CH 9 Flashcards
2 essential functions of the DNA
- genetic material for inheritance
- directs and regulates the construction of proteins
WHAT contains the full complement of DNA within a cell
genome
smaller discrete units of genomes
genes
genes are arranged where
chromosomes and plasmids
3 important processes
- Replication
- Transcription
- Translation
genotype vs phenotype
genotype: genes
phenotype: physical characteristics
DNA replication location in :
1. eukaryotes
2. prokaryotes
- nucleus
- nucleoid
4 phases of DNA Replication
- Unwinding
- Primer Bonding
- Elongation
- Termination
Enzymes included in DNA Replication
- Topoisomerase (unwind)
- Helicase (unzip)
- Primase (sets primer)
- DNA polymerase 3 (adds bases)
- Ligase (joins together Okazaki fragments)
- Exonuclease (removes primer
- DNA polymerase 1 (proofreads bases and adds where primer is removed)
Replication process that is unidirectional
Rolling Circle Replication
a specific genomic locus where DNA replication begins in Rolling Ciruclar Replciaton
ori
What enzyme binds to ori and what does it do and where does it bind
Rep-A - breaks a single strand called “NICK” and binds to 5’
Purines vs Pyramidines
Purines (adenine and guanine) are two-carbon nitrogen ring bases
Pyrimidines (cytosine and thymine) are one-carbon nitrogen ring bases
Direction of RNA initiation for start of transcription process
5’ -> 3’
kaya didikit si enzyme kay 3’ -> 5’ na dna strand
What short sections in the DNA signals when and where to start transcription process
Promoters
What binds to promoters to start transcription and how:
- eukaryotes
- prokaryotes
- Basal transcription factors bind first THEN RNA polymerase
- RNA Polymerase directly binds
What happens in ELONGATION process-transcription
RNA polymerase makes mRNA strand which is similar to non-template dna strand but uses URACIL
What happens in TERMINATION process-transcription
short DNA sequences “terminators” signal end of process
mRNA is released from polymerase
2 types of termination (transription) in BACTERIA
- Rho-independent (forms TERMINATING HAIRPINS and independent of external proteins)
- Rho-dependent (requires Rho Proteins which interacts with RNA polymerase)
What happens after transcription and process
RNA modifications
SPLICEOSOME removes introns (non-coding segments) and leaves exons
what do you call the sequence of three nucleotides that code for a specific amino acid
codons
How many possible codons are there
64 (61 coding + 3 stop codons)
what is the starting codon and the 3 stop codons
AUG (methionine)
UGA
UAA
UAG
What happens in initiation - translation
- Initiaion Factors 1 & 2 attach to small ribosomal unit
- tRNA with anticodon attaches to SRU
- Big ribosomal unit attaches to tRNA
What is the subunits of rRNA
Small subunit (30S in P; 40S in E)
Big subunit (50S in P: 60S in E)
What are the sites present in BIG SUBUNIT
E site (exit site
P site (polypeptide)
A site (Amino acid)
What happens in Elongation process - translation
AUG enters P site first and A site is for 2nd amino acid. The amino acids leaves thru the E site after forming peptide bonds
What happens in termination process - translation
stop codon enters A site
release factors breaks down sobrang peptide bonds at the end
What do you call redundancy in the genetic code
Degeneracy
What is found in codon chart
the CODON, not the ANTICODON
Where does transcription and translation occur in prokaryotes and eukaryotes
P: both occur simultaneously in cytoplasm
E: transcription: nucleus ; translation: cytoplasm
what is a mutation
heritable change in DNA sequence of organism
2 causes of mutations
- spontaneous
- induced
Causes of Mutations
mistakes in the process of DNA replication
Spontaneous
Causes of Mutations
exposure to mutagens
Induced
What is the error rate of DNA polymerase 3
one base per billion base pairs
How much can exposure to mutagen increase rate of mutation
1000-fold
2 types of mutations in DNA sequence
- Point Mutation (single base is substituted or replaced)
- Insertion/Deletion/Frameshift (addition or removal of base)
4 effects of mutation on protein structure and function
- Silent (no effect)
- Missense (amino acid substitution)
- Nonsense (stop codon substitutes for amin acid)
- Frameshift (insertion or deletion of one or more bases)
Types of Chemical Mutagens
structure is similar to normal nucleotide bases
Nucleoside analogs
Nucleoside analog of Adenine and Thymine
A: 2-aminopurine
T: 5-bromouracil
Types of Chemical Mutagens
modifies normal DNA bases
Nucleotide base modifiers
Type of nucleotide base modifiers
Nitrous acid
Types of Chemical Mutagens
molecules that slide between normal bases that distorts molecule and create spacing
intercalating agents
Type of intercalating agents
acridine
How does the DNA counter mutations? (3)
- Proof-reading (DNA polymerase 1, during replication)
- Mismatch Repair (after replication)
- Repair of Thymine Dimers
2 types of Thymine Dimers
- Nucleotide Excision Repair (dark repair) - use enzymes
- Direct Repair (light repair) - photoreactivation in the presence of visible light
What can an F+ (fertility factor) bacteria produce?
Sex Pilus
What is a sex pilus? (Step 1-Conjugation)
A protein tube used to connect to an F- bacteria. This is produced from a gene sequence in an F+ bacteria plasmid.
What happens after an F+’s protein tube connects with an F- (Step 2-Conjugation)
- Plasmid in F+ is duplicated.
- Duplicated plasmid is passed to the F-
Step 3 - Conjugation
2 F+ bacteria are now available
High Frequency Recombinant (HFR) cell CONJUGATION - Step 1
A DNA section of the F+ bacteria Plasmid is incorporated into the Chromosomal DNA of F+ Bacteria
High Frequency Recombinant (HFR) cell CONJUGATION - Step 2
Sex pilus (protein tube) of HFR cell is created and connected to the F- bacteria.
An Hfr cell may attempt to transfer the entire bacterial chromosome (w plasmid dna) to an F− cell,
High Frequency Recombinant (HFR) cell CONJUGATION - Step 3
now you have:
HFR cell
Recombinant F- Cell with chromosomal and plasmid portion of HFR cell **
*not F+ kasi not entire plasmid dna is transferred. sex pilus lacks gene sequence to be made.
TRANSFORMATION - Step 1
“Pathogenic” Bacteria gets destroyed-> chromosomal DNA is released and becomes NAKED DNA
TRANSFORMATION - Step 2
“Harmless” Bacteria near it may actively bind to
to the DNA, transport it inside, make it single-stranded.
Harmless bacteria now becomes harmful
Main reason for transformation
many bacteria are NATURALLY COMPETENT
What types of bacteria have the ability to do transformation process
S - Streptococcus pneumoniae
H - Haemophilus influenzae
N - Meningococcus
Generalized Transduction - Step 1
Bacteriophage (virus) attaches to a bacterial cell and injects a PHAGE RECEPTOR
Generalized Transduction - Step 2
PHAGE DNA replicates and breaks down chromosomes of bacterial cell
Generalized Transduction - Step 3
Some bacterial phages have PHAGE DNA, and some have BACTERIAL DNA
Generalized Transduction - Step 4
Bacterial cell will pop, and bacterial phages with bacterial dna may inject it to another cell.
RESULT: cell #2 with a mixture of its dna and another bacteria’s dna
Specialized Transduction - Step 1
Bacteriophage (virus) attaches to a bacterial cell and injects a PHAGE RECEPTOR
Specialized Transduction - Step 2
PHAGE DNA gets incorporated to the bacterial DNA
Specialized Transduction - Step 3
Sections of the phage and bacterial DNA will be released and form CAPSIDS
Specialized Transduction - Step 4
Bacterial cell will pop, and bacterial phages with phage and bacterial dna may inject it to another cell.
RESULT: cell #2 with a mixture of its dna, bacteria’s dna, and phage dna
What example of toxin can be made as a result of transduction
Cholera Toxins by Vibrio cholerae
