Unit 5 Flashcards
chemical concept of a gene
structurally stable, self-replicating, resists alterations, inheritable
Molecular hierarchy
DNA-genotype-RNA-phenotype-protein
Simplified Central Dogma
DNA - Transcription - RNA - amino acid chain - folding - protein
DNA is _________ transferred to RNA molecules
unidirectionally
What is self-replicating?
DNA and RNA
RdRP
dependent RNA Polymesase
How do RNA viruses work?
Use antisense (non-coding strand) as genetic material via the activity of RdRP
antisense
non-coding strand
Retrotranscriptase (RT)
Enzyme that allows RNA to be transcribed back to DNA
Exception to self-replicating rule
Prion diseases
Molecular mechanisms behind the transfer of genetic info
Transcription and translation
Where does transcription and translation happen in prokaryotes
Cytoplasm
Transcription
DNA to RNA
Translation
RNA to protein
Where is RNA synthesized then transported to?
Synthesized in nucleus, transported to the cytoplasm
Where does most of our understanding of transcription processes come from?
Study of E. coli infection
Phages
DNA viruses that infect bacteria by hijacking the transcription and translation mechanisms
Characteristics of RNA molecules
Single stranded
OH group in position 2 of the ribose
uses U instead of T, but when RNA folds U can pair with A or G
Can catalyze reactions
Ribozyme
catalytic RNA
Small nuclear RNA
snRNA
structural components of spliceosomes
Messenger RNA
m RNA
intermediates that carry genetic info from DNA to the ribosomes
Transfer RNA
tRNA
adaptors between amino acids and the codons in mRNA
ribosomal RNA
rRNA
structural and catalytic components of ribosomes
micro RNA
miRNA
short single-stranded RNA that blocks expression of complementary mRNA
general features of RNA synthesis
catalyzed by RNA polymerases
processed in 5-3 direction
only coding strand used as template
U instead of T
will be complementary to DNA antisense template strand and identical to DNA contemplate (sense) strand
cDNA
the complementary DNA synthesized from RNA template
Which DNA strand is used in RNA synthesis
template strand
What is the RNA produced by transcription of the template strand referred to?
sense (+) RNA
Transcription is a dynamic event, what does this mean?
several events of transcription can be going on at the same time
What type of genes are transcribed nonstop
housekeeping genes, such as ribosomal RNA
Stages of transcription in prokaryotes
RNA chain initiation
RNA chain elongation
RNA chain termination
RNA polymerases
enzymes responsible for decoding DNA to RNA
RNA chain initiation
RNA polymerase binds to promorter region (forms phosphodiester bonds)
Promoter region
conserved cis-elements (sequence of DNA) that mark site of binding
Only present on template strand
RNA chain elongation
chain grows from 5-3
RNA chain termination
RNA polymerase arrives at termination site, decouples from DNA template, and RNA strand is released
Factor dependent termination
requires a protein factor (p-dependent)
Intrinsic termination
requires cis elements (inverted repeat) at end of transcript (p independent)
post-transcriptional modifications of mRNA
intron splicing
5’ capping
3’ poly-adenylation
differences between prokaryotic and eukaryotic transcription
one RNA polymerase vs 3 (5 in plants)
naked DNA vs chromatin
simple vs complicated transript
RNA polymerase 2
transcribes mRNA and some functional/non-coding RNA
capping
unusual 5-5 phosphodiester bond between a methylated guanine nucleotide to the first transcribed nucleotide in the RNA
cap purpose
transport across nuclear envelope
protect mRNA from cytoplasmic nucleases
recognition on signal for translation machinery
poly a tail
poly a polymerase recognizes cleaved and processed transcripts as templates to add poly a tail (200 adenines)
Poly(a) tail purpose
enhance mRNA stability in cytoplasm
promotes translation
mature mRNA
only coding sequences (no introns)
capped on 5
poly-A tail on the 3
What does splicing allow?
more alternative genes and to remove introns
introns
noncoding sequences
exons
coding sequences
R loops
formed by 2 nucleic acid strands. Its boundaries mark the interval of an exon in the gene
what does a single r loop mean
all coding sequence present in the RNA has direct correspondence in its gene. They are the exons
Do prokaryotes have introns?
no
2 mechanisms of splicing in eukaryotes
Self splicing and RNA/protein complex mediated splicing
self splicing
primary transcript with enzymatic activity/ribozyme. No protein involvement or energy required
RNA/Protein complex mediated splicing
enzymes/snRNA needed to recognize and mediate intron excision (spliceosome). Requires energy
Which RNA polymerase does translation use
RNA pol 2 - mRNA
RNA pol 1 - all RNA
RNA pol 3 - tRNA
tRNA job
acts as adapter between codons and amino acids. They fold into 3 different structures that determine its function
Which codons don’t have a corresponding tRNA
stop codons
Hachimoji DNA
8 nucleotides
4 biological (A,C,T,G)
4 new synthetic (Z,P,S,B)
can be replicated and transcribed to RNA
Properties of genetic code
composed of nucleotide triplets, stop, and start codons
non-overlapping
comma-free
is degenerate and nearly universal
Wobble Rules
tRNA can interact with more than 1 condon
amber mutation
a premature stop codon
amber suppressors
mutations in tRNA genes that change the anticodon specificity can re-engineer the genetic code in cells
