Unit 2 Flashcards
What is a genome?
complete set of genetic information
What is a gene?
functional unit
What is DNA replicaiton?
duplication of chromosome
What is gene expression?
going from DNA to protein
What is transcription?
going from DNA to RNA
What is translation?
going from RNA to protein
Information flows in which direction?
DNA——->RNA———->protein
What is the function of enzymes?
catalyze chemical reactions
What is molecular transport?
move small molecules into/out of cells
What is motility/mobility?
moves the cell
What is the function of sensors?
recognize extracellular conditions (nutrients, other cells, infectious agents, etc.)
What is the function of gene expression?
bind to DNA
What do proteins do for our body?
-produce enzymes
-molecular transport
-motility/mobility
-structure
-sensors
-gene expression
True or False
A:T nucleic acids base pairing have two hydrogen bonds.
True
True or False
G:C nucleic acids base pairing have one hydrogen bonds
False, there are three hydrogen bonds
How do antiparallel strands go?
5-3 and 3- 5
5PO4 attached to the 5th carbon and 3OH attached to 3rd carbon
What is replication?
DNA—–>DNA
What happens during initiation of DNA replication?
-proteins bind to origin of replication
-DNA gyrase and helicases
How do proteins bind to origin of replication?
-bacterial chromosomes/plasmids contain only one binding area
-eukaryotic cells multiple binding sites
What is the function of DNA gyrase and helicases?
-bind to origin of replication
-break and unwind DNA
-Primers (temporary bases are added) are added for replication
What is the function of DNA Polymerase?
-Synthesize DNA in the 5 to 3 direction
-Nucleotides added on the expanding 3` strand of the new DNA
-Can only add to pre-existing nucleotides (purpose of RNA primers)
What is step two of DNA replication?
- Synthesize DNA in the 5
to 3direction
Nucleotides added on the expanding 3` strand of the new DNA
Can only add to pre-existing nucleotides (purpose of RNA primers)
What is step one of DNA replication?
- Synthesize DNA in the 5
to 3direction
Nucleotides added on the expanding 3` strand of the new DNA
Can only add to pre-existing nucleotides (purpose of RNA primers)
What is step three of DNA Replication?
After helicase untwists and separates the strands, DNA polymerase binds to each strand. Scientists have identified several kinds of bacterial DNA polymerase. These vary in their specific functions, but all of them share one important feature—they synthesize DNA by adding nucleotides only to the hydroxyl group at the 3′ end of a nucleic acid. All DNA polymerases replicate DNA by adding nucleotides in only one direction—5′ to 3′—like a jeweler stringing pearls to make a necklace, adding them one at a time, always moving from one end of the string to the other. DNA polymerase III is the usual enzyme of DNA replication in bacteria.
What is step four of DNA replication?
An enzyme called primase synthesizes a short RNA molecule (4–15 nucleotides long) that is complementary to the DNA strand being copied. This RNA primer provides a 3′ hydroxyl group, which is required by DNA polymerase III.
What is step five of DNA replication?
Triphosphate deoxyribonucleotides form hydrogen bonds with their complements in the parental strand. Adenine nucleotides bind to thymine nucleotides, and guanine nucleotides bind to cytosine nucleotides.
What is step six of DNA replication
Triphosphate deoxyribonucleotides form hydrogen bonds with their complements in the parental strand. Adenine nucleotides bind to thymine nucleotides, and guanine nucleotides bind to cytosine nucleotides.
What is step seven of DNA replication?
Triphosphate deoxyribonucleotides form hydrogen bonds with their complements in the parental strand. Adenine nucleotides bind to thymine nucleotides, and guanine nucleotides bind to cytosine nucleotides.
What is step eight of DNA replication?
Primase synthesizes RNA primers, but in contrast to its action on the leading strand, primase synthesizes multiple primers—one every 1000 to 2000 DNA bases of the template strand.
What is step nine of DNA replication?
DNA polymerase III joins neighboring nucleotides and proofreads. In contrast to synthesis of the leading strand, however, the lagging strand is synthesized in discontinuous segments called Okazaki fragments, named for the Japanese scientist Reiji Okazaki (1930–1975), who first identified them. Each Okazaki fragment uses one of the new RNA primers, so each fragment consists of 1000 to 2000 nucleotides.
What is step ten of DNA replication?
Nucleotides pair up with their complements in the template—adenine with thymine, and cytosine with guanine.
What is step eleven of DNA replication?
DNA polymerase I replaces the RNA primers of Okazaki fragments as well as the RNA primer in the leading strand with DNA and proofreads the short DNA segment it has just synthesized.
What is step twelve of DNA replication?
DNA ligase seals the nicks between adjacent Okazaki fragments to form a continuous DNA strand.
What are the enzymes of DNA replication?
DNA gyrase, DNA helicase, RNA primase, DNA polymerase, Okazaki fragments, and DNA ligase.
What is the function of DNA gyrase?
Enzyme that temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix.
Unique to PROKARYOTES
What is the function of DNA helicase?
Unwinds the double helix by breaking hydrogen bonds
What is the function of RNA primase?
Builds an RNA primer on leading and lagging strands
What is the function of DNA polymerase?
Adds daughter nucleotides on the parent strands
What is the function of Okazaki fragments?
Nucleic acid fragment produced during discontinuous synthesis of the lagging strand of DNA.
What is the function of DNA ligase?
Joins Okazaki fragments to form a continuous strand
What is the origin of replication?
Distinct region of a DNA molecule at which replication is initiated.
What is primer?
Fragment of nucleic acid to which DNA polymerase can add nucleotides (the enzyme can add nucleotides only to an existing fragment).
What is replisome?
The complex of enzymes and other proteins that synthesize DNA.
What are characteristics of RNA?
-Ribose instead of deoxyribose
-Uracil in place of thymine
-Usually shorter single strand
-Synthesized from DNA template strand
–RNA molecule is transcript
–Base-pairing rules apply except uracil pairs with adenine
–Transcript quickly separates from DNA
What are the 3 types of RNA?
-messenger RNA (mRNA)
-Ribosomal RNA (rRNA)
-Transfer RNA (tRNA)
What is RNA?
ribonucleic acid
-single stranded
What are the 5 steps of transcription?
- Sigma factor binding
- RNA polymerase splits the DNA
- RNA polymerase adds nucleotides (A, U, G, C)
- RNA polymerase links the nucleotides
- Hydrogen bonds between RNA & DNA are broken
What is transcription?
Process in which the genetic code from DNA is copied as RNA nucleotide sequences
RNA polymerase binds to sequence called a
promotor
What does the promoter do?
-Synthesizes in 5’ to 3’ direction
-Can initiate without primer
Where does transcription stop at?
a sequence called a terminator
RNA sequence is complementary, __________ to DNA template strand.
antiparallel
What strand is the DNA template?
minus strand
What strand is the RNA strand?
plus strand
RNA has the same sequence as (+) DNA strand except
Uracil instead of Thymine
What is genotype?
the actual set of genes in its genome
What is phenotype?
refers to the physical features and functional traits of an organism
What are the steps of transcription initiation, sigma factor?
- Initiation
RNA polymerase binds to the promoter and melts a short stretch of DNA - Elongation
Sigma factor dissociates from RNA polymerase, leaving the core enzyme to complete transcription. RNA is synthesized in the 5’ to 3’ direction as the enzyme adds nucleotides to the 3’ end of the growing chain - Termination
When RNA polymerase encounters a terminator, it falls off the template and releases the newly synthesized RNA
What are the types of prokaryotic mRNA transcripts?
Monocistronic and polycistronic
What is monocistronic?
one gene
What is polycistronic?
multiple genes
What is translation?
process of decoding information in mRNA
What are the major components of translation?
mRNA, ribosomes (contain rRNA), tRNAs, and accessory proteins
What is genetic code?
every three nucleotides make up a codon which is one amino acid
How do ribosomes function in translation?
-Aligns and forms peptide bond between amino acids
-Locate punctuation sequences on mRNA molecule
==Begins at start site, moves along in 5′ to 3′ direction
-Maintain correct reading frame
Prokaryotic comprised of 30S and 50S subunits
==Made up of protein and ribosomal RNA (rRNA)
How does a tRNA get its amino acid?
Aminoacyl tRNA synthetase
ENZYMES
How are the polypeptide chains elongated during translation?
-peptide bind formed between amino acids
-ribosome advances one codon on mRNA
==tRNA exits E-site
==tRNA with growing protein occupies P site
==new tRNA occupies A-site
-the process repeats
What happens during the termination stage of translation?
-elongation continues until ribosome reaches stop codon
==not recognized by tRNA
==Enzymes break covalent bond joining to polypeptide to tRNA
-Ribosome falls off mRNA
==disassociates into component subunits (30s and 50s)
==subunits can be reused to initiate translation at other sites
what is an anticodon?
Sequence of three nucleotides in a tRNA molecule that is complementary to a particular codon in mRNA. The anticodon allows the tRNA to recognize and bind to the appropriate codon.
What is mRNA Polyribosome (polysome) reading frame?
Type of RNA molecule that contains the genetic information decoded during translation.
Multiple ribosomes attached to a single mRNA molecule.
Grouping of a stretch of nucleotides into sequential triplets that code for amino acids; an mRNA molecule has three potential reading frames, but only one is typically used in translation.
What is a ribosome?
Structure that facilitates the joining of amino acids during the process of translation; composed of protein and ribosomal RNA. The prokaryotic ribosome (70S) consists of a 30S and a 50S subunit.
What are ribosome binding sites?
Sequence of nucleotides in mRNA to which a ribosome binds; the first time the codon for methionine (AUG) appears after that site, translation generally begins.
What are rRNA start codons?
Type of RNA molecule present in ribosomes.
Codon at which translation is initiated; it is typically the first AUG after a ribosome-binding site.
What is a stop codon?
Codon that terminates translation, signaling the end of the protein; there are three stop codons.
What is tRNA?
Type of RNA molecule involved in interpreting the genetic code; each tRNA molecule carries a specific amino acid dictated by its anticodon.
What are components of translation in bacteria?
anticodon, mRNA Polyribosome (polysome) reading frame, ribosome, ribosome-binding site, rRNA start codon, stop codon and tRNA
What are the differences between Prokaryotes and Eukaryotes in transcription/translation?
Prokaryotes:
-All in the cytoplasm: No Nucleus!
-Translation begins as transcription is still occurring (simultaneous)
-Start codon codes for formylmethionine (f-Met)
==So do mitochondria & chloroplasts
-Multiple ribosomes (polyribosome) can be translating a strand of mRNA at the same time (quick)
Eukaryotes:
-Complete transcript is sent out of the nucleus where it is translated by ribosomes
-Start Codon is for methionine (Met)
-One ribosome translates a strand of mRNA before translation can begin again
How do Eukaryotes go through gene regulation?
Eukaryotic cells produce pre-mRNA
Capped with methylated guanine (5` end)
Poly A tail, ~200 adenine derivatives added (3` end)
Splicing introns out and exons together
What are the differences between prokaryotic and eukaryotic transcription and translation?
Prokaryotes:
-mRNA is not processed
-mRNA does not contain introns
-translation of mRNA begins as it is being transcribed
-mRNA is often polycistronic; translation usually begins at the first AUG codon that follows a ribosome-binding site
Eukaryotes:
-a cap is added tot he 5’ end of mRNA, and a poly A tail is added to the 3’ end
-mRNA contains introns, which are removed by splicing
-the mRNA transcript is transported out of the nucleus so that it can be translated in the cytoplasm
-mRNA is Monocistronic; translation begins at the first AUG
What is quorum sensing?
-cell/population density (expression at critical mass)
-biofilm formation
-“Sense” the density of cells within their own population
-Allows the expression of certain genes only when a certain mass has been reached
-Bacteria talk, via synthesized molecules
What is transduction?
transmission of information from the outside of a cell to the inside
What is phase variation?
involved switching genes on and off
__________ _________ is alteration of characteristics of surface proteins.
antigenic variation
What are the three main ways genes can be on or off?
Constitutive, inducible, and repressible
What is constitutive?
always on
-enzymes of the central metabolic pathways
What is inducible?
not routinely produced at significant levels
enzymes involved in the breakdown and transport of specific nutrients
What is repressible?
produced routinely, but can be turned off when they are not required
enzymes involved in building macromolecules (anabolic)
What are alternative sigma factors of bacterial gene regulation in transcription?
-sigma factors recognize specific promoters
-cells can produce specialized sigma factors to transcribe genes
-anti-sigma factors can inhibit transcription
What is an operon?
-consists of a promoter and a series of genes
What is an operator?
Controls the operon and is a regulatory element
What are repressors?
-protein that blocks transcription
-binds to the operator downstream of the promoter
What are activators?
-facilitates transcription (positive)
-protein binds to an activator binding site that helps RNA polymerase bind to the promoter
What is the lactose operon?
-includes genes involved in the transport and catabolism of lactose
-there are two events that activate the lac operon
What two events activate the lac operon?
-positive regulation by a protein called CAP
-deactivation of repressor molecule
What happens when both glucose and lactose are present?
-Caron catabolite repression (CCR) prevents expression of genes that metabolize lactose in presence of glucose.
What is the unique feature of gene regulation in eukaryotes?
RNA interference: RNAi
-microRNA (miRNA)
-short interfering RNA (siRNA)
What happens during regulation of genetic expression in eukaryotes?
RNA molecules can control translation
-Regulatory RNAs can regulate translation of polypeptides
==microRNAs bind complementary mRNA and inhibit its translation
==small interfering RNA. RNA molecule complementary to a portion of mRNA, tRNA, or DNA that binds and renders the target inactive
==Riboswitch: RNA molecule that changes shape to help regulate translation
What two mechanisms do bacteria have to adjust to new circumstances?
-regulation of gene expression
-genetic change
What are the two mechanisms of genetic change in bacteria?
-mutation
-horizontal gene transfer
What is mutation?
changes in existing nucleotide sequence
What is horizontal gene transfer?
movement of DNA from one organism to another
Changes are passed to progeny by _____ _______ _______
vertical gene transfer
Change in organism’s DNA alters __________
genotype
True or False
DNA has sequences of nucleotides
True
True or False
Bacteria are haploid
True
Change in genotype often changes observable characteristics or ________ that are influenced by environmental conditions.
phenotype
______________ __________ are genetic changes that result from normal processes
spontaneous mutations
____ ______ most common spontaneous mutation
Base substitution
What happens during base substitution?
-Incorrect nucleotide
-incorporated during
-DNA synthesis
-Point mutation is change of a single base pair
What are the three possible outcomes in base substitution?
-silent (synonymous) mutation
missense mutation
-nonsense mutation
What are silent mutations?
wild-type amino acid
What are missense mutations?
different amino acid
-resulting protein often does not function normally
What is a nonsense mutation?
specifies stop codon
-yields shorter, often non-functional protein
How many hydrogen bonds do A-T have?
2 Hydrogen bonds
How many hydrogen bonds do G-C have?
3 hydrogen bonds
Base substitutions that inactivate a gene is termed a _____ or __________ mutation
null or knockout
What environments are base substitutions more common in?
aerobic environments
What is spontaneous mutations?
Deletion or addition of nucleotides
-3 pairs change one codon
-one or two pairs yields frameshift mutation
What are transposons (jumping genes)?
pieces of DNA that can move from one location to another in a cell’s genome; process of transposition
-most have transcriptional terminators
What is insertional inactivation?
gene into which transposon jumps is inactivated; function disrupted
What are induced mutations?
result from outside influence
-agent that induces change in mutagen
-geneticists may use mutagens to increase mutation rate
-two general types:
==chemical agen
==radiation
How do chemicals that modify nucleobases?
-change base-pairing properties; increase chance of incorrect nucleotide incorporation
-alkylating agents add alkyl groups onto nucleobases
What are base analogs?
resemble nucleobases, but have different hydrogen-bonding properties
–can be incorporated into DNA by DNA polymerase
-wrong nucleotide is incorporated into complementary strand during DNA replication
What are intercalating agents?
Increase frameshift mutations
-flat molecules that insert between adjacent base pairs in DNA strand.
What do intercalating agents do?
-pushes nucleotides apart, produces space
-causes errors during replication
True or False
Radiation can be used as a mutagen
True
UV light cause _______ _______ (covalent bonds between adjacent thymines)
thymine dimers
What is the function of thymine dimers?
-distorts molecule; replication and transcription stall
-mutations result from cell’s SOS repair mechanism
_________ cause single-and-double-strand breaks in DNA
X-rays
True or False
Mutations are rare because alterations in DNA generally repaired before being passed to progeny.
True
During replication, _____ ________ sometimes incorporates wrong nucleotide.
DNA polymerase
What are the two mechanisms of repair that takes place before DNA replication?
Proofreading and mismatch repair
What is mismatch repair?
fixes errors missed by DNA polymerase
What are the steps of mismatch repair?
-enzyme cuts sugar-phosphate backbone of new DNA strand
-another enzyme degrades short region of DNA strand with error
-DNA polymerase, DNA ligase fill in and seal the gap
What happens when modified nucleobases lead to base substitutions?
-Glycosylase removes oxidized nucleobase
-Another enzyme cuts DNA at this site
-DNA polymerase removes short section; synthesizes replacement
-DNA ligase seals gap
What is photoreactivation?
light repair
How is photoreactivation used?
-enzyme uses energy form light
-breaks covalent bonds of thymine dimer
-only found in bacteria
What is excision repair?
dark repair, no light involved
How is excision repair used?
-enzyme removes damage
-DNA polymerase, DNA ligase fill in and seal the gap
What is SOS repair?
last-ditch repair mechanism used when other systems fail
When is SOS repair used?
Induced following extensive DNA damage that stalls DNA and RNA polymerases
What are carcinogens?
cause many cancers; most are mutagens
What is the Ames test?
measures effect of chemical on reversion rate of histidine-requiring Salmonella auxotroph
-uses direct selection on glucose-salts plate
-if chemical is mutagenic, reversion rate increases relative to control (more colonies grew)
What are the 3 recombinant mutations of horizontal gene transfer?
Transformation, transduction, conjugation
What is transformation?
a recipient cell takes up DNA from the environment. Involves uptake of short fragments of naked DNA by naturally transformable bacteria.
What is transduction?
DNA is transferred from one cell to another via a replicating virus. Transfer of DNA from one bacterium into another via bacteriophages. Dead bacterial cells
What is Conjugation?
bacterium containing a fertility plasmid forms a conjugation pilus that attaches and transfers plasmid genes to a recipient in reproduction of ciliates: Coupling of mating cells. Transfer of DNA material via sexual pilus and requires cell to cell contact
What happens during transduction?
Phages infect bacterial cells
-Attaches to cell and injects its nucleic acid
-Phage enzymes cut bacterial DNA into small pieces
-Bacterial cell enzymes produce phage nucleic acid and a phage coat – components of new phage particles
-Phage particles are released from bacterial cell
What is generalized transduction?
results when a fragment of bacterial DNA enters the phage protein coat
-produces a transducing particle
What type of horizontal transfer involved the transfer of DNA via a virus?
Transduction
What are the steps of transduction?
- phage injects its DNA
- phage enzymes degrade host DNA
- Cell synthesizes new phages that incorporate phage DNA and, mistakenly, some host DNA
- Transducing phage injects donor DNA
- Donor DNA is incorporated into recipient’s chromosome by recombination
What are the steps of conjugation?
- donor cell attaches to a recipient cell with its pilus
- pilus draws cells together
- one strand of F plasmid DNA transfers to the recipient
- the recipient synthesizes a complementary strand to become an F+ cell with a pilus; the donor synthesizes a complementary strand restoring its complete plasmid
What are the requirements in order for transformation to begin?
free DNA in the environment and a competent recipient
What are the requirements in order for transduction to begin?
bacteriophage
What are the requirements in order for conjugation to begin?
cell-to-cell contact and F plasmid, which is either in a cytosol or incorporated into chromosome of donor Hfr cell
