6. Genetics Flashcards
nucleoside
sugar plus base
nucleotide
sugar, base, and phosphate
pyrimidine
guanine and adenine
purine
cytosine and thymine
is DNA or RNA more stable?
DNA is more stable
strong G=C content
hydrogen bonds
phosphodiester bonds
hydrogen bonds connect the strands through the bases
phosphodiester bonds are the phosphate to sugar groups
topoisomerases
insert and remove supercoils
negative supercoiling:
twisted in opposite sense relative to right-handed double helix; found in most cells
DNA gyrase
introduces supercoils into DNA via double-strand breaks
positive supercoiling
helps prevent DNA melting at high temperatures
viruses contain either RNA or DNA genomes
-can be linear or circular
-can be single or double stranded
plasmids
double-stranded DNA that replicate separately from chromosome
-usually circular
-generally beneficial for the cell (antibiotic resistance)
-NOT extracellular, unlike viruses
(can be lost)
plasmids are diverse- multiple can exist in one cell
operon
group of genes transcribed together
DNA replication
semi conservative
parent + daughter strand
DNA polymerase I
fills in the gaps (bw okazaki)
removes RNA primers
DNA polymerase III
replicates majority
DNA ligase
reconnects broken DNA strands
transcription in bacteria
produces RNA from a DNA template
mRna
tRNA
rRNA
terminator regions
RNA contains ribose
-uracil
-less stable
polycistronic
multiple ribosomes reading messenger molecule
transcript for more than one gene
RNA polymerases in bacteria archaea and eukarya
bacteria
-1 RNA polymerase
-only need sigma
archaea
-transcription more complex
-require other transcription factors
eukarya
-transcription more complex
-3 RNA polymerase
sigma subunit
recognizes promoter sequences
binds between the -35 region and the pribnow box in the promoter sequence
operon parts
promoter
5’ leader
gene 1
gene 2
gene 3
transcription terminator
go through transcription to form a polycistronic mRNA with ORF 1, 2, and 3
transcription in bacteria: termination of RNA synthesis is
governed by specific DNA sequences
EX: GC-rich sequences with inverted repeat and central nonrepeating segment
rho-dependent termination
rho-dependent termination
rho protein recognizes specific DNA sequences and causes a pause in the RNA polymerase, releasing RNA and RNA polymerase
amino acids, polypeptides, and proteins
proteins play a major role in cell function
-catalytic proteins (enzymes)
-structural proteins (membranes, walls, ribosomes)
-regulatory proteins
proteins are polymers of amino acids
amino acids are linked by peptide bonds to form a polypeptide
proteins are one or more polypeptides
genetic code
a triplet of nucleic acid bases (codon) encodes a single amino acid
-64 possible codons
-specific codons for starting and stopping translation
degenerate code
multiple codons encode a single amino acid
wobble
irregular base pairing allowed at third position of tRNA
start and stop signals
AUG - methionine
UAA stop
UAG stop signal
translation
synthesis of polypeptide directed by sequence of nucleotides in mRNA
direction of synthesis N-TERMINAL to C-terminal
ribosome
site of translation
-coupled transcription/ translation in bacterial/ archaea
polyribosome- complex of mRNA with several ribosomes
transfer RNA
tertiary structure due to base pairing within the tRNA molecule
-anticodon is present
–complementary to the mRNA codon
–located on the anticodon arm
amino acid activation
attachment of amino acid to tRNA
-catalyzed by aminoacyl-tRNA synthetases
at least 20- each specific for a single amino acid and for all the tRNAs to which each may be properly attached (cognate tRNAs)
elongation of the polypeptide chain consists of three phases
aminoacyl-tRNA binding
transpeptidation reaction
translocation
involves several elongation factors (EFs)
tRNA binding sites of ribosome
aminoacyl (acceptor; A) site
-binds incoming aminoacyl-tRNA
peptidyl (donor; P) site
-binds initiator tRNA or tRNA attached to growing peptide (peptidyl-tRNA)
exit (E) site
-briefly binds empty tRNA before it leaves ribosome
assisted protein folding and chaperones
chaperones catalyze macromolecular folding events
chaperones can also refold partially denatured proteins (helper proteins)
translocases
transport proteins into or through bacterial and archaeal membranes
Sec systems
exports unfolded proteins and inserts integral membrane proteins
Tat systems
transports folded proteins through membranes
protein secretion: sec and tat systems
-signal sequence
15-20 residues
found at N-terminus
signals secretory system
prevents protein from completely folding
antibiotics that inhibit bacterial translation
erythromycin prevents the shift on ribosome
tetracyline blocks tRNA attachment to mRNA
chloramphenicol prevents peptide bond formation between amino acids
gentamicin and streptomycin are aminoglycosides that distort ribosome shape
