Unit 6 - Gene Expression and Regulation Flashcards
function of nucleic acids
- hereditary information
- store and transmit genetic expression
structure of nucleic acids
- double stranded
- alpha helix
nucleotide composition
- nitrogenous base
- phosphate
- pentase sugar
how do nucleotide monomers join together to form a polymer
- complementary bases are bonded with hydrogen bonds
purines
A-G
- double rings
pyramidines
C-T
- single rings
how many hydrogen bonds between A-T
2 hydrogen bonds
how many hydrogen bonds between C-G
3 hydrogen bonds
what is meant by “DNA is antiparallel”
DNA runs in opposite directions
how are bases added to a DNA strand
- bases are added 5’ -> 3’
building of nucleic acids: arrival with 3 P groups
- nucleotides arrive with 3 phosphate groups
- that nucleotide is energy
building of nucleic acids: DNA polymerase III
- use the energy from breakin the 3-phosphate to bond nucleotides together
- energy coupling
energy coupling
- exergonic gives energy for endergonic reaction
when does DNA replicate
s-phase in mitosis
why does DNA replicate
- growth
- repair
- reproduction
topoisomerase
- loosens DNA, unwinds DNA
helicase
- breaks hydrogen bonds between bases
- “unzips DNA”
replication fork
dna helicase unzips here
DNA polymerase III
- adds complementary bases on the new daughter strand
**cannot start strand
primase / rna primase
- starts the DNA replication process
- adds rna primer
templet strand
- original strand
leading strand
- continuous replication at DNA
- replicated in the direction of the replication fork
lagging strand
- opposite the direction of the replication fork
- replicated in fragments
- okazaki fragments
- DNA ligase binds these fragments together
- forms phosphodiester bonds
DNA polymerase I
- removes rna primers
- adds the correct nucleotides in place of primers (only in lagging strand)
what about the first RNA primers on the leading strand?
- they are removed and not replaced with nucleotides
telomeres
- repeating sequences of DNA (TTAAGGG)
- they get shorter everytime DNA replicates
- as they get smaller, eventually it will enter apoptosis
dna polymerase??
- add nucleotides
- proof read/check
- remove primers
- add bases
shape of prokaryotic DNA
circular DNA
semi-conservative replication
- the original parent strand is always going to be in at least one offspring
where does RNA processing occur?
in the nucleus
does RNA processing occur in prokaryotes and eukaryotes?
no, only eukaryotes
- prokaryotes do not have a nucleus
3 events in RNA processing
- modified guanine cap is added
- introns are removed and exons are spliced together
- poly a tail is added
RNA Processing: guanine cap
- 3 phosphates added to it
- function: attaches to the ribosome (for protection)
RNA Processing: introns and extrons
- introns are removed and exons are spliced together
introns
- noncoding regions of mRNA
- “in the way”
- these are removed using an SnRNP
exons
- coding regions for amino acids
SnRNP
- small nuclear RNA and proteins
- cut out introns
spliceosomes
- groups of SnRNPs
- splice = cut out introns and attach exons
RNA Processing: poly A tail
- poly A tail is added
- 50 to 250 adenine bases are added to the 3’ end of mRNA
- used for protection
alternate RNA splicing
- we can use different combinations of exons to produce different proteins
mRNA
instructions to make proteins
ribosomes
- reads mRNA 3 bases at a time (codon)
how many RNA bases call for an amino acid
3 RNA bases call for 1 amino acid
steps for translation
- initiation
- elongation
- termination
anti codon
initiation
- mRNA binds to ribosome (small ribosomal subunit)
- ribosome calls for an amino acid
- tRNA will bring amino acid, and bind with mRNA codon
elongation
-polypeptide is made, peptide bonds formed through dehydration synthesis
primary structure of a protein
polypeptide chain
termination
- a stop codon is reached
- polypeptide is released
** mutations
how many nitrogenous bases are in a polypeptide made from 219 amino acids
219 * 3 = 657
657 + 3 (stop codon) = 660 total bases
tRNA
transfer RNA that carries amino acids to the ribosome
prokaryotic translation
- no nucleus; DNA gets transcribed and RNA gets translated at the same time
what is the source of heritable information found in cells?
DNA and (sometimes) RNA are the primary sources of heritable information
what are the characteristics of DNA and RNA that allow them both to be used as hereditary materials?
- they store information as nitrogen base sequences
- base pairing occurs with specific pyramidines always pairing with specific purines
what differences exist between the heritable information found in prokaryotes and eukaryotes
- prokaryotes typically have circular chromosomes while eukaryotes have linear chromosomes
how is genetic information stored
- stored as a sequence of bases in DNA and RNA
in what ways are DNA and RNA structurally similar
- both are polymers containing nucleotides
- both are chain like
- both follow base pairing rules
pyramidines: rings
single ring structure
purines: rings
double ring structure
what is the purpose of DNA replication
- to ensure the continuity of hereditary information
- allows transmission of genes from one gen to the next
what does it mean for the replication process to be semiconservative
- results in a DNA molecule containing one og strand and a newly synthesized compliment
how does the directionality of a DNA molecule influence the replication process
what are the specific enzymes involved in replication and what is the function of each?
- helicase
- topoisomerase
- DNA Polymerase
- ligase
structure of DNA molecule in terms of phosphate and hydroxyl
- each DNA strand has a terminal phosphate group on one end and a terminal hydroxyl group (OH) on the other end
what is the phosphate terminus referred to as
5’ end
what is the hydroxyl terminus referred to as
3’ end
in what direction can nucleotides be added
- nucleotides can only be added to a growing strand in a 5’-3’ direction
- this means one strand will continously be made (leading strand)
which strand will always be synthesized continuosly
- leading strand
which strand will always be synthesized discontinuously, in fragments
- lagging strand
helicase
unwinds DNA strand
topoisomerase
- relaxes the supercoil at the replication fork
replication fork
- the location where the two strands are separated
DNA polymerase
- synthesizes new strands
- requires RNA primers to initiate synthesis
- attaches to the 3’ end of the template strand
- builds strands in the 5’-3’ direction
ligase
joins DNA fragments on the lagging strand
what is meant by the flow of genetic information
- genetic information flows from DNA to RNA to protien
what is transcription
- the process in which RNA polymerase uses the noncoding strand of DNA as a template to produce an mRNA molecule
RNA polymerase directionality
- RNA polymerase synthesizes mRNA in the 5’-3’ direction while reading DNA in the 3’-5’ direction
what are the diff types of RNA molecules and what is the function of each
- mRNA
- tRNA
- rRNA
mRNA
- carries genetic information from DNA to the ribosomes
- information is used to direct protein synthesis at the ribosomal site
- codons are found on mRNA
tRNA
- recruited to the ribosomes to help create a specific polypeptide sequence as directed by mRNA
- various tRNA molecules, each carrying a specific amino acid
- anti codon
anti-codon
- a 3-base sequence on tRNA
- correct base pairing of tRNA anti-codons with mRNA codons will result in the release and addition of an amino acid to a growing polypeptide
rRNA
- Ribosomal RNA
- functional units of ribosomes responsible for protein assembly
what are the mRNA transcript modifications that occur in eukaryotic cells
- addition of a poly-A tail
- addition of a GTP cap
- introns and exons
what is alternative splicing?
- when introns are excised from a primary mRNA transcript and exons are retained and joined together
how does alternative splicing result in different proteins
- different combinations of exons can be retained in a mature mRNA transcript
- diff exon combinations encode for different proteins
what does addition of a poly-A tail do
- 100-200 adenine nucleotides
- increases stability
- helps with exporting from nucleus
what does the addition of GTP cap do
- modified guanine nucleotide
- protects the transcript
- helps ribosome attach to mRNA
introns
- sequences of mRNA transcript that DO NOT CODE for amino acids
- these are removed during RNA processing
- not included in mature mRNA transcript
what is translation
- the process of generating polypeptides using the information carried on an mRNA molecule
exons
- sequences of mRNA transcript that code for amino acids
- retained during RNA processing
- different exons are connected in the mature mRNA transcript
what are the main steps of the translation process
initiation, elongation, termination
when does translation occur in prokaryotes
protein synthesis objective
- this is how we get the directions from DNA about how to make proteins and bring them to the ribosomes so that the ribosomes can join amino acids in a specific order to synthesize a protein
what are phenotypes dependent on
they depend on presence or absence of particular proteins
how do we get the directions from our genes into an actual protein
transcription and translation
where does translation / transcription occur in prokaryotes
the cytoplasm at the same time
miRNA
- Micro RNA
- promotion of genes
transcription simply put is just
- copying the code from DNA to RNA
DNA is read in what direction
3’-5’
coding strand
- 5’-3’
- codes for the proteins
template strand
- non coding strand
- minus strand
- antisense strand
- DNA that is used for transcription (3’-5’)
how does RNA polymerase know where to attach to begin transcription?
promoter region - RNA polymerase attaches and begins transcription
how does the RNA polymerase know where the promoter is
TATA box
TATA box
a repeating sequence of TATA nucleotides
how does RNA polymerase know where to stop
termination sequence
transcription factors
- proteins that grab RNA polymerase (this attaches to them) in order to start transcription
transcription initiation complex
- transcription factors, promoter, RNA polymerase - all bind to start transcription
RNA Processing
- results in mature mRNA
- only happens in eukaryotes
RNA Processing: 1
- modified guanine cap is added for protection
RNA Processing: 2
- introns are removed and exons are spliced together
what are mutations that could occur during termination in translation
how is it possible to have over 200 different types of human cells if we all start from one cell
- different genes are turned on and off (expressed)
histones
- proteins that DNA coils around
- 8 Histones coiled up is a nucleosome
what regulates gene expression in eukaryotes
- transcription factors (proteins that help RNA polymerase bind to the promoter)
- DNA coiling
euchromatin
- loosely/unwounded chromatin
- able to do transcription or translation
heterochromatin
- densly packed chromatin
- hidden
- no transcription therefore no translation
how do we modify the histone proteins and DNA
- add acetyl groups to the histone proteins
- relaxes the histone so that DNA is available for transcription
what happens if you remove the acetyl group from histones
- DNA ends up as heterochromatin
what happens during histone acetylation in relation to transcription
- if you acetylate the histone, gene transcription can be turned on
deacetylation in relation to transcription
- gene transcription is turned off
what is DNA methylation
- CH3
- add a methyl to the actual DNA
- brings you from euchromatin to heterochromatin
- **turns off gene transcription
how does DNA polymerase replicate DNA
- DNA polymerase reads the template strand in the 3’-5’ direction and carries complementary base pairs to create a new strand
how does DNA polymerase build the complimentary strand
- DNA polymerase reads the parent strand from 3’-5’ then builds the complementary strand from 5’-3’
role of the DNA polymerase
- DNA polymerase proofreads and corrects errors with the help of nucleases
- incorrect base pairs are removed, and correct ones inserted
DNA Ligase
bonds the nucleotides and the okazaki fragments together
helicase function
unwinds the parental double helix
DNA Replication - leading strand
- the DNA polymerase reads the parent strand from 3’-5’ and synthesizes continuosly in the leading strand in 5’-3’ direction, moving towards the replication fork
telomeres
- ends of eukaryotic DNA molecules
- protects coding genes from being eroded during multiple rounds of DNA replication
DNA replication vs Transcription + Translation
- DNA replication occurs only when the cell is ready to divide
- Translation and Transcription occur constantly to make proteins needed as the cell carries out metabolic activities
where does transcription occur in eukaryotes
transcription of DNA to RNA occurs in the nucleus
where does translation of RNA occur in eukaryotes
the cytoplasm
transcription: promoter
- TATA Box
- the part of the DNA where RNA Polymerase binds to start transcription
- noncoding DNA
transcription: transcription factors
- in eukaryotes
- proteins that bind to the promoter region and ease the binding of RNA polymerase to the promoter
why does the RNA get modified before it exits the nucleus into the cytoplasm?
purpose of 5’ cap and poly-A tail: prevent enzymatic degradation of the mRNA when it moves out of the nucleus into the cytoplasm
purpose of RNA splicing
removes the introns so that only the exons will remain in the mRNA that goes out into the cytoplasm to be translated
length of final mRNA vs. og mRNA
final mRNA is much shorter than the initial RNA transcript due to the removal of introns
function of mRNA
- carries the instruction for making a protein from a gene and delivers it to the site of translation (ribosome)
- this mRNA is a complementary copy of a segment of DNA
ribosomal RNA (rRNA) function
- part of the structure of the ribosome
mutations are caused by…
- a change in the sequence of DNA nucleotides
- error in DNA replication or as a result of environmental factors (mutagens)
phenotypic plasticity
- the ability of one genotype to produce several phenotypes when exposed to different environments
what are the bonds between nucleotides
phosphodiester bonds formed by dehydration synthesis
translation: initiation
- mRNA binds to small ribosomal subunit
- ribosome calles for tRNA to bring amino acid
- tRNA will bring amino acid and bind with mRNA codon
start codon is
AUG
translation: elongation
building a polypeptide by forming peptide bonds through dehydration synthesis
explain why a normal polypeptide may have 100 amino acids whereas a mutated polypeptide may only have 10
there was a stop codon earlier in the sequence so the mutated polypeptide ended up shorter
translation: termination
- a stop codon is reached
- polypeptide is released
tRNA
transfer RNA that carries amino acids to the ribosome
prokaryotic translation
- no nucleus
- DNA gets transcribed and RNA gets translated at the same time
list two factors that are unique to eukaryotic trans.
- they are separated by the nuclear envelope
- RNA processing in Eukaryotes
structure of a virus
- they have a protein coat (capsid)
- sometimes theres an envelope that surrounds capsid
- glycoproteins are used to connect to cells
capsid
- protein coat on viruses
- DNA/RNA (genome) is found inside the capsid
spikes
- found on the virus
- how our body recognizes the virus
explain how a lytic cycle works? (7 steps)
- virus attaches to the cell
- virus enters the cell
- capsid breaks open and the DNA (genome) is exposed
- virus transcribes mRNA using the cells RNA polymerase
- virus uses cells organelles to make proteins
- viral proteins will aggregate (come tg) and make new viruses
- viruses lyse the cell and leave
retroviruses
- copy RNA into host DNA
- enzyme: reverse transcriptase
- RNA -> DNA -> mRNA
- host’s RNA polymerase now transcribes viral DNA into viral mRNA
- mRNA codes for viral components
- hosts ribosomes produce new viral proteins
how is it possible to have over 200 different types of human cells if we all start from one cell (a zygote)
- different genes are turned on and off (expressed)
- not all genes are active in every cell
transcription factors
- proteins that help RNA polymerase bind to the promoter
- regulate gene expression
histones
- the proteins that DNA coils around
nucleosome
- 8 histones coiled up
euchromatin
- loose/unwound chromatin
- able to do transcription/translation
heterochromatin
- densely packed chromatin
- hidden
- no transcription therefore no translation
how can we modify the histone proteins and DNA
- add acetyle groups to the histone proteins
- this relaxes the histone -> DNA is available for transcription
- if you remove acetyl group, you end up with heterochromatin
how are histone acetylation/deacetylation related to transcription?
- if you acetylate the histone, gene transcription can be turned on
- deacytelation: gene transcription is turned off
DNA Methylation
- methyl groups: CH3
- add a methyl group to the actual DNA
- brings you from euchromatin -> heterochromatin
- this turns off gene transcription
epigenetics
- how chemicals/behaviors can affect gene expression without altering the genetic code
ex: cigarettes
specific gene regulation expression occurs in what
eukaryotes
promoter
- where gene transcription begins
- where RNA polymerase binds
proximal control elements
- any control element near the gene
activators
enhancer regions
distal control elements/enhancers
- control elements that are far away from the gene
ex: enhancer - amplifies transcription
enhancers
- amplifies transcription
- it is a sequence of DNA
activators binding to enhancers
- these activators (proteins) are specific to the cells they are in
alternative RNA splicing
non-coding RNA’s
- miRNA’s: mini RNA’s that block gene translation at the ribosome
- these are RNA (not proteins!!)
- blocks protein synthesis
how does miRNA affect gene expression
- micro RNA base pairs with mRNA
- ribosome cannot translate it
prokaryotic DNA characteristics
- circular shape
- they have plasmids
how do prokaryotes regulate gene expression?
they use operons
regulatory gene
- LAC I
- TRPR
- these produce repressors
will the bacteria express the tryp operon when tryp levels are low or high?
- Low
what happens when there is too much tryptophan
repressed - turned off
what do you notice about the repressor protein in the LAC operon?
- it is the correct shape to bind to the operator, no need for a corepressor
in the absense of lactose, the lac operon is…
inactive (off)
LAC Operon: inducer
allolactose - binds to the repressor
- changes shape
- repressor is removed from operator
repressible operon
- TRP
- when you have high levels of TRP, operon will turn off
- no gene expression
inducible operon
- LAC
- high levels of lactose, operon will turn on
mutations: are they all bad?
no, they provide genetic variety
point mutations
- mutations in one single base (DNA)
- often substitution
ex: sickle cell anemia
silent mutations
- same amino acid regardless of base change
missense mutation
- new amino acid
- problematic
nonsense mutation
- causes a shorter protien
- problematic
frameshift mutations
- change the reading frame of the mRNA codon via a deletion/addition of a base
- largest effect on a protein
what about frame shift mutations in introns?
- will likely have no effect on the protein because they are cutout anyway BUT…
- could have an effect if the mutation pushes in the exon
how are mutations inherited
if the mutations occur in the gametes DNA; not if they’re in the somatic cells
bacteriophage
- the virus that infects bacteria
lytic cycle
- virus injects the DNA into host cell (bacteria)
- uses cells organelles to make more of itself
- virus will lyse the cell and infect more cells
lysogenic cells
- virus injects DNA into bacteria (host cell)
- virus DNA incorporates itself into the host genome “prophase”
- as bacteria replicates the viral genome gets replicated; when there is a trigger, the virus enters lytic stage
genetic variation in prokaryotes mechanisms
- transformation, transduction, conjugation, transposons
transformation
- altering the DNA of a bacteria through the uptake of foreign bacterial DNA
transduction
- bacteriophage could uptake bacterial DNA and then pass it to its host (bacteria)
conjugation
- “bacterial sex”
- an F+ cell contains a plasmid, F- cell doesn’t
- F+ cell uses a pilus to insert plasmid into F- cell
transposons
- aka Jumping Genes
- transposons can insert themselves anywhere in the DNA
- causes mutations (+/-)
recombinant DNA
- DNA that comes from 2 or more different sources
restriction enzyme
- this will cut the DNA at specific sites
ex: ECOR1
plasmid
- circular DNA in bacteria; double stranded
what is gene expression
the process by which instructions in the DNA are transcribed and translated into a functional protein
what types of interactions regulate gene expression?
interactions between regualtory proteins and regulatory sequences, due to the presence of certain transcription factors, or due to modifications of DNA or histones
what is epigenetics
they are reversible modifications of DNA or histones which help regulate gene expression
how is the phenotype of a cell or organism influenced by differential gene expression?
the phenotype of a cell or organism is determined by the combination of genes that are expressed
what are promoter sequences
they are sequences upstream of the transcription start site where RNA polymerase and transcription factors bind to initiate transcription
what is the connection between the regulation of gene expression and phenotypic differences in cells and organisms
the interaction of promoters and other transcription factors helps determine phenotypic differences between tissues within an organism or between individual organisms
what roles do small RNA molecules have in regulating gene expression
they can regulate gene expression post transcription by either blocking transcription or by breaking down mRNA
how do errors during mitosis or meiosis result in changes in the phenotype of a cell or organism?
errors in mitosis can change the number of chromosomes in an organism, which can result in increased vigor in plants, sterility, or disorders in humans
how are changes in genotype subject to natural selection?
genetic changes that enhance survival and reproduction can be selected for based on specific environmental conditions
what are horizontal aquisitions of genetic information
horizontal acquisitions of genetic information include the transfer of DNA segments between cells, viruses and cells, or movement of DNA sequences with and between DNA segments
what reproduction processes increase genetic variation
- sexual reproduction
- independent assortment of chromosomes
- crossing over
all the cells in the same organism have
THE SAME DNA SEQUENCES
tissues are groups of cells that have
the same funciton
- the presence of specific proteins within the cells of tissues give the tissue its function
cell differentiation refers to
cells within the same organism having different phenotypes
operons
are closely linked genes that produce a single mRNA molecule during transcription
- they are under the control of the same regulatory sequence
promoters
DNA sequences upstream of the transcription start site where RNA polymerase and transcription factors bind to initiate transcription
whether a mutation is detrimental, beneficial, or neutral depends on
the environmental context
what is the primary source of genetic variation
mutations
horizontal aquisition entails
- transformation, transduction, conjugation, and transposons
gel electrophoresis separates molecules based on
size and charge
DNA molecules are what charge
negative
DNA moves towards what end in gel electrophoresis
positive end
PCR (polymerase chain reaction)
- DNA fragments are amplified
watson and crick’s model of DNA
- double helix
- antiparallel
- backbone of phosphates and sugars are covalently bonded
why are there so few mistakes when DNA replicates?
- proof reading of the DNA by DNA polymerase
- error corrections by repair enzymes
**only one strand of DNA is transcribed??????
promoter
- noncoding stretch of DNA where RNA polymerase binds to initiate trancription
purpose of 5’ cap and poly A tail addition:
prevents enzymatic degradation of the mRNA when it moves out of the nucleus into the cytoplasm
mutations are in actuality
a change in the sequence of DNA nucleotides
frameshift mutations
- shifts the reading frame of the gene so that the protein mat not be able to perform its function
what does “a gene is expressed” actually mean
the gene is trasncribed into RNA and the translated into a protein specific for that gene
regulatory gene
- produces a repressor protein that binds to the operator and prevents gene expression by blocking RNA polymerase
structural genes
code for enzymes for a particular pathway
do prokaryotic cells have histones?
no
pre transcriptional regulation of gene expression at the level of DNA
- Modifying the DNA packaging to either impede or aid RNA polymerase to begin transcription
- DNA methylation
- Histone Acetylation
regulation at the level of transcription
- transcripiton factors: enhancers and inhibitors
- silencing
enhancers
- facilitate binding of RNA polymerase to promoter
inhibitors
- inhibit binding of RNA polymerase to promoter
regulation at the level of translation
block translation by modifying the activty of the ribosome via phosphorylation
most significant cause of genetic variation in bacteria
mutations because bacteria replicate so frequently
restriction enzymes
- produced by bacteria to chop up viral DNA to protect themselves from infection
if all cells have the same DNA, how do we have different cells?
by expressing different parts of the DNA via RNA splicing or activators
function of LAC Operon
to break down lactose
location of a promoter region is ALWAYS
upstream of the gene
what happens if there is no promoter?
RNA Polymerase will not bind and gene transcription will not occur
CDK’s
they regulate the cell cycle
how do cyclin dpeendent kinases regulate the cel cycle
P53
tumor suppressor gene that stops the cell cycle
how does P53 stop the cell cycle
how does diversity exist in prokaryotes?
transformation, transduction, conjugation
in gel electrophoresis, the end of the chart in terms of size holds
the smallest fragments
what does the size or thickness of the bands in gel electrophoresis indicate
- not size but rather the number of fragments
PCR (polymerase chain reaction)
- uses TAQ Polymerase to amplify DNA
why does PCR use TAQ polymerase
because it won’t be denatured at high temperatures
AMP
ampiclin (antibiotic)
when does DNA replication occur
s-phase of interphase
simply explain enzymes involved in DNA Replication
helicase - unzips DNA
topoisomerase - relieves tension ahead of the fork
primase - lays down an RNA primer
DNA Polymerase 3 - adds nucleotides in the 5’ -> 3’ direction
dna polymerase 1 - replaces RNA primers with DNA
ligase - seals gaps in the lagging strand
coding strand is AKA
- non-template strand
- plus strand
- has the same sequence as mRNA but does not serve as template for RNA synthesis
template strand is AKA
- antisense strand
- noncoding strand
- minus strand
- used by RNA Polymerase to synthesize complimentary mRNA in the 5’ -> 3’ direction
