BIOL 3450 - Exam 1

How do peripheral proteins associate to the membranes?

-Via charge (usually +protein/-membrane) -Specific lipid binding motifs-- for example PH domain for PIP2, PIP3 -Binding to other proteins in membrane

Characteristics of transformed or stem cell lines

-can grow in liquid suspension -"immortal" / can be cultured indefinitely -not contact inhibited; form 3D mounds or balls -relatively undifferentiated

Why is reverse transcriptase a key step?

-mRNA have a poly-A tail which then can use a primer to make cDNA -mRNA/DNA hybrid is created after first cycle

What is the charge of the peptide A-G-S-E-K at pH 7?

0 E = glutamic acid, charge = -1 K = lysine, charge = +1 net charge = 0

At equilibrium, what does delta G equal?

0; therefore, Delta G naught = -RTlnKeq

How does molecular cloning work?

1. A DNA fragment to be cloned is enzymatically inserted to plasmid vector 2. Mix E. coli with plasmids in presence of calcium chloride; heat pulse culture on nutrient agar plates containing ampicillin 3. Transformed cell will survive because of antibiotic resistance 4. Plasmid is replicated 5. Cells multiply with the DNA inside

How does base excision repair work?

1. A DNA glycosylase flips the thymine base out of the helix 2. APEI cuts the DNA backbone 3. AP lyase removes the deoxyribose phosphate 4. DNA Pol Beta and DNA ligase fix it

How is cholesterol synthesized?

1. Acetyl CoA + acetoacetyl CoA 2. HMG-Coa is reduced to mevalonate 3. Isopentenyl pyrophosphate (IPP) forms isoprenoids and farnesyl pyrophosphate 4. Farnesyl pyrophosphate forms squalene 5. Cholesterol is formed from squalene

In what direction does tRNA read mRNA?

5'-3'

In what direction is the new DNA strand made?

5'-3'

Eukaryotic pre-mRNA processing

5'-methylated G cap 3' polyA tail Splicing

How is translation initiated?

elF4 complex binds to both polyA binding protein (PABPC) and to 5' cap

What is the free energy change in kcal/mol for Glucose + ATP -> Glucose 6-P + ADP? Glucose 6-P -> Glucose + Pi ΔGo' = -3.3 kcal/mol ATP -> ADP + Pi ΔGo' = -7.3 kcal/mol

-4 First we reverse one of the chemical reactions to get the desired half-reaction: Glucose + Pi -> Glucose 6-P ΔGo' = +3.3 kcal/mol (if we reverse the reaction, we reverse the sign of the free energy change) ATP -> ADP + Pi ΔGo' = -7.3 kcal/mol Adding the two chemical reactions together, and also adding their deltaG values, Glucose + ATP -> Glucose 6-P + ADP (the Pis cancel out), ΔGo' = -4 kcal/mol

What is the delta G naught of... 1. ATP to ADP +Pi 2. AMP + PPi

-7.3 for both

What are types of covalent modifications of a protein?

-Acylation: association with protein on amino terminus. reversible (cytosol) -Prenylation: association with protein on carbon terminus. Anchored by hydrophobic interaction (cytosol) -GPI: carbohydrate linked to phosphoglyceride and attached to protein (exterior) -Palmitoylation: associates fatty acids covalently to N-terminus of a protein

Characteristics of cryo-electron microscopy

-Biological samples preserved in native state, frozen in vitrified water, stable even in high vacuum -Low energy electrons preserve sample, no need for staining or coating with heavy metals -Direct electron detectors for high sensitivity -For uniform particles, can average tens of thousands of images for details imagining and 3D reconstruction

Characteristics of immunofluorescence microscopy

-Can detect specific proteins in fixed cells -Uses antibody that has a fluorescent dye attached to it covalently

Methods of isolating cell organelles: how to break through cell wall / membrane

-French press with hypotonic solution -Sonication -Enzymes (lysozyme) and detergent -Bead beating (microscopic glass, ceramic, steel beads)

What are some tools used to locate regions of expression?

-In situ hybridization to visualize location of the mRNA -Fusion constructs when making plasmid insert polynucleotides to make protein of interest -Promoter-fusion: what cells are actually transcribing that promoter -Protein fusion: where in the cell the protein actually goes

How can molecular tools be used to study a protein?

-Locate regions of expression -analyze protein function

Characteristics of Fluorescence microscopy

-Most versatile and powerful for localizing molecules within a cell by light microscopy -Use molecular genetics approaches to express a fusion between a protein of interest and a naturally fluorescent protein -Localize and quantify specific molecules in living cells -Use fluorophores-molecules that absorb or emit light at specific wavelengths

What are some tools used to analyze protein function?

-Overexpression of the protein -Elimination or alteration of the protein and/or its activity -edit genome with Crispr-Cas9

How do you analyze the elimination or alteration of the protein and / or its activity?

-Replace normal gene with other sequences in cells and organisms (Knock-out/Knock-in) using homologous recombination or targeted gene disruption (knock-out) -Introduce an allele whose protein inhibits function of normal protein (dominant negative) -Activate mRNA degradation (knock-down) using RNA interference

Characteristics of primary cultures

-Require attachment -Senescence after limited number of cell divisions -Contact inhibited; grow as monolayers on culture dishes -differentiated cell types may require 3D structure support or "feeder" layers of cells

Limitations of electron microscopy

-Sample is dried -High vacuum required -High energy electron beam will destroy biological samples, so have to stain with heavy metals

Types of DNA sequencing technologies

-Sanger dideoxy sequencing reactions -Massively parallele sequencing reactions -3rd generation single-moleucle sequencing

How do you do cre-lox?

1. Cross a mouse with loxP sequences that are surrounded by introns with a mouse heterozygous for gene X knock-out, carrying cre gene that is beneath a promoter that is cell-specific 2. Some progeny will have the gene and the cre gene on separate chromosomes probably. 3. Turn on cre, block the gene between the loxP sites 4. All cells in the loxP-Cre mouse will carry one copy of loxP-modified gene X, one copy of gene X knockout, and cre genes

What are the steps to non-homologous end joining?

1. DNA-PK and KU80/KU70 heterodimer bind to the break and cut it to make it even 2. Other proteins bind 3. Ligase seals it back together

What are the steps to homologous repair?

1. Ends are digested by exonucleases, leaving 3' single-stranded ends 2. RecA- or Rad51-mediated strand invasion 3. 3' end of invading strand is extended by DNA polymerase until the displaced single-strand base-pairs with the other 3' single strand generated initially 4. 3' end is extended by DNA polymerase 5. Ends are ligated 6. Cleave phosphodiester bonds indicated with arrows and ligate alternative ends

How do you knock-out a gene?

1. Form a gene with the mutation and tkHSV. Take out the middle of the gene and replace it with antibiotic resistance. 2. Put the genes in a nucleus of a culture cell through direct micro injection or transfection 3. Through homologous recombination, the tkHSV stays behind and through nonhomologous recombination, everything gets inserted 4. In homologous recombination, mutation in the gene X clls are resistant to G-418 and ganciclovir. In nonhomologous recombination, no mutation in gene X cells are resistant to G-418 but sensitive to ganciclovir

Differences in transcription in prokaryotes and eukaryotes

1. Genes encoding proteins that function together are most often found in a row; In Euks, they're usually on different chromosomes 2. No splicing

How does nucleotide excision repair work?

1. Initial damage recognized. 2. transcription factor TFIIH recruited, whose helicase subunits, powered by ATP hydrolysis, partially unwind the double helix. XP-G and RPA proteins then bind to the complex and further unwind and stabilize the helix until a bubble is formed 3. XP-G and XP-F cut the damaged strand on each side of the lesion 4. This releases the DNA fragment with the damaged bases, which is degraded to mononucleotides. 5. Finally the gap is filled by DNA polymerase exactly as in DNA replication, and the remaining nick is sealed by DNA ligase

How do you create a transgenic mouse?

1. Inject ES cells into blastocoel cavity of early embryos 2. Surgically transfer embryos into pseudopregnant female 3. Select for chimeric mice for crosses to wild-type black mice (A/X+; A/X-; a/X+ crossed with a/X+) 4. ES-cell-derived progeny will be brown (A/a, X+/X+; A/a, X-/X+) 5. Screen brown progeny DNA to identify X-/X+ heterozygotes 6. Mate X-/X+ heterozygotes 7. Screen progeny DNA to identify X-/X- homozygotes

How does mismatch repair work?

1. MSH2 and MSH6 cover the error to distinguish the template from the replicated strand 2. MLHI and PMS2 bind which brings in an endonuclease that cuts the newer strand. A DNA helicase unwinds and a DNA exonuclease removes several nucleotides 3. The gap is filled by DNA polymerase and ligase

Steps for protein folding through chaperonins

1. Partially folded or misfolded protein binds in the chamber 2. ATP is reduced to ADP and the GroES comes off. 3. Unfolded protein is in the upper chamber 4. More ATP is used and GroES is added to the top 5. Folding within upper chamber 6. Phosphate comes off in slow step, ATP is added, another GroES cap comes on 7. Cap and ADP come out and protein is released

Steps to Transcription: Elongation

1. Polymerase advances 3'-5' down template strand, melting duplex DNA and adding rNTPs to growing RNA

Steps to Transcription: Initiation

1. Polymerase binds to promoter sequence in duplex DNA. 2. Polymerase melts duplex DNA near transcription start site, forming a transcription bubble 3. Polymerase catalyzes phosphodiester linkage of two initial rNTPS

Steps to prepare a sample of immunofluorescence microscopy

1. Prepare sample and place on microscope slide 2. Incubate with primary antibody; wash away unbound antibody 3. Incubate with fluorochrome-conjugated secondary antibody; wash away unbound antibody 4. Mount specimen and observe in fluorescence microscope

How does RT-PCR work?

1. Reverse transcriptase is used to make cDNA to RNA. This makes a copy of the DNA without mRNA 2. cDNA is amplified using PCR

How does CRISPR-Cas9 work?

1. Scientists make guide RNA and attach it to Cas9 2. Cas9 roams the DNA in search of the DNA that matches the gRNA 3. Once it finds it, it cuts the dsDNA to make sure it's a match 4. Then it cuts out the target DNA 5. Two possible results occur: nonhomologous end joining or homology-directed repair 6. Nonhomolgous end joining results in short deletion disrupting the open reading frame 7. Homology-directed repair involves adding a specific change through a template and homologous recombination

How do you express genes in animals?

1. Start with a fertilized egg to microinject the DNA into the pronuclei 2. Implant it into a pseudo pregnant mouse 3. About 10-30% of offspring will contain foreign DNA in chromosomes of all their tissues and germ lines 4. Breed mice expressing foreing DNA to propagate DNA in germ line

Phospholipid synthesis in the ER membrane

1. Two fatty acids from fatty acyl CoA are esterified to the phosphorylated glycerol backbone, forming phosphatidic acid, whose two long hydrocarbon chains anchor the molecule to the membrane. 2. A phosphatase converts phosphatidic acid into diacylglycerol. 3. A polar head group (e.g., phosphorylcholine) is transferred from cytosine diphosphocholine (CDP-choline) to the exposed hydroxyl group. 4. Flippase proteins catalyze the movement of phospholipids from the cytosolic leaflet in which they are initially formed to the exoplasmic leaflet.

Lodish et al. describes an example of a protein (P) binding to DNA (D); P + D ⇔ PD, where Kd = 10-10 M total concentration of P ([P] + [PD]) = 111 x 10-10 M (calculated concentration of 10 molecules of P per cell) total concentration of D ([D] + [PD]) = 10 x 10-10 M (just 1 molecule of DNA per cell) and calculated that the DNA molecule would have P bound to it 99% of the time. What would be the ratio of unbound to bound DNA if phosphorylation of P altered the Kd to 10-8 M?

1:1 Let's start with the equation: Kd = [P][D]/[PD] We can approximate [P] (concentration of free protein) as being about 100 x 10-10 M, because there is a 10-fold excess of P for every DNA molecule (if no protein is bound, [P] = 111 10-10 M, and if the DNA always has protein bound, [P] = 100 x 10-10 M). Then Kd = 100 x 10-10 M [D]/[PD] Then Kd of phosphoP = 10-8 M = 100 x 10-10 M = 100 x 10-10 M [D]/[PD] [D]/[PD] = 1; the DNA molecule will have P bound to it about half the time.

What is the pH of a 1 mM solution of a strong acid (HCl)? Enter your answer as just a number (no units).

3 pH is the negative log of the hydrogen ion concentration. A 1 mM solution of HCl, which dissociates completely, will have a H+ ion concentration of 1 mM = 1E-3. Negative log of that is 3.

In what direction is the DNA template read?

3'-5'

Lodish et al. describes an example of a protein (P) binding to DNA (D); P + D ⇔ PD, where Kd = [P][D]/[PD] = 10-10 M If the total concentration of DNA ([D] + [PD]) = 10 x 10-10 M, what is the total concentration of P ([P] + [PD]) in the cell needed to have the DNA bound to protein half the time? Enter your answer in the form: 1E-5 for 1 x 10-5 M

6E-10 Let's start with the equation: Kd = [P][D]/[PD] = 10-10 M If the DNA is bound to protein half the time, then the concentration of free DNA is the same as the concentration of protein-bound DNA. Therefore, [D] = [PD] and [D]/[PD] = 1 Then Kd = 10-10 M = [P] We also know that [PD] = 5 x 10-10 M, because [D] + [PD] = 10 x 10-10 M The total concentration of protein = [P] + [PD] = 6 x 10-10 M

Tris is a common buffer used in biochemistry and molecular biology. The pKa of Tris is 8.3 Tris is available as powder in 2 forms: TrisHCl is the acid form, and Tris base as the free base. What will be the pH of a solution that contains 100mM Tris base and 10 mM TrisHCl? Enter your answer as just the number: e.g., 10 Henderson-Hasselbach equation: pH = pKa + log {[A-]/[HA]}

9.3 Henderson-Hasselbach equation: pH = pKa + log {[A-]/[HA]} log {[A-]/[HA]} = log (10) = 1 pH = 8.3 + 1 = 9.3

A genetic mutation that results in a R ⇒ K substitution at the site indicated by the arrow labeled "I" in the diagram on the right would be predicted to: A. have little or no effect because the sidechains of R and K both have a postive charge B. likely cause disruption of the 3D structure because the replacement of R by K would cause charge repulsion C. likely cause disruption of the 3D structure because R has a very small sidechain whereas K has a much larger sidechain

A

DNA and RNA is replicated and transcribed, respectively, in which direction? A. 5' to 3' B. 3' to 5' C. both 5' to 3' and 3' to 5' D. none of the above

A

Is the reaction: Succinate + 1/2 O2 -> Fumarate + H2O exergonic or endergonic? You are given that: Succinate -> Fumarate + 2H+ +2e- -0.03V 1/2 O2 + 2e- +2H+ -> H2O +0.82 V A. exergonic B. endergonic

A

To separate organelles that are close in size, one employs the technique called sucrose gradient centrifugation. This technique separates organelles by: A. Density B. Surface area C. Morphology D. Buoyancy

A

What causes degeneracy of the genetic code at the third position of the codon? A. many tRNA anticodons have inosine as the first (most 5') base B. it is a position where no base-pairing occurs between the tRNA anticodon and mRNA codon C. many tRNA anticodons have inosine as the last (most 3') base D. the amino-acyl tRNAs vary in their anticodons at that position

A

What is true for DNA replication? A. DNA replication is semi-conservative B. Both prokaryotic and eukaryotic cells employ a uni-directional mechanism of DNA replication. C. Only the lagging strand requires a short primer for the initiation of replication. D. The replication fork has one molecule of DNA polymerase

A

Which of the DNA repair occurs 'before' DNA replication? A. Base excision repair B. Mismatch excision repair C. Nucleotide excision repar D. Non-homologous end joining repair

A

Which of the following technique can be used to evaluate the expression of many genes at one time? A. microarray B. gel electrophoresis C. restriction enzyme digestion D. PCR

A

Which of these proteins or complexes generate ~21 nucleotide dsRNA fragments from longer dsRNA or miRNA? A. Dicer B. RISC C. Argonaute

A

Which post-translational modification of proteins tags them for degradation by the proteasome? A. ubiquitination B. phosphorylation C. glycosylation D. proteolytic cleavage

A

A combination of 2 or more secondary structure elements that form a characteristic 3-D structure, like EF-hands or zinc-fingers, is called ____ A. a motif B. a domain C. a supramolecular complex

A A motif is defined by Lodish as a structure that is formed by two or more secondary structures in combination to form a distinctive 3-D structure. A domain is a unit of protein structure - a module - that may contain a motif. So in general, a domain is larger than a motif. A supramolecular complex is something like a ribosome, or a viral capsid, that is assembled from multiple proteins.

A human protein you are studying is found to be reversiblly palmitoylated and depalmitoylated in response to extracellular signals. Based on this information, you hypothesize that ____ A. the protein associates with the membrane in response to extracellular signals B. the protein flips across the membrane in response to extracellular signals C. the protein regulates lipid biosynthesis in response to extracellular signals D. the protein is a phospholipase activated by extracellular signals

A For some signaling pathways, the reversible membrane association is important to regulate target membrane proteins.

What are SNPs?

A DNA sequence variation occuring within a population. More often found in non-coding regions but can be in coding regions

CRISPR-Cas9 is a programmable endonuclease that cuts DNA at sites where the sgRNA binds. What is (are) limitation(s) on what sgRNAs can be used? A. Cas9 cuts only if there is also a PAM (protospace adjacent motif) sequence adjacent to the sgRNA target site B. The sgRNAs should not bind elsewhere in the genome C. sgRNA sequences have to be palindromic

A and B

What are the possible outcomes after CRISPR-Cas9 mediated cleavage of DNA? Select all that apply A. The cleavage site is joined by non-homologous end joining, usually resulting in a mutation at the joint B. The cleavage site is repaired by recombination repair with a homologous sequence

A and B

Which of the following would yield better resolution (smaller value of D)? Select all that apply. A. immersion of the objective in oil (refractive index = 1.56) instead of exposed to air (refractive index = 1) B. an objective with a shorter focal length (designed to work closer to the specimen) C. a longer wavelength of light

A and B

Select all true statements about chemical equilibrium A. Keq = kf/kr (rate constant for forward reaction/rate constant for reverse reaction) B. for the reaction A <-> B, Keq = [B]/[A] at equilibrium C. reactions in cells tend to be at chemical equilibrium

A and B These statements correctly state or arise from the definition of the equilibrium constant. Cells maintain steady-state (homeostasis), which is different from chemical equilibrium. See Fig. 2-23 - the product of one reaction is used as the reactant for another reaction, so reactions never actually reach equilibrium. This is really important from an energetics point of view, because at equilibrium ΔG = 0. No free energy is released at equilibrium, so no energy will be available for cells to do any work.

Which of these lipids would you expect to find enriched in a lipid raft of the plasma membrane of a eukaryotic cell? Select all that apply A. cholesterol B. phosphatidyl choline C. sphingomyelin D. phosphatidyl serine

A and C cholesterol and sphingomyelin both increase the rigidity (decrease the fluidity) of the membrane; lipid rafts are more rigid and a little thicker (sphingomyelin tails are straighter and longer than most phospholipid fatty acid tails).

How do integral proteins associate to the membrane?

A region of the protein having hydrophobic amino acids that are more stable in the lipid bilayer (sometimes a short sequence that anchors the mostly soluble protein to the membrane, and sometimes via one or more transmembrane domains)

Dominant negative

A mutation whose gene product adversely affects the normal, wild-type gene product within the same cell. This usually occurs if the product can still interact with the same elements as the wild-type product, but block some aspect of its function.

Why is the code degenerate?

A particular amino acid can be specified by multiple codons

What is Cre-Lox?

A way to be able to turn off a gene at a place and time of our choosing

What is needed in the culture medium of animal cells? select all that are minimally necessary for all animal cell cultures A. nutrients such as glucose B. growth factors C. any amino acids or vitamins that the cells cannot make themselves D. bovine serum albumen E. carbon dioxide

A, B, C

Which of the following statements about cDNA is (are) true? Select all true statements. A. cDNA contains no introns B. cDNA is synthesized from an mRNA template by reverse transcriptase C. cDNA stands for cytoplasmic DNA D. cDNA can be expressed in E. coli to make a eukaryotic protein

A, B, D

Which of the following statement(s) about the lipid composition of mammalian membranes is/are correct? Select all true statements. A. the lipid compositions of many of the subcellular organelles differ from each other B. the lipid compositions of the two sides of the plasma membrane bilayer are different C. the lipids in a biological membrane can sometimes be sub-localized into structures like "rafts"

A, B, and C

The eukaryotic translational initiation factor eIF4 binds to which of the following? select all that apply A. ribosomal small subunit in a pre-initiation complex B. ribosomal large subunit C. tRNAi Met D. 5' cap on the mRNA E. polyA-binding protein (PABP) bound to the 3' polyA tail on the mRNA

A, D, and E

How are nucleotides paired?

A-T with two H bonds G-C with three H bonds

What do you know about ∆G for the energetically favored reaction in the previous question? A. it is negative B. it is positive C. it = zero D. none of the above

A; Any energetically favored reaction must have a negative delta G

What is the most common intiator codon?

AUG

When does mismatch repair occur?

After DNA replication

Hydrophobic amino acids

Alanine (Ala or A); Valine (Val or V); Isoleucine (Ile or I); Leucine (Leu or L); Methionine (Met or M); Phenylalanine (Phe or F); Tyrosine (Tyr or Y); Tryptophan (Trp or W) pKa ~10

Possible configurations for polysaccharides

Alpha (down) or Beta (up)

Names of monomers and polymers of four main building blocks of life

Amino acid -- polypeptide Nucleotide -- nucleic acid Monosaccharide -- polysaccharide Phospholipid -- Phospholipid bilayer

What features do plasmids have to have?

An origin of DNA replication for E. coli, a selectable marker (antibiotic resistance gene), a multiple cloning site for insertion of the sgRNA or spCas9 DNA sequences

What do you call a lipid in contact with an amino acid?

Annular lipid

Acidic amino acids

Aspartic acid (Asp or D)r group = CH2-COO; glutamic acid (Glu or E) r group = CH2CH2COO

Steps to Transcription: Termination

At transcription stop site, polymerase releases completed RNA and dissociates from DNA

If the gene product still interacts with the same elements as the wild-type product, but block some aspect of its function, it acts as a ( ). A. recessive B. dominant negative C. haploinsufficient D. all of the above

B

In fluorescence microscopy, the sample is excited by absorption of light at certain wavelengths. The sample then emits light at A. shorter wavelength B. longer wavelength C. same wavelength

B

In the CRISPR-Cas9 system, what is the function of the guide RNA? A. it carries out the catalytic cleavage of the target DNA molecule B. it binds to the target DNA sequence by base-pairing C. it holds CRISPR and Cas9 together as a complex D. it initiates homologous recombination with the target DNA sequence E. it serves as the template for the break repair of the DNA after cleavage by Cas9

B

Introduction of foreign DNA into eukaryotic cells is called ______? A. transformation B. transfection C. ligation D. elongation

B

Suppose that this graph shows Michaelis-Menten kinetics for two enzymes. The enzyme represented by the red curve (upper) has _____ A. a higher Km than the enzyme represented by the blue curve B. a lower Km than the enzyme represented by the blue curve C. a higher Vmax than the enzyme represented by the blue curve D. a lower Vmax than the enzyme represented by the blue curve

B

The base in the wobble position of a codon A. is the 5 ́ (first) base. B. is the 3 ́ (third) base. C. is the second base. D. often contains adenine.

B

The enzymes for fatty acid biosynthesis are located in the cytoplasm, but synthesis of membrane phospholipids occurs primarily in___ A. mitochondria B. the endoplasmic reticulum C. the Golgi D. lipid bodies E. the nucleus

B

What DNA repair mechanism will most likely be used to repair a mismatched basepair caused by an error in DNA replication, after S phase but prior to cell division? A. base excision repair B. mismatch repair C. nucleotide excision repair D. non-homologous end joining E. homologous recombination

B

What do chaperons such as Hsp70 and Hsp90, and chaperonins have in common? A. they all form barrel-shaped chambers to fold denatured proteins B. they all bind and hydrolyze ATP in the process of folding proteins C. they are all associated with ribosomes D. all of the above

B

What limits the resolution, D, of ordinary light microscopy? A. the size of the objective lens B. the wavelength of visible light C. Show fast our optical neurons can fire D. the resolution of the human iris E. none of the above

B

What protein relieves torsional stress caused by unwinding the DNA double helix during DNA replication? A. helicase B. topoisomerase C. RPA D. PCNA E. primase

B

Which of the following is not one of the lipids that is covalently attached to proteins to bind them to membranes: A. a GPI anchor B. a succinyl group C. a fatty acyl group D. a prenyl group

B

what would you predict to be the structural/functional consequences of a genetic mutation that results in a K -> E substitution at the site indicated by the box above? A. little or no effect B. likely disruption of protein A binding to protein B C. binding of proteins A and B to each other will probably be stronger D. cannot even guess

B

Flavins and pyridine nucleotides are major mediators of redox reactions in cells. The standard redox potential for them are: Reaction (OXIDIZED « REDUCED) ∆Eo (volts) FAD + 2H+ + 2e- ⇔ FADH2 (in flavoproteins) 0 NAD+ + H+ + 2e- ⇔ NADH -0.315 Given these data, which of the following reactions is energetically favored? A. the reduction of NAD+ by FADH2 (NAD+ + FADH2 ⇔ FAD + NADH) B. the reduction of FAD by NADH (FAD + NADH ⇔ NAD+ + FADH2) C. neither of these electron transfers can occur

B A positive deltaE for a reaction is energetically favored: the deltaG is negative. The reduction of NAD+ by FADH2 will have a deltaE of -0.315 V; deltaG is positive and the reaction is not favored The reduction of FAD+ by NADH will have a deltaE of +0.315 V because the half-reaction shown in the table is reversed (now NADH <=> NAD+ + H+ + 2e-). With a positive deltaE, this reaction has a negative deltaG and will occur spontaneously.

You are interested in an enzyme that uses ATP for a critical biological process. You wonder if the enzyme loses a substantial amount of its activity (and hence the biological proces is affected) when cells become partially hypoxic (i.e., have reduced access to oxygen) which decreases the cellular ATP concentration. You know that the enzyme has a Km for ATP of 0.1 mM, and you look up in the literaturę that the normal ATP concentration of the cells is 5 mM and decreases to 1 mM when the cells are partially hypoxic. Based on this information, you would predict that: A. the activity of the enzyme will decrease by >50% due to this 5-fold decrease in cellular ATP concentration B. the activity of the enzyme will decrease by much less than 50% due to this 5-fold decrease in cellular ATP concentration C. the activity of the enzyme will INCREASE due to this 5-fold decrease in cellular ATP

B Since the enzyme has a Km for ATP of 0.1 mM, it will be operating at near Vmax at 1 mM (10x Km). So a decrease in ATP concentration from 5 mM to 1 mM will have only a small effect on enzyme activity.

What happens when a membrane contains a substantial amount of lipids that have chemical features that make them prone to forming more ordered structures (i.e., have saturated alkyl chains, such as sphingolipids, or are planar, such as cholesterol), even though it also contains other phospholipids with more fluidity (such as phosphoglycerolipids with unsaturated fatty acyl chains)? A. the membranes will be uniformly fluid B. some of the membrane lipids will probably be present in membrane rafts C. the membranes will be very thin because alkyl chains will tend to bend out into the aqueous phase because they don't fit together well D. these membranes will be so unstable that they cannot be present in cells.

B lipid rafts are regions of the plasma membrane enriched in sphingolipids and cholesterol, making them substantially more rigid than the surrounding membrane area. The presence of sphingolipids make them distinctly thicker, as well. They can facilitate signaling and other membrane functions by holding together functional complexes of membrane proteins.

A genetic mutation that results in a V ⇒ E substitution at the site indicated by the arrow labeled "II" in the diagram on the right would be predicted to: A. have little or no effect B. likely cause disruption of the tertiary structure of the mutant protein C. likely disrupt quaternary structure or the interaction between the two proteins

B and C

What information does mass spectrometry provide most directly? A. the shape of the peptide fragment B. the amino acid sequence of a peptide fragment C. the mass to charge ratio of an ion D. the length of a molecule

C

How is a thicker membrane acheived?

Cholesterol and sphingolipids can increase the thickness of the lipid bilayer. Bulkier head groups also lead to a thicker and more rigid membrane.

The latest super-resolution fluorescence microscopy techniques such as PALM and STORM use which of the following to defeat or circumvent the limits of light microscopy? A. They illuminate the sample with x-rays B. They use very low amounts of excitation light so only a few molecules give off fluorescence at any given time C. The techniques assign the center of a Gaussian spatial distribution of photons as the location of the fluorecence emitting molecule. D. They use high-intensity lasers to deliver extremely high levels of excitation energy to the sample.

B and C

Which of these lipids are usually highly enriched in the exoplasmic face of the plasma membrane? Select all that apply. A. cholesterol B. phosphatidyl choline C. sphingomyelin D. phosphatidyl serine E. phosphatidyl inositol

B and C

what are the advantages of cryo-EM compared to traditional transmission EM? Select all that apply. A. Cryo-EM has better resolution B. Cryo-EM images samples in their native, hydrated state C. Cryo-EM does not require staining or coating with heavy metals D. Cryo-EM does not require vacuum

B and C

What is the purpose of RT-PCR?

Bacteria cannot splice out introns so E. coli need a copy of a eukaryotic gene without introns

DNA repair systems

Base Excision repair Mismatch repair Nucleotide excision repair Non-homologous end joining Recombinational repair

Which binds to the 5'-cap on the mRNA as part of the translation initiation process? A. The ribosomal small subunit B. The ribosomal large subunit C. A component of the eIF4 complex D. initiator met-tRNA E. polyA binding protein

C A subunit of eIF4 binds to the 5' cap of eukaryotic mRNAs.

What is the function of RPA?

Binds single-stranded DNA

How does mass spectrometry separate ions?

By mass/charge ration (m/z)

How does gel electrophoresis separate proteins?

By size

How does lipid composition vary?

By species, cell type, organelle, and leaflet (cytoplasmic vs exoplasmic)

If you wanted to isolate just vesicles coated with COPI protein from cells, what method would give you the cleanest results? A. Differential centrifugation B. Sucrose density gradient centrifugation C. Immuno-affinity purification with antibodies to COPI coat protein

C

Scanning electron microscopy is BEST described by which of the following terms A. Electron beam, electromagnetic lenses, objective lens, negative staining sample, detector B. Light source, convex and concave lenses, objective, fixing sample, eyepiece C. Electron beam, electromagnetic lenses, condenser lens, scanning coils, metal sputter coating, detector D. Light source, condenser and objective lenses, sample, phase contrast

C

Suppose an enzyme has a Km for substrate of 10 micromolar. The concentration of the substrate changes from 50 micromolar to 100 micromolar. What happens to the rate of the enzyme-catalyzed reaction? Try using the equation and express in terms of the Vmax (the maximal velocity of the enzyme): v = Vmax[S]/([S] + Km) Then choose the best answer below. A. the rate of the enzyme-catalyzed reaction will increase 2x when the substrate concentration increases from 5x Km to 10x Km B. the rate of the enzyme-catalyzed reaction will increase more than 2x when the substrate concentration increases from 5x Km to 10x Km C. The rate of the enzyme-catalyzed reaction will increase by less than 2x when the substrate concentration increases from 5x Km to 10x Km

C

Which of the following statements are generally true about lipids in cell membranes? Select all true statements. A. cell membranes have only phospholipids B. fatty acid chains in phospholipids frequently have both cis- and trans- double bonds between carbons C. phospholipid can have different "head" groups covalently linked to diacyl glycerol (glycerol plus 2 fatty acid chains)

C Although phospholipids are a main component, cell membranes also have other lipids such as sterols (e.g. cholesterol). Celll membranes also have significant amounts of proteins, and glycosyl groups. Naturally occuring fatty acids with double bonds almost always have the cis-configuration; trans-fatty acids in foods occur as a result of chemical processing (hydrogenation). most common phospholipids consist of glycerol with two fatty acid chains, a phosphate and a polar "head group" linked to the phosphate - see Fig 2-20 and Table 2-5.

Which of these PCR primers will have to highest Tm for binding to the complementary template DNA strand? A. 5'-AACCATGCAATACGGATGAC-3' B. 5'-ATAAGGCATGCCAGAACGTG-3' C. 5'-ATGGAGCCATCGTGCACCGA-3' D. 5'-GATACCATATTACGAATCGA-3

C The biggest factor determining the Tm of a DNA duplex is the percent G:C base-pairs. Primer C has the highest percent G+C.

What mediate protein folding?

Chaperones and chaperonins

What are the parts of the hydrophilic head?

Choline; phosphate; glycerol; fatty acid chains

How do you analyze the over expression of the protein? What are the uses of this?

Clone and over express in cells and organisms (transgenic) Uses: structural analysis; examination of the effects of elevated amounts/activity on cell function

How does the sample need to be prepared in electron microscopy?

Coat the sample in a metal vapor, place it in a vacuum, and then you scan the coating

Types of motifs

Coiled-coil EFhand/helix-loop-helix Zinc-finger

Special amino acids

Cysteine (Cys or C); Glycine (Gly or G); Proline (Pro or P) pKa ~8.4

Proteasomes ___ A. are supramolecular complexes that synthesize proteins B. are supramolecular complexes that refold proteins C. are supramolecular complexes that degrade proteins bound to chaperones D. are supramolecular complexes that degrade ubiquitinated proteins

D

How do lipid anchored proteins associate to the membrane?

Covalent modification of the protein with a lipid (GPI, fatty acid, etc)

The "activated" form of fatty acids that is utilized for most biosynthetic reactions is: A. the anhydride of the fatty acid with another one of the same kind (e.g., palmitic anhydride) B. a mixed anhydride of two different fatty acids (e.g., palmitic-oleic anhydride) C. the N-hydroxysuccinimide ester of the fatty acid D. the fatty acyl-coenzyme A thioester

D

What methods may be used to introduce Cas9 protein and sgRNAs into cultured mammalian cells? A. transfection of cells with plasmids containing the Cas9 and sgRNA genes to achieve transient expression B. transfection of cells with Cas9 and sgRNA gene constructs with a selectable marker for stable integration into the cell's chromosomes C. electroporation of recombination Cas9 protein and sgRNAs D. any of the above methods

D

Which imaging technique has the best resolution (smallest D)? A. optical microscopy B. super-resolved fluorescence microscopy C. scanning electron microscopy D. transmission electron microscopy

D

Which of the following biosynthetic precursors is NOT correctly matched to the lipid pathway it is used for? A. fatty-acyl coA + glycerol 3-phosphate for phosphatidylcholine B. palmitoyl-coA + serine for sphingomyelin C. HMG-CoA for cholesterol D. pick this if all of the above are correctly matched

D

Which of the following categories of bonds or interactions is usually the strongest (takes most energy to break) between a pair of atoms? A. covalent single bonds B. electrostatic interactions C. van der Waals interactions D. covalent double bonds E. hydrogen bonds

D

Which of the following is NOT the component of DNA replication fork? A. okazaki fragment B. primase C. helicase D. reverse transcriptase

D

Which of the following is NOT the key feature of plasmid cloning vectors? A. replication origin B. antibiotic resistance gene C. polylinker D. inverted repeats

D

Which of the following lipids would increase the fluidity of a lipid bilayer membrane? Select all that apply. A. saturated fatty acids B. cholesterol C. trans-unsaturated fatty acids D. cis-unsaturated fatty acids

D

Which of these bonds or interactions requires the least amount of energy to disrupt or break? A. a covalent C-C bond B. a covalent C=O double bond C. a hydrogen bond between a water molecule and an -OH group D. van der Waals interaction between two carbon atoms

D

What is the central dogma?

DNA gets transcribed to RNA and then translated to protein. DNA gets replicated.

What seals Okazaki fragments?

DNA ligases

What elongates primers?

DNA polymerases

What is the equation for delta G?

Delta G = Delta G naught + RT ln([Products/Reactants]) Delta G naught = the standard free energy change of the rxn OR Delta G= -nF(delta E)

Molecular chaperones, such as Hsp70, ____. A. bind ATP B. stabilize unfolded or partly folded proteins C. help newly synthesized proteins fold into their proper conformation D. help unfolded proteins to fold back into their proper conformation E. all of the above

E

The sequence of a portion of the template strand of DNA is: 5'-...GTATAGCGAATGCAGT....3' What is the sequence of the RNA that is transcribed from this DNA sequence? A. 5'-...GTATAGCGAATGCAGT....3' B. 5'-...GUAUAGCGAAUGCAGU....3' C. 5'-...CATATCGCTTACGTCA....3' D. 3'-...CATATCGCTTACGTCA....5' E. 3'-...CAUAUCGCUUACGUCA....5' F. 3'-...GUAUAGCGAAUGCAGU....5'

E

What approache(s) is/are often employed to perturb specific gene or protein functions in the cells? A. Expression of GFP fusion proteins B. Using chemical inhibitors of a specific pathway C. Knockdown of specific genes by RNAi D. a and c E. b and c

E

What drives the "hydrophobic effect"?

Entropy. Water populations is less ordered; higher entropy means it is more energetically favored.

What are the downsides to non-homologous end joining?

Error prone Leads to deletion mutations

If a reaction is exergonic, the energy reaction will look like...? Endergonic?

Exergonic: The products will be lower than the reactants. Delta G < 0. Endergonic: The products are higher than the reactants. Delta G > 0

How do membrane proteins associate with membranes?

Extrinsic (peripheral) Intrinsic (integral) Lipid anchored

How is the position of a single fluorescent molecule determined?

From its point spread function; localizing millions of point sources sequentially paints a high-resolution picture

What does DNA denaturation depend on?

G:C and salt content. The more G:C, the higher the temperature it'll take

How are lipids made?

Go through the ER and then vesicle transport them to the membrane

Steps to Transcription

Initiation Elongation Termination

RNA secondary structures

Hairpin Stem-loop Pseudoknot

What does it mean for lipids to have more ordered structure?

Have saturated alkyl chains, such as sphingolipids, or are planar, such as cholesterol

What unwinds DNA?

Helicases

Tris is a common buffer used in biochemistry and molecular biology. The pKa of Tris is 8.3 Tris is available as powder in 2 forms: TrisHCl is the acid form, and Tris base as the free base. What molar ratio of TrisHCl and Tris base will form a solution of pH 8.0?

Henderson-Hasselbach equation: pH = pKa + log {[A-]/[HA]} log {[A-]/[HA]} = 8 - 8.3 = -0.3 [A-]/[HA] = 0.5 [HA]/[A-] = 2 or 2:1 ratio

What does loss of function of MLH1 or MSH2 lead to?

Hereditary nonpolyposis colorectal cancer

What does salt concentration do to DNA denaturation?

High salt concentrations neutralizes the phosphates and stabilizes the molecule

Functions of Topoisomerase I and II

I: making nicks (unwinding), relegate II: making double stranded breaks (unwinding), relegate

Biochemistry often involves molecular complementarity, or the lock-and-key fit between two molecules. List non-covalent bonds, interactions, or factors that determine whether two molecules will associate with each other into a stable complex, or not.

If the shapes of the two molecules are complementary, so that their surface atoms can be very close over a large area, then van der Waals interactions can help hold them together Hydrogen bonds between an electronegative atom of one molecule (O or N) and a near-by hydrogen with a partial positive charge (because it's bonded to O) on the partner molecule electrostatic interactions, where a positive charge on one molecule is close to a negative charge on the partner molecule. hydrophobic interactions, where the exclusion of water molecules from the interaction of the two molecules results in an increase in entropy. All of the above interactions work only at very short distances, so it's important that the two molecules are able to fit together.

Where is cholesterol synthesized?

In the ER

What is haploinsufficiency an example of?

Incomplete or partial dominance, as a heterozygote (with one mutant and one normal allele) displays a phenotypic effect

What is transfection?

Introduction of foreign DNA into eukaryotic cells

What causes dsDNA breaks?

Ionizing radiation (x-ray, gamma radiation), chemotherapy, etc

What is important about sgRNA?

It contains uracil

How does centrifugation of cell lysates work?

It separates the cell organelles by density

How is translation stopped?

It stops at the stop codon. Then a release factor binds to ribosome and ribosome dissociates

What's the use of CRISPR-Cas9?

Knock out or edit any gene in cells or organisms

What is knock-out / knock-in?

Knock-out: genetic engineering to disrupt the gene Knock-in: when you design the mutation to know what that mutation will do by changing an amino acid to see if its critical

What is deamination

Leads to point mutations; Changes C to T; Can be fixed by base excision repair

What is the function of the clamp loader (Rfc)?

Loads PCNA onto end of primer template

What are some of the advantages of assembly of proteins into multi-protein complexes?

Localization, efficiency, specificity, and regulation

Basic amino acids

Lysine (Lys or K) r group= NH3+; Arginine (Arg or R) r group = Amide?; Histidine (His or H) r group = pentagon

What does tkHSV do?

Makes cells sensitive to ganciclovir (nucleotide analog)

How do you study gene functions?

Molecular cloning Transformation Transfection

How are dsDNA breaks fixed?

Non-homologous end joining Homologous recombination

What are the essential elements of plasmids?

ORI, origin of replication Polylinker, a site to enter DNA Promoter, to transcribe the gene Selectable marker such as antibiotic resistance

Common structural peculiarities in lipid images?

Odd carbon number in fatty acid chain Trans bonds

Where do post-translational modifications with carboyhydrates occur? What do they do?

On extrinsic membrane proteins; especially on the outer leaflet of the plasma membrane. They enable protein-protein and protein-lipid interactions for cells in tissues, and serve as signals for cell-cell interactions and communication (for cells in circulation as well as cells in tissues)

What enzymes cleave lipids?

PLase A2, C, D

What are the variable head groups for phosphoglycerides?

Pe PC Ps PI

What is molecular cloning?

Preparing large numbers of identical DNA molecules

Levels of protein hierarchy

Primary structure Secondary Tertiary Quaternary

When does base excision repair occur?

Prior to DNA replication

Adenine

Purine

Guanine

Purine

Cytosine

Pyrimidine

Thymine

Pyrimidine

Uracil

Pyrimidine

What are SSRs?

Repeating sequences of 2-5 base pairs of DNA

What is the equation for resolution?

Resolution (D)= 0.61 (lamda) / N sin(alpha) N= refractive index of medium between specimen and objective lens (1 for air; 1.56 for oil) lamda= wavelength of light alpha= half angle of the cone of light that enters the objective

What are the variable head groups for sphingolipids?

SM GlcCer

Cell culture media

Sals and buffering agents Nutrients -Glucose -Vitamins -Essential Amino Acids -Glutamine (nitrogen source) Growth factors -serum from fetal calves -serum-free media has insulin, transferrin + growth factors

What is the function of DNA ligase

Seals phosphodiester bonds between Okazaki fragments

Polar amino acids with uncharged R groups

Serine (ser or s) r group = CH2OH; threonine (thr or T) r group = CHOHCH3; Cysteine (R group = -SH); Asparagine (Asn or N) r group = CH2CONH2; Glutamine (Gln or Q) r group = CH2CH2CONH2

What are examples of DNA polymorphisms?

Single nucleotide polymorphisms, SNPs Simple-sequence repeats, SSR (or microsatellites)

What is the function of PCNA?

Sliding clamp that stabilizes DNA pol binding to template strand

What are the major and minor grooves?

Spaces between the intertwined strands on the outside of B form DNA. They interacted with the grooves to stabilize the structure.

What does STORM stand for?

Stochastic Optical Reconstruction Microscopy

What is the function of primase?

Synthesizes short RNA segments complementary to template DNA strand

What is transformation?

The genetic alteration of a cell resulting from the direct uptake, incorporation and expression of exogenous genetic material (exogenous DNA) from its surrounding and taken up through the cell membrane(s). Most commonly occurs in bacteria.

What is the purpose of Cre-lox in biological research?

The key here is that the Cre recombinase is expressed under the control of the cell-type specific promoter, or an experimentally inducible promoter. The loxP-modified copy of the target gene (gene X) is functional, because loxP sites have been added to introns and do not affect the coding sequence. In mice that are heterozygous for a knockout of gene X and a loxP-modified gene X, only the cells that express the Cre recombinase will have no functional copy of gene X. This system is used to eliminate the function of the target gene only in particular cells or tissues of the body, or at particular times.

What is the difference between phosphoglycerides and sphingolipids?

The linkage between fatty acid chains (glycerol vs serine respectively)

On a titration curve, where can you find the pKa?

The pH where half of the acid is dissociated

What is the wobble position?

The position in tRNA that has non-standard bases, and non-standard base pairing Third position in mRNA; first in the anticodon

How does super resolution microscopy work?

Uses properties of fluorophores to acheive sub-wavelength resolution, down to tens of nanometers

How do lipids reach their final destination?

They are made there or transported there -vesicle diffusion -two membranes in direct contact. membrane protein facilitates transfer of lipids -carrier proteins bind lipids and transport them (important for mitochondria)

What's the difference between DIC and phase contrast microscopy?

They utilize differences in refractive index to enhance contrast

What happens if the lipids are prone to more ordered structures?

They will tend to form more ordered domains in biological membranes ("rafts")

Subunits that make up ribosomes

Top: 23S, 5S; (50S) Bottom: 16S; (30) Combined to make 70S

Subunits that make up eukaryotic ribosomes

Top: 5S; 28S; 5.8S; (60S) Bottom: 18S; (40S) Combined to make 80S

What relieves torsional stress?

Topoisomerases

What are the differences between transient and stable transfection?

Transient is not segregated during mitosis and never integrates. In stable, you select for the integration.

What do enzymes lower?

Transition state

How do you select for cells that have inserted the gene through homologous recombination?

Treat the cells with G-418 to positively select for the cells that have the DNA. Then treat the cells with ganciclovir to negatively select against the cells that still have tkHSV

Why do lipids self-associate spontaneously?

Triacylglycerols (and most other lipids) will aggregate to reduce the area of the surface that is in contact with water

What are the stop codons?

UAA, UGA, UAG

When is nucleotide excision repair necessary?

UV radiation causes T-T dimers which can cause melanomas

What happens to proteins that can't be folded properly?

Ubiquitinated and destroyed

Why do lipids with saturated fatty acids have higher melting temperatures?

Unsaturated fatty acids interfere with aligned of the alkyl chains for van der Waal interactions

What all can light microscopes see?

Up to 100 nm; Tissues, cells, organelles; bacteria

Haploinsufficiency

When a diploid organism only has a single functional copy of a gene (with the other copy inactivated by mutation) and the single functional copy of the gene does not produce enough of a gene product (typically a protein) to bring about a wild-type condition, leading to an abnormal or diseased state

What is cell electroporation?

When you put everything into a medium and provide a sharp electric pulse to cause the cell membrane to open up temporarily some holes. The electric field drives things inside and then the membrane closes

Can membrane proteins move?

Yes, laterally but they can also flip over.

How can you suppress protein function by RNA interference?

You put double-stranded RNA or a plasmid construct that transcribes both strands of a segment of DNA that contains a gene sequence into a cell 2. A gene silencing mechanism involving DICR or Argonaut is used to cleave dsRNA into short segments 3. Segments base-pair with endogenous mRNA 4. Paired molecules cleave by specific nucleases

Rank the predicted G+C content of the genomic DNAs of the bacteria listed below, from lowest to highest a bacterium like E. coli that lives in a mammal's intestines a thermophilic bacterium that lives in hot springs a cryophilic bacterium that lives under the arctic ice

a cryophilic bacterium that lives under the arctic ice < a bacterium like E. coli that lives in a mammal's intestines < a thermophilic bacterium that lives in hot springs Organisms that live in cold temperatures will have DNA with lower Tm and be A:T-rich, so they can replicate and transcribe their DNA at the cold temperatures. Conversely, organisms that live in high temperatures will have DNA with high Tm and be G:C-rich so their DNA stays double-stranded at the high temperatures.

What are the differences in hydrogen bonds that stabilize alpha-helices, beta-sheets, and tertiary/quarternary structures?

alpha-helix - hydrogen bonds between peptide backbone atoms of amino acids spaced 3 residues apart along the polypeptide chain beta-sheet - hydrogen bonds between peptide backbone atoms of amino acids that are far apart along the polypeptide chain tertiary and quaternary structure - hydrogen bonds between side chain atoms of amino acids that are far apart along the polypeptide chain

Why does lipid turnover occur?

for membrane dynamics, signaling, and lipid digestion

Proteins associate with the membrane as integral membrane proteins, peripheral membrane proteins, or via lipid anchors. Describe how each of these classes of membrane proteins physically associate with cell membranes.

integral membrane proteins have a domain, such as a transmembrane domain, with hydrophobic amino acid residues that interact with the hydrophobic lipids in the bilayer, via hydrophobic interactions and van der Waals interactions. peripheral membrane proteins associate witht the charged head groups of the membrane via ionic bonds, or associate with integral membrane proteins via protein-protein interactions (hydrophobic interactions, van der Waals, hydrogen bonds, ionic bonds) lipid-anchored proteins may have a fatty acid covalently attached at the N-terminus, or be prenylated at the C-terminus, or have a GPI-anchor bonded at the C-terminus

Where do the phospholipases A1, A2, C, and D cleave?Why?

phospholiipases A1 or A2 - lysophospholipid + fatty acid phospholipase C - diacyl glycerol + phopho-head group phospholipase D - phosphatidic acid + head group Phospholipases act on membrane phospholipids to generate second messengers. For example, both diacylglycerol and inositol triphosphate, generated by phospholipase C, act as important second messengers for some cell signaling pathways.

What synthesizes RNA primers?

primase

What is the Michaelis-Menten equation?

vi = Vmax x [S]/ ([S+Km])

What all can electron microscopes see?

~1nm - 0.1nm; Tissues, cells, organelles, bacteria, molecules, ribosome virus, proteins, small molecules, atoms