Test 3 Chapter 11 Study Guide Flashcards
Central Dogma of Molecular Biology
DNA will be transcribe into RNA which will be translated into proteins. Can only move in one direction.
Genotype
Genes contained within a cell
Phenotype
Physical characteristics.
Semiconservative Replication
Two strands of DNA separate during replication. Each strand serves as a template for the new strand. The new double stranded DNA has one “old” strand and one “new” strand
Origin of replication
where replication begins, only 1 origin in bacteria
Topoisomerase II (DNA gyrase)
Relaxes the super coil
Helicase
Separates the DNA strands. Unzips the genes only a short distance
Replication Fork
one side of the now open DNA strands and the still helixed end –{
Single-Stranded Binding Proteins
Prevent the newly separated DNA strands from hydrogen bonding together again.
Primase
Adds RNA primers
RNA primers function
Allows DNA polymerase III to attach as it can only attach to RNA primers
Initiation
DNA Gyrase relaxes super coil at origin of replication. Helicase separates DNA. Bidirectional Replication. Primase adds RNA primers.
DNA Polymerase III
Adds new nucleotides in 5’ -> 3’ direction
Leading Strand
Complementary to the 3’->5’ parent strand. Extended continuously
Lagging Strand
Complementary to the 5’->3’ parent strand. Has Okazaki fragments.
Okazaki Fragments
Short spurts of 5’->3’ chunks on the lagging strand.
DNA polymerase I
replaces RNA primers with DNA
DNA Ligase
Seals the cracks between okazaki fragments in the lagging stand
Elongation
DNA polymerase III starts adding nucleotides. DNA Poly I replaces RNA primer with DNA. DNA Ligase seals cracks.
Termination
Not a lot of information about this process. Topoisomerase IV unlocks the newly synthesized chromosomes.
DNA polymerase III and errors during replication
Has proofreading abilities which reduce errors during DNA replication.
Telomere
Noncoding sequence at ends of chromosomes.
Telomerase
Extends the telomeres
Rolling Circle Replication occurs in
Plasmids
Rolling Circle Replication Steps
Nick (separates parental strands) forms a double-stranded origin site.
DNA Poly III replicates nicked strand in one direction using the un-nicked strand as template.
Nicked strand is displaced and re-circularizes into a single-stranded DNA molecule.
Which Strand of DNA is used for transcription
Template strand is used for synthesizing RNA
Initiation RNA
RNA transcription initiation begins at a promotor.
Most common promotor
TATA box (TATAAT) about 10 base pairs upstream of gene to be transcribe
RNA polymerase
Main enzyme in Elongation. No proofreading skills
Why are there more errors in RNA than DNA?
RNA polymerase does not have any proofreading skills.
Elongation
RNA polymerase unwinds DNA, seperates double helix, and can add new RNA nucleotides.
Termination Begining
RNA polymerase reaches a Stop codon and ends the process.
Termination Post Stop Codon
RNA polymerase stalls and releases the DNA template. Gets stopped and falls off when it hits termination signal
Termination Releasing the RNA
final step of termination
Prokaryote in cytoplasm Unique RNA transctipion
Prokaryote in cytoplasm perform transcription and translation at the same time.
Modifications made to the pre-mRNA in eukaryotes
In eukaryotes a 5’ cap is added to pre-mRNA. A poly-A tail is added to the 3’ end of pre-mRNA. Primary transcript (pre-mRNA) must be processed before leaving the nucleus
5’ cap function
Capping of mRNA 5′ ends modification that allows efficient mRNA translation, directs pre-mRNA splicing and mRNA export from the nucleus. limits mRNA degradation. Allows recognition of foreign RNAs (including viral transcripts) as ‘non-self’.
Poly-A tail 3’ end of pre-mRNA function
export of the mature mRNAs from the nucleus to the cytoplasm. Also promotes the translation of the mRNAs and protects them from degradation.
RNA splicing
remove the introns and reconnect the exons. Facilitated by a spliceosome.
“Degeneracy” of the genetic code
Multiple codons can code for the same amino acid.
Wobble position
3rd position in a codon that can vary while still coding for the same amino acid
Codon
Sequence of 3 nucleotides on the mRNA
codes for the same amino acids in essentially all organisms
How many Codons? How many nonsense/stop codons?
64 total codons, 3 nonsense or stop codons.
AUG - Codon relevance
Methionine and start codon
Components of ribosomes
Made of rRNAs (act as enzymes) and peptides
Ribosome size in Prokaryotes
70s
Ribosome size in Eukaryotes
80S
Small subunit of the ribosome
Binds mRNA template
Large subunit of the ribosome
bind tRNA for initiation with the thymine attached.
Polyribosomes
have multiple ribosomes translating the same mRNA
Direction Polypeptide is formed in
Polypeptides are formed from the N-Terminus -> C-Terminus
Structure of a tRNA
Single stranded RNAs with a lot of intramolecular base pairing. Kind of looks like a clover
Anticodon
Base pairs with the codon on the mRNA
aminoacyl tRNA transferases
Charges tRNA
Shine-Delgarno Sequence
where 30S ribosomes can bind.
What are the three sites on ribosomes
A (aminoacyl), P (peptidyl), and E (exit)
A site
Charged tRNA enters at this site.
Peptide bond formation
Catalyzed by peptidyl transferase with GTP as energy source
Between the amino group of the A site and the carboxyl group in the P site
E site
Where tRNA is released from
Nonsense codon and the Sites
Codon aligns with the A-Site. Release factors lead to detachment of chain from the P-site tRNA.
Mutation
A change within a gene
Point Mutations
Where a single nucleotide in the DNA is changed
Silent Mutation
Is a point mutation where there is no change to the protein coded.
Missense Mutation
Point mutation where incorrect amino acid in the protein. May be good or bad or nothing at all
Nonsense Mutation
Point mutation which codes for an early stop codon. Maybe good, bad, or nothing, but more likely to be bad than missense
Insertion mutation
Add a nucleotide or two into the DNA
Deletion Mutation
Remove a nucleotide or two from the DNA
Frameshift Mutation
Most likely to be bad. Nucleotides have been added or removed
Why is spontaneous mutation rare?
There are fail safes in play to avoid mutation during replication
Mutagen
Something that can cause a mutation
Carcinogen
Things that can cause cancer
Nucleoside analogs
Structurally similar to normal nucleotides, but use different base-pairing rules
Modification of normal bases
Different base-pairing rules
Intercalating agents
Distort the double helix impairing enzyme funtion.
Ionizing Radiation on DNA
Breaks in the sugar-phosphate back bone. Modification of bases
Nonionizing Radiation on DNA
Dimer formation between two adjacent pyrimidine basses (usually thymine)
Nucleotide Excision Repair of Thymine Dimers
Nuclease cuts strand. Helicase removes cut section. DNA Pol I and DNA Ligase make repair. DNA Pol I adds the nucleotides back, DNA ligase seals the cracks
Direct Repair of Thymine Dimers
Photolyase binds distorted helix. When exposed to visible light breaks the thymine dimer. No longer works in humans
Vertical Gene Transfer
Sexual Reproduction
Meiosis
Sexual Reproduction
Horizontal Gene Transfer
Across same generation -> Prokaryotes.
Transformation
Uptake of DNA from the environment and incorporating it.
Competent Bacteria
Common. Those that can take up DNA from its environment and incorporate it into their genome.
Generalized Transduction
Transducing phage carries random DNA segment from donor to recipient
Specialized Transduction
Transducing Phage carries DNA from either side of the Phage’s intergration site
Conjugation
DNA is directly transferred via a conjugation pilus.
Conjugation Pilus
Bring cells close togethere and forms a bridge for DNA transfer
F-Plasmid
Required for genes to conjugate
Conjugation of the F Plasmid
F pilus (F+ cell on an HFR) contacts an F- cell. Form a cytoplasmic bridge at site of conjugation pilus. Rolling circle replication of the F Plasmid begins. Single-Stranded copy is transferred and then the complementary strand is synthesized. The F- cell is now F+
Conjugation of F+ and HFR Cells
F Plasmid integrates into bacterial chromosome
Hfr
High frequency of recombination.
R Plasmids
genes for antimicrobial resistance and conjugation
Toxin Production
Bacillus anthrakus (production of two toxins on two plasmids)
Colonization factors
Capsule
Transposons
“jumping genes” cut and paste or copy and paste movement.
Imprecise cutting of the transposon
Transposon may carry additional genes with them.
Operons
Unique to Prokaryotes. Group of genes for a single metabolic pathway.
Upstream regulatory gene
impacts the level of transcription.
trp operon
makes the amino acid tryptophan. Repressible operon
Repressible Operon Function
It is always on. so it can be turned off or repressed
trp operon repression
When typyophan is present in the environment it activates the repressor which binds to the operator
Inducible Operon Fucntion
Usually off, can be turned on or induced.
lac operon
Activates Lactose Catabolism.
Activation by catabolite activator protein
CAP induces lac operon
lac Operon and cAMP
When glucose levels are low the cell produces less ATP for catabolism. This leads to activation of adenylyl cyclase producing cAMP. cAMP binds to catabolite activator protein (CAP) binds upstream of RNA polymerase binding site in promoter
