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BIOL130 Study Guide - Final Guide: Polysaccharide, Autophagosome, Tethering

Course Code
Niels C Bols
Study Guide

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Transcription = copying the nucleotide sequence of that (protein) gene into RNA
RNA = linear polymer made of A, U, G, C; single stranded
Transcription produces RNA that is complementary to one strand of DNA (template strand)
Transcription vs. DNA Replication
RNA does not remain hydrogen-bonded to DNA template strand (single stranded)
RNA are copied from limited region of DNA polymer is much shorter than DNA molecules
Types of RNA
Messenger RNA = direct synthesis of proteins
Nonmessenger RNA = proteins with various roles: regulatory, structure and catalytic component of cell
Ribosomal RNA = form structural and catalytic core of ribosomes (translate mRNA into protein)
Transfer RNA = adaptors that select amino acids and hold them in place on ribosome (translation)
microRNA = regulators of eukaryotic gene expression
**RNA other than mRNA used for regulation of gene transcription, processing mRNA prior to translation,
translation (transport of amino acids, catalyze formation of peptide bonds)
Transcription Process
RNA polymerase catalyze formation of phosphodiester bonds that link nucleotide together allows free template
strand to be copied
Adds nucleoside triphosphate monomer (RNA), one by one through hydrogen bonding
oRNA polymerase vs. DNA polymerase
RNA polymerase can start an RNA chain without primer (unlike DNA polymerase)
RNA is not made for genetic storage, so mistakes in RNA have minor consequences
RNA strand transcribed from 5’-to-3’, template strand has to be the 3’-to-5’ strand
Signals in DNA tell RNA polymerase where to start/stop
oRNAp collide with DNA molecule, slides along
until latches onto promoter
Opens helical structure in front of
promoter region is not transcribed
Bacterial Transcription
Holoenzyme = made up of core enzyme + sigma factor
Contains subunit if RNAp called sigma factor helps
recognize promoter regions
oOnce transcription has begin, sigma factor is released and polymerase moves forward chain elongation
until terminator enzyme halts and released both DNA template and new RNA transcript RNAp binds
to free sigma factor
When terminated, codes for RNA folds back on itself (short double helix) – hairpin structure
Hairpin disrupts transcription complex, RNApol separates from RNA transcript
Eukaryotic Transcription vs. Bacterial
Eukaryotes contain RNAp I. II and III
oI and III transcribe gene encoding transfer RNA, ribosomal RNA, and other RNA for structural and
catalytic roles in cell
oII transcribes majority of eukaryotic genes, encode for proteins, miRNA
Bacterial RNAp (with sigma) can initiate transcription on its own, eukaryotic requires large complex accessory
proteins general transcription factors
Eukaryotes have longer DNA strands with genes spread out controlled by large variety of regulatory DNA
sequences, enables eukaryotes to engage in more complex form of transcriptional regulation
Eukaryotic transcription initiation takes account the packing of DNA in nucleosomes and more compact forms of
chromatin structure

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General Transcription Factors
Similar role to sigma factor assemble at promoter, and pulls apart DNA helix to expose template strand
oFactors (some) are called: TFIIB, TFIID, TFIIH = transcription initiation complex
TFIIB recognize TATA (promoter) box binds and enables adjacent binding of TFIID
Allows all other factors to pile on, forming transcription initiation complex
TFIIH (contains protein kinase) pries apart double helix at transcription start point, uses ATP
Then phosphorylates RNA polymerase II, release polymerase from most GTF to begin
Only dephosphorylated form of RNAp can begin synthesis of RNA
RNA processing (Eukaryotic)
Unlike bacteria, eukaryotes must transport RNA strand to cytosol for translation RNA must undergo processing
before exported = RNA processing
oRNA capping = modifies 5’ end of RNA transcript capped with addition of Guanine bearing methyl
oPolyadenylation = (unlike 3’ end of bacterial RNA an mRNA is the end of chain) 3’ end of eukaryotic
mRNA is trimmed by enzyme (cuts RNA chain at particular nucleotide)
Then use of second enzyme, addition of poly-A tail
oIncreases stability of mRNA molecule, marks RNA as mRNA for export
Most eukaryotic genes have coding sequences interrupted by long, noncoding, intervening sequence = introns
oCoded genes = exons (expressed sequences)
Introns are removed from pre-mRNA by RNA splicing enzymes (snRNA) exons are stitched together
oSpecial nucleotide sequence in pre-mRNA signal beginning and end of intron for removal
Excised intron = lariat
snRNA and snRNP
Splicing carried out by RNA molecules small nuclear RNA, small nuclear ribonucleoproteins
osnRNA + snRNP = spliceosome complex
spliceosome complex consist of 5 small nuclear ribonucleic particles (RNA-protein complex)
Catalytic activity provided by RNA component (ribozymes)
Advantages of splicing:
oAlternative splicing (genes can be spliced in different ways) produce distinct proteins allows different
proteins to come from same gene increase coding potential of genome
oSpeeds up emergence of new and useful proteins novel proteins rise from mixing-matching pre-existing
Disadvantages of splicing
oMore steps = more work
oMore steps = more opportunity for error
Mutations result in loss of exons, inclusion of introns, shift in location of splice
Export of mRNA
mRNA must have poly-A-binding protein, cap-binding complex and appropriate spliced proteins that bind to
oOnly way for it to leave selective nuclear pore complex
Waste RNA remain in nucleus for degradation
Transfer RNA
mRNA is decoded in sets of three nucleotides = codon 64 possible combinations of codons, only 20 amino
acids that it can code for
anticodon = complementary base paring for the codon of mRNA strand
tRNA molecules = molecular adaptors link amino acids to codons
tRNA to Correct Amino Acid
Recognition and attachment of right amino acid depends on enzyme aminoacyl-tRNA synthetase

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oCovalently couple each amino acid to appropriate set of tRNA molecules
oDifferent synthetase for each amino acids 20 synthetases
Translation occurs in the cytosol, with the help of ribosome
oRibosome = large complex made from dozens of small proteins and rRNA
Composed of a large and small subunit attached together
Small ribosomal subunit matches tRNA to codons of mRNA
Large subunit catalyzes formation of peptide bonds that link amino acids together in polypeptide chain
oUses tRNA as adaptors
When synthesis is complete, subunits of ribosome separate
A site, P site and E site
A site = appropriate charged tRNA enter A site by base-pairing with complementary codon on mRNA
P site = amino acid is then linked to peptide chain held by tRNA in P site
E site = large ribosomal subunit shifts forward, moves tRNA to E site before ejection
oNew protein growing from its amino to carboxyl end until stop codon in mRNA is encountered
Translation Initiation in Eukaryotes
Specific codon (sequence) needed to initiate translation AUG; special charged tRNA is required to initiate
translation = initiator tRNA
oAlways codes/carries the amino acid methionine (or modified form, formyl-methionine in bacteria)
Always at N-terminus
Initiator tRNA charged with methionine is loaded into P site of small ribosomal unit with additional proteins
called translation initiation factors
omRNA slides through small subunit + TIF (starting from 5’ cap) until AUG is encountered recognized
by initiator tRNA
Initiation factors dissociate from small ribosomal subunit to make room for large subunit to bind
and complete ribosomal assembly
Exceptions to Genetic Code
oAlmost always universal (codons) except in mitochondria; UGA stop codon, encode for tryptophan
oCytosolic protein-synthesizing machinery reading mitochondrial gene will stop when it should be
inserting tryptophan
Mistakes in Transcription
oDeletions/insertions shifts reading frame
oFrame shift mutations = can lead to
beneficial novel proteins or be disastrous
Translation Initiation in Bacteria
Doesn’t have 5’ cap contain specific ribosome-
binding sequence located few nucleotides upstream of AUG where
translation begins
oRibosome can readily bind to start codon that lies inside mRNA
as long as ribosome-binding site precedes it
Prokaryotic mRNA = polycistronic encode different
proteins from same translated mRNA
Eukaryotic mRNA usually carry information for
one protein
Wobble hypothesis (Francis Crick)
oProposes that anticodon of tRNA can bind successfully to codon whose
third position requires nonstandard base pairing
oExplains how tRNA is able to base pair with more than one type of
Terminator in Bacteria and Eukaryotes
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