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fundamentals of nutrition and metabolism > Macromolecular Synthesis > Flashcards

Macromolecular Synthesis Flashcards

1
Q

Structure of DNA

A
  • nucleotides: one pentose sugar, base (ATGC), phosphate
  • pentose deoxyribose
  • AT base pair with 2 hydrogen bonds
  • GC base pair with 3 hydrogen bonds
  • C and T Are pyrimidine bases (one ring sugar)
  • G and A are purine bases (two ring sugar)
  • DNA stability encouraged by stacking interactions (VDWF), hydrophilic outside (phosphates), hydrophobic center (base pairs)
  • instability caused by electrostatic repulsion between charged phosphates; mitigated by histones
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2
Q

Structure of RNA

A
  • ribose (pentose), base (AUGC) and phosphate
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3
Q

The cell cycle stages and regulation

A
  • cell cycle regulated by checkpoints: cyclin, cyclin-dependent kinases to ensure environment is favourable
  • G1: cell checks if environment is stable and if cell is big enough
  • S: cell growth and development (duplication of genetic material)
  • G2: checks all DNA is replicated, and if enviroment is stable
  • M: mitosis
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4
Q

DNA replication

A

1) DNA helicase unwinds DNA to form the replication fork, single strand binding protein prevents reannealing
2) Leading strand is replicated via DNA polymerase I (3’ to 5’), 3’OH group nucleophilic attacks 5’P on adjacent nucelotide, catalysed bond formation by pyrophosphatase- exergonic reaction
3) lagging strand (anti-parallel) replicated in discontinuous fashion (5’ to 3’= unfavourable), short RNA primers bind and DNA polymerase III catalyses elongation in short bursts (Okazaki fragments). DNA polymerase I exonuclease activitu removes primers and adds DNA. DNA ligase stitches fragments together

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5
Q

The nucleosome and chromatosome

A
  • the nucleosome: x2 of each H2A, H2B, H3, H4 (octamer), 146bp of DNA wrapped around 1.75 turns
  • chromatosome: nucelosome + H1 histone
  • key role in reducing repulsion between DNA and condensation of genetic material
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6
Q

mRNA synthesis

A
  • occurs in 5’ to 3’ orientation (opposite to DNA)
  • TFIID binds to TATA box upstream of core promoter using TBP
  • TFIIA & B bind
  • TFIIF binds with RNAPII
  • TFIIE & H then bind
  • Zn finger motifs in TF help bind to DNA in stable manner
  • RNAPII is phopshorylated at C terminus (rich in serine and threonine), TFs dissociate and gene is transcribed
  • protein complex which cleaves at terminating region and is involved with poly(A) tail associated with C terminus of RNAPII
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7
Q

regulation of mRNA synthesis: enhancers

A
  • activator proteins bind to enhancer regions upstream of core promoter
  • bind and interact with TF on the initiation complex, stimulating transcription
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8
Q

Regulation of mRNA synthesis: repressors

A
  • repressor proteins bind upstream of core promoter in a silencing region
  • this silencing region typically overlaps with enhancer region, meaning activator proteins cannot bind and transcription is repressed
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9
Q

Regulation on mRNA synthesis: co-activators

A
  • histone modifcation to make DNA more readily accessible to RNAPII and associated basal TFs
  • N terminus of histone proteins can be modified, usually on R group of lysine (nitrogen rich)
  • acetylation, methylation, phosphorylation
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10
Q

Regulation of mRNA synthesis: co-repressors

A
  • histone deacetylase activity

- removes modification on histones so they aren’t as readily accessible

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11
Q

Post transcriptional modification of mRNA: splicing

A
  • splicing removes introns so only coding exons are on mature mRNA
  • snRNA (small nuclear RNAs) and proteins come together to form the spliceosome, through series of transesterifcation reactions
  • the 2’OH of the branch site in the intron nucleophilically attacks the 5’P at the donor site, forming a lariat structure
  • the 3’OH on the exon at the previous donor site attacks the 5’P at the acceptor site
  • phosphodiester bond formed and intron removed
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12
Q

Post- transcriptional modification of mRNA: 5’ capping

A
  • 7 methylguanine cap added to 5’ end
  • prevents degradation
  • acts as a protein binding site to allow for export of out the nucleus into the cytosol
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13
Q

Post-transcriptional modification of mRNA: poly(A) tail

A
  • poly(A) tail added to 3’ end of mRNA to prevent degradation
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14
Q

Different types of RNA: siRNA

A
  • small or short interfering RNAs
  • complementary sequences to mRNA
  • form part of the protein- containing RISC complex (RNA induced silencing complex) whcih base pair to the mRNA and induce mRNA degradation
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15
Q

Different types of RNA: miRNA

A
  • fragments of RNA which move from nucleus to cytosol
  • processed by Dicer in the cytosol to give rise to mature miRNA to form part of the RISC complex
  • if binding to mRNA is complete this can cause degradation
  • if binding to mRNA is incomplete this causes inability for the translational machinery to bind
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16
Q

Structure of tRNA

A

Anticodon loop
Anticodon stem
Acceptor stem
CCA 3’OH terminus which binds to amino acid

17
Q

Charging of tRNA

A
  • aminoacyl tRNA synthetases catalyse charging
  • tRNA acceptor can be an ‘iso acceptor’ for wobble base pairs
    1) amino acid is adenylated
    2) charging: transfer of adenylated amino acid on the tRNA involves binding of hydroxy group at the CCA 3’OH end and releases AMP
18
Q

Translation

A
  • eIF1,2,3,4 bind to the small ribosomal subunit which is bound to cahrged aminoacyl tRNA, with GTP
  • small subunit scans mRNA until reach start codon
  • large subunit (60s) binds (ribozyme with peptidyl transferase activity)
  • new charged tRNA enters the A site, and clamo slides along, old tRNA moves to P site
  • E site is exit site
  • adjacent amino acids condense and form peptide bond, catalysed by ribozyme
  • continue until meet STOP codon (no charged tRNA for this)
19
Q

Protein targeting by the ER

A
  • as N terminus of synthesised protein is exposed in cytoplasm, if has signal sequence, this is recognised by signal recognition particle (complex of proteins and non coding RNA)
  • SRP binds to N terminus and to SRP receptor on RER, which is coupled to translocon
  • GTP is hydrolysed, causing conformational change and dissociation of SRP
  • translocon opens, peptide moves through
  • signal peptidase clips N terminal signal sequence
  • peptide folds in ER lumen and is moved by secretory vesicles to the golgi (where modified by glycosylation etc)
20
Q

Glycosylation of proteins

A
  • N linked: occurs in ER, attached to amine N of asparagine

- O linked: less common, attached to hydroxyl groups of Ser, Thr, hydroxylysine (less common)

21
Q

Protein targeting for secretion or insertion into the plasma membrane

A
  • proteins packaged into secretory vesicles from the RER
  • move to the golgi apparatus, where glycosylation (O linked) can occur
  • vesicles bud off from the golgi, where can be targeted for degradation in lysosomes, insertion into plasma membrane or secretion
22
Q

Proteolytic processing of insulin

A
  • human insulin gene has 3 exons and 2 introns which are processed to form mature insulin in the cytosol
  • hydrophobic signal sequence (N terminal leader sequence) causes binding of SRP and movement onto RER, so transcription can continue in the lumen
  • introns are spliced following transcription of mRNA, forming preproinsulin
  • N terminal leader sequence is cleaved (24 residue) is cleaved post-translation, forming proinsulin in the RER lumen (by signal peptidase)
  • proinsulin is transported from the RER to the golgi
  • in the golgi, proinsulin is then cleaved again to form insulin A and insulin B, with a connecting peptide (which retains the conformation of A and B); A and B are then connected by disulfide bridges
  • secretory granules are secreted by exocytosis releasing mature insulin and C peptide
23
Q

The proteasome pathway for degradation

A
  • breakdown of skeletal muscle during starvation
  • predominately for abnormal proteins, short lived proteins (regulatory), long lived normal proteins i.e. contractile proteins in muscle, membrane proteins
  • ubiquitin is constitutively expressed but can be upregulated in stress, this tags proteins for degradation
  • enzyme cascade activated: ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2), ubiquitin protein ligase (E3), ubiquitin ubiquitin lovase
  • proteasome degrades tagged proteins in an energy dependent process, into di and tri peptides
  • peptides are transported to the lysosome via peptide transporter (PEPT1) on lysosome membrane, then subsequently degraded
24
Q

Lysosome degradation

A
  • predominately for endocytosed proteins (hormones) and membrane proteins i.e insulin receptors
  • lysosomes fuse with vesicles and release hydrolases/ proteases

fundamentals of nutrition and metabolism (12 decks)

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