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BIOL 130 > Unit 3 > Flashcards

Unit 3 Flashcards

1
Q

Template strand

A
  • The strand that is transcribed
  • RNA is built from its complementary base pairs
  • Read in a 3’ to 5’ direction
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2
Q

Coding strand (non-template)

A
  • Identical sequence to the produced RNA (except for uracil)
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3
Q

In which direction is a new RNA molecule synthesized?

A

5’ to 3’ direction (new nucleotides added to the 3’ end of the strand)

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4
Q

What is a requirement in the formation of phosphodiester bonds?

A
  • A nucleoside triphosphate monomer
  • 2 P required for energy input to form bond
  • Nucleoside monophosphate becomes part of polymer
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5
Q

Which protein complex transcribes DNA?

A

RNA polymerase

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6
Q

Modifications to the Central Dogma

A
  • Many genes do not code for proteins
    Examples:
  • miRNA (regulation of gene transcription)
  • tRNA (AA transport)
  • rRNA (catalyze peptide bond formation)
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7
Q

E. coli is the model organism for…

A

DNA replication, gene transcription, translation

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8
Q

Prokaryotic RNA Polymerase

A
  • Large globular enzyme w/ several channels
  • Active site at intersection of channels
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9
Q

Holoenzyme

A
  • Component of prokaryotic RNApol
  • Core enzyme + sigma factor
  • Synthesize RNA + regulatory subunit (sigma factor)
  • Core RNApol combines w/ sigma factor –> RNApol holoenzyme
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10
Q

Promoter

A
  • Sequence directly upstream of start of gene
  • Region on non-template stand, 40-50bp long
  • RNApol must recognize it + bind firmly
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11
Q

Sigma factor

A
  • Recognizes promoter sequence
  • Positions DNA for correct transcription
  • Uses -35 and -10 box sequences to position itself on non-template strand
  • Most bacteria have several types of sigma proteins (E coli –> 7 types)
  • Each sigma binds to promoters w/ slightly different sequences
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12
Q

When does transcription begin? (pro)

A
  • Starts at +1
  • When sigma identifies + binds to -10 and -35 boxes, properly orienting RNApol holoenzyme for transcription at start site
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13
Q

Steps of initiation + elongation (transcription in bacteria)

A
  1. Sigma factor binds to RNApol
  2. Sigma factor bind to promoter region
  3. Double helix of DNA is unwound (comp. strands broken apart)
  4. RNA synthesis begins
  5. Sigma factor released
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14
Q

Termination (transcription in bacteria)

A
  • RNApol reaches transcription termination sequence in DNA template
  • Term. sequence codes for RNA to fold in on itself (hairpin) –> disrupts transcription complex (destabilizes –> falls apart)
  • RNApol releases RNA transcript + DNA template
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15
Q

Which strand is used as the template strand?

A
  • Promoters are asymmetric –> binds RNApol in only one direction
  • Depends on gene
  • RNApol binds to a promoter (specifies the non-template strand) –> transcription of the template stand
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16
Q

Transcription in eukaryotes vs prokaryotes

A
  • Euks have DNA tightly packed + wrapped in histones (DNA packaging)
  • Euk RNApol –> 3 types (vs one)
  • Many euk promoters are more diverse+ complex (RNApol II –> TATA box, RNApol I + II w/ a diff set of promoters)
  • Euk RNApols require large team of accessory proteins (general transcription factors assemble at promoter w/ RNApol)
  • mRNA is processed before export from nucleus
  • Euk genes spread out w/ gaps of 100,000 bps of untranscribed DNA between them (allows complex regulation by regulatory sequences throughout genome)
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17
Q

Chromatin

A

DNA + protein (histone)
- DNA molecules combine w/ proteins –> higher order structure
- Allows for compact packaging + strict regulation of gene expression

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18
Q

In what form does DNA spend most of its time?

A

Chromosome in extended form

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19
Q

Initiation of transcription (euk)

A
  1. TATA box recognized by TBP (subunit of TFIID)
  2. Binding of TFIID distorts helix (kink), allowing other factors (TFIIA/B/C/etc) to pile on to form transcription initiation complex
  3. TFIIH pries apart double helix at transcription start point
  4. Once transcription starts, most of transcription factor team members come off (can help at another site) –> rNTPs come in, polymerization starts, TFIID stays
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20
Q

TATA binding protein

A

Subunit of TFIID that recognizes + binds to TATA box within promoter –> causes kinks and partial unwinding of double helix

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21
Q

Processing of euk mRNAs in nucleus

A
  • Capping, splicing, polyadenylation –> mature mRNA
  • Done by enzymes that ride on RNApol II
  • Required before export from nucleus
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22
Q

Capping

A
  • Guanine + 3P + methyl group (7mG + 3P)
  • 5’ cap
  • Recognition signal for translation machinery
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23
Q

Polyadenylation

A
  • Poly-A tail
  • 150-250 As
  • Stabilizes msg
  • Protects from degradation (extends 1/2 life)
  • Newest part of strand
24
Q

Exons vs introns

A
  • Exons: “express”, coding sequences for euk genes, will be expressed –> dictate peptide sequence
  • Introns: need to be removed, non-coding sequences
25
Q

Organization of pro vs euk genes

A
  • Pro: continuous sequence
  • Euk: exons (coding) interrupted by introns (non-coding)
26
Q

Removing introns

A
  • After capping, while still being transcribed, RNA splicing begins
  • Each intron contains a few short sequences at/near ends –> cues for removal
27
Q

Structure of introns

A
  • Branch points A ‘attacks’ 5’ splice site –> cuts sugar-phosphate backbone
  • Cut end forms covalent bond w/ ribose sugar group
  • Lariat (branched structure formed from intron) eventually degraded
28
Q

Splicing

A
  • Carried out by spliceosomes (RNA-protein complexes from non-coding RNA) –> consists of 5 small nuclear ribonucleic particles (snRNPs)
  • RNA + 100+ proteins
  • Catalytic activity provided by RNA component
  • ‘Ribozymes’
  • Bring intron loop together, catalyze joining + breaking
29
Q

Advantages of RNA splicing

A
  • Can create diff. proteins from same gene/same primary mRNA transcript depending on cell type, stage development, gender, etc. –> ‘splice variants’
  • Depending on cell type: choose which exons to keep
30
Q

Disadvantages of RNA splicing

A
  • More steps –> more work
  • More steps –> more opportunity for error
  • Mutations of splice sites can result in: loss of exons, inclusion of introns, shift in locations of splice
31
Q

Mature mRNA export from nucleus

A
  • Cap + poly-A tail ‘marker’ by proteins
  • EJC (exon junction complex (proteins)) binds to properly spliced mRNAs
  • Only then mRNA transported out of nuclear pore into cytoplasm
32
Q

Genetic Code

A
  • Relationship b/w sequence of nucleotides in DNA/RNA and sequence of amino acids in protein
  • 64 (4^3) possible codons, only 20 AAs
  • 1 codon NEVER specifies more than 1 AA
  • Almost universal (start and stop codons are the same in majority of genes in animals, plants, and microbes) –> exceptions: some fungi + protozoa, mitochondria (animal)
33
Q

What amino acids are specified by only one codon?

A

Met (methionine) and Trp (tryptophan)

34
Q

Exceptions to genetic code

A
  • Assign some of the three STOP codons to an amino acid

Mitochondria (animal cells):
- Use UGA to encode tryptophan (instead of stop)
- Implications for transferring of mitochondrial genes to nuclear genome
- Cytosolic protein-synthesizing machinery reading mitochondrial gene will always STOP when it should be inserting Trp
Plant mitochondria (use universal code –> not an issue)

35
Q

Reading frame mutations

A
  • Loss or gain of bases (deletions/insertions) that shift reading frame (frame shift mutation) can lead to novel beneficial/disastrous proteins
36
Q

How does mRNA codon specify an amino acid?

A
  • Francis Crick: ‘adapter molecule’ held AAs in place while interacting directly + specifically w/ codon in mRNA
  • Adapter –> tRNA
  • tRNA + AA –> aminoacyl tRNA (covalent bond catalyzed by aminoacyl tRNA synthetase)
  • Each AA has its own aminoacyl tRNA synthetase
37
Q

Structure of tRNA

A
  • 3’ end –> binding site for AA
  • Anticodon loop –> 3 ribonucleotides that base pair with mRNA codon
  • Cloverleaf shape (hydrogen bonding b/w complementary base pairs creating loops)
  • L-shape, 90 degree bend
38
Q

Redundancy in genetic code + tRNAs

A
  • Several different codons can specify the same AA
    Specificity of tRNAs:
  • Some AAs have more than 1 tRNA
  • Some tRNA need accurate base-pairing at only first 2 based of a codon (can tolerate mismatch (‘wobble’) at 3rd position)
39
Q

Wobble hypothesis

A

anticodon of tRNAs can still bind successfully to codon whose 3rd position requires a nonstandard base pairing

40
Q

Loading tRNA w/ AA: aminoacyl-tRNA synthetase

A
  • Total of 20 aminoacyl-tRNA synthetases (each AA has its own) –> must recognize its AA + all anticodons that recognize that AA
  • Hydrolysis of ATP (spent) couples to attachment of AA to tRNA
  • Combined action of tRNA + synthetases ensures each mRNA codon is matched to correct AA
41
Q

‘Charging’ of tRNA

A
  • Active site binds ATP (hydrolysis –> AMP) + AA
  • AA bound to AMP is now ‘activated’
  • activated AA is transferred to tRNA (moves onto enzyme) from aminoacyl-tRNA synthetase (checked in 2 places: receiving end for AA, anticodon loop)
  • AMP + enzyme separate from tRNA (ready for translation)
42
Q

Components of ribosome

A
  • Large subunit: catalyzes formation of peptide bonds (euk: 3 RNA + 39 proteins)
  • Small subunit: matches tRNA to codons, initiates translation (euk: 1 RNA + 33 proteins)
  • Made of RNA + proteins
  • Larger than largest proteins
  • Large + small subunits free in cytosol until they come across mRNA that needs to be translated
43
Q

When does translation of a particular codon begin and end?

A
  • Begins: anticodon of ‘charged’ tRNA binds to codon in mRNA
  • End: AA forms peptide bond with growing chain
44
Q

4 steps of translation cycle

A
  1. New AA diffuses into A (acceptor) site (if codon in mRNA doesn’t match with anticodon in tRNA, AA diffuses out)
  2. If match, P site AA-tRNA bond breaks + peptide bond forms between P site and A site AAs
  3. Large subunit moves 1 triplet to the right to move severed tRNA to E site + empty A site
  4. Small subunit moves 1 triplet to the right to align with large subunit and mRNA, E site tRNA exits
    Cycle is ready to repeat
45
Q

What initiates translation?

A
  • Always begins with AUG codon
  • Initiator tRNA always loaded with met (formyl-met in bacteria)
  • Initiator tRNA binds tightly to P site (only indicator tRNA can do this) along with translation initiation factors
  • Small subunit w/ bound initiator tRNA, moves along mRNA searching for first AUG
  • AUG found, translation initiation factors dissociate, large subunit binds
  • Translation cycle begins with 1st AA (w/ tRNA) binding to A site
  • All new proteins start with Methionine (typically snipped off in a later step)
46
Q

What terminates translation?

A
  • Presence of several STOP codons in mRNA (not recognized by a tRNA; do not specify an AA
  • Any STOP codon that reaches A site will bind a release factor –> alters catalytic activity, causing addition of a water, rather than forming a peptide bond
  • Frees the carboxyl end of the peptide chain –> peptide, mRNA, large + small subunits released
47
Q

Is the ribosome an enzyme or a ribozyme (is catalytic activity provided by RNA or protein compartments)?

A
  • A,P, E sites –> primarily RNA
  • Catalytic site (where peptide bond is formed) between P and A sites in large subunit is entirely RNA
  • Ribosomal proteins are mostly superficial (helping to create + maintain shape of RNA core)
48
Q

RNA world hypothesis

A
  • RNA did it all, including catalyzing rxns
    (RNA predates DNA as a molecule)
49
Q

Polyribosomes (polysomes)

A
  • Many ribosomes translating the same mRNA at the same time
  • Takes from 50 sec to 1-2 mins for a single ribosome to translate a protein
  • Greatly increases output (as soon as first ribosome out of way)
  • In both bacteria + eukaryotes
50
Q

Simultaneous transcription + translation in prokaryotes

A
  • No nucleus –> transcription + translation in same location
  • Can greatly increase output
  • Translation of mRNA while transcription of DNA is still happening
  • Can have polyribosomes (polysomes) translating the mRNA
51
Q

When do proteins fold?

A
  • Begins during translation, long before termination + disassembly of ribosomes
  • Although it doesn’t require energy (spontaneous), often assisted by proteins called molecular chaperones
  • Some chaperone proteins bind to ribosome near ‘tunnel’ where growing peptide exits
52
Q

What is post-translational modification (PTM)?

A
  • Chemical modifications of protein structure (20 AAs)
  • Addition of functional groups or small molecules
  • Major effects on charge, shape, activity
53
Q

What are some types of post-transcriptional modifications (PTMs)?

A
  • Glycosylation (addition of CHO)
  • Lipid addition
  • Phosphorylation
  • Ubiquitination
  • Methylation, hydroxylation, acetylation
  • proteolysis (cleavage of peptide bonds)
    Over 30+ types
54
Q

How do PTMs increase protein diversity?

A
  • Increase proteome complexity
  • So many different combinations of PTMs that can be done on a single protein, let alone all of the proteins a cell can make
55
Q

Regulation of protein production in euk cells

A
  • Nucleus: control of protein amount (initiation of transcription)
  • Cytosol: stabilization of mRNA (poly-A tail) to prevent degradation
  • Degradation of fully folded proteins in cytosol

Is more being made than degraded?

BIOL 130 (6 decks)

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