e3 super set bioc

Question

Answer

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)

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

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 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 function of snRNPs (small nuclear ribonucleoproteins) in splicing?

U1, U2, U4, U5, U6 bind splice sites and catalyze 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

What percentage of human genes undergo alternative splicing?

95%

What is the function of enhancer sequences?

Stimulate transcription at start sites thousands of bases away

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

Hutchinson-Gilford Progeria Syndrome

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 empirical formula for carbohydrates?

(CH2O)n

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)

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

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

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 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

Why is sucrose non-reducing?

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

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

What are glycosaminoglycans (GAGs)?

Long unbranched repeats of amino sugar + uronic acid, often sulfated and strongly negative, holding water

What are examples of GAGs?

Hyaluronan, chondroitin sulfate, heparan sulfate (ground substance of gingiva, PDL, cartilage)

What determines ABO blood type?

Terminal sugar on H antigen: Type O has H only; Type A adds GalNAc; Type B adds galactose

What is the function of lysozyme in saliva?

Hydrolyzes β(1→4) bond between NAM and NAG in peptidoglycan, lysing bacteria (especially Gram-positive)

Where does carbohydrate digestion begin?

Mouth, with salivary α-amylase (ptyalin)

What does salivary α-amylase do?

Cleaves internal α(1→4) bonds of starch into maltose, maltotriose, and α-limit dextrins

Why does salivary amylase stop working in the stomach?

Gastric acid (pH 1.5-3.5) denatures it

Where does starch digestion resume?

Small-intestinal lumen with pancreatic α-amylase after bicarbonate neutralizes chyme

What enzymes are in the brush border for carbohydrate digestion?

Maltase, sucrase, isomaltase, lactase

What is the only form of carbohydrate that can be absorbed?

Monosaccharides

What transporter carries glucose and galactose into enterocytes?

SGLT1 (Na+-coupled secondary active transport)

What transporter carries fructose into enterocytes?

GLUT5 (facilitated diffusion)

What transporter releases monosaccharides from enterocytes into blood?

GLUT2 (facilitated diffusion)

What is the cause of lactose intolerance?

Lactase deficiency → lactose reaches colon → osmotic diarrhea and bacterial fermentation (gas, acids)

What are the three types of lactose intolerance?

Primary (age-related decline), secondary (gut injury), congenital (rare)

What is the basis of oral rehydration therapy?

SGLT1 cotransports glucose and sodium, and water follows osmotically

Which GLUT transporter is insulin-responsive?

GLUT4 (skeletal muscle, adipose tissue)

Which GLUT transporter is the glucose sensor in liver and β-cells?

GLUT2 (high Km, low affinity)

Which GLUT transporter supplies the brain?

GLUT1 (high affinity, always active)

Where does glycolysis occur?

Cytosol