Exam 2(post ME 2) Flashcards
Results of transcription, what happens after?
mRNA, rRNA and tRNA. These types of RNA then undergo translation
T.H. Morgan
Showed that genes are located on chromosomes and that chromosomes have 2 components-DNA and protein.
Frederick Griffith
Proved the “transforming principle” of genetic material. He did this in an experiment with 2 types of a virus. S cells killed mice and R cells did not. He found that mice lived when injected with heat-killed S cells but died when injected with a mixture of heat killed S-cells and living R cells. The R cells added carbs, protein and DNA to the heat-killed S-cells
Alfred Hershey and Martha Chase
Showed that DNA is the genetic material of a phage in an experiment in which the protein and then the DNA of the phage were radioactively labeled. The phages were allowed to infect a bacterial cells then a centrifugation was performed and the phage protein was found in the liquid whereas the DNA was found in the solid pellet(bacteria)
Rosalind Franklin
x-ray crystallographic images of DNA enabled Watson to deduce that DNA was helical. She concluded that there were two outer sugar-phosphate backbones with nitrogenous bases paired in the molecule’s interior
Watson and Crick
built models of a double helix to conform to the x-rays and chemistry of DNA, enabled by Rosalind Franklin. Watson built a model in which the backbones were antiparallel
Chargaff’s rules
- The base composition of DNA varies between species
2. In any species that number of A and T bases are equal and the number of G and C bases are equal
of H bonds in A/T and G/C
A and T: 2 H bonds
G and C: 3 H bonds
bases present in DNA and RNA
DNA: A, T, G, C
RNA: A, U, G, C
In what direction does DNA grow
from the 5’ and 3’
DNA structure
double helix with H bonds, complementary strands, antiparallel, more stable than RNA
Models for DNA replication modes
- Conservative model: two strands reassociate after acting as templates for new strands, thus restoring the parental double helix.
- Semiconservative model: two strands of parental molecules separate and each functions as a template for synthesis of a new, complementary strands
- Dispersive model: Each strand of both daughter molecules contains a mixtures of old and newly synthesized DNA
Experiment to determine mode of DNA replication
Bacteria were cultured in medium with heavy N isotope then transferred to medium with a lighter isotope. The sample was centrifuged twice(once after each replication) and the more dense centrifugations went closer to the bottom of the solution. This proved the semiconservative model correct. This rejected both replications of the conservative model and the second replication of the dispersive model.
What DNA replication looks like in bacteria
Happens in a single, circular, chromosome with a single origin of replication
What DNA replication looks like in eukaryotes
Multiple, linear chromosomes, much longer than bacterial chromosomes, multiple origins of replications, occurs in both directions
Helicase
unwinds parental double helix at replication forks
Single-strand binding protein
Binds to and stabilizes single-stranded DNA until it is used as a template
Topoisomerase
Relieves overwinding strain ahead of replication fork by breaking, swiveling, and rejoining DNA strands
Primase
Synthesizes RNA primer at 5’ end of leading strand and at 5’ end of each okazaki fragment of lagging strand, using parental DNA as a template
DNA polymerase I
Removes RNA nucleotides of primer from 5’ end and replaces them with DNA nucleotides adde to the 3’ end of adjacent fragment
DNA polymerase III
Using parental DNA as a template, it synthesizes new DNA strand by adding nucleotides to an RNA primer or pre-existing DNA strand, elongates leading strand continuously in the 5’ to 3’ direction as fork progresses
DNA ligase
Joins okazaki fragments of lagging strand; on leading strand, join 3’ end of DNA that replaces primer to rest of leading strand DNA. Also performs this function in proofreading and repairing DNA
Overall purpose of DNA polymerases
Catalyze the synthesis of new DNA by adding nucleotides to the 3’ end of a preexisting chain. They also repair damaged DNA by filling in missing nucleotides, suing the undamaged strand as a template
direction of DNA elongation
5’ to 3’, leading strand is elongated continuously in the 5’ to 3’ direction as the fork progresses
synthesis of lagging strand
synthesized discontinuously, synthesized as a series of okazaki fragments which are joined together by DNA ligase. Primase makes RNA primer from 5’ to 3’ starting closer to the replication fork and moving away, the DNA pol III makes an okazaki fragment starting at the end of the primer furthest from the fork. Then they both detach and repeat this closer to the replication fork. DNA pol I replaces RNA with DNA, DNA ligase bonds fragments
Ends of leading and lagging strands
leading strand is 5’ to 3’, lagging is 3’ to 5’
trombone model
a recently supported model of DNA replication in which DNA polymerase molecules “reel in” parental DNA and extrude newly made daughter DNA
nuclease
enzyme that cuts damaged DNA strand at 2 point, removing the damaged section
Eukaryotic chromosome structure components from smallest to largest
- DNA: double helix, 2nm in diameter
- nucleosome: 10nm in diameter, histones wrapped in DNA with histone tails sticking out
- Fiber: 30 nm in diameter, many nucleosomes
- Looped domain: 300 nm in diameter, has scaffolding pattern, fiber
- chromatid: 700nm
- Chromosome: 1400nm, 2 chromatids
General mechanisms of gene regulation
- structural and chemical changes to the genetic material
- binding of proteins to specific DNA elements to regulate transcription
- Mechanisms that modulate translation of mRNA
operons
clusters of genes with one promoter, serving several adjacent genes
operator
site of DNA that switches operon on or off, resulting in coordinate regulation of genes, part of operon
repressible operon
usually on, repressors bind to them to shut off transcription
inactive repressor
repressor with no corepressor present
active repressor
repressor with corepressor bound
tryptophan
a co-repressor that activates the repressor, therefore turning the operon off
inducible operon
usually off, inducers inactivates repressor and turns on transcription
Lactose
when present, allolactose acts as an inducer to inactive the repressor and turn on the operon. It promotes the transcription of the enzymes that use lactose
histone tails
protrude outward from a nucleosome, providing amino acids that are available for chemical modification
Acetylation/unacetylated histone tails
acetylation of histone tails promotes loose chromatin structure that permits transcription. Unacetylated histone tails are compact and DNA is not accessible for transcription
Purpose of alternative splicing
allows for an increase in the size of the proteome while maintaining the size of the genome, conserves energy by not increasing genome size
miRNA
microRNA, binds to target mRNA. If the bases are complementary, the mRNA is degraded, if the match isn’t complete, translation is blocked
What do all viruses have?
Genome and a capsid protein coat
Viral genome
may consist of either double stranded or single stranded DNA or RNA
What do all viruses NOT have?
cell membranes, ribosomes, cell walls, organelles
Viral envelope
extra layer of protection found in SOME viruses
How do viruses affect host gene expression?
They make the host cell, replicate viral genome, transcribe viral genes and translate viral proteins
HIV
Virus that causes AIDS. It is a retrovirus that uses reverse transcriptase and infects helper T cells
CRISPR-Cas system
- Infection by phage triggers transcription of the CRISPR region of the bacterial DNA, where phage has inserted its DNA.
- RNA transcript is processed into short RNA strands
- Each short RNA strands binds to a Cas protein, forming a complex
- Complementary RNA binds to DNA. Cas protein cuts the phage DNA
- Phage DNA can no longer replicate
How do scientist take advantage of viral element that control gene expression?
They give “guide RNA” to a Cas9 protein to target a gene, making a Cas9-guide RNA complex. It will then cut the target part of the gene. The target gene can then be isolated so its function can be studied, or if it has a mutation it can be repaired
siRNA
stands for small interfering RNA
Methlyation
methylation of DNA increases its density and decreases expression of methylated genes
promoter
sequences of DNA(a control element) that are part of the operon where RNA polymerase first binds to start transcription
where do transcription and translation occur?
Transcription: nucleus
Translation: cytoplasm
Enhancers
Region of DNA(a control element) that can be bound by activators to increase the likelihood that transcription of a particular gene will occur, transcription factors can also bind to enhancers
transcription factor
proteins that turn specific genes on or off by binding to nearby DNA.
Activators
transcription factors that boost a gene’s transcription
control element
region of DNA that allows the regulation of gene expression by binding of transcription factors
Mendel definition of a gene
discrete unit of inheritance that affects phenotypic character
Morgan definition of inheritance
specific loci on chromosomes
One gene-one enzyme hypothesis
Hypothesis by beadle and Tatum, included that not all proteins are enzymes
One gene-one protein hypothesis
Many proteins are constructed from two or more different polypeptide chains, and each polypeptide is specified by its own gene
One gene-one polypeptide hypothesis
still not entirely accurate, a eukaryotic gene can code for a set of polypeptides via a process called alternative splicing
General definition of transcription
Synthesis of RNA using information in DNA, produces mRNA
General definition of translation
synthesis of a polypeptide using the information in mRNA
Role of RNA in transcription and translation
bridge between genes and proteins for which they code
Role of ribosomes in transcription and translation
sites of translating nucleic acid to amino acid
DOGMA sequence including transcription and translation
DNA➡️transcription➡️RNA➡️translation➡️protein
Difference between transcription/translation in prokaryotes vs eukaryotes
In prokaryotes, there is no barrier between the two processes and translation can begin in prokaryotes before transcription is finished, eukaryotic RNA transcripts are modified through RNA processing to yield finished mRNA, in termination of transcription: RNA passes polyadenylation signal sequence and the transcript is released 10-35 nucleotides past this sequence
What separates transcription and translation in eukaryotes?
Nuclear envelope
Differences between transcription and DNA replication
RNA polymerase does not need a primer, uracil is used instead of thymine, DNA is split where one strand is the template strand and one strand is ignored, then strands are rejoined once transcript is made and DNA is left as it originally was before
Initiation in transcription
RNA pol and transcription factors bind to promoter, DNA strands unwind, polymerase initiates RNA synthesis at the start point on the template strand
Elongation in transcription
RNA pol moves downstream, unwinding the DNA and elongating the RNA 5’ to 3’(adding to 3’ end), Once RNA pol passes, DNA strands reform double helix and RNA transcription peels away from template strand
Termination in transcription
RNA transcript is released and polymerase detaches from DNA
Eukaryotic promoters in transcription
Include a TATA box about 25 nucleotides upstream from the transcription site
Role of transcription factors in transcription initiation
One recognizes the TATA box and binds to the DNA so RNA pol II can bind in the correct position/orientation, then additional transcription factors form a transcription initiation complex with RNA pol II
RNA processing
Occurs in eukaryotes in nucleus
- A 5’ cap with a modified guanine nucleotide and 3 phosphates is added to 5’ end
- 50-250 adenine nucleotides are added to the 3’ end, forming a poly-A-tail
- RNA splicing: removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence
These modifications facilitate the export of mRNA to the cytoplasm, protect mRNA from hydrolytic enzymes and help ribosomes attach the 5’ end
Spliceosome
Large complex made of proteins and small RNAs used in RNA splicing
Triplet code
The genetic code of different combinations of 3 nucleotides forming 64 different combos that code for polypeptides.
AUG
start codon
Stop codons
UAA, UAG, UGA
What are ribosomal units(for translation) made of?
Proteins and rRNA
tRNA
Each tRNA molecule enables a translation of a given mRNA codon into a certain amino acid, carries a specific amino acid on one end and an anticodon on the other end
Difference between prokaryotic and eukaryotic ribosomes in translation
Prokaryotic: 50S and 30S subunit(70S) total
Eukaryotic: 60S and 40S subunit(80S) total
Components of ribosome during translation
Large subunit, small subunit, exit tunnel through large subunit for polypeptide, mRNA entering and exiting in small subunit, tRNA molecules in the middle for mRNA to pass through
binding sites in tRNA
P site: holds tRNA that carries the growing polypeptide chain
A site: holds tRNA that carries the next amino acid to be added to the chain
E site: Exit site, discharged tRNAs leave the ribosome
In what order is mRNA read in the ribosome?
5’ to 3’
Amino end
first amino acid to be made, at the end of polypeptide chain, opposite of carboxyl end, doesn’t change
What is required in all 3 steps of translation?
protein factors that aid in the translation process
Initiation in translation
small ribosomal unit binds to mRNA, initiator tRNA binds at the start codon(AUG) , large ribosomal subunit arrives and uses GTP to bind to small ribosomal unit
Met
an amino acid called methionine produced by the start codon, AUG
Elongation in translation
Codon recognition occurs, anticodon of an incoming tRNA base-pairs with complementary mRNA codon in the A site, peptide bonds are formed
anticodons
located on tRNA, bind to codons of mRNA
Carboxyl end
end of polypeptide that has been most recently added to the chain in translation, opposite of amino end
How are new amino acids attached to the growing polypeptide chain in translation?
an rRNA molecule from the large ribosomal subunit catalyzes the formation of a peptide bond between the new amino acid from site A and the growing peptide in the P site
What form of energy is used in translation?
GTP
translocation
Ribosome translates tRNA to their next sites using GTP, while the empty site is simultaneously replaced with the next tRNA. mRNA moves along with it’s in bounds tRNA
Termination in translation
Ribosome reaches stop codon on mRNA, A site accepts a release factor, polypeptide is freed and ribosomal subunits and other components dissociate(uses 2 GTP)
Release factor
A protein shaped like tRNA, promotes hydrolysis of the bond between tRNA in the P site and the last amino acid of the polypeptide
Polyribosomes
aka polysomes, this is the result when multiple ribosomes can translate a single mRNA simultaneously, enables cells to make multiple copies of a polypeptide very quickly. This can occur on another level when the same strand of DNA is transcribed multiple times and each strand of resulting mRNA has polysomes
Site of polypeptide synthesis
Synthesis always starts in cytosol, it finishes in cytosol unless the polypeptide signals the ribosome to attach to the ER. It is attached to the ER by an SRP and a signal-cleaving enzyme cuts of the signal polypeptide
Bond between ribosomes and amino acids
covalent
Glycocalyx
A pink coating/layer of molecules external to the cell wall that serves as a protective, adhesive, and receptor functions. It can fit tightly or be loose
Bacterial chromosome/nucleoid
Composed of condensed DNA
Plasmid
double-stranded DNA circle containing extra genes
Pilus
long, hollow appendage used in transfers of DNA to other cells
Flagellum
Specialized appendage attached to the cell by a basal body that holds a long, rotating filament. The movement pushes the cell forward and provides motility
Outer membrane
extra membrane similar to cell membrane, except it also contains lipopoly saccharide. It controls flow of materials and portions of it are toxic to mammals when released
Gram positive vs gram negative
Positive: has a thick cell wall, purple
Negative: pink, thin or no cell wall, more difficult to kill because they have 2 cell membranes
What grams stains are and are not useful for
Useful in providing info on cell wall and can reveal which antibiotics are useful against a certain type of bacteria. Not useful in classifying bacteria or identifying their ancestry
What determines cell shape?
the way peptidoglycan is layered around a cell
Which part of a bacteria is more selective?
the cell membrane
What makes gram negative cells pink after a stain is performed?
Crystal violet is easily rinsed away, revealing red safranin dye.
Why is the cell wall a good target for antibiotics?
Humans don’t have cell walls and bacteria do, so there will be less side effects. Targeting organelles present in human cells will cause side effects.
Lipopolysaccharides
aka LPS, they are embedded in the outer membrane of gram negative cells. Human immune systems are sensitive to LPS and it’s recognized as a foreign substance. This causes gram negative infections to tend to be more harmful
What is the result of bacterial cell division
In theory, two identical daughter cells
What allows bacteria to grow rapidly?
They have no nuclear membrane, making division faster and more energetically efficient
Which cells have circular chromosomes?
bacteria
Where can the origins of replication be found in bacterial cell division and why?
Anchored on the cell membrane, this happens because there is no mitotic spindle to pull anything apart, the elongation of the cell acts as the pulling force
Parts of a growth curve for bacterial population
- lag phase: cells adjust to new environment
- logarithmic phase: aka exponential phase, population grows very rapidly, cells double at maximum rate
- Stationary phase: growth plateaus, more cells can’t be supported, population stops increasing due to lack of resources, space or buildup of toxins. Some bacteria population maintain this stage for a very long time, competition has increased
- Death phase: not experienced by all cells
Events that occur at stationary phase
- Production of spores/endspores
- biofilm production
- toxin production
Production of endospores
endospores receives half of bacterial DNA while the rest of the DNA builds the coat, they have very little water, process of complicated
Main type of endospore
anthrax
Quorum sensing
Genes are regulated by an autoinducer and production of proteins in density-dependent. This is what allows stationary phase events to occur
Quorum
minimum number of individuals needed to make decision in bacterial population
Autoinducers
signaling molecules produced in response to cell population density, allows interspecies communication, new drug targets
Types of autoinducers
Autoinducer 1: tends to be species specific
Autoinducer 2: conserved among many bacterial species
How do prokaryotic cells target eukaryotic cells?
A large number of prokaryotes group up to target a eukaryotic cell to make up for the size difference
Vibrio fischeri
autoinducer, bioluminescent, lives in light organ of Hawaiin bobtail squid, doesn’t glow when free living, gene expression for glow increases in concentrated numbers
What can bacteria produce in large numbers and how are these produced?
Biofilm components, enzymes and toxins produced from changes in gene expression
Metabolic processes found in both eukaryotes and prokaryotes
- Oxygenic photosynthesis
- Calvin cycle
- Aerobic respiration
- Citric acid/TCA/Krebs cycle
- glycolysis
- Lactic acid fermentation
- Alcohol fermentation
Which metabolic processes take place in the cytoplasm of prokaryotes?
- Glycolysis
- Krebs cycle
- Calvin cycle
- Fermentation
Which metabolic processes take place in the plasma membrane of prokaryotes?
- ATP synthesis
- chemiosmosis
- light reactions
Most abundant metabolic membrane
thylakoid membranes
Where do proteins that will be secreted from he cell or function inside cellular compartments go?
from the cytosol to the ER lumen
What is a common theme among metabolic processes found in ONLY prokaryotes?
many them are associated with prokaryotes that do not or can not use oxygen, a lot of them came from ancient earth where there was no oxygen
Lithotrophy+example
Metabolic process only found in prokaryotes, inorganic molecules are used to generate energy and build cells, example includes ammonia oxidizers, which use ammonia as a source of electrons for production of ATP
How do eukaryotes and prokaryotes get nitrogen
Some bacteria and archea can fix nitrogen themselves, every other organism gets N from these organisms
Why must nitrogen be fixed in order to be made available to most organisms
It is unavailable in its atmospheric form to most organisms
Sequence of N fixation
N2➡️ammonium➡️nitrite➡️nitrate
Process of nitrogen fixation
- Plant releases signal in soil that bacteria respond to
- Specific species of bacteria respond
- Plant root hair curls around bacterial cells and bacteria enter plant cells via an infection thread
- Plant creates anaerobic environment for N fixation
Lephemoglobin
A protein produced by a plant that binds to oxygen to make an anaerobic environment needed for N fixing bacteria
Methanogenesis
Production of methane as a waste product, only in archea, found in anaerobic environments, critical to carbon cycle, made by obligate anaerobes
Biogas system
Organic material is inserted into a digestion tank, producing biogas(heats homes) and co-products(nutrients, compost, livestock bedding)
Where is H+ released to when H20 is split in photosystem II
the thylakoid space
Primary electron acceptor
first electron acceptor in the ETC after P680/P700 gets excited
In the chemiosmosis gradient in photosynthesis, where are electrons pumped to and from?
ETC pumps H+ into the thylakoid space, they H+ drives ATP synthesis as they diffuse back into the stroma
Where is there high and low H+ concentrations in photosynthesis?
High in thylakoid space low in stroma
what occurs in bundle sheath cell
CO2 and pyruvate are released by PEP, 1ATP is used ti fix pyruvate in PEP, CO2 undergoes carbon fixation
What type of molecule is NAD+?
a coenzyme
How is energy released in photosynthesis/cellular respiration, or what actually carries the energy?
passing electrons to another substance releases energy, electrons hold the energy
Number of carbons in pyruvate
3
Where is the cellular respiration ETC?
The inner membrane(cristae) of mitochondria
Where do organisms get electrons for cellular respiration?
Organic molecules(food) and O2
Where is H+ pumped to and from in cellular respiration? Where are there high and low H+ concentrations?
Pumped from matrix to intermembrane space, then they go through ATO synthase back into the matrix.
High H+: Intermembrane space
Low H+: matrix
What occurs in substrate-level phosphorylation?
Phosphate is directly transferred from an organic molecule to ATP
What is a main characteristic of fermentation other than ATP production?
recycling of NAD+ into NADPH
Purines and pyrimidines
Purines: adenine, guanine, wider
Pyrimidines: Thymine, Uracil, cytosine, narrower
Which nucleotides pair with which?
A and T(DNA) and U(RNA)
G and C
Which DNA strand is the template in transcription?
3’ to 5’
tRNA
molecule with anticodons on one end, has H bonds and an amino attachment site on the 3’ end
Which part of elongation in translation requires GTP?
Translocation/movement of tRNA
What can possibly occur after translation?
protein processing
Cell type-specific transcription
Certain activators for certain genes are available in certain cells
What regulations occurs at initiation of transcription?
Promotors/transcription factors, enhancers/activators
