Exam 1 Biochemistry Thread Flashcards
Gibbs free energy (G)
The potential energy of a chemical reaction or system with the capacity to do work.
High Energy Bond
Any bond that releases > -7 kcal/mol upon dissociation.
Gibbs Free Energy Equation
The change in free energy of a system (∆G) at constant pressure and temperature.
∆G = ∆H - T∆S
∆G ⇒ change in free energy
∆H ⇒ change in enthalpy
∆S ⇒ change in entropy
T ⇒ absolute temperature in Kelvin
Reaction Spontaneity
∆G > 0 ⇒ Reaction proceeds in the reverse direction (endergonic)
∆G = 0 ⇒ equilibrium
∆G < 0 ⇒ Reaction proceeds in the forward direction (exergonic)
Equilibrium Constant
(K or Keq)
Defined as the ratio of the concentration of products to concentration of reactants.
A + B ↔︎ C + D
Free Energy Change
The free energy change for a reaction (∆G) is given by:
Standard Free Energy
At Equilibrium
∆G = 0.
Concentrations of reactants and products are at equilibrium values.
Standard free energey change is related to the equilirium constant (Keq).
Reaction Kinetics
Rate of ractions determined by the rate constants (k) and concentrations of reactants.
Equilibrium occurs when the rate of the forward reaction equals the rate of the backwards reaction.
∆G Trends
As we approach equilibrium:
Keq gets bigger because [products] > [reactants]
∆G gets smaller
More negative K ⇒ more positive ∆G.
D & L
Isomers
D & L isomers are enantiomers.
D if OH on the farthest chiral C is on the right
L if OH on the farthest chiral C is on the left
D form in the body.
α and β
Isomers
α and β isomers are the result of ring formation ⇒ anomers
Fischer projections:
alpha ⇒ OH on the same side as oxygen ring
beta ⇒ opposite side
Hayworth projections:
alpha = trans
beta = cis
Fisher to Hayworth
Projections
right side ⇒ up
left side ⇒ down
Anomeric C
The anomeric C is linked to two oxygens.
C#1 → anomeric C in aldoses
C#2 → anomeric C in ketoses
Epimers
Isomers that differ in the position of OH at only one carbon.
Considered diasteriomers.
Galactose
C4 epimer of glucose.
Mannose
C2 epimer of glucose
Reducing Sugar
Anomeric C has available OH.
All monosaccharides are reducing sugars.
Ketose must tautomerize to an aldose first.
Keto-Enol Tautomerization
Sugars freely interconvert between the keto and aldo forms in solution.
Catalyzed by base.
Mutarotation
Cyclic sugars undergo epimerization between the alpha and beta anomeric forms in solution.
Forms a racemic mixture ⇒ racemization.
Shows mutarotation of plane polarized light.
Glucose Test
Urine test for glucose:
Glucose oxidase used to oxidize glucose to gluco-lactone and H2O2.
Peroxidase used to visualize the H2O2.
Clinitest
Uses Benedict’s reagent (copper reduction) to test for the presence of reducing sugars in urine.
Monosaccharide Reactions
Oxidation of terminal OH group
Monosaccharide Reactions:
Reduction of Carbonyl C
Yields new OH and creates a polyol.
Monosaccharide Reactions:
Reduction of OH
Reduction of OH on C#2 yields a deoxy sugar
Monosaccharide Reactions:
Replacement Reactions
Replacement of OH (usually at C#2) yields an amino sugar.
NH2 can then be acetylated.
Activated Monosaccharides
Monosaccharides activated as first step in metabolism.
Glycosides
Monosaccharides can be linked together via glycosidic bonds to form glycosides.
Glycosidic bonds form by glycosyltransferases via condensation of OH on anomeric C with OH of another sugar.
Glycosidic bonds cleaved by glycosidases and glycosylases.
Glycosidic Bonds
α linkages → cis
β linkages → trans
Lactose
galactosyl-β (1→4)-glucose
Sucrose
glucosyl - α (1→2) - fructose
Maltose
glucosyl - α (1→4) - glucose
Glycogen
Storage form of glucose in animals.
Branched chain polymer of α-D-glucose.
α 1→4 chains
α 1→6 branches
Starch
Storage form of glucose in plants.
Contains:
Unbranched polymer of α-D-glucose via α 1→4 linkages ⇒ amylose
&
Branched polymer of α-D-glucose α 1→6 linkages ⇒ amylopectin
Cellulose
Structural component of plant cell walls.
Unbranched polymer of β-D-glucose via β 1→4 linkages.
Glycoproteins
Proteins with short, often branched chains of oligosaccharides attached.
Proteoglycans
Large complexes of negatively charged heteropolysaccharides associated with a small amount of protein (core protein).
Important components of the extracellular matrix.
Large negative charge favors extended conformation and extensive hydration ⇒
GAGs
Proteoglycan containing glycoaminoglycan (GAG) a.k.a mucopolysaccharides
Long, unbranched, negatively charged.
Contains a repeating unit [acidic sugar-amino sugar]n
Usually [glucuronate glucosamine].
Glucosamine is frequently acetylated and often sulfated to increase negative charge.
Chondroitin Sulfates
The most abundant proteoglycan GAGs in humans.
Contains the repeating unit:
[D-glucuronate - N-acetyl-D-galactosamine-6(4)-sulfate]n
Bonds in DNA
Sugar and phosphoryl group linked via an ester bond.
Nucleotide monophosphate (NMP) monomers linked by 3’-5’ phosphodiester bond.
Nitrogenous base linked to sugar via N-glycosidic bond.
Base Pairing
Nitrogenous bases of DNA linked via hydrogen bonds.
Adenine - Thymine stabilized by 2 H-bonds.
Guanine - cytosine stabilized by 3 H-bonds.
DNA
Secondary Structure
Twisted right-handed helix
- Base stacking decreases contact between water and hydrophobic face ⇒ hydrophobic effect
- Van der Waals forces further stabilize the base
- Forms major and minor grooves
DNA Denaturation
- Alkali treatment (pH > 11.3)
- Cause H-bonds to break
- Does not destroy phosphodiester bonds
- Heat
- Midpoint of heat denaturation (Tm) correlated with GC/AT ratio
DNA Renaturation
Denatured DNA can realign and base-pair.
Denatured DNA can undergo hybridization and anneal with complementary mRNA strands.
Forms of DNA
- B - DNA
- normal DNA
- R-handed helix
- predominants
- A - DNA
- DNA / RNA hybrid
- Z - DNA
- L-handed helix
- via stretches of alternating purine and pyrimidine nucleotides
- L-handed helix
A-DNA and Z-DNA are rare and thought to be involved in regulation of transcription.
mtDNA
Double stranded
Circular
Codes for 13 proteins.
Found in multiple copies in the mitochondrial matrix.
Nucleohistone
Consists of DNA and histones.
[H2A, H2B, H3, and H4]2 forms octomer nucleosome core
H1 binds to linker DNA acts as linkages
Forms beads on a string structure.
Nucleosomes wind into coils ⇒ nucleofilaments / solenoid structures
Solenoid structures further compact forming chromosomes.
mRNA
Structure
- Has considerable secondary and tertiary structure due to loop-like structures within RNA single strand
- When 2 regions of ssRNA complementary, can base pair to form stem-loop or hairpin structure.
tRNA
Structure
- High percentage of modified bases
- 2º structure ⇒ cloverleaf
- Base pairing occurs in stem regions resulting in ds regions
- 3º structure ⇒ inverted “L”
- D-loop ⇒ contains dihydrouridine (D)
- Anticodon loop ⇒ base-pairs with codon on mRNA
- TψC loop ⇒ contains ribothymidine (T) and pseudouridine (ψ)
- Variable loop ⇒ varies in size
- 3’ CCA sequence ⇒ attachment site for amino acid
Ribozyme
RNA with catalytic activity.
Ex. rRNA ⇒ forms peptide bond linking AA in proteins
Peptide Bond
- Amide bond links AA in a protein ⇒ peptide bond
- Acts as a double bond due to resonance
- Planar
Protein Bond Angles
- omega (ω) angle ⇒ peptide bond ⇒ 0º or 180º
- phi (φ) angle ⇒ nitrogen and alpha carbon
- psi (ψ) angle ⇒ carbonyl carbon and alpha carbon
If phi and psi angles for the whole protein is known, the 3-D structure of the protein is also known.
Beta Strand
2º structure of protein
Elongated straight chain stabilized by hydrogen bonding across the backbone (i.e. perpendicular).
H-bonds can be intra-chain or inter-chain.
Same orientation ⇒ parallel
Opposite orientations ⇒ anti-parallel
Can zig-zag to form β pleated sheets.
α-Helix
2º structure of protein
Stabilized by intra-chain hydrogen bonds parallel to central axis.
Cannot incoorporate proline residues.
β-Turn
2º structure of protein
Loop in the protein.
Stabilized by backbone hydrogen bond that causes chain to change direction.
Typically involves four amino acids including a pro and gly.
DNA-Binding Motifs
- Helix-loop-helix (dimer)
- Tandem array of Zinc Fingers
- Leucine zipper (dimer)
- Homeodomain (contains helix-turn-helix)
- From homeobox complex with DNA
Protein Folding
- Starts immediately after translation
- Largely dictated by the amino acid sequence
- Forms molten globule structure
- Added by chaperones
- Ex. GroEl
Protein
Quarternary Structure
Arrangement of multiple folded protein subunits to form a multi subunit complex.
Usually bind via non-covanlent interactions:
hydrophobic interactions
hydrogen bonding
electrostatic interactions
Prosthetic Groups
Non-amino acid groups required by a protein to be functional.
Protein Isoforms
Protein with the same function as another protein but which is encoded by the same or a differnt gene and may have small differences in sequence.
Amino Acid
Basic Structure
- At physiological pH 7.4, carboxyl group dissociated and amino group protonated
- α-carbon is chiral except for glycine
- L-form found in mammals
- R-group determines solubility
Non-Polar
Amino Acids
GLAM VIP For Women
Polar Uncharged
Amino Acids
Queens Never Take Your Silly Crown
Polar (+) Charge
Amino Acids
HRK
Polar ( - ) Charge
Amino Acids
Cystine
2 cysteines form a covalent disulfide bond ⇒ cystine
Histidine
Histidine’s heterocyclic imidazole side chain weakly basic and largely uncharged at physiological pH.
When incorporated into a protein, can be neutral or positively charged depending on environment.
R group has a pI ~ 6.5-7.4 in proteins meaning it can serve as a buffer at physiological pH.
Essential Amino Acids
HV MILK FTW
Histidine
Valine
Methionine
Isoleucine
Leucine
Lysine
Phenylalanine
Threonine
Tryptophan
Isoelectric Point (pI)
The pH at which the net charge on a molecule is zero.
The average of the pK’s for amino acids with 2 ionizable groups:
pK1 for the α-carboxyl group ~ 2-3
pK2 for the α-amino group ~ 9-10
The average of the two pK’s on either side of the isoelectric form for those with 3 ionizable groups.
Plasma Protein
Electrophoresis
Carried out at pH above pI values for most plasma proteins.
Proteins will carry a negative charge and move towards the positive electrode at a rate dependent on their net charge.
Apoenzyme
The inactive enzyme without its coenzyme.
Holoenzyme
The active form of an enzyme with a coenzyme component.
Co-factor
A metal ion coenzyme.
Coenzyme
A small organic molecule coenzyme.
Cosubstrates
Coenzymes that are loosely associated with the enzyme and leave in a changed state.
Prosthetic Group
Coenzyme that is permanently attached and is not altered during the reaction.
Classification of Enzymes
Michaelis Menten
Equation
Describes the kinetics of enzyme-catalyzed reactions.
Vmax ⇒ the maximal rate of the reaction when all of the enzyme is occupied by substrate.
Km is a reflection of the enzyme’s affinity for substrate.
(Not when Kcat is included)
When [S] = Km ⇒ v = 1/2 Vmax
Turnover Rate
(Kcat)
The maximum number of substrate molecules converted to produce per enzyme molecule per second.
Measures the efficiency of the enzyme.
Theoretical upper limit of 109 M-1sec-1 ⇒ catalytic perfection
Reaction becomes diffusion limited.
Lineweaver-Burke
Linearized version of the Michaelis-Menten Equation
Irreversible Inhibition
The destruction or modification of one or more functional groups of the enzyme resulting in a permanent reduction in enzyme activity.
Decreases Vmax.
Reversible Inhibition
Takes place only in the presence of a specific inhibitor.
Competitive inhibition vs Noncompetitive inhibition
Competitive inhibition
Inhibitor binds to the active site
Can be reversed by increasing [substrate]
No change in Vmax
Apparent increase in Km
Noncompetitive Inhibition
Inhibitor binds somewhere other than the active site.
No change in Km.
Apparent decrease in Vmax.
Allosteric Regulation
Effector or ligand binds to the regulatory site.
Enzymes often have more than one subunit.
Shows a sigmoidal v vs [S] curve.
Increase activity ⇒ positive allosteric effector
Decrease activity ⇒ negative allosteric effector
Can alter Km, Vmax, or both.
Homotrophic effector ⇒ substate for that enzyme
Heterotrophic effector ⇒ seperate molecule
Covalent Modification
of Enzymes
Regulation of enzymes via reversible covalent modification.
Most often phosphorylation/dephos at serine, threonine, or tyrosine residues.
Prokaryotic DNA Replication
-
Helicase seperates DNA strands at the AT rich ‘origin’ of replication.
- Topoisomerase relieves supercoils
- Single strand binding proteins prevent reannealing
- DNA primase lays down an RNA primer
-
DNA polymerase III replicates DNA continuously in 5’→3’ direction on the leading strand and in Okazaki fragments in the 3’→5’ direction on the lagging strand.
- Sliding clamp complex holds DNA pol on the DNA ⇒ processivity
- DNA polymerase I degrades RNA primer and fills in with DNA.
- Fragments joined by DNA ligase.
*DNA pol II with repair function.
Eukaryotic DNA Replication
- Origin Recognition Complex (ORC) binds to the origin of replication.
- ORC recruits cell division cycle 6 (CDC6) to coordinate replication with mitosis.
-
Minichromosome maintenance complex (MCM) acts as helicase to seperate DNA strands. (ATP dependent)
- Topoisomerase undoes supercoils formed
- Replication Protein A (RPA) [SSB] prevents reannealing
- DNA polymerase α lays down RNA primer.
-
DNA polymerase ε (epsilon) elongates leading strand.
* *DNA polymerase δ** (delta) elongates lagging strand.- Both have 3’→5’ exonuclease activity for proofreading.
- Replication Factor C (RFC) [clamp loader] loads Proliferating Cell Nuclear Antigen (PCNA) [clamp] which holds Pol on the DNA ⇒ processivity
-
RNase H1 or Fen1 degrades RNA primer on lagging strand.
- Fen1 has 3’→5’ exonuclease activity for proofreading.
- DNA polymerase δ fills in the gap with DNA.
- DNA ligase I joins Okasaki fragments.
Telomeres
Non-coding hexanucleotide repeats (AGGGTT) at the ends of linear chromosomes that maintain the structural integrity of eukaryotic chromosomes.
Lagging strand end problem arises with removal of RNA primer during synthesis.
Shorter and shorter daughter DNA molecules with incomplete 5’ ends result with each round of replication.
Telomerase
Ribonucleoprotein present in constantly replicating cells.
Addresses lagging strand end problem.
“Template-bearing reverse transcriptase”
- Telomerase has RNA molecule that acts as a template for telomere elongation.
- Telomerase has polymerase activity that places new telomere repeat at the 3’ end of leading strand.
- DNA pol α inserts RNA primer on the 5’ end of lagging strand and elongates in the 5’→3’ direction.
- RNA primer removed after.
Prokaryotic
Mismatch Repair
(MMR)
Corrects single base mismatches or small insertions/deletions.
- MutS dimer follows behind DNA Pol looking for distortions in helix
- Mut S binds to mutated DNA and recruits MutH and MutL
- MutH r_ecognizes methylated parent_ strand
- MutL activates the complex to form a loop
- MutH nicks daughter strand near methylated site and recruits a helicase
- Complex slides past site of mismatch followed by exonuclease, leaving gap extending beyond mismatch.
- Gap filled by DNA Pol III
- Sealed by DNA ligase
Eukaryotic
Mismatch Repair
(MMR)
Corrects single base mismatches or small insertions/deletions.
- MutS and MutSβ recognize mismatch, bind, and recruit complex.
- MutLα binds and activates exonuclease activity removing mismatched base
- Synthesis of repaired strand requires RFC (clamp loader), PCNA (sliding clamp), Pol-δ, and DNA ligase.
Microsatellite Instability
Microsatellites are tandem repeats of 2-5 base pairs x thousands.
Microsatellite instability is genetic hypermutability due to defect in MMR.
Can cause Hereditary Non-Polyposis Colorectal Cancer aka Lynch syndrome.
Nucleotide Excision Repair
(NER)
Corrects damaged DNA containing bulky adducts.
Ex. Thymine dimers from UV damage or chemical carcinogens
- Region of damaged strand excised by excision endonuclease (aka exinuclease)
- Hydrolyzes phosphodiester bonds on both sides of the lesion
- DNA Pol copies undamaged strand with help from RFC and PCNA
- DNA ligase seals gap
Xeroderma pigmentosum and basal cell carcinomas result from defects.
Base Excision Repair
(BER)
Used to repair damaged single bases (non-bulky damage) caused by oxidation, alkylation, hydrolysis, or deamination.
-
Glycosylase cuts N-glycosidic bond of damaged base and removes base
- Leaves either apyrimidinic or apurinic site
- Endonuclease removes sugar
- Lyase removes phosphate
- DNA Pol and ligase finishes repair
Homologous Recombination
(HR)
Uses homologous dsDNA as template ⇒ error-free
- Broken dsNDA processed by exonucleases to produce DNA duplex with a protruding 3’-ssDNA tail
- RAD51, homologous pairing protein, loaded onto ssDNA
- RAD51 searches for an intact homologous DNA template
- Template used for complementary DNA synthesis
Non-homologous ends joining
(NHEJ)
Repairs DS breaks in template-independent manner ⇒ error prone.
Some DNA lost.
- KU proteins and DNA-PKcs (DNA-dependent protein kinases) recognize and link broken DNA ends
- Recurits nucleases to make ends better substrates for ligation
- Ligases connect ends
DNA ⇒ RNA
Template
RNA produced is complimentary to the template strand.
The non-template strand is identical (except for U’s) to the RNA produced ⇒ called the coding strand.
Ribosomal RNA
(rRNA)
Major building blocks of ribosomes.
Prokaryotes: 5s, 16s, 23s
Eukaryotes: 5s, 5.8s, 18s, 23s
Small Non-coding RNAs
(ncRNA)
Involved in regulation and are not translated into proteins.
Three main types:
- Small nuclear RNAs (snRNAs)
- Small nucleolar RNAs (snoRNAs)
- MicroRNAs (miRNA)
Small nuclear RNAs
(snRNAs)
Used in the spliceosome.
Small nucleolar RNAs
(snoRNAs)
Guide chemical modifications of rRNA, tRNA, and snRNA.
MicroRNAs
(miRNA)
Function in RNA sliencing and post-transcription regulation of gene expression.
Prokaryotic Transcription
-
Initiation
- Holoenzyme of RNA polymerase (core + sigma factor) recognizes and binds to the -35 consensus sequence and inserts into DNA at the -10 TATA box of the promotor ⇒ closed complex
- Hydrolysis of ATP activates helicase activity of RNA pol seperating DNA ⇒ open complex
- RNA pol makes several abortive attempts, sigma factor dissociates, and elongation begins.
-
Elongation
- Ribonucleotides added to 3’ end of RNA transcript
- RNA pol does not have exonuclease activity but will halt at mismatched base-pairs and remove it
-
Termination: two methods
-
Intrinsic termination sites
- Palindromic GC-rich region followed by oligo U’s on nascent mRNA
- Forms stem-loop that interacts with RNA pol causing it to pause and dissociate
- Oligo U’s after stem-loop cause nascent RNA transcript to dissociate from DNA
-
Rho-dependent
- Nascent mRNA has 5’ Rho binding site
- Rho factor [RNA-dependent ATPase with helicase activity] binds to mRNA
- Rho moves up mRNA and strips it from RNA Pol and DNA
-
Intrinsic termination sites
Prokaryotic mRNA
- 5’ UTR or leader sequence (Shine-Delgarno Sequence) ⇒ recognizes ribosome for translation
- AUG start codon codes for N-formyl-Met
- 3’ UTR or trailing sequence
- Polycistronic
Chromatin Modification
-
Histone acetyltransferases (HATs)
- Transfer acetyl group to 1º amine of lysine side chain on histone ⇒ neutralizes charge-charge interaction
- Works with chromatin remodelers to form euchromatin
-
Histone deacetyltransferases (HDACs)
- Removes acetyl group from histones
- Works with chromatin remoders to change euchromatin to heterochromatin
Nucleosome and REmodeling and Deacetylase Complex
(NuRD)
ATP-dependent chromatin recomdeling complex.
Has histone binding proteins and deacetylase activity.
Important role in regulation of gene transcription, genome integrity, and cell cycle regulation.
RNA Polymerase I
- Found in the nucleolus
- Synthesizes rRNAs except 5S rRNA
- Recognized by general transcription factors (GTFIs)
- Regulation linked to cell growth and protein translation
RNA Polymerase II
- Synthesizes mRNA
- Synthesizes most small noncoding RNAs
- Has a wide variety of regulatory elements
- Most controlled Pol
RNA Polymerase III
- Makes tRNA
- Makes 5S rRNA
- Makes some snRNA and snoRNA
- Most are ‘housekeeping’ genes needed all the time
- Regulation tied to cell growth and cell cycle
- Requires fewer regulatory proteins compared to RNA Pol II
-
Requires no control sequences upstream of the gene
- Relies on internal control sequences within the transcribed gene
Core Promoter
The minimal DNA sequence required to direct the initiation of transcription.
Region where RNA polymerase and general transcription factors interact.
No consensus sequence in eukaryotes.
Ex. TATA box or Hogness Box
General Transcription Factors
(GTFs)
aka basal transcription factors
The most basic set of proteins needed to activate gene transcription.
Binds to the template DNA.
Help to localize RNA polymerase and regulation initiation of elongation.
Proximal Control Elements
DNA sequences within 250 base pairs of the start site that alter the rate of transcription initiation by interacting with regulators.
Are typically position dependent.
Usually upstream.
Ex:
CAAT box ⇔ CAAT box transcription factor (CTF)
GC box ⇔ Sp1
Distal Control Elements
DNA sequences which are farther away from the start site that alter transcription.
Position and orientation independent.
Can be enhancers or silencers.
Specific Transcription Factors
(STFs)
Interact with proximal and distal control elements to modulate the level of transcription.
DNA binding domain (BD) ⇒ recognizes the control elements
Transactivation domain ⇒ binds chromatin remodeling factor, co-activators, or co-repressors, and other factors.
Mediator Proteins
Forms a complex that acts as a bridge betwee the regulators and core promoter.
RNA Polymerase II
Pre-initiation Complex
- TATA Box Binding Protein (TBP) binds to the TATA box and marks site for RNA polymerase recruitment
-
TFIID recognizes the core promoter DNA sequence and TBP
- Binding causes sharp bend dramatically marking spot
- TFIIF finds RNA Pol II and ferries it to the initiation complex.
-
TFIIH joins and helps activate RNA Pol II
- Has helicase activity to create transcription bubble
- Has kinase activity that phosphorylates the Carboxy Terminal Domain (CTD) of RNA Pol II
- Activates polymerase
- Positions it directly over the DNA
- As RNA pol II escapes the promoter it leaves the initiation complex behind
Eukaryotic Transcription
Elongation and Termination
- Once all initiation complex components and regulatory proteins in place, polymerase escapes the promotor
- Makes several small abortive transcripts and starts elongation
- Transcript is terminated when RNA Pol II reaches an AAUAAA polyadenylation signal
- GU-rich region after polyadenylation signal causes polymerase to fall off DNA.
mRNA Processing
7-methyl cap
- Capping enzyme complex adds a 7-methylguanosine triphosphate cap to 5’ end of primary transcript
- Connected via a 5’-5’ triphosphate linkage
- Helps protect from endonucleotytic degradation
- Serves as marker that transcript is mRNA
mRNA Processing
Poly-A Tail
- AAUAAA polyadenylation signal recognized by polyadnylation factors
- Recruit endonuclease to cut the RNA
- Recruits polyadenylate polymerase to add poly A tail
- Important for nuclear export
- Length affects stability and half-life of mRNA
mRNA Splicing
Spliceosome removes introns and joins exons
snRNAs complex with proteins to form small nuclear ribonucleoprotein particles (snRNPs)
-
Intron Splice Sites
- 5’ consensus GU ⇒ 5’ splice donor site
- 3’ consensus AG ⇒ 3’ splice acceptor site
- conserved adenosine towards 3’ end ⇒ branch site
-
Process:
- snRNP bind the ends of the intron and the branch site A to loop out the intron
- 2’ OH from branch point A nuc. attacks G at 5’ end creating a lariat
- Free 3’ OH of exon 1 attacks 5’-P at splice acceptor site joining exons 1 and 2
tRNA Processing
- 5’ leader sequence cleaved by RNase
- 14 nucleotide intron removed by endonuclease
- Uracil residues at 3’ end replaced by “CCA”
- Certain bases modified
Operons
A region comprised of several structural genes controlled by a common promoter and regulated by a common operator.
An operator is a segment of DNA that binds a repressor which regulates gene expression.
LAC Operon
Structural Genes
- β-Galactosidase [Lac Z] ⇒ intracellular enzyme that cleaves lactose into glucose and galactose
- β-Galactosidase permease [Lac Y] ⇒ membrane-bound transport that mediates lactose entry into cells
- β-Galactosidase transacetylase [Lac A] ⇒ transfers an acetyl group from acetyl-CoA to galactose
LAC Operon
Regulation
-
Lactose only ⇒ Lac operon induced (Positive regulation)
- Lactose → allolactose
- Allolactose binds repressor protein ⇒ inactivates
- Repressor leaves operator
- When glucose absent, adenylate cyclase active ⇒ makes cAMP
- cAMP binds catabolite activator protein (CAP) activating it
- CAP binds CAP binding site causing ↑ transcription
-
Glucose only ⇒ Lac operon repressed (Negative regulation)
- Repressor bound to operator site downstream of promotor region
- Prevents RNA Pol from binding to promotor
- Transcription blocked
-
Glucose + Lactose ⇒ derepressed state
- Lactose → allolactose ⇒ repressor
- Repressor leaves operator
- Transcription on but negligible since RNA Pol cannot efficiently initiate transcription without active CAP protein
- Basal levels of gene expression
Trp Operon
Structure
- Transcriptional control region ⇒ operator within the promoter region
- Unlinked Trp R gene codes for repressor protein
- Not part of operon
- 5 structural genes involved in last steps of tryptophan biosynthesis
- Contains a leader peptide with an attenuator sequence (in mRNA transcript)
Trp Operon
Regulation
Operon sensitive to ratio of charged to uncharged tRNAtrp.
Attenuation allows fine control.
Repressor/Operator Control
- High [trp], trp combines with trp R repressor protein
- Complex binds operator site
- Transcription blocked
- Tryptophan acts as a corepressor (negative control)
Attenuation
Leader peptide with attenuation sequence (contains 2 trp codons) can form two hairpin loops.
- High [trp] ⇒ trp incorporated quickly ⇒ ribosome moves quickly and blocks site 2 ⇒ hairpin forms between sites 3 and 4 making a termination signal ⇒ kicks off RNA pol and premature transcript forms
- Low [trp] ⇒ trp incorporated slowly ⇒ ribosome stalls ⇒ alternative hairpin forms between sites 2 and 3 ⇒ trancription continues ⇒ full transcript made
Eukaryotic Regulation of Expression
Overview
The main level of control is at the transcriptional level.
Cis-acting DNA elements recruit trans-acting factors to initiate, modulate, or repress gene transcription.
Eukaryotic systems use coordinated transcription control ⇒ one master transacting factor regulating multiple genes.
Multiple levels of regulation exist outside of transcription.
Ex. alternative mRNA splicing, control of mRNA stability, and control of translational efficiency.
GAL4
Transcriptional Control
Structural genes: Gal 1, Gal 10, Gal 2, Gal 7, Mel 1
Regulatory genes (constitutively expressed): Gal 4, Gal 80, Gal 3
GAL4 binds to the upstream activating sequence (UAS) of all 5 structural genes activating transcription.
Galactose Absent:
- GAL80 binds GAL4 preventing it from binding the UAS ⇒ represses transcription
Galactose Present:
- Galactose binds Gal 3 ⇒ conformational change ⇒ complex binds Gal 80 in cytoplasm
- Causes an equilibrium shift that recruits the intranuclear Gal 80 bound to Gal 4 into the cytoplasm
- Free Gal 4 binds UAS and stimulates transcription
Alternative Splicing
Results in a single gene coding for multiple proteins.
-
Splicing silencers (cis-acting) bind splicing-repressor proteins (trans-acting) to reduce the chance that nearby site will be used as a splice junction.
- Located in neighboring exon ⇒ exonic splice silencer (ESS)
- Located whtin the intron itself ⇒ intronic splice silencers (ISS)
-
Splicing enhancers (cis-acting) bind splicing-activator proteins (trans-acting) to increase the chance that nearby site will be used as a splice junction.
- Located in neighboring exon ⇒ exonic splice enhancer (ESE)
- Located whtin the intron itself ⇒ intronic splice enhancer (ISE)
RNA Editing
mRNA undergoes nucleotide changes before translation.
Increases protein diversity without increasing gene pool.
Substiution editing most common.
Two major systems both involve deamination reactions:
- Cytidine → uracil by cytidine deaminase
- Adenosine → inosine by adneosine deaminase
Apolipoprotein B
Example of RNA editing.
In liver, full mRNA transcript translated ⇒ apoB100
In small intestines, editosome changes C → U creating a stop codon.
Only first 48% of transcript translated ⇒ apoB48
Iron Metabolism
Regulation
Expression of transferrin and ferritin regulated by iron response elements (IREs) [cis-acting].
- IREs form stem-loop structure which can bind iron response proteins (IRPs) [trans-acting].
- 5’ IRE prevents transcription.
- 3’ IRE allows transcription and stabilizes MRA.
- [IRP] high when [iron] low.
- Transferrin mRNA has 3’ IRE
- Ferritin mRNA has 5’ IRE
When [iron] low, [IRP] high ⇒ IRP binds IRE ⇒ transferrin activated and ferritin repressed.
When [iron] high, [IRP] low ⇒ IRP does not bind IRE ⇒ ferritin expressed and transferrin mRNA degraded.
RNA Interference
(RNAi)
RNA molecules used to interfere with gene expression.
Via destruction of mRNA or inhibition of translation.
Role in defending against parasitic nucleotide sequences i.e viruses and transposons.
- microRNAs (miRNAs) transcribed and processed.
- In cytoplasm, Dicer (endonuclease) processes miRNA to produce short DS miRNA.
- Guide/Antisense strand of DS miRNA hybridizes with RNA-induced silencing complex (RISC)
- Guide strand targets mRNA for degradation or prevents translation
RNAi can also be induced by exogenously added siRNA.
Epigenetics
Mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence.
Ex.
ATP-dependent chromatic remodeling by HATs and HDACs.
DNA methylation
DNA Methylation
DNA hypermethylation silences genes.
Cytosine bases in CpG-rich regions of promoters methylated by DNA methyltransferases (DNMTs).
Unmethylated CpGs often grouped into CpG islands, present in 5’ regulatory regions of most genes.
Hunters Syndrome
(MPS II)
- Defective iduronate 2-sulfatase
- Removes sulfate from sulfated alpha-L-induronic acid
- GAG present in heparan sulfate and dermatan sulfate
- X-linked recessive
- Presentation:
- Mild type: lives to adulthood
- Severe type: intellectual decline and rapid disease progression, lose basic function skills by 6-8 y/o, terminal around 10-12 y/o
Hurler Syndrome
(MPS I)
- Defect in alpha-L-iduronidase
- Hydrolysis of unsulfated alpha-L-iduronic acid
- Present in heparan sulfate and dermatan sulfate
- Heparan sulfate: glucuronic acid & N-acetylglucosamine
- Dermatan sulfate: L-iduronate & N-acetylglucosamine
- Autosomal recessive
- More severe than other subtypes (MPS IS and MPS IH/S)
