Cell Bio Ch. 11

Genes ____ information for producing all _______.

Mutation in a single gene causes a single ______ in an _______ of a
single polypeptide.

•Overview
of Flow of Information through the Cell

–Messenger
RNA (mRNA): ______________

–Transcription: __________________

–Translation: _________________

Overview of flow of information in eukaryotes
Explain.
5 steps

Three classes of RNA in a cell

•rRNA means and does what?

•tRNAs means and does what?

_____________ are responsible for transcription in both prokaryotes and eukaryotes.

•Incorporate nucleotides into a strand of RNA from a DNA template.

–The ______ is where the enzyme
binds prior to initiating transcription.

–The enzyme requires the help of _____________ to
recognize the promoter.

Chain elongation during transcription.
Explain

•Newly synthesized RNA chain grows in a 5’ to
3’ direction ___________ to the DNA.

•Nucleotides enter the polymerization reaction as ____________ precursors.

•The reaction is driven forward by the _____ of
a pyrophosphate: PP_i -> 2P_i

•Once polymerase has finished adding nucleotides, the DNA-RNA hybrid _________ and
the DNA double helix ______.

•Two enzymatic activities of RNA polymerase:

•Transcription in Bacteria

–One type of RNA polymerase in prokaryotes: five subunits associated to form a core enzyme.

–________-competent cells also have a ______ attached to the RNA
polymerase before attaching to DNA.

•__________ are located upstream from the site of initiation.

–Two conserved regions:

–Differences in the DNA sequences at both –35 element and the Pribnow box may regulate
_________.

•Termination in bacteria can either require a _________ or may reach a terminator
sequence without _____.

Explain the promoter region in bacteria.

•Transcription and Processing
–Three types of RNA polymerases in eukaryotes:
•Most rRNAs are transcribed by ________
•tRNAs are transcribed by ________
•mRNAs are transcribed by ___________
–_______ regulate the activity of RNA
polymerases.

•Newly transcribed RNAs are processed.
–A transcription unit is the DNA segment corresponding to a _______ transcript.
–A primary transcript (or pre-RNA) is _________
•A variety of small RNAs are required for RNA processing.

•A eukaryotic cell may contain millions of_______.
•The DNA sequence encoding rRNA is called____
and is usually clustered in the genome.
•In nondividing cells, rDNA are _____ in the
_______, where_____ are produced.

•Synthesizing the rRNA Precursor
–rRNA genes are arranged in _____.
–rRNA transcription has a “_________” pattern.
–Proteins that convert rRNA precursors into mature rRNA become associated with pre-rRNA during
______.
–The _______ separates transcription units in a ribosomal gene cluster.

•Processing the rRNA Precursor
–A single primary transcript (pre-rRNA) can be spliced into three rRNAs: __________
–Pre-rRNA contains large numbers of ______ and ___________.
–Unaltered sections of the pre-rRNA are _____.

•The Role of snoRNAs:
- Processing of________
•packaged with proteins into ________
•modify bases in _______

•Synthesis and Processing of the 5S rRNA

–The 5S rRNA genes are located outside the nucleolus.
–It is transcribed by __________, which uses an
internal ______.

•Transfer RNAs
–Genes are located in small clusters scattered around the
__________.
–tRNAs have_____ within the coding region of the gene.
–During processing, the tRNA precursor is ____and numerous bases must be modified.

•The precursors of mRNAs are represented by diverse RNAs called _________.
–Found only in the _______.
–Have large molecular weights.
–Degraded after a very short time.

•The Machinery for mRNA Transcription
–RNA polymerase II is assisted by general transcription
factors (GTFs) to form the _________.
–The critical portion of the promoter lies ________ from the initiation site and contains the TATA box.
–The preinitiation complex of GTFs and polymerase assemble at the ____ box.

•The preinitiation complex assembly
starts with the ________________
–TBP is a subunit of the _________
–Binding to the promoter causes a _______
in DNA

•Binding of TFIID sets the stage for the assembly of the complete PIC.
•The three GTFs bound to the promoter allow the binding of RNA polymerase with its TFIIF.
-As long as TFIID
remains bound to the promoter, additional _____________
for additional rounds of transcription.

•RNA polymerase is heavily phosphorylated at the
_____________.
–(answer from above) phosphorylation can be catalyzed by different _______.
–TFIIH acts as the ____________.
•Termination of transcription is not well understood.

•Messenger RNAs share certain structural properties
–Each code for a specific ______.
–Are found in the _______.
–Are attached to ______ when translated.
–Most have a noncoding segment.
Eukaryotic mRNAs
modifications at their 5’ (guanosone cap) and 3’ poly(A) tail.

•Split Genes: An Unexpected Finding
–The difference between heterogenous nuclear RNA (hnRNA) and mRNA provided early clues about RNA processing.
–Eukaryotic genes contain intervening sequences which are missing from mature mRNAs.
–The presence of genes with intervening sequences are
called ______.
–The parts of the split gene that contribute to the
mature mRNA are called _____.
–The intervening sequences are called _____.

•Hybridization experiments supported the concept of mRNA precursors (pre-mRNAs).
•Loops in the DNA-RNA complex were the introns.
–Resulted from introns that were not __________ to any part of the gene.

•RNA transcripts become associated with _______ as they are synthesized.
•During processing, a 5’ methylguanosine cap and a 3’
poly(A) tail are added.
•Intervening sequences are ______ and exons are connected by ________.

•RNA Splicing: _______ of _____ from a Pre-mRNA
–Breaks are introduced at the 5’ and 3’ ends of the
splice sites.
–Sequences between exon-intron boundaries are highly _________.
–Sequence most commonly found at the boundary is g/GU at the 5’ end and AG/G at the 3’ end.

•Studying RNA splicing has led to the study of RNA enzymes, or __________.
–RNA splicing is thought to have evolved from
___________.
–An example of a self-splicing intron is the _________, discovered in various organisms.

•The pre-mRNA is not capable of self-splicing
–requires small nuclear RNAs (snRNAs)
•As each hnRNA is transcribed, it
becomes associated with a_________.
•Processing occurs as each intron becomes associated
with a complex called ______.
•The spliceosome consists of ____________.
•Removal of an intron requires
–Several snRNP particles.
Each snRNP contains a dozen or
more proteins, such as the Sm protein family.

Assembly of the Splicing machinery. Explain.

•Evolutionary Implications of Split Genes and RNA Splicing
–The idea of an “RNA world” suggests that RNA was the earliest molecule to both store information and catalyze reactions.
–RNA splicing via spliceosomes could have evolved from _________.
–Exon shuffling could have played a role in the evolution of many genes.

•________ results in the
destruction of some mRNAs.
•RNAi is produced when a double-stranded RNA shares the __________ as the target ____.
•RNAi is part of a broader phenomenon of RNA silencing, in which small RNAs
inhibit gene expression in various ways.
•3 Types:

•The steps involved in RNAi include:
–dsRNA is cleaved into small interfering RNAs (siRNAs) by an enzyme called ____.
-The small dsRNAs are loaded into a complex named _____ that bind ____ to a target RNA.

•Micro RNAs (miRNAs)
–Are derived from a single-stranded precursor RNA that
contain ________ that allow them to fold back to form _____.
–The pseudo dsRNA is cleaved to generate a ________.
–The single-stranded miRNA binds to a complementary region on an ______ and inhibits
translation of the message. Are thought to play a regulatory role in development.

Know and Explain

•_____________ are
small RNAs that suppress the movement of transposable elements in the __________.

•Strategies for using RNAi to combat cancer,
viruses, and some genetic disorders.
•Some obstacles:
–Delivering genes for siRNAs can lead to complications.
–Viral genes mutate rapidly, making some siRNAs ___________.

•Information stored in a gene is present in the form of a _______.

•Properties of the Genetic Code
–The _______ for amino acids are
non-overlapping triplets of nucleotides.
–It is _________, some of the amino
acids are specified by more than one codon.

•Identifying the Codons

–Codon assignment was determined by transcription of
________.
–The first two codon bases for a particular amino acid are ______, whereas the third base may vary.

•Structure of tRNAs

•The secondary structure resembles a _______, while
the tertiary structure is an _____.
–The amino acid is attached to the 3’ end of tRNA.
–The anticodon on tRNA complements the codon of the ______.
–The wobble hypothesis suggests that a ____ can recognize codons with variable third bases.

•Amino Acid Activation
–Specific _______ link amino acids with their respective tRNAs.
–Energy from ATP is used to activate the amino acid,
which is then transferred to the tRNA molecule.
–Codons of the mRNA are interpreted according to the
recognition abilities of the ______.

•________ is the most complex
activity of the cell.
•Translation is divided into: (3 parts)

•Initiation
–Translation begins at the ________, which then puts the ribosome in the proper ________.
–The small ribosomal subunit identifies the correct AUG codon.
–Initiation requires proteins called________
–In bacterial cells, the ________ sequence guides the small ribosomal subunit to the correct initiation codon.
–In eukaryotes, the smallest ribosomal subunit recognizes
the 5’ end of the message and finds the first _______ by scanning.

•Bringing the First aa-tRNA Into the Ribosome
–AUG codes for ______ so it is always the first amino acid to be incorporated into the polypeptide chain.
–There are two differenet methionyl-tRNAs: one for ______ and one for the____________.
-After the initiation tRNA is _____, the large
subunit of the ribosome _____ the complex.

•The Role of the Ribosome
–Ribosomes have three sites for tRNAs: ____
–Ribosomes receive each tRNA in successive steps of the ________.

•Elongation
–The process of ______ each subsequent amino acid to the ___________.
•With the charged amino acid in the P site, the next aminoacyl-tRNA binds to the _______.
•Several elongation factors are required.
-Peptidyl trasnferase catalyzes the peptide bond formation between ______.

•Elongation
–The ribosome moves three nucleotides (one codon) along the mRNA in the 5’ -> 3’ direction during translocation.
–Translocation is driven by conformational changes in an
elongation factor (EF-G or eEF2).
–Mutations that add or delete nucleotides that affect
translocation are called frameshift mutations, and produce an abnormal sequence of amino acids.