Cell molec

What features are shared by prokaryotic and eukaryotic cells?

Plasma membrane, DNA, and ribosomes

Why are viruses not considered cells?

They are not cellular and depend on host cells to reproduce

What type of genetic material can viruses contain?

DNA or RNA

Best microscopy for living, unstained transparent cells?

Phase-contrast microscopy

What is DIC microscopy useful for?

Living, unstained cells with a 3D-like appearance

Which microscopy has the highest resolution?

Electron microscopy; specimen is not living

Which microscopy tracks a specifically labeled molecule?

Fluorescence microscopy

Why can bright-field be poor for living transparent cells?

They often need staining, which may be toxic

~500–1,000 × g primarily pellets what?

Nuclei and other large/heavy material

~20,000 × g primarily pellets what?

Mitochondria

~50,000–100,000 × g pellets what?

Microsomal fraction

~200,000 × g pellets what?

Large complexes such as ribosomes

After all major pellets are removed, what remains?

Cytosol in the supernatant

640 × g followed directly by 100,000 × g: final pellet?

Mitochondria and microsomal fraction

Adult stem cells are usually what potency?

Multipotent

Embryonic stem cells are what potency?

Pluripotent

Which has greater teratoma risk: multipotent or pluripotent?

Pluripotent

What are iPS cells?

Somatic cells reprogrammed to a pluripotent state

Differentiated cell → another differentiated cell directly?

Transdifferentiation

Autologous vs allogeneic transplant?

Autologous = self; allogeneic = another person

Why use a cell line for repeated experiments?

It provides a renewable population of cells

Which bases are purines?

Adenine and guanine (A and G)

Which bases are pyrimidines?

Cytosine, thymine, and uracil (C, T, U)

Nucleoside vs nucleotide?

Nucleoside = sugar + base; nucleotide = sugar + base + phosphate

Ribose vs deoxyribose?

Ribose has a 2′ OH; deoxyribose lacks it

Base attaches to which sugar carbon?

1′ carbon

Phosphate is associated with which sugar carbon?

5′ carbon

What bond connects nucleotides?

Phosphodiester bond

What charge does the DNA backbone have?

Negative, from phosphate groups

DNA strands are oriented how?

Antiparallel

DNA base pairing?

A–T and G–C

More GC content does what to Tm?

Raises Tm

Why does GC-rich DNA have a higher Tm?

GC base pairs stabilize the duplex more strongly

PCR steps in order?

Denaturation → annealing → elongation

PCR annealing temperature compared with Tm?

Annealing temperature is the same as Tm

Why does PCR require heat-resistant polymerase?

It must survive repeated high-temperature denaturation

RNA polymerase reads which DNA strand?

Template strand

RNA polymerase reads the template in what direction?

3′ → 5′

RNA is synthesized in what direction?

5′ → 3′

Coding DNA compared with mRNA?

Same sequence except DNA T becomes RNA U

What does a Northern blot assess?

Relative RNA expression

RT-PCR first converts RNA into what?

cDNA, which PCR then amplifies

What bond joins amino acids?

Peptide bond

Which amino acids are usually buried inside globular proteins?

Nonpolar/hydrophobic residues

Which residues are usually exposed on globular-protein surfaces?

Polar/charged residues

Which residues dominate transmembrane segments?

Nonpolar/hydrophobic residues

What substitution can disrupt a transmembrane segment?

Hydrophobic residue → polar or charged residue

Aspartate: abbreviation, code, property?

Asp, D, negatively charged

Glutamate: abbreviation, code, property?

Glu, E, negatively charged

Lysine: abbreviation, code, property?

Lys, K, positively charged

Arginine: abbreviation, code, property?

Arg, R, positively charged

Histidine: abbreviation and code?

His, H

Phenylalanine: abbreviation, code, property?

Phe, F, nonpolar/aromatic

Tyrosine: abbreviation and code?

Tyr, Y; aromatic with an OH

Valine: abbreviation and code?

Val, V

Which amino acid did the homework identify as the largest?

Arginine

In tandem mass spectrometry, which bonds are fragmented to determine a peptide’s amino-acid sequence?

Peptide bonds

ΔG < 0 means what?

Forward reaction is thermodynamically favorable

ΔG > 0 means what?

Forward reaction requires energy input

At equilibrium, ΔG equals what?

0

Keq > 1 generally corresponds to what ΔG°′?

Negative ΔG°′; products favored

Keq < 1 generally corresponds to what ΔG°′?

Positive ΔG°′; reactants favored

Does negative ΔG mean a reaction is fast?

No; thermodynamics does not determine reaction rate

What do enzymes lower?

Activation energy

Do enzymes change ΔG or equilibrium?

No

Three ways enzymes lower activation energy?

Orientation, reactivity/proton transfer, and strain

Chymotrypsin catalytic triad?

Ser195, His57, Asp102

Chymotrypsin nucleophilic attack residue?

Ser195

Chymotrypsin proton-transfer residue?

His57

What is Vmax?

Maximum rate when enzyme active sites are saturated

How do you find Km on a graph?

Substrate concentration at ½ Vmax

Lower Km generally indicates what?

Less substrate is needed to reach ½ Vmax

Competitive inhibitor effect?

Km increases; Vmax stays the same

How can competitive inhibition be overcome?

Increase substrate concentration

Noncompetitive inhibitor effect?

Vmax decreases

Lower Kd means what?

Higher ligand affinity

Carbonyl at end of monosaccharide?

Aldose

Internal carbonyl in monosaccharide?

Ketose

Glucose classification?

Aldohexose

Fructose classification?

Ketohexose

Ribose classification?

Aldopentose

α vs β sugar in professor's ring convention?

α = anomeric OH below; β = anomeric OH above

What bond joins two monosaccharides?

Glycosidic bond

Glycogen/amylopectin main-chain bond?

α-1,4

Glycogen/amylopectin branch bond?

α-1,6

Amylose structure?

Unbranched glucose polymer with α-1,4 bonds

Cellulose structure?

Unbranched glucose polymer with β-1,4 bonds

Lactose composition and linkage?

Glucose + galactose; β-1,4

Sucrose contains what?

Glucose + fructose

Chitin consists mainly of what?

Acetylated glucosamine units; structural polymer

What are GAGs?

Modified sugar polymers important in extracellular matrix

Gain electrons = ?

Reduction

Lose electrons = ?

Oxidation

Glycolysis occurs where?

Cytosol

Net products emphasized for glycolysis?

2 pyruvate, 2 ATP, and 2 NADH per glucose

G6P, F1,6BP, and PEP belong to what?

Glycolysis

Citrate and succinate belong to what?

Krebs/Citric Acid/TCA cycle

Krebs cycle occurs where in eukaryotic cells?

Mitochondrial matrix

NADH and FADH₂ mainly carry what?

High-energy electrons to the ETC

ETC/oxidative phosphorylation occurs where?

Inner mitochondrial membrane