e3 biochem slop

What is the process by which an enzyme system converts genetic information in dsDNA into an RNA strand with a complementary base sequence?

Transcription

What are the four stages of DNA transcription?

Binding of RNA polymerase to promoter; Initiation; Elongation; Termination

What is the function of the sigma (σ) subunit in bacterial RNA polymerase?

Directs the enzyme to specific DNA binding sites (recognizes promoter) and initiates synthesis

What is the core enzyme of bacterial RNA polymerase composed of?

All subunits except the sigma subunit (α2, β, β', ω)

What is the holoenzyme of bacterial RNA polymerase?

Core enzyme plus the sigma subunit

What is the most common sigma factor in E. coli?

σ70

What is the function of the rho (ρ) factor?

Helps terminate transcription at rho-dependent termination sites

Which eukaryotic RNA polymerase synthesizes pre-ribosomal RNA (28S, 18S, 5.8S rRNA)?

RNA polymerase I (in nucleolus)

Which eukaryotic RNA polymerase synthesizes mRNA precursors and snRNA?

RNA polymerase II (in nucleoplasm)

Which eukaryotic RNA polymerase synthesizes tRNA and 5S rRNA?

RNA polymerase III (in nucleoplasm)

Which eukaryotic RNA polymerase is strongly inhibited by α-amanitin?

RNA polymerase II

What is the TATA box sequence found in eukaryotic promoters at about -25?

TATA(A/T)A(A/T)(A/G)

What are the two common promoter motifs in prokaryotes?

-35 sequence (TTGACA) and -10 sequence (Pribnow box, TATAAT)

What is the CAAT box?

A promoter element located ~40-110 bp upstream of the start site in eukaryotes

What is the GC box?

A promoter element (GGGCG) located upstream of the start site in eukaryotes

What is the Inr sequence?

Initiator sequence at +1 in Pol II promoters

What type of termination involves a self-complementary region forming a hairpin and a string of U residues?

Rho-independent termination

What is the function of the spliceosome?

Carries out nuclear pre-mRNA splicing (removes introns)

What are the consensus sequences at splice sites?

GU at 5' end of intron and AG at 3' end

What is the branch site?

An internal site 20-50 nucleotides upstream of the 3' splice site; contains an A residue that forms a lariat intermediate

What is the function of U1 snRNP?

Binds the 5' splice site

What is the function of U2 snRNP?

Binds the branch site and forms part of the catalytic center

What is the function of U6 snRNP?

Catalyzes splicing

What autoimmune disease is caused by antibodies blocking snRNP function in splicing?

Systemic lupus erythematosus

What is alternative splicing?

Process where a particular exon may or may not be incorporated into the mature mRNA transcript; occurs in >95% of human genes

What is the function of enhancer sequences?

Stimulate transcription at start sites thousands of bases away; can be upstream, downstream, or within introns; orientation-independent

What type of transcription factor is required at every Pol II promoter?

General transcription factors

What is the function of the TATA box binding protein (TBP)?

Recognizes the TATA box as part of TFIID to initiate transcription

What are zinc finger transcription factors?

DNA-binding proteins with zinc coordinated to cysteine and histidine residues (C2H2) that bind the major groove of DNA

What is the function of TFIIIA?

A zinc finger protein required for RNA polymerase III transcription of 5S rRNA genes

What are intracellular hormone receptors?

Receptors for steroid and thyroid hormones that bind DNA response elements and regulate transcription

What are the domains of intracellular hormone receptors?

Variable region, DNA-binding domain, ligand-binding domain

What happens when a hormone binds its intracellular receptor?

The receptor dissociates from chaperones, translocates to the nucleus, binds response elements, and regulates transcription

What disease results from a silent mutation that activates a cryptic splice site in the lamin A gene?

Hutchinson-Gilford Progeria Syndrome

What is the significance of the GGC to GGT mutation in progeria?

It is predicted to be silent but activates a cryptic splice site, causing disease

What is the function of reverse transcriptase?

Synthesizes DNA using RNA as a template

What are ribozymes?

RNA molecules that can catalyze chemical transformations

What is the RNA world hypothesis?

The idea that RNA's dual capacity as genetic information carrier and catalyst supports RNA as the origin of life

What is the function of the lac repressor?

Binds to operator and blocks transcription of the lac operon in the absence of lactose

What is the inducer of the lac operon?

Allolactose (an isomer of lactose)

What is IPTG?

Isopropylthiogalactoside; a nonmetabolizable inducer of the lac operon used experimentally

What is the function of CAP (catabolite activator protein) in the lac operon?

Activates transcription when cAMP levels are high (low glucose)

What is the effect of glucose on cAMP levels in E. coli?

Glucose decreases cAMP, reducing CAP binding and lowering lac operon transcription

What is the function of thiogalactoside transacetylase?

Modifies toxic galactosides to facilitate their removal

What is the 5' cap structure?

m7G cap formed by condensation of GTP with the 5' triphosphate of the transcript; methylated at N-7 of guanine

What is the poly(A) addition signal?

AAUAAA; directs endonuclease cleavage 10-15 bases downstream and addition of poly(A) tail

What is the average half-life of eukaryotic mRNA?

~3 hours

What is the example of RNA editing in the ApoB gene?

In liver, full-length ApoB100 is produced; in intestine, C-to-U editing creates a stop codon, producing truncated ApoB48

What is the significance of the MDR1 gene silent mutations?

Combinations of silent mutations change codon usage, slowing translation and altering cotranslational folding, changing protein conformation

What is the formal definition of a carbohydrate?

Polyhydroxy aldehydes or ketones, or molecules that yield them on hydrolysis; empirical formula (CH2O)n, though amino and deoxy sugars do not fit exactly

What is an aldose?

A monosaccharide with a carbonyl group (C=O) at C-1 (aldehyde)

What is a ketose?

A monosaccharide with a carbonyl group (C=O) at C-2 (ketone)

What is a triose?

A 3-carbon monosaccharide (e.g., glyceraldehyde, dihydroxyacetone)

What is an aldohexose?

A 6-carbon monosaccharide with an aldehyde group (e.g., glucose, galactose)

What is a ketohexose?

A 6-carbon monosaccharide with a ketone group (e.g., fructose)

What is an oligosaccharide?

A carbohydrate of 3-10 monosaccharide units (e.g., glycoprotein glycans)

How do you determine D vs L configuration in a Fischer projection?

Look at the highest-numbered chiral carbon; -OH on right = D, -OH on left = L

Why are nearly all human sugars D-configuration?

Enzymes are stereospecific and recognize D-sugars; D-glucose is the biological form

How many stereoisomers exist for a molecule with n chiral centers?

2^n. An aldohexose has 4 chiral centers → 16 isomers (8 D, 8 L)

What is the relationship between D-glucose and L-glucose?

Enantiomers (mirror images, differ at every chiral center)

What is the relationship between D-glucose and D-galactose?

Epimers (differ only at C-4)

What is the relationship between D-glucose and D-mannose?

Epimers (differ only at C-2)

What is the relationship between D-glucose and D-fructose?

Constitutional isomers (same formula, different connectivity; aldose vs ketose)

What is the relationship between α-D-glucose and β-D-glucose?

Anomers (differ only at the anomeric carbon C-1)

What is the relationship between D-galactose and D-mannose?

Diastereomers, not epimers (differ at C-2 and C-4)

What is the anomeric carbon?

The new chiral center formed when a sugar ring closes (C-1 of aldoses, C-2 of ketoses)

What is mutarotation?

Interconversion of α and β anomers through the open-chain form until equilibrium

What is the equilibrium composition of D-glucose in solution?

~63% β-D-glucose, ~36% α-D-glucose, <1% open chain

In a Haworth projection, what does α mean for D-glucose?

Anomeric -OH is down (trans to CH2OH)

In a Haworth projection, what does β mean for D-glucose?

Anomeric -OH is up (cis to CH2OH)

What type of ring does glucose form?

Pyranose (6-membered)

What type of ring does fructose form?

Furanose (5-membered)

What is a reducing sugar?

A sugar with a free anomeric carbon that can reduce Cu2+ to Cu+ (Benedict's test)

Are all monosaccharides reducing sugars?

Yes, including fructose

What makes sucrose non-reducing?

Both anomeric carbons (glucose C-1 and fructose C-2) are involved in the glycosidic bond

What are amino sugars?

Sugars where -OH is replaced by -NH2 (often N-acetylated), e.g., glucosamine, GlcNAc, GalNAc

What are sugar acids?

Sugars where carbon is oxidized to -COOH, e.g., glucuronic acid, sialic acid

What are sugar alcohols?

Sugars where carbonyl is reduced to -OH, e.g., sorbitol, xylitol, mannitol

What are deoxy sugars?

Sugars with an -OH replaced by -H (e.g., 2-deoxyribose in DNA; fucose in blood-group antigens)

Why can't sugar alcohols form glycosidic bonds?

They have no anomeric carbon (no carbonyl to cyclize)

Why is xylitol used in sugar-free gum?

It is poorly fermented by oral streptococci, producing little acid

What is the glycosidic bond?

Bond formed when the anomeric -OH of one sugar reacts with an -OH of another, releasing water

What is the standard notation for a glycosidic bond?

e.g., Glc-α(1→4)-Glc: anomer, first carbon number, arrow, second carbon number

What is an O-glycosidic bond?

Sugar-sugar (di/polysaccharides) or sugar-Ser/Thr linkage

What is an N-glycosidic bond?

Sugar-base in nucleotides or sugar-Asn in N-linked glycoproteins

What are the monosaccharides and linkage of maltose?

Glucose-α(1→4)-Glucose; reducing; digested by maltase

What are the monosaccharides and linkage of lactose?

Galactose-β(1→4)-Glucose; reducing; digested by lactase (β-galactosidase)

What are the monosaccharides and linkage of sucrose?

Glucose-α(1↔2)-β-Fructose; non-reducing; digested by sucrase

How does Streptococcus mutans use sucrose to promote caries?

Glucosyltransferases split sucrose to build sticky insoluble glucans (plaque matrix) and release fermentable sugars

What is the critical pH below which enamel hydroxyapatite dissolves?

~5.5

What is the Stephan curve?

Graph showing plaque pH drops below 5.5 within minutes of sugar exposure and recovers over 30-60 min

Why does frequency of sugar exposure matter more than amount?

Each exposure restarts the pH drop, keeping plaque acidic longer

What is the linkage in amylose?

α(1→4) glucose; linear, coils into helix

What is the linkage in amylopectin?

α(1→4) backbone with α(1→6) branches every ~24-30 residues

What is the linkage in glycogen?

α(1→4) backbone with α(1→6) branches every ~8-12 residues

What is the linkage in cellulose?

β(1→4) glucose; straight chains H-bond into fibrils

Why can humans digest starch but not cellulose?

Human amylase and α-glucosidases cleave α bonds but not β(1→4) bonds

What are N-linked glycoproteins?

Glycans attached to asparagine (Asn) residues

What are O-linked glycoproteins?

Glycans attached to serine or threonine (Ser/Thr) residues

What are salivary mucins (MUC5B, MUC7)?

Heavily O-glycosylated proteins that lubricate oral tissues, form acquired pellicle, and aggregate bacteria