of genetic information
reverse transcriptase
retroviruses contain this enzyme, which makes a DNA copy of the RNA genome of the virus, inserting it into the genome of the infected host cell; the host cell then transcribes and translates the information in the viral DNA; less accurate than RNA polymerase
gene regulation
an organism’s phenotype is determined by the levels at which genes are expressed; gene regulation is important in determining an organism’s phenotype; regulation is through the interaction of regulatory proteins with regulatory sequences in the genome
regulatory proteins
proteins that can turn on or turn off genes by binding to specific nucleotide sequences
regulatory sequences
the sequences to which regulatory proteins bind
operon
cluster of genes with a common function under the control of a common promoter; contain regulatory sequences, genes for regulatory proteins, and genes for structural proteins
promoters
noncoding regulatory sequences that serve as binding sites for RNA polymerase
operators
noncoding regulatory sequences that serve as binding sites for repressor proteins (type of regulatory protein)
structural genes
coding sequences that contain the genetic code for the proteins required to perform the function of the operon
inducible operons
- catabolic function (digesting molecules) in prokaryotes
- are turned off unless the appropriate inducer molecule is present
- repressor protein binds to operator sequence, blocking transcription of operon by RNA polymerase
inducer
when present, it binds to the repressor protein, changing the shape so that it can’t bind to the operator sequence, which allows RNA polymerase to begin transcribing the operon
corepressor
sometimes, repressor protein must bind to corepressor before binding to operator
repressible operons
- anabolic function (synthesizing molecules) in prokaryotes
- turned on unless the product of the operon is in abundance in the cell
regulatory switches
sequences to which activator proteins or repressor proteins may bind in eukaryotes
silencers
regulatory switches to which repressor proteins bind in eukaryotes
enhancers
regulatory switches to which activator proteins or transcription factors bind in eukaryoties
repressors
bind to regulatory switches to turn off/suppress gene expression
activators
bind to regulatory switches and upregulate gene expression
mediators
connectors between other regulatory proteins, allowing them to communicate
epigenetic changes
reversible modifications to the nucleotides of the DNA sequence, like methylation
methylation
adding a methyl group to lessen gene transcription
acetylation
addition of acetyl groups to histone proteins, which makes DNA wound more loosely and more accessible to RNA polymerase, increasing gene trasncription
euchromatin
DNA more loosely wound around histone proteins, more accessible to RNA polymerase, and usually results in more expression of the genes within it
heterochromatin
DNA tightly wound around histone proteins, which is less accessible to RNA polymerase and therefore less expressed
siRNA (small interfering RNA) molecules
single-stranded, binds to complementary mRNA molecules, forming dsRNA that is detected and destroyed by enzymes to prevent translation
differential gene expression
regulation of gene expression that results in different genes being expressed in different cells; influences the functions of cells and phenotype of the organism
mutations
- changes in genetic material of an organism
- may result in changes to the organism’s phenotype if the mutation interferes with/changes the function of a protein
- provide genetic variation in populations
- can be caused by environmental factors
- can be caused by mistakes in meiosis or mitosis, like failure of homologous chromosomes to separate causing aneuploidy
horizontal transmission of genetic information
genetic mutations can be transmitted horizontally between members of the same generation; types include transformation, transduction, conjugation, transposition
transformation
uptake of naked foreign DNA by a cell
transduction
transmission of DNA from one organism to another by viruses; as the DNA is transferred by the virus, the sequence may be recombined or changed, causing mutations
conjugation
transmission of DNA through cell-to-cell contact, usually through a pilus
transposition
movement of DNA between chromosomes or within a chromosome; sometimes referred to as jumping genes
bacterial transformation
- introduces foreign DNA (circular plasmid DNA) into bacterial cells
- DNA integrates into the host cell’s chromosome or remains separate from the host cell DNA in the cell’s cytoplasm
- heat shock used to create pores for foreign DNA to pass through
recombinant DNA
DNA that has been recombined from different source organisms
gel electrophoresis
- separates DNA fragments by size and charge
- fragments created by treating a DNA sample with restriction enzymes
- short fragments are found at the bottom of the gel, whereas longer fragments are found at the top
polymerase chain reaction
- used to amplify specific DNA fragments and create their copies
- involves cycles of DNA replication using primers specific to the beginning and end of the fragment to be amplified
1) denaturing the DNA (separating strands)
2) annealing of the primers (primers form bonds with beginning and end of fragment)
3) extension of the primers (new nucleotides added to primers)
CRISPR-Cas9
- adaptive immune system in bacteria
- edits DNA sequences using guide RNA so that the cell can repair its damaged DNA
