Biochem Final

Mannose-6-PO4^3- is a signal for a. lysoenzymes to move into the lysosomes b. sialic acid degradation c. protein degradation in lysosomes d. glucose absorption

A

Membrane lipids in a lipid bilayer are held together primarily by a. hydrophobic forces b. electrostatic forces c. hydrogen bonds d. covalent bonds

A

Name this compound (24) a. galactose -beta- 1, 4- glucose b. galactose -alpha -1, 4- glucose c. glucose - alpha- 1, 4 - glucose d. galactose -alpha -1, 6- glucose

A

Oil in water a. organizes the water molecules b. make water stable c. disorganize the water molecules d. none of the above

A

One of these bonds is not capable of hydrogen bonding a. C-H b. N-H c. O-H d. F-H

A

One of these fatty acids is non-essential a. oleic c. γ-linolenic b. linoleic d. α-linolenic

A

One of these is not a function of sugars on glycoproteins a. degradation of proteins b. increase solubility c. cell signaling d. protection from degradation

A

Restriction enzymes are? a. endonucleases b. are found in eukaryotes and prokaryotes c. ribonucleases d. cut on non-palyndromic sites e. all of them

A

The ability of a polymerase to attach several nucleotides before detaching is called a. processivity b. reactivity c. high Km d. connectivity e. efficiency

A

The antibiotic Rifampicin, which targets RNA polymerase, should be more or less toxic than than tetracyclins (target ribosomes and protein synthesis)? a. less toxic, since RNA polymerase is different from RNA pol II b. Tetracyclins are less toxic because the ribosomes of mitochondria are similar to prokaryotic ones and tetracyclins will target both c. more toxic since RNA polymerases are almost identical in prokaryotes and eukaryotes and eukaryotic ones are more abundant d. They are equally toxic

A

The carbon where the phosphate attaches to ribose in RNA is? a. highest numbered b. alpha c. anomeric d. beta e. glycosidic

A

The extracellular buffer in humans is a. CO2/H2CO3/HCO3- system b. the anserine system c. H2PO4- /H1PO42- system d. the acetate system

A

The fact that ribonuclease (Anfinsen's experiment) can be renatured implies that? a. the primary sequence is all you need for its native conformation b. it must have a great number of disulfide bonds c. the protein must be heat stable d. it will not be digested by our stomachs

A

The following figure depicts a chromosome pair with restriction sites 1, 2, 3 in one chromosome( "A" allele) and restriction sites 1,3 in the other chromosome ( "a" allele). After cutting the chromosomes with restriction enzymes and visualizing the fragments with radioactivity on the whole length of the chromosomes (not with the probe shown), how many bands would you see in a gel for both chromosomes? (26) a. 3 b. 4 c. 2 d. can not tell

A

The following question is related to the figure below (27) How would you clone the gene of interest shown above into the plasmid below? Careful with polarities! a. Using Pst1 and EcoR1 c. Cla1 and EcoR1 b. BamH1, EcoR1 d. All of them would work

A

The following question is related to the structures below: (14) What is the name of the amino acid A? a. valine b. proline c. leucine d. tyrosine

A

The isolation of nascent Okazaki fragments during DNA replication led to the surprising discovery of uracil in the fragments. This uracil is present due to which of the following? a. Hydrolysis of cytosine b. Failure of mismatch a repair c. Chemical modification of thymine d. C deamination by the cytidine deaminase enzyme e. An error in the Primase enzyme

A

The name of the following sugar is (20) a. maltose b. lactose c. cellobiose d. galactose

A

The reason why we can not digest cellulose is because a. it has beta glycosidic bonds b. our lactase can not break it down c. cellulose has alpha glycosidic bonds d. it is too well packed

A

The region of DNA shown below is to be amplified by PCR. The appropriate pair of primers to use is which of the following? (28) a. B and C b. B and D c. A and D d. C and D e. A and C

A

This enzyme has 2 activities: Polymerase and helicase. a. RNA polymerase b. integrase c. reverse transcriptase d. telomerase e. pol III

A

Three different enzymes (no inhibitor present) gave the plots below. If the enzymes concentrations were identical, which enzyme is the least efficient? (25) a. A b. B c. C d. I can not tell from graphs

A

What in incorrect, in general, about an Alpha-helix? a. The helix has a left handed pitch b. The helix is right handed c. The helix has 3.6 amino acids per turn d. The helix possesses an overall dipole moment

A

What is not true of facilitated diffusion a. is found in some types of cells d. allow only diffusion with the gradient c. allow only diffusion down a gradient d. pores have affinity for solute

A

What is not true of lipid anchors in membranes a. are permanently attached to membrane b. are transient in nature c. are used as signaling devices d. are not always anchored through thioesters

A

What is the ratio of the weak acid, citric acid (pK1 = 3.09) to monosodium citrate in a 1.0 M citric acid solution with a pH = 2.09? a. 10:1 b. 1:10 c. 1:1 d. 1:11

A

When is the lac operon activity called leaky (very little activity)? a. It reads the complement of the consensus sequence on the antisense strand b. it reads the consensus sequence on the sense strand c. it reads either one of the strands

A

Which E. coli enzyme has the greatest frequency of incorporating the incorrect nucleotide into its nucleic acid polymer? a. RNA polymerase b. Klenow fragment from DNA polymerase I c. DNA Polymerase III d. Reverse transcriptase e. DNA polymerase I

A

Which of the enzymes DNA pol-I and DNA pol-III is the most abundant in E. coli? a. Pol I b. Pol III c. equal amounts d. none of the above

A

Which of the following molecules does not fit in a general category with the other three molecules? a. phosphatidyl choline b. cerebrosides c. gangliosides d. glycosphingolipids

A

Which of the following pKAs represents the strongest acid? a. 3 b. 5 c. 6 d. 10

A

Which of the following peptides would absorb the most light centered at 280 nm? a. trp-tyr-thr-lys-phe b. thr-thr-phe-tyr-lys c. lys-ala-trp-trp-val d. tyr-thr-va-thr-thr

A

Which of the following sugars is a hemiketal? a. -D-fructofuranose b. -D-glucopyranose c. -D-ribofuranose d. methyl--D-glucopyranoside

A

Which of the following transport processes does not require a transport protein? a. passive diffusion b. symport transport c. active transport d. facilitated transport

A

Which amino acid would migrate the furthest toward the anode (positive electrode) during paper electrophoresis at pH 7.0? a. aspartic acid b. alanine c. lysine d. glutamine

A Asp. is the only negatively charged

Which of the following amino acids is the least water soluble at pH 7.0? a. tryptophan b. glutamic acid c. cysteine d. histidine

A Trp is aromatic and nonpolar, nonpolar does not dissolve in polar

Of the unsaturated fatty acids listed below, which of them are essential? - Arachidonic acid (20:4) Omega 6 - Docosahexaenoic acid (22:6, DHA) - Linoleic acid (18:2) Omega 6 - α-Linolenic acid (18:3) Omega 3 - γ-Linolenic acid (18:3) Omega 6 - Oleic acid (18:1) - Palmitoleic acid (16:1)

- Linoleic acid (18:2) Omega 6 - α-Linolenic acid (18:3) Omega 3 - γ-Linolenic acid (18:3) Omega 6

Basis for oligo- and poly-saccharides.

Acetals, ketals, and glycosides

Most buffers consist of a weak (acid / base) and its conjugate (acid / base).

Acid ; Base

How many carbons are in saturated lauric acid?

12 C

Glucose is transported into the blood from the small intestine lumen via a. a symport and facilitated diffusion (uniport) b. a symport and an antiport c. a symport only d. a uniport only e. an antiport

A

In Eukaryotes, how many translation termination release factors attach to the stop codons? a. RF1 b. RF3 c. RF2 d. all of them

A

In order to relieve supercoiling in transcription, this is needed a. gyrase ahead of the fork and topoisomerase 1 behind the fork b. gyrase and helicase c. topoisomerase 1 ahead of the fork and gyrase behind the fork d. primase and gyrase

A

In prokaryotes, tRNA is made by? a. RNA polymerase b. RNA polymerase I c. several RNA polymerases d. RNA polymerase III e. reverse transcriptase

A

Nucleic acids are linear polymers of nucleotides linked ______ to ______ by phosphodiester bridges.

3' to 5

All template strands are read in the (5'-3' / 3'-5') direction, so DNA synthesis proceeds in the (5'-3' / 3'-5') direction.

3'-5' ; 5'-3'

Correct registration of mRNA on ribosome requires alignment of a pyrimidine-rich sequence on ________ of 16S RNA with a purine-rich part of ________ of mRNA.

3'-end ; 5'-end

H2O can diffuse into a cell or go via __________.

Aquaporins

What are the acidic amino acids?

Aspartic Acid (Asp) Glutamic Acid (Glu)

The cell membrane is (asymmetric / symmetric).

Asymmetric

A transport system which can be described as a partial symport system is a. Na+,K+ATPase b. Glucose transport from kidney to blood c. H+,K+ ATPase d. Ca++‚ ATPase

B

An isoelectric amino acid was dissolved in water and the resulting pH was approximately 7.6. What amino acid would possess this property? a. alanine b. histidine c. glutamic acid d. lysine

B

At pH 1, lysine (pKs are α-carboxylate 2.16, α-amino 9.06, α-amino 10.54) would be charged as follows: a. -2 b. +2 c. +1 d. +4 e. +5

B

Calculate the enthalpy of formation per mol of NH3. Bond energies: H2 ,436 kJ/mol; N2 , 945KJ/mol; H-N 391 kJ/mol. N2 + 3H2 → 2NH a. 1080kJ b. -1080kJ c. -93kJ d. - 46.5kJ e. 45kJ

B

Camels and other desert mammals get their water from a. dessert plants b. water from lipid metabolism c. a pouch to store water in their bodies d. dew condensation

B

E. coli DNA polymerase I has one, or all, of these characteristics a. a 3'-5' endonuclease activity b. modest processivity c. a 5'-3' DNA primase activity d. a 5'-3' exonuclease activity on a second subunit in the polymerase e. all of them

B

For the amino acids histidine, alanine, and aspartic acid, list the amino acids in order of increasing isoelectric points. a. ala, his, asp b. his, ala, asp c. asp, ala, his d. ala, asp, his

B

If snake venom phosphodiesterase (3' -"a"cutter) cleaved the molecule pGATAG, what fragments would you expect as a result? a. pG , pATAG b. pGATA, pG c. pGp, ATAG d. pGATAp,G

B

In order to achieve nick translation, a DNA synthesizing enzyme can not have a. 3' exonuclease, 5'-3'polymerase activity and 5'exonuclease activities b. 5' to 3' polymerase and 3' exonuclease activity only c. 5'-3' polymerase activity and 5' endonuclease d. none of them

B

In the synthesis of the prokayotic DNA, this keeps the fork from re-annealing a. multiple RNA primers b. ss binding protein c. Pol I d. helicase e. primase

B

Iodoacetate is used to a. acetylate enzymes b. block sulfidryl (thiol) groups c. iodinate proteins d. none of the above

B

Living systems are characterized by these, EXCEPT a. Organisms are complicated and highly organized b. Living systems are always at equilibrium c. Biological structures serve functional purposes d. Living systems are able to replicable

B

One of these is not a characteristic of most fatty acids a. have an even number of carbons b. are found unassociated c. if unsaturated, they have cis double bonds d. are non conjugated

B

One of these is not used to separate the subunits in a protein a. 6 M guanidine HCl b. chymotrypsin c. high salt concentration d. 8M urea

B

Oxidation of allose on the carbon 6 will produce a. allonic acid b. alluronic acid c. allaric acid d. allopuric acid

B

Reverse transcriptase has all these activities except a. RNA directed DNA polymerase b. DNA directed RNA synthesis c. RNase H activity d. DNA directed DNA polymerase e. none of them are correct answers

B

Since every third amino acid faces the crowded center of the tropocollagen molecule, one finds there the amino acid? a. proline b. glycine c. hydroxyproline d. alanine

B

Some people say they do not use masks againts Covid19 because masks will? a. lower [CO2 (g)] in the blood and increase blood pH b. raise [CO2 (g)] in the blood and decrease blood pH c. raise [CO2 (g)] in the blood and increase blood pH. d. lower [CO2 (g)] in the blood and increase [HCO3-] e. lower [CO2 (g)] in the blood and decrease blood pH

B

The Okazaki fragments are a consequence of? a. Pol I lack of processivity b. Pol III being unable to read the lagging template in the 5' to 3' direction c. Helicase priming the DNA synthesis d. the need to have a ligase enzyme

B

The Shine-Dalgarno sequence is found a. upsteam from the promoter b. in mRNA c. downstream from the promoter d. as part of the promoter e. in rRNA

B

The enzyme that extends the 3' end at the replication primer gap in eukaryotes is a. polymerase b. pol delta c. telomerase d. primase

B

The following are part of DNA replication in E. coli, except a. the lagging strand b. the TATA box c. OriC d. Pol III e. DNAa

B

The following structure is that of (17) a. cellulose b. amylose c. cellobiose d. sucrose

B

The ionization constant of pure water is a. 1 x 10^-7 b. 1 x 10^-14 c. 1 x 10^7 d. 1 x 10^14

B

The organ that controls the pH of the small intestine is? a. gallbladder b. pancreas c. kidneys d. liver

B

The promoter site is? a. the start site for transcription in DNA b. the site on DNA at which RNA polymerase binds to initiate accurate transcription c. the binding site in DNA for regulatory proteins which stimulate or further promote the level of transcription d. the general region of DNA downstream from the start site

B

The sequence of part of a DNA strand is the following: -ATTCGATTGCCCACGT-. When this strand is used as a template for DNA synthesis, the product will be which one of the following? a. TAAGCTAACGGGTGCA b. ACGTGGGCAATCGAAT c. UAAGCUAACGGGUGCA d. TGCACCCGTTAGCTTA e. ACGUGGGCAAUCGAAU

B

What is the factor (protein) that is crucial in translation in eukaryotes? a. all of them are needed b. eIF2alpha c. TFIIB d. TFIID

B

What would be the resulting pH following addition of 0.5 moles of sodium hydroxide to 1.0 mole of isoelectric alanine? The pKas for alanine are 2.4 and 9.7. a. 2.4 b. 9.7 c. 6.0 d. 12.0

B

Which molecule or class of molecules is not derived from cholesterol? a. progesterone b. prostaglandings c. testosterone d. cortisone

B

Which of the following statements about water is incorrect? a. Water is an excellent solvent for polar molecules b. Non-polar molecules dissolve in water, if shaken vigorously c. Pure water has a concentration of approximately 55.5 M d. Amphiphilic detergents often form micelles with the polar groups on the outside exposed to the water (solvent) and the non-polar groups sequestered in the interior

B

Which of the peptides below will give a stronger Ellman's test? a. lys-lys-cys b. pro-cys-cys c. val-lys-pro d. arg-pro-pro

B

Which of these acids will not obey the Henderson-Hasselbalch equation? a. CH3COOH b. HI c. H3PO4 d. H3BO3

B

_________ in glucose provides a mechanism for quickly releasing (or storing) glucose units for (or from) metabolism.

Branching

__________ are solutions that resist changes in pH as strong acid or base are added.

Buffers

When the base pairing is imperfect, a variety of _________ and _________ can form, including _________ stem-loop structures

Bulges ; Loops : Hairpin

_________ _________ is found in all cells and performed by proteins.

Facilitated Diffusion

Drives protein synthesis.

GTP

Ceramides with 3 or more sugars, one of which is a sialic acid.

Gangliosides

Label the fluid mosaic model of the cell membrane. (11)

Green & Pink: Integral Glycoprotein Blue: Membrane channel Yellow: Integral protein Red: Peripheral protein Branch: Carbohydrate of glycoprotein

DNA _________ (topoisomerase) and DnaB __________ unwind the DNA double helix

Gyrase ; Helicase

___________ make up 99+% of atoms in the human body

H, O, C and N

Glucose (an aldose) can cyclize to form a cyclic (hemiacetal / hemiketal) while fructose (a ketose) can cyclize to form a cyclic (hemiacetal / hemiketal).

Hemiacetal ; Hemiketal

In order to analyze the N-terminal, the most common reagent used is...

Edman's reagent

One of these enzymes is diffusion controlled a. Carbonic anhydrase (kcat = 1.0 x 106/s, Km =0.12M) b. Chymotrysin (kcat = 5.1 x 10-2/s, Km = 0.44M ) c. Crotonase (kcat = 5.7 x 103/s, Km = 2 x 10-5 M) d. Urease ( kcat = 1.0 x 104/s, Km = 2.5 x 10-2M )

C

Starting with the translation initiation codon in prokaryotes, the following sequence encodes a polypeptide of how many amino acids? note: you will need the genetic code table for this question. 5'-CUGCCAAUGUGCUUUUAAUCGCGGGGG-3' (29) a. two b. eight c. three d. six e. none of them

C

Movement of the ribosome along mRNA, aa-tRNA:codon recognition, and synthesis of all peptide bonds - with tRNAs bound to acceptor (A) and peptidyl (P) sites.

Elongation

The __________ ________ binds the second incoming NTP.

Elongation site

Stereoisomers that are mirror images of each other are _________.

Enantiomers

__________ fragmentation utilizes trypsin, chymotrypsin, clostripain, and staphylococcal V8 protease, while _________ fragmentation utilizes cyanogen bromide.

Enzymatic ; Chemical

In order to analyze the C-terminal, the process used is...

Enzymatic analysis

_________ are the agents of metabolic function.

Enzymes

Two sugars that differ in configuration at only one chiral center are _________.

Epimers

Which of the following is the force that makes your bones? a. covalent b. hydrogen bond c. ionic d. van de Waals force

C

Which of the following mRNA molecules would form the most stable hairpin? (23) a. I b. IV c. II d. V e. III

C

Which of the following sugars is not oxidized to an aldonic acid by the treatment with alkaline CuSO4-- (Fehling's solution)? a. glucose b. galactose c. sucrose d. maltose

C

Which of these enzymes is a better plasma indicator of cardiac damage? a. lactate dehydrogenase b. aspatate aminotransferase c. creatine kinase MB d. lipase

C

Which one of these characteristics is not true for the α helix? a. There are 3.6 amino acids per turn. b. A hydrogen bond forms between the carbonyl oxygen of the nth amino acid residue and the -NH group of the (n + 4)th amino acid residue. c. There is a requirement for glycine every third amino acid residue in the helix d. It is right-handed.

C

What volume of 2 M HCl is required to completely titrate a 4 mmol monosodium aspartate (Asp.Na) solution? a. 2 ml b. 3 ml c. 4 ml d. 6 ml or more

C For Asp.Na to be completely titrated we need 2 mols of HCl per mol of Asp.Na or 8mmolof HCl per 4mmol of Asp.Na. mmol HCl = V HCl xM HCl or V = 8mmol/2M = 4mL

Inhibition of _________ produces renal toxicity and stomach bleeding. Inhibition of _________ causes heart attacks.

COX1 ; COX2

Only RNA pol II whose ______ is NOT phosphorylated can initiate transcription, however transcription elongation proceeds only after protein phosphorylation within the ______.

CTD

Drives lipid synthesis.

CTP

After muscle contraction, _____ must leave the cell. If not, the muscle will contract too much. _____ outside is needed to pump it out (antiport).

Ca++ ; Na+

Primary transcripts (aka pre-mRNAs or heterogeneous nuclear RNA [hnRNA]) are usually ___________ by addition of a guanylyl group.

Capped

DNA repair systems include...

Direct reversal damage repair Single-strand damage repair Double-strand break repair Translesion DNA synthesis

Enzymatic reactions that reverse the damage, returning DNA to its proper state, are ________ _________ ________ ________.

Direct reversal repair systems

_____________ _____________ are a particular threat to genome stability, because lost sequence information cannot be recovered from the same DNA.

Double-strand breaks (DSBs)

For D-sugars, alpha (OH anti to 6C) has OH (up / down), beta (OH syn to 6C) (up / down). For L-sugars, the reverse is true.

Down ; Up

Why does Pol I have exonuclease activity?

It removes incorrectly matched bases, so that the polymerase can try again and acts as a proofreader.

Regions where several stem-loop structures meet are termed __________.

Junctions

_____ and _____ are found within the cell while _____ is found outside the cell.

K+ ; ATP ; Na+

The (lagging / leading) strand is synthesized continuously while the (lagging / leading) strand is synthesized in segments.

Leading ; Lagging

Define the different structures of asparagine based on the image. (9)

Left to Right: High Mannose, Complex, Hybrid

Label the diagram using the different methods of facilitated diffusion. (12)

Left to Right: Uniport, Symport, Antiport

Name the three unnamed molecules below. (8) Hint: GalLoMan

Left to Right: Galactose, Allose, Mannose

DNA _________ seals the "nicks" between Okazaki fragments

Ligase

_________ _________ (aka Anexxin) is a PLA2 Inhibitor whoseexpression is activated by cortisone.

Lipocortin peptide

A (liposome / micelle) has water both inside and outside separated by a bilayer while a (liposome / micelle) has no water inside.

Liposome ; Micelle

Polymerase binds nonspecifically to DNA with (high / low) affinity and migrates along it, looking for promoter.

Low

When S is (low / high), the equation for rate is 1st order in S. When S is (low / high), the equation for rate is 1st order in S

Low ; High

_________ _________ and _________ _________ make the cell membrane rigid.

Low cholesterol ; Saturated lipids

The (lower / higher) the pKa, the stronger the acid.

Lower

The more unsaturated a fatty acid is (more C=C) the (higher / lower) the melting point.

Lower

Enzymes accelerate reactions by (raising / lowering) the free energy of activation.

Lowering

Transcription activation requires ___________.

Mediator

_________ proteins (hydrophobic/hydrophilic) are used for cell signaling and transport.

Membrane

________ proteins have more hydrophobic residues, whereas _________ proteins may have atypical sequences.

Membrane ; Fibrous

Systems repairing single-strand breaks include...

Mismatch repair (MMR) Base excision repair (BER) Nucleotide excision repair (NER)

Reverse transcriptase has three enzyme activities including (DNA / RNA)-directed DNA polymerase activity, ________ H activity (an exonuclease activity that degrades RNA chains in DNA:RNA hybrids), and (DNA / RNA)-directed DNA polymerase activity (which replicates the ssDNA remaining after RNase H degradation of the viral genome), yielding a DNA duplex which directs the remainder of the viral infection process.

RNA ; RNase ; DNA

Are nucleic acids susceptible to hydrolysis?

RNA is resistant to dilute acid DNA is depurinated by dilute acid DNA is not susceptible to base RNA is hydrolyzed by dilute base

Transcription is initiated in bacteria by _______ ___________ ___________, with the subunit composition α2ββ'σ.

RNA polymerase holoenzyme

______ _____________ link NTPs (ATP, GTP, CTP, and UTP) in the order specified by base-pairing with a DNA template.

RNA polymerases

DNA Pol III uses an _____ _________ (12 nucleotide __________)

RNA primer

(RPB1 / RPB2) has a DNA-binding site; (RPB1 / RPB2) binds to NTP.

RPB1 ; RPB2

Like amylopectin, glycogen gives a _________ color with iodine.

Red-violet

_________ _________ convert the sugar to a sugar acid.

Redox Reactions

__________ sugars with free anomeric carbons - they will _________ oxidizing agents, such as peroxide, ferricyanide and some metals (Cu++ and Ag+)

Reduce(ing)

___________ ___________ work with operators and promoters to control transcription of the genes.

Regulatory proteins

When comparing the 16S rRNA structures of multiple organisms, it is easy to see that they are...

Relatively similar

Proteins known as _________ _________ recognize the stop codon at the A site and promote polypeptide release from the ribosome.

Release factors

Activation of eukaryotic transcription depends on....

Relief from repression imposed by chromatin structure and interaction of RNA polymerase II with promoter and transcription regulatory proteins

Intestinal mucosa Na-glucose linked transporter, (SGLT1 / SGLT), is a symport driven by Na+ (Na+ is ATP transported). Reabsorption of glu in kidneys uses a similar symport, (SGLT1 / SGLT). Blocking (SGLT1 / SGLT) can help treat diabetes.

SGLT1 ; SGLT2 ; SGLT2

Cleaves on the C-side of Glu, Asp in phosphate buffer.

Staphylococcal V8 protease

(Saturated / Unsaturated) chains pack tightly and form more rigid, organized aggregates (i.e., membranes). (Saturated / Unsaturated) chains bend and pack in a less ordered way, with greater potential for motion

Saturated ; Unsaturated

Amino groups form _________ & _________.

Schiff bases ; Amides

A protein structure involving the α helix and β sheets is known as the _________ structure.

Secondary

Ribosomal RNA has a complex ___________ structure due to many intrastrand H bonds.

Secondary

The shape that a polypeptide takes according to its individual amino acids attractive/repulsive forces and their steric conformation.

Secondary Structure

The sterically favorable combinations are the basis for preferred _________ _________.

Secondary Structures

Know the specific structures of cholesterol and steroid hormones.

See image 10.

DNA replication is ______________- one of the two original strands is conserved in each progeny molecule

Semiconservative

DNA replication is ______________- the lagging strand is formed from newly synthesized short segments (Okazaki fragments), which are joined to form the final product

Semidiscontinuous

_________ comes in two forms, a linear form (10-30% amylose) and a branched, 1-6 form (70-90% amylopectin). It is a storage polysaccharide in plants.

Starch

_________ and _________ are energy storage molecules.

Starch ; Glycogen

The two most common core promoters in protein-encoding genes are the ________ _______ and the _____________ element.

TAT box ; Inr (Initiator)

_________ (simple sugars) cannot be broken down into simpler sugars under mild conditions.

Monosaccharides

G:C-rich regions of DNA are (more / less) stable.

More

Sugars make nucleosides (more / less) water-soluble than free bases.

More

The interconversion of the cyclic forms ( or anomers) is called _________.

Mutarotation

These change the sequence of bases in DNA, either by substitution of one base for another (so-called point ___________) or by the insertion or deletion of one or more base pairs (insertions or deletions).

Mutations

___________ are compounds formed when a base is linked to a sugar via a glycosidic bond.

Nucleosides

DNA packaging is made possible by wrapping the DNA around protein spools called __________ and then packing these in helical filaments.

Nucleosomes

Recognizes and repairs larger regions of damaged DNA than base excision repair.

Nucleotide excision repair

_________ are nucleoside phosphates.

Nucleotides

Splicing occurs exclusively in the __________.

Nucleus

_____-linked monoglycosidation can occur via serine and threonine residues.

O

Whether a glycoprotein is _____-linked or _____-linked affects the physical and chemical properties of proteins, alters solubility, mass, and electric charge, or its ability to protect proteins against proteolysis.

O ; N

________ are glycolipids and glycoproteins found in cell membranes or secreted proteins. Their function may be to allow attachment and solubility of proteins, help proper folding (steric crowding), protection from degradation, or in cell signaling (recognition).

Oligosaccharides

Genes for enzymes in pathways are grouped in clusters on the chromosome and are called __________.

Operons

Passive diffusion of a neutral particle.

Osmosis

__________ form bone.

Osteoblasts

An H+ATPase remodels bone in __________ by dissolving it (bone resorption).

Osteoclasts

Stimulates Pitocin. Bonding, labor inducing and milk letdown).

Oxytocin (from the Pituitary)

During translocation, deacylated tRNA must be removed from the _______.

P site

_________ is the eukaryotic counterpart of the E. coli β2-sliding clamp; _________ clamps δ to the DNA template

PCNA

Diacylglycerol activates _________, a crucial kinase for many pathways.

PKC

_________ releases arachidonic acid from the C-2 position of a phosphatidylglycerol (In the cell membrane).

PLA2

Cellulose strands are (parallel / antiparallel), chitins can be parallel or antiparallel.

Parallel

_________ _________ arise when a base pairs with an inappropriate partner.

Point mutations

Water forms H-bonds with (polar / nonpolar) solutes.

Polar

_________ tail enhances mRNA stability.

Poly(A)

_________ are short polymers of amino acids.

Polymers

_________ functions include storage, structure, recognition.

Polysaccharides

(Positive / Negative) supercoiling has the potential to cause localized unwinding in DNA.

Positive

Enzymes called topoisomerases introduce (positive / negative) supercoils and unwind (positive / negative) supercoils, while gyrases introduce (positive / negative) supercoils and unwind (positive / negative) supercoils.

Positive ; Negative ; Negative ; Positive

Transcription initiation in eukaryotes proceeds through assembly of a ____________ ____________.

Preinitiation complex (PIC)

Refers to linking of "isoprene"-based groups.

Prenylation

An alkylating agent like iodoacetate is used in order to...

Prevent recombination.

A family of glycoproteins whose carbohydrates are mostly O-linked glycosamine glycans, are used for cell growth, make cartilage flexible, resilient (cushion), and glue cells to their matrix.

Proteoglycans

The angle about the C(alpha)-C bond in a peptide chain is denoted as _________.

Psi

(DNA / RNA) and protein are replaceable, but (DNA / RNA) must be preserved.

RNA ; DNA

80% of DNA-binding proteins belong to one of three principal classes based on their structures....

The helix-turn-helix (HTH) motif The zinc-finger (or Zn-finger) motif The leucine zipper-basic region (or bZIP)

Male Drosophila mark females with _________ when they mate, rendering them unattractive to subsequent suitors.

Triacylglycerols

_________ are a major energy source for many organisms.

Triacylglycerols / Triglycerides

The genetic code is a _________ code, read from a fixed starting point in each mRNA where each group of ________ bases codes for one amino acid.

Triplet ; Three

Cleaves on the C-side of Lys, Arg.

Trypsin

Water, glucose, amino acids, and needed ions are transported out of the filtrate into the tubule cells and then enter the capillary blood.

Tubular reabsorption

H+, K+, creatine, and drugs are removed from the peritubular blood and secreted by tubule cells into the filtrate.

Tubular secretion

______ protein (contrahelicase, reanneals DNA) must be bound to ______ to prevent helicase activity. Halts polymerase

Tus (terminus utilization substance) ; Ter

In the secondary protein structure, ________ can occur about either of the bonds linking the alpha carbon to the other atoms of the peptide backbone

Twists

A and T share _____ H bonds.

Two

Hemoglobin has _____ α and _____ β subunits. Each one has a heme group. (How many?)

Two

In a peptide chain, there are _____ degrees of freedom per residue.

Two

_______ GTPs are hydrolyzed for each amino acid incorporated into peptide.

Two

________ restriction enzymes require no ATP and can leave staggered or "sticky" ends or can produce "blunt" ends.

Type II

__________ and _________ restriction enzymes cleave DNA chains at selected sites

Type II ; Type III

Ultraviolet light absorption of proteins between 260 and 280 nm is due their aromatic amino acid content. What are the three aromatic amino acids?

Tyr, Trp, Phe

snRNPs _____ and _____ bind at the 5'- and 3'- splice sites, and _____ snRNP binds at the branch site

U1 ; U5 ; U2

Drives carbohydrate metabolism.

UTP

In type of inhibition, the inhibitor (I) binds only to ES, not to E.

Uncompetitive inhibition

What is the Michaelis-Menten (MM) Equation? (2)

V = Vmax [S] / (Km + [S])

_________ _________ promotes calcium absorption in the gut and maintains adequate serum calcium and phosphate concentrations to enable normal mineralization of bone and to prevent hypocalcemic tetany (spasms).

Vitamin D

_________ are esters of long-chain alcohols with long-chain fatty acids that are highly insoluble.

Waxes

Amino acids are (weak / strong) polyprotic acids.

Weak

Subunit interactions depend on (weak / strong) forces.

Weak

___________ ___________ Maintain Biological Structure, Determine Biomolecular Interactions, as well as Narrow Range for Life Conditions.

Weak Forces

_________ inhibits factor Xa, so no Trombin can be made, and therefore, Fibrinogen can not be made into Fibrin to form a clot.

Xarelto

This DNA is left-handed, longest, thinnest, 3.8 A, and has 12 bp per turn.

Z DNA

Blood clotting is a series of _________ cleaved sequentially.

Zymogens

Codon recognition is achieved by _______________________.

aminoacyl-tRNAs

_____, the turnover number, is the number of substrate molecules converted to product per enzyme molecule per unit of time, when E is saturated with substrate.

kcat

Carries the message for protein synthesis.

messenger RNA (mRNA)

What is the equation for determining pH?

pH = -log10 [H+]

What is the Henderson-Hasselbalch Equation?

pH = pKa + log10 [A ̄ ] / [HA]

What is the isoelectric point?

pH at which a species is neutral

What is the equation for the isoelectric point? - Basic: highest pKas, highest pI - Acid : lowest pKas, lowest pI

pI = (pKa1 + pKa2) / 2

What is the equation for determining pKa?

pKa = - log Ka

What is the Nerst law equation? (Passive diffusion of a CHARGED particle.)

ΔE = RT/zF x Log [ion]out/[ion]in

What is the Gibbs free energy equation?

∆G = ∆H - T∆S

The requirements for peptide chain elongation are:

1. An mRNA:70S ribosome:peptidyl-tRNA complex (peptidyl-tRNA in the P site) 2. Aminoacyl-tRNAs 3. A set of proteins known as elongation factors 4. GTP

The four stages of transcription, in order, are...

1. Binding of RNA polymerase holoenzyme to template DNA at promoter sites 2. Initiation of polymerization 3. Chain elongation 4. Chain termination

The three steps in chain elongation are...

1. Codon-directed binding of the incoming aminoacyl-tRNA at the A site. 2. Peptide bond formation 3. Translocation of the "one-residue-longer" peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A site.

Arrange these intermolecular forces from strongest to weakest: - Dipole-Dipole - Ion-Dipole - Ion-Ion in solid / gas phase - Dipole-Induced Dipole - Ion-Ion in water - London Dispersion Forces / Induced Dipole-Induced Dipole

1. Strong: Ion-Ion in solid / gas phase 2. Ion-Dipole (water - ions, NaCl in H2O), 1/r4 3. Weak: Ion-Ion in water, 1/r, ~ 20KJ/mol 4. Dipole-Dipole, 1/r3, 4 KJ/mol 5. Dipole-Induced Dipole 6. London Dispersion Forces: Induced Dipole-Induced Dipole, weakest but universal. All have them.

Proteins: The rise per residues in an alpha helix is _____ Angstroms Hint: Rise per turn (pitch) = 3.6 x _____A = 5.4

1.5

What is the Lineweaver-Burk form of the Michaelis-Menten (MM) Equation? (3)

1/ V = Km/Vmax(1/[S]) + 1/Vmax

How many carbons are in saturated myristic acid?

14 C

How many carbons are in saturated palmitic acid?

16 C

How many carbons are in saturated stearic acid?

18 C

What pentose sugars are found in DNA and RNA respectively?

2-deoxy-D-ribose (in DNA) D-ribose (in RNA)

How many carbons are in saturated arachidic acid?

20 C

How many carbons and how many double bonds are in Arachidonic acid (20:4)?

20 Carbons 4 C=C double bonds

A nucleic acid sequence is always read _____ to _____.

5' to 3'

Proteins: The rise per residues in a parallel (skewed) beta sheet is _____ Angstroms

3.25

Proteins: The rise per residues in an antiparallel (straight) beta sheet is _____ Angstroms

3.47

Proteins: In the alpha helix, C=O and N-H hydrogen bridge every _____ residues or n with n+4 residue Hint: Rise per turn (pitch) = _____ x 1.5A = 5.4

3.6

DNA polymerase adds nucleotides in _________ direction to the 3'-end of the primer

5'-3'

The _________ of an intron in higher eukaryotes is always GU and the _________ is always AG

5'-end ; 3'-end

Eukaryotic mRNAs are characterized by two post-transcriptional modifications: The _____________ 7methyl-GTP cap The _____________ poly(A) tail

5'-terminal ; 3'-terminal

Aldoses with _____ or more and ketoses with _____or more are chiral.

3C ; 4C

Cleavage on the a-side of a polynucleotide chain leaves the phosphate attached to the _____-position of the adjacent nucleotide. B-side hydrolysis yields _____-phosphate products.

5' ; 3'

In the chain termination method, the bottom of the gel represents the _____ end of the DNA while the top represents the _____ end of the DNA. You read from the top to bottom to get the complimentary strand.

5' ; 3'

Mutations can be induced by base analogs such as _________________ or ______________.

5-bromouracil (5-BU) ; 2-aminopurine

Loss of the initiation factors leads to binding of _____ __________.

50S subunit

Cap G residue is methylated at ____________.

7-position

Addition of the ionophore gramicidin to erythrocytes in serum would a. break the cell membrane lysing the erythrocytes b. cause the net movement of Na+ out of the cells into the blood serum c. eliminate the electrical charge of the membrane d. eliminate other proteins from the membrane

A

Aldohexose prefer the following type of structure a. pyranose ring b. furanose ring c. linear structure d. none of the above

A

All amino acids derived from proteins have the same configuration as: a. L-glyceraldehyde b. L-glucose c. D-glyceraldehyde d. glycine

A

An college student is rushed to the hospital because he drank the alcohol methanol, which is converted into toxic formaldehyde in the liver by alcohol dehydrogenase. The ER physician says; " get him as drunk as possible with pure ethanol" Why did she say that? a. ethanol must be a competitive substrate for the active site of the liver enzyme that processes methanol b. ethanol is transformed by lactate dehydrogenase into lactic acid, which protects the liver c. ethanol must be an non-competitive inhibitor of alcohol dehydrogenase d. ethanol converts formaldehyde back into methanol, which is then excreted

A

An isoelectric amino acid was dissolved in water and the resulting pH was approximately 10.7 . What amino acid would possess this property? a. arginine c. histidine b. glutamic acid d. lysine

A

Are silent mutations always harmless? a. Not always, if the codon reading speed changes, too much or too little protein can be made b. No, because, if synonymous, they are found in introns, not exons c. Always harmless, because they code for the same amino acid d. all of them

A

Based in the following melting points, which fatty acid is more likely to be found in the cell membrane of a tropical plant a. myristic, 45°C b. oleic, 13°C c. linoleic, -5°C d. palmitoleic, 0°C

A

Collagen is characterized by a. having long streches of gly-pro-pro/hyp b. has no lysine in its composition c. formula has repeats of abcdefg amino acids d. being made of alpha helices

A

Consider the DNA replication fork shown below. DNA ligase will be required to finish synthesis at which labeled points on the figure? Hint: there are two pol III enzymes moving in opposite directions (21) a. A and D b. D and B c. C and D d. B and C e. A and B

A

Covalent forces a. are intramolecular forces b. are both intra and intermolecular forces c. are intermolecular forces d. none of the above

A

DNA pol III replicates the lagging strand by using a. a loop on the lagging strand b. by moving backwards c. by reading in the 5'-3' direction d. Okazaki fragments e. by using one enzyme per strand

A

Fill the blanks: If the pI of a peptide is 4.6, then ____ might be present while ____would probably be absent a. Glu / Lys b. Asp / Gly c. His / Ser d. Cys / Tyr e. Arg / His

A

Globular proteins are usually all EXCEPT a. Insoluble in water b. Roughly spherical c. Folded so that the hydrophobic amino acids are in the interior of the molecule d. All of them

A

This DNA is right-handed, short and broad, 2.3 A, and has 11 bp per turn.

A DNA

Km is a _________ derived from rate constants.

Constant

Aminoacyl-tRNA binds to _______ of ribosome in the form of an EF-Tu:GTP:aminoacyl-tRNA complex

A site

During translocation, peptidyl-tRNA must be moved (translocated) from the _______ to the _______.

A site ; P site

Insulin is a polypeptide hormone that contains two short polypeptide chains linked by two interstrand disulfide bonds. The most logical order of events to perform in order to sequence this protein would be? A: The peptides are reduced with mercaptoethanol. B: The peptides are sequenced using Edman chemistry. C: The peptides are separated by chromatography techniques. D: The peptides are alkylated with iodoacetate

A, D, C, B

According to Chargaff's rules, the molar ratios of G-C and A-T in humans are 1:1, but the ratios of _______ is 1.56:1 and _______ is 1.75:1.

A-G ; T-C

Oxidative deamination of adenine in DNA yields hypoxanthine, which base-pairs with cytosine, resulting in an ________ to ________ transition.

A-T to G-C

Which statement is incorrect about the nature of the hydrogen bond? a. The donor is a hydrogen atom bonded to a less electronegative atom than hydrogen. b. The more linear the bond, the stronger the interaction. c. The acceptor is a fairly electronegative atom containing a nonbonding pair of electrons. d. It is a type of noncovalent bond.

A. The donor is a hydrogen atom bonded to a less electronegative atom than hydrogen.

The repeating secondary structures as found in beta-strands, beta-turns, and alpha-helices of folded proteins primarily result from a. hydrogen bonds b. electrostatic interactions c. hydrophobic interactions d. van der Waals interactions

A. hydrogen bonds

Which of the following is not a characteristic of hemoglobin? a. it is an allosteric enzyme b. it contains two different subunits c. it contains a prosthetic group d. is a transport protein for molecular Oxygen

A. it is an allosteric enzyme Not an enzyme

Stimulates resorption of water by the distal tubules: antidiuretic, for D. Insipidus, labor contractions.

ADH (from the Pituitary)

When determining whether or not a patient suffers from liver disease, it is important to note that damage NOT of viral origin will result in an ALT / AST ratio (< / >) 1.

ALT / AST < 1

Central to energy metabolism.

ATP

Multidrug resistant in cancer is due to the cancer making use of the cell's __________ __________ to remove chemotherapeutic drugs from the cell.

ATP pumps

Spliceosome assembly requires _______________ RNA rearrangements catalyzed by spliceosomal DEAD-box ATPases/helicases.

ATP-dependent

Antibodies raised to bind the transition state of a reaction of interest.

Abzymes

_________ _________ requires energy to move against concentration gradient.

Active Transport

What are the different purines and where are they found?

Adenine (DNA, RNA) Guanine (DNA, RNA)

Galactose polymers.

Agarose and Agaropectin

What are the nonpolar amino acids?

Alanine (ala) Valine (Val) Leucine (Leu) Isoleucine (Ile) Methionine (Met) Tryptophan (Trp) Phenylalanine (Phe) Proline (Pro)

_________ and _________ contain aldehyde and ketone functions, respectively.

Aldoses ; Ketoses

Ca-binding polymers in algae.

Alginates

In the core enzyme, the ______ subunit is the polymerase.

Alpha (α)

Carboxyl groups form _________ & _________.

Amides ; Esters

Proteins are made of _________ _________.

Amino Acids

Contain an amino group in place of a hydroxyl group.

Amino sugars

Refers to molecules that contain both polar and nonpolar groups. Ex: Fatty acids

Amphiphilic Molecules (Amphipathic)

__________ is poorly soluble in water, but forms micellar suspensions. Iodine fits into the helical suspensions to produce a blue color.

Amylose

Persons suffering chest pain due to angina only will not likely have altered LDH levels. Why?

Angina pectoris does no damage.

A chemically diverse series of ____________ targets the PTC and/or the adjacent peptide exit tunnel.

Antibiotics

The DNA double helix has a (parallel / antiparallel) nature.

Antiparallel

This DNA is right-handed, longer, thinner, 3.32 A, and has 10 bp per turn.

B DNA

A phylogenetic tree depicts ___________ of proteins. a. folding patterns b. evolutionary relationships c. hypervariable residues d. gene sequences e. appropriate purification strategies

B. evolutionary relationships

Using the graph, determine which line represents Competitive inhibition, Noncompetitive inhibition, 1 / Vmax, and -1 / Km. (5)

Blue: Noncompetitive inhibition Green: Competitive inhibition A: -1 / Km B: 1 / Vmax

__________ __________ can form when a purine interacts with one pyrimidine by Hoogsteen base pairing and another by Watson-Crick base pairing.

Base triplets

The ___________________ _________ is the "primary" structure of chromatin.

Beads-on-a-string motif

Tay sachs is a _________ _________ _________ deficiency.

Beta hexosaminidase A

DNA replication is ______________- it proceeds in both directions from the starting point

Bidirectional

A 42-amino acids peptide related to the extracellular Alzheimer amyloid deposits has the last few residues immersed in the membrane bilayer. Based on your knowledge about membrane proteins, which of the following sequences most probably identifies the last few amino acids in this 42 residue peptide? a. Ala-Glu-Phe-Arg b. Lys-Val-His-His-Gln c. Val-Val-Ile-Ala d. Asp-Val-Gly-Ser e. Asp-Ser-Gly-Tyr

C

A group of genes transcribed at the same time and controlled by only one protein is called a. polycystrionic genes b. split genes c. operon d. a replicon e. operator

C

A plasmalogen is a. a glycerophospholipid with an amide bond b. a fatty acid attached to protein c. an ether glycerophospholipid d. a triglyceride found in plasma

C

An aspect which is not a characteristic of the Na+,K+ATPase is a. it is an electrogenic pump b. its function is to pump Na+ ions out of and K+ ions into the cell c. the process requires the hydrolysis of ATP and the subsequent hydrolysis of the ADP side product d. the ATPase activity is associated with the cytoplasmic side of the pump

C

Analysis of a cell line that rapidly transforms into a tumor cell line demonstrated an increased mutation rate within the cell. Further analysis indicated that there was a mutation in the DNA polymerase enzyme that synthesizes the leading strand. This inactivating mutation is likely to be in which of the following activities of this DNA polymerase. a. 5'-3' Exonuclease activity b. Uracil-DNA glycosylase activity c. 3'-5' exonuclease activity d. Ligase activity e. Phosphodiester bond making capability

C

Carbon is essential for life is because a. it has four bonds b. it can be used to make CO2 c. it makes versatile, complex structures d. none of the above

C

Consider the in vivo turnover rates (half life) for proteins, mRNA and DNA. Which order, from most turnover to less turnover, should you find in vivo? a. mRNA > DNA > protein b. protein > mRNA >DNA c. mRNA > protein > DNA d. DNA > mRNA > protein

C

Dideoxynucleotides are effective agents against DNA synthesis, but appear to have little, or no effect, on RNA synthesis. This is most likely due to which of the following? a. Lack of a 3'-OH group b. Presence of an N-glycosidic bond at carbon 1 c. Lack of a 2'-OH group d. Factor TFIID of RNA polymerase does not recognize deoxyribonucleotides e. Presence of a 5'-phosphodiester bond

C

Give the name of the sugar show below (15) a. sialic acid b. galactosamaine acetate c. glucosamineacetate d. heparin acetate

C

How many amino acyl t-RNA synthetases are there in prokaryotes? a. 10 b. 21 c. 20 d. class I and II

C

If a solution of lysine, histidine and aspartic acid at pH 12 were loaded on a strong anion exchange column and eluted from the column with a gradient of decreasing pH, what would be the order (first to last) in which these amino acids would elute from the column? a. his, lys, asp b. asp, his, lys c. lys, his, asp d. asp, lys, his

C

If equal volumes of 0.8M sodium lactate and 0.4M lactic acid are mixed, and the pKa of lactic acid is 3.86, the final of the solution pH should be a. 3.86 b. lower than 3.86 c. higher than 3.86 d. neutral

C

If the following section of a polypeptide is folded into an Ɐ-helix, to which amino acid is the CARBONYL GROUP OF ALANINE noncovalently bonded? ala-ser-val-asp-glu-leu-gly a. serine b. aspartic acid c. glutamic acid d. leucine

C

If you want to clone a gene and you can either use one enzyme to make two flanking cuts or two enzymes each one flanking one of the ends of the gene, which choice will be better? a. one enzyme, because I get the same two types of sticky ends b. one enzyme, because I get the same two types of sticky ends and it is cheaper c. two enzymes, because having two different sticky ends gives the right orientation d. either way you get the right insert

C

In eukaryotes, the first tRNA used is? a. the same as per prokaryotes, tRNAfMet b. the same as per prokaryotes, tRNAMet c. A non codon directed tRNAiMet, but that starts at the AUG codon d. able to bind EF-TU

C

In order to prevent a disulfide bond in a protein from re-forming, we need a. two cysteine molecules b. mercaptoethanol c. iodoacetate d. all of the above e. urea

C

In prokaryotic DNA synthesis, one of these enzymes does not use an RNA primer a. E. coli Pol III b. telomerase c. E. coli Pol I d. reverse transcriptase

C

In the majority of α-helixes, each peptide carbonyl is hydrogen-bonded to the peptide N-H group ______ residues farther _____ the chain a. 2, down b. 3, down c. 4, up d. 2, up

C

Lactate dehydrogenase combines two subunits in variable ratios to control its activity. This is an example of? a. holoenzymes b. zymogen c. isozymes d. heteroterameric e. proenzymes

C

Membrane proteins differ from globular proteins in that a. membrane associated amino acids usually have polar side chains b. globular proteins are water insoluble c. membrane proteins are much more soluble in detergents than water d. membrane proteins usually have more hydrophobic amino acids e. All are true

C

Which carbon in ribose determines whether it is the D- or L-stereoisomer? a. 1 b. 5 c. 4 d. 6

C

Termination of translation occurs when a. the tRNA for termination reads a stop codon b. the peptidyl transferase becomes a hydrolase when termination tRNA attaches to stop codon c. the RF1, RF2 or RF 3 and GTP bind to a stop codon d. all of the the choices

C

The co-inducer in negative control of the lac operon is a. CAP b. glucose c. lactose d. repressor

C

The common activities of DNA pol I and pol III are? a. polymerase, 5' and 3' exonuclease b. polymerases and 5' exonuclease only c. polymerase and 3' exonuclease d. polymerase only

C

The enzyme trypsin has an optimal pH of 7.8. If the pH is decreased to 3, the enzyme loses activity. If the pH is increased back to 7.8 , the activity is recovered. This is most likely due to? a. The active site is not protonated at pH = 7.8 b. the enzyme cleaves aromatic amino acids c. the enzyme reversibly loses quaternary structure at pH = 3 d. the enzyme is denatured at pH = 3 e. all of them

C

The enzyme which catalyzes the reaction below is classified as a? aldehyde + NADH + H+ --> alcohol + NAD+ a. lyase b. hydrolase c. reductase d. esterase e. isomerase

C

The eukaryotic enzyme used to replicated mitochondrial DNA is? a. Reverse transcriptase b. Unable to replicate circular DNA c. Similar to Pol III d. DNA polymerase epsilon

C

The fact that DNA synthesis inhibitors in humans prevent retroviruses from being infective led to hypothesize the existence of? a. telomerase b. restriction enzymes c. reverse transcriptase d. DNA polymerase

C

The information needed to define the structure of a protein is essentially contained in a. amino acid composition b. secondary structure c. amino acid sequence d. tertiary structure

C

The pH of a 0.05M solution of Ca(OH)2 is a. 1 b. -1.3 c. 13 d. 5

C

The portion of an integral protein that is located within the bilayer of a plasma membrane is most likely to contain which of the following amino acids? a. aspartic acid b. histidine c. leucine d. serine

C

The reason vitamin C is necessary for collagen structure is a. without it no crosslinking can occur b. it helps the collagen to form an alpha helix c. is needed for the production of hydroxyproline d. if not present, collagen becomes water soluble

C

The reason why restriction enzymes (RE) do not cut the bacterial DNA of the organism from which they were isolated is? a. Because the bacterial DNA lacks the restriction sites (sequences) to be cleaved b. the viral DNA activates the RE as soon as it is injected in the cell c. because the bacterial DNA is methylated and the RE can not cut it d. all of them

C

The relationship between the structures below is (18) a. they are mirror images b. they are hexoketoses c. they are anomers d. they are furanoses

C

The separation between two proximal beta strands of a beta sheet is wider in the? a. parallel arrangement b. the have the same separation c. antiparallel arrangement d. none of them

C

The thermodynamic driving force for passive diffusion depends on a. the thickness of the membrane b. the hydrophobic character of the species c. the chemical potential gradient d. the permeability coefficient of the species

C

The unique composition of collagen is accommodated in a structure called a(n): a. β-pleated sheet. b. coiled coils. c. triple helix. d. helix-turn-helix motif e. all are true

C

The upper most stream consensus sequence of the prokaryotic promoter is located at? a. at -35 bp from starting promoter b. at -10 from the enhacer element c. at -35 bp from the initiation site d. it can be found up or downstream e. at -35 bp from the operator

C

Treatment of cells with oubain inhibits the Na+/K+ pump and causes the cells to swell and burst. This could be explained by? a. The ATP not used forces the Mg++ and Na+ ions to enter the cells b. there are also leaky K+ channels that are not inhibited by oubain c. the Na+ ions can not leave the cell, which swells the cells with water by osmosis d. there are also K+ channels that are activated by oubain

C

Tyrosine has pKas at 2.2, 9.1, and 10.1. What is the charge of tyrosine at pH 12? a. -1 b. -3 c. -2 d. +2 e. +1

C

Water is an acid and a base, therefore water is? a. amphiphilic b. can be either c. amphoteric d. polyprotic/polybasic

C

Water is the solvent of life because? a. dissolves organic and ionic compounds b. has a high heat capacity c. all of them d. it is a liquid at room temperature e. it is amphoteric

C

What is not true about cognate t-RNA recognition by the aminoacyl-tRNA synthetases a. they recognize invariant bases b. their code is universal c. all recognize the anticodon loop d. their discriminatory base is number 1

C

What is the name of the sugar show below? (16) a. glucose b. galactose c. allose d. mannose

C

What is the pH of a serine solution in which the α-NH3+ group (pKa 9.2) is one-third dissociated? a. 8.7 b. 9.5 c. 8.9 d. 9.8 e. 9.0

C

What is true of this compound? (22) a. it is deoxyuridine b. it not found as part of DNA c. it is deoxycytidine d. all of them e. it does not have a glycosidic bond

C

Which of the following characteristics is not associated with the solvent water? a. high surface tension b. a chemically inert solvent, which has a great capability to dissolve a diverse spectrum of molecules and ions c. low heat capacity d. a high dielectric constant

C. low heat capacity

Some promoters require an accessory protein to activate transcription. An example of this is the protein _____.

CAP (Catabolite activator protein)

_________ cleaves any residue except Pro, Arg, and Lys.

Carboxypeptidase A

_________ only works on terminal Arg and Lys.

Carboxypeptidase B

_________ or __________ cleave all residues.

Carboxypeptidases C or Y

_________ _________ inhibit the Na/K pump. This accumulates Na+ and Ca++ (Ca++ pump inhibited by Na+) inside the cells producing hypertension.

Cardiac glycosides

Made of lipid bilayer of phospholipids, proteins and cholesterol.

Cell Membrane

_________ _________ _________ are recognition molecules

Cell surface polysaccharides

__________ is the most abundant natural polymer on earth. It is the principal strength and support of trees and plants.

Cellulose

_________ have amide linkages of fatty acids to the nitrogen of sphingosine.

Ceramides

Glycosphingolipids with one sugar are _________.

Cerebrosides

__________ makes up the exoskeletons of crustaceans, insects and spiders, and cell walls of fungi.

Chitin

_________ and _________ are structural molecules.

Chitin ; Cellulose

The nucleoprotein complex, consists of histones and nonhistone chromosomal proteins

Chromatin

____________ is remodeled through the actions of enzymes that covalently modify side chains on histones within the core octamer.

Chromatin

This factor for chromatin remodeling mediates ATP-dependent conformational changes in nucleosome structure.

Chromatin-remodeling complexes

Cleaves on the C-side of Phe, Tyr, Trp.

Chymotrypsin

RNA polymerases adopt a _____________ structure, to grasp the DNA duplex.

Claw-like

The first step in determining a protein's sequence is to...

Cleave the disulfide bridges.

In prokaryotic chain termination, clusters of GTGTGTTGT consensus sequences block the ________ and ____________forks.

Clock ; Counterclock

RNA polymerase holoenzyme and promoter form a (open / closed) promoter complex (in which the DNA is not unwound). Polymerase then unwinds about 12 pairs to form "(open / closed) promoter complex

Closed ; Open

Like trypsin, but attacks Arg more than Lys.

Clostripain

In type of inhibition, the inhibitor (I) binds only to E, not to ES.

Competitive inhibition

______ enzyme has three subunits - α, ε, and θ

Core

Pol II promoters consist of two separate sequence features, the ______ ___________ and the more distantly located __________ _________ (enhancers and silencers).

Core promoter ; Regulatory elements

_________ indirectly inhibits PLA2, preventing inflammation.

Cortisone

Irreversible inhibitors interact with an enzyme via covalent associations (aspirin, both COX).

Covalent

_________ _________ is found primarily in heart and skeletal muscle as well as the brain. Therefore, measurement of serum _____ levels is a very good diagnostic for injury to these tissues.

Creatine phosphokinase (CPK)

Acts only on the C-side of methionine residues.

Cyanogen bromide

Prenylation always involves the...

Cys of CAAX (C=Cys, A=Aliphatic aa, X=any residue)

What are the different pyrimidines and where are they found?

Cytosine (DNA, RNA) Thymine (DNA) Uracil (RNA)

Why does DNA contain thymine instead of uracil?

Cytosine spontaneously deaminates to form uracil.

A DNA is found to exhibit a melting temperature of 750C in 0.1 M NaCl in 0.01 guanidinium chloride. Under what experimental conditions would the Tm be decreased? a. Increasing the concentration of guanidium chloride b. decreasing the concentration of NaCl in the solution. c. adding 1% urea (an organic denaturant). d. all of the above.

D

All of these are examples of globular proteins EXCEPT a. hemoglobin b. myoglobin c. ribonuclease d. alpha keratin

D

Alpha keratin has a structure with a sequence that a. has 7 repetitive residues b. disulfide bridges connect the polypeptides c. the first and the fourth are nonpolar d. all of them

D

Ceramides, cerebrosides and gangliosides have all in common a. glycerol b. phosphate groups c. fatty acids d. sphingosine

D

Chymotrypsin is secreated as a zymogen by the acinar cells of the pancreas. This is most likely due to? a. the zymogen is inactive and will no attack the pancreas cells b. another enzyme, trypsin, is needed to cleave the zymogen c. the chymotrysin is needed in the duodenum only d. all of them

D

_________ is due to loss of tertiary and quaternary structure. The later loss is enough to lose activity and function.

Denaturation

Dextrans formed by bacteria are components of _________ _________.

Dental Plaque

Covid 19 is this type of virus a. a coronavirus b. a (+)RNA virus c. an enveloped virus d. all of them

D

Fibrous proteins, such as collagen, have which of the following properties? a. highly soluble in water b. exhibit enzymatic activity c. their hydrophilic residues are directed into the interior of the protein d. serve structural roles in the cell

D

For a weak acid and its conjugated base the following is true a. KAH x KA- = 10-14 b. pKa + pKb = 14 c. pH = pKa + Log [A-]/[AH] d. all are true

D

In a beta keratin molecule made of alanine and glycine you would find a. all alanines and glycines on the same face b. random alanine glycine on both faces c. alternant alanines and glycines on the same face d. alternant alanines and glycines on opposite faces

D

In eukaryotes, the DNA sequences called enhancers are characterized by? a. are distantly located from the initiation site b. can be found within the gene itself c. transcription factors bind to them d. all of them

D

In relaxed "B" DNA, one of these group of numbers is correct a. W= 0, L= 22, T = 20 b. L = 40, W= 20, T = 20 c. W = 20, L = 20, T = 0 d. W= 0, L= 23, T = 23 e. T = 20, L = 20, W = 40

D

One of these is not found in alpha helices a. methionine b. aspartic acid c. lysine d. proline

D

One of these is not found in collagen a. 3-hydroxyproline b. 5-hydroxylysine c. 4-hyrdroxyproline d. 3-hydroxy-glycine

D

Phospholipids which have an ether linkage are a. phosphatidic acid b. sphingomyelin c. ceramide d. plasmalogens

D

Reverse transcriptase has all these activities except a. RNA directed DNA polymerase b. DNA directed DNA polymerase c. RNase H activity d. RNA polymerase

D

The "permanent" part of adding wave in hair is primarily due to: a. rearrangement of hydrogen bonds between hair fibers b. rearrangement of hydrophobic interactions in hair fibers c. reestablishment of new ionic interactions between hair fibers. d. reduction and re-oxidation of disulfide bonds in hair fibers. e. breaking and reforming peptide bonds in the hair polypeptides.

D

The ATPase which is responsible for maintaining the greatest ion gradient is the a. Na+-/K+ATPase b. Ca++‚ ATPase c. erythrocyte anion transporter d. H+,K+ ATPase

D

The Henderson-Hasselbalch equation applies a. only to acids b. to weak acids c. only to bases d. to very weak conjugated bases e. to strong acids

D

The amino acid residues which are directly involved in the sugar-protein linkage in glycoproteins are a. gly, thr & ser b. lys, his & glu c. gln, ser & tyr d. asn, thr & ser

D

The difference between starch and glycogen is a. starch has a and glycogen b glycosidic bond b. starch has 1,6 glycosidic linkages and glycogen does not c. starch has only 1,4 glycosidic linkages d. glycogen is more branched than starch

D

The following question are related to the structures below: (14) What is the name of the amino acid D? a. valine b. asparagine c. leucine d. serine e. proline

D

The rate of passive diffusion depends on a. the chemical potential gradient b. the partition coefficient for the species c. the thickness of the membrane d. all of the above

D

The tertiary structure of a protein is usually a result of which of the following interactions? a. intramolecular hydrogen bonding b. hydrophobic interactions c. electrostatic interactions d. all of the above interactions

D

The tus protein function is a. to cut DNA and stop replication b. that of a primase c. that of a gyrase d. to prevent unwinding of the DNA/DNA duplex

D

To what target sequence on DNA is the oligonucleotide pAATTCCTA complementary? a. TTAAGGCC b. CCGGAATT c. UAGGAAUU d. TAGGAATT

D

What is not true about cell membranes a. made of lipid bilayer b. composed of glycerophospholipids, proteins, cholesterol c. have a wide range of composition d. same composition in the inner and outer face

D

What is not true about the following sugar (19) a. it is a reducing sugar b. it has a beta glycosidic bond c. it is lactose d. it has an alpha glycosidic bond

D

What is the mRNA sequence corresponding to the sense DNA sequence: TTAATATAAAAAAAAATAAAGCGC, if the internal run of 8 A's correspond to an intron? GOOD a. UUUAUAUAUAUAGCGC b. GCGCTATATATATAAA c. AAATATATATATCGCG d. UUAAUAUAUAAAGCGC e. CGCGAUAUAUAUAUUU

D

Which molecule is not a glycosaminoglycan? a. heparin d. keratan sulfate c. chondroitin- 4- sulfate d. chitin

D

Constituents of DNA, etc.

Deoxy sugars

Which of the following molecules cannot undergo mutarotation? a. Glucose b. Fructose c. Ribose d. Sucrose

D

Which of the following would be the best in buffering capacity? a. 2M CH3COOH/ 2M CH3COO-Na b. 0.1M H2PO4^-1 and 0.1M HPO4^2- c. 1M PO4^3- and 1M HPO4^2- d. 5M H3PO^4 and 5M H2PO4^1- e. 0.1M CH3COOH/ 0.1M CH3COO-Na

D

Which statement is CORRECT about the peptide ala-ser? a. Alanine is at the N-terminal of the peptide b. The Ɐ-carbon of alanine is sp3 hybridized c. There are a total of six atoms that lie in the plane of the peptide bond linking alanine to serine d. All the above are correct statements

D

Which statement is INCORRECT about the classification of amino acids? a. Alanine and valine are neutral, nonpolar amino acids b. Lysine and arginine are basic amino acids c. Tryptophan and phenylalanine are aromatic amino acids d. Aspartic acid and asparagine are acidic amino acids

D

Which statement is incorrect about the mechanism of the Na+-/K+ pump? a. The pump gets phosphorylated when ATP, Mg++ and Na+ are bound b. The cartiotonic steroid, digitalis, inhibits the pump by binding to a site on its extracellular face. c. One mole of ATP is hydrolyzed for every three moles of Na+ transported out of the cell. d. The phosphorylated pump has a lower affinity for K+ than for Na+.

D

Which these is a strong promoter? Consensus is TTGACATATA a. GCGACATATA b. CCGAGAGGG c. TTTATATATA d. TTGACATAAA e. none of them

D

Which would be the best strategy for cloning gene w? The most efficient (30) a. Use KpnI to cut both the plasmid and the gene, then clone it b. Use NdeI and Xho I to cut the gene, EcoRI and Sal I to cut the vector. Clone it c. Use EcoRI and BamH I to cut the gene and EcoRI and Sal I to cut the plasmid. Clone it d. Use NdeI and Xho I to cut the gene, NedI and Sal I to cut the vector. Clone it

D

D,L designation refers to the configuration of the highest-numbered asymmetric center. Which type of sugars (D- / L-sugars) predominate in nature?

D-sugars

Which factors will influence the native conformation of a protein? a. pH of the solution b. concentration of salt in solution c. its sequence of amino acids d. all of the above

D. all of the above -pH of the solution -concentration of salt in solution -its sequence of amino acids

Which of the following pKbs represents the strongest conjugated acid? a. ammonia, 4.75 b. pyridine, 8.77 c. ethyl amine, 3.25 d. phenoxide, 4.11

D. phenoxide, 4.11

Quaternary structure is associated with a. the overall shape of a polypeptide chain b. the sum of the secondary and tertiary interactions c. simple proteins with only one subunit d. the relative orientation of one polypeptide to another polypeptide in a multi-subunit protein

D. the relative orientation of one polypeptide to another polypeptide in a multi-subunit protein

Reaction of the peptide, ala-met-lys-ser, with phenylisothiocyanate (PITC) at pH 8.0 followed by mild acidification (first cycle of Edman chemistry): a. would release the labeled peptide PTH-ala-met-lys-ser b. would release PTH-ala, PTH-ser, PTH-lys, and PTH-ser c. would release PTH-ser and the peptide ala-met-lys d. would release PTH-ala and the peptide met-lys-ser

D. would release PTH-ala and the peptide met-lys-ser

If you change the main linkages between glucose from alpha(1,4) to alpha(1,6), you get a new family of polysaccharides. What are they?

Dextrans

Pairs of isomers that have opposite configurations at one or more chiral centers but are NOT mirror images are _________.

Diastereomers

The chain termination method of DNA sequencing employs ____________ (ddNTPs) as chain terminators. (13)

Dideoxynucleotides

Downstream on the lagging strand, ______ _________ ______ excises the primer and replaces it with DNA

DNA polymerase I

_______ _____________ _____ is the chief DNA-replicating enzyme of E. coli

DNA polymerase III

Mismatch repair systems scan DNA duplexes for mismatched bases, excise the mispaired region and replace it by _______ __________ _________ local replication

DNA polymerase-mediated

The enzymes that replicate DNA are called ______ _____________.

DNA polymerases

The genetic code is in mRNA is ______________- in most cases, each amino acid can be designated by more than one codon, except Met, Trp.

Degenerate

Formation of ADP from ATP requires use of a __________ __________.

Dehydration synthesis

DNA polymerase _______ is the principal lagging-strand DNA replicase in eukaryotes.

Delta (δ)

Alpha keratin has all of these characteristics EXCEPT? a. it is made of alpha helices b. it is right handed c. it is found in hair d. it has a polar axis e. it is the main component of silk

E

If 0.01 M HCl is added to pure water, what is the [OH-] in that solution? a. 1 x 10^-7 b. 1 x 10^7 c. 1 x 10^12 d. 1 x 10^-2 e. 1 x 10^-12

E

One of these enzymes participate in telomeres extension a. polymerase gamma b. polymerase epsilon c. polymerase delta d. polymerase beta e. polymerase alpha

E

The enzyme that extends the 5' end of a primer at the telomere gap in eukaryotes is? a. delta polymerase b. primase c. telomerase d. Reverse transcriptase e. pol alpha

E

This is true of an alpha helix a. all carbonyl groups point in the same direction b. its has a pitch that is smaller than that of collagen c. the helix has axial polarity d. the helix is found in human keratin e. all of the above

E

Which of the following statements does not apply to collagen? a. It contains hydroxylated amino acids. b. There is an absolute requirement for glycine every third position. c. The polypeptide forms a left-handed helix. d.. The triple helical structure twists in the right-handed direction. e. Its main component is lysine

E

premRNA from eukaryotes differs from that of prokaryotes in that? a. it does not have introns b. none of them c. it has telomeres d. it must have a SECIS recoding sequence e. it has the Kozak consensus sequence

E

DNA polymerase ______ is the principal leading-strand DNA replicase in eukaryotes.

Epsilon (ε)

In the core enzyme, the ______ subunit is a 3'-exonuclease.

Epsilon (ε)

When the chemical and electrical gradients are equal in size, the ion is said to be in electrochemical __________, and the membrane potential established is the __________ potential (Veq.) for the ion.

Equilibrium

In (eukaryotes / prokaryotes), the initiator tRNA that carries only Met and functions only in initiation is called tRNAiMet, but the Met it carries is not formylated.

Eukaryotes

DNA glycosylase removes damaged base, creating an apurinic or apyrimidinic "AP" site.

Excision repair

In addition to 5'-3' polymerase, DNA polymerase I also has 3'-5' _____________ and 5'-3' _____________ activities

Exonuclease

_________ proteins are structural and normally H2O insoluble.

Fibrous

Total of ________ high-energy phosphate bonds are expended per amino acid residue added.

Four

The third step in determining a protein's sequence is the...

Fragmentation of the chains.

The elongation rate is slower in G-C rich regions because...

G-C base pairs share 3 H bonds, whereas A-T base pairs, with 2 H bonds, are less stable.

____________ are cyclic arrays of four G residues united through Hoogsteen base pairing.

G-quadruplexes

Telomeres are short (5 to 8 bp) tandemly repeated, _______ nucleotide sequences that form protective caps 1-12 kbp long on the chromosome ends

G-rich

They present a three-dimensional shape that is structurally and chemically complementary to the surface of a DNA sequence.

Gene regulatory proteins

_________ proteins are compact, H2O soluble and used for transport or metabolism.

Globular

Water and solutes smaller than proteins are forced through capillary walls and pores of the glomerular capsule into the renal tubule.

Glomerular filtration

Because ________ is a reducing sugar, redox reactions are the basis for diagnostic tests for blood sugar.

Glucose

_________ constitutes up to 10% of liver mass and 1-2% of muscle mass. It is a glucose storage device in animals.

Glycogen

_________ _________ is an enzyme that crosslinks peptidoglycan chains to build the bacterial cell wall.

Glycoprotein transpeptidase

Long chain, repeating disaccharides with (usually) amino sugars in one and negative charges (COO- or SO3-) on both.

Glycosaminoglycans

Mutated genes/defective enzymes in the degradation pathways of _________. These enzymes are required to establish steady state concentrations of these lipids. If some enzyme is defective, the substrate will build-up and these myelins become toxic for cells.

Glycosphingolipids

_________ are ceramides with one or more sugars in beta-glycosidic linkage at the 1-hydroxyl group.

Glycosphingolipids

In E. coli, the DNA double helix is unwound by ____________.

Helicases

The _______ motif is a protein structural domain consisting of two successive α-helices separated by a sharp β-turn.

Helix-turn-helix (HTH

This polysulfated polysaccharide, similar to chondroitin sulfate, binds to positive sites of the natural anticoagulant antitrombin III (which binds Xa and thrombin, both are coagulant agents) activating it (more than usual) by keeping the AT-III attached to Xa and Trombin to prevent blood clotting.

Heparin

Enzymes produce products in very (high / low) yields.

High

Prominent forms of _________ __________ __________ are lysine acetylation, lysine methylation, serine phosphorylation, lysine ubiquitination, and lysine sumoylation.

Histone covalent modification

This factor for chromatin remodeling introduces covalent modifications into the N-terminal tails of the histone core octamer.

Histone-modifying enzymes

Ligation following strand invasion forms a ________ ________.

Holliday junction

Recombination involving similar DNA sequences is called ___________ recombination.

Homologous

_________ proteins from different organisms have _________ sequences.

Homologous

_________ __________ _________ are abundant, baby indigestible oligosaccharides, that are food for a good type of bacteria (Bifidobacterium bifidus) preventing pathogenic bacteria from colonizing the large intestine.

Human Milk Oligosaccharides (HMOS)

If DNA from two different species are mixed, denatured, and allowed to cool slowly, __________ __________ may form, provided the DNA from one species is similar in sequence to the other.

Hybrid duplexes

Proteins: The alpha helix is stabilized by _________ _________.

Hydrogen Bonds

__________ __________ are not true bonds, but are the strongest of all non-covalent interactions. About 1.9-6.9 kcal/mol

Hydrogen Bonds

The stability of the DNA double helix is due to...

Hydrogen bonds, electrostatic interactions, and base-pair stacking.

Presence of release factors with a nonsense codon at A site transforms the peptidyl transferase into a _____________, which cleaves the peptidyl chain from the tRNA carrier.

Hydrolase

A "secret of life"—necessary for cell membranes.

Hydrophobic Interactions

What are other naturally occurring purine derivatives?

Hypoxanthine Xanthine Uric acid

Polymerases _____, _____, and _____ function principally in DNA repai.

I ; II ; V

_________ is an ether glycerophospholipid produced by platelets and inflammatory cells like neutrophils and monocytes.

Platelet activating factor (PAF)

_______ delivers the initiator tRNA in a GTP-dependent process.

IF-2

RNA pol ______ must be capable of transcribing a great diversity of genes, but must also function at any moment only on the genes whose products are appropriate to the needs of the cell.

II

The second step in determining a protein's sequence is to...

Identify N- and C-terminal residues.

What happens if "F" inhibits Enz 1? (7)

If "F" inhibits Enz 1, it regulates its owns synthesis. And the regulation is usually allosteric (in a site other than active).

The Michaelis-Menten (MM) Equation assumes that the ES complex is...

In rapid equilibrium with free enzyme.

When DNA is heated to 80°C or more, its UV absorbance (increases / decreases) by 30-40% due to hyperchromic shift.

Increases

Increased synthesis of enzymes in response to the presence of a metabolite is ___________.

Induction

Isozymes combine their subunits to suit the needs of the cell. Muscle makes (lactate / pyruvate) (from (lactate / pyruvate), anaerobic resp.) while heart (aerobic) uses it to make (lactate / pyruvate).

Lactate ; Pyruvate ; Pyruvate

Many drugs (47%) are enzyme _________.

Inhibitors

In eukaryotes, DNA polymerase α functions in ___________ of nuclear DNA replication.

Initiation

Involves binding of mRNA and initiator aminoacyl-tRNA to the small subunit, followed by binding of the large subunit.

Initiation

In bacteria, N-formyl-Met-tRNAifMet is only used for _____________, and regular Met-tRNAmMet is used for ______________ of Met internally

Initiation ; Incorperation

The __________ _______ prefers to bind ATP and GTP (most RNAs begin with a purine at 5'-end)

Initiation site

Single-strand damage repair relies on the _______ _________ ________ to guide repair.

Intact complementary strand

_________ _________ (green) are covalently regulated. The kinase/phosphatase activities are part of same converter enzyme, the one that phosphorylates/dephosphorylates the _________ _________. (6)

Interconvertible enzymes

Complementary sequences in RNA can join via __________ __________ __________.

Intrastrand base pairing

The second termination mechanism is termed _________ _________, where termination is determined by sequences in the DNA called termination sites.

Intrinsic termination

In eukaryotic mRNA, ________ are an intervening sequence while ________ are a coding sequence. The poly A tail is there for ________.

Introns ; Exons ; Stability

Termination sites consist of which 3 structural features?

Inverted repeats, rich in G:C, which form a stable stem-loop structure in RNA transcript A nonrepeating segment that punctuates the inverted repeats A run of 6-8 As in the DNA template, coding for Us in the transcript

What is the equation for determining Ka?

Ka = ([H+] [A-]) / [HA]

The (keto / enol) tautomers of uracil, thymine, and guanine predominate at pH 7. By contrast, the (keto / enol) form of cytosine predominates at pH 7.

Keto ; Enol

The aromaticity and electron-rich nature of pyrimidines and purines enable them to undergo _______-_______ _________.

Keto-enol tautomerism

Enzymes endow cells with the remarkable capacity to exert _________ _________ over thermodynamic potentiality.

Kinetic Control

_________ _________ make the cell membrane fluid.

Kinked lipids

_____ = _____ + _____ where L= linking, W=writhe, T=twist

L = T + W

The measurement of lactate dehydrogenase (LDH) is especially diagnostic for myocardial infarction because this enzyme exist in 5 closely related, but slightly different forms (isozymes). Of the 5 forms, where is each found?

LDH 1: Heart (Aerobic) LDH 2: Heart LDH 3: Nonspecific LDH 4: Nonspecific LDH 5: Liver (Anaerobic)

Measurement of AST is not diagnostic for myocardial infarction, but taken together with _________ and _________ measurements.

LDH ; CPK

What are the basic amino acids?

Lysine (Lys) Arginine (Arg) Histidine (His)

Proteins that recognize nucleic acids do so by the basic rule of _______________ _______________.

Macromolecular recognition

Gene regulatory protein contacts with the bases of DNA usually occur within the (major / minor) groove of the DNA (but not always)

Major

The "tops" of the bases (as we draw them) line the "floor" of the (major / minor) groove.

Major

_________ is signal for lysoenzymes to move to lysosomes.

Mann-6-P

_____-linked monoglycosidation can occur via asparagine residues.

N

A protein is translated from mRNA from the _____-terminus to the _____-terminus.

N ; C

________________ _______________ is first amino acid in all E.coli proteins.

N-formyl methionine

Genes under (positive / negative) control are transcribed unless they are turned off by the presence of a repressor protein, while genes under (positive / negative) control are expressed only if an active regulator protein is present.

Negative ; Positive

The structural genes of the lac operon are controlled by __________ __________.

Negative regulation

The 5'-exonuclease activity, working together with the polymerase, accomplishes "_______ __________"

Nick translation

In type of inhibition, the inhibitor (I) binds either to E and/or to ES.

Noncompetitive inhibition

Reversible inhibitors interact with an enzyme via (noncovalent / covalent) associations (Ibuprofen, both COX).

Noncovalent

_________ _________ are regulators of gene expression.

Nonhistone proteins

Recombination involving very different nucleotide sequences is ___________ recombination

Nonhomologous

Double-strand breaks (DSBs) can be joined through _________ _________ ________ ________ if the ends are blunt, or through _________ _______ _________ if the ends are sticky.

Nonhomologous DNA end joining ; Homologous DNA recombination

A (polar / nonpolar) solute, like oil, "organizes" water?

Nonpolar

_________ is a competitive, suicide, inhibitor of glycoprotein transpeptidase.

Penicillin

___________ __________, or transpeptidation, is the central reaction of protein synthesis, the actual peptide bond-forming step

Peptidyl transfer

The _____________ ____________, the activity catalyzing peptide bond formation, is a property of the 23S rRNA of the 50S ribosomal subunit

Peptidyl transferase

The angle about the C(alpha)-N bond in a peptide chain is denoted as _________.

Phi

__________ are used to store energy from sugars.

Phospho-ester bonds

_________________________ / _________________________ of translational components is a dominant mechanism for control of protein synthesis.

Phosphorylation ; Dephosphorylation

Pyrimidine dimers can be repaired by ___________.

Photolyase

Using the graph, determine which line represents Competitive inhibition, Noncompetitive inhibition, and No inhibitors. (4)

Pink: No inhibitor Blue: Competitive inhibition Green: Noncompetitive inhibition

Due to the double bond character, the six atoms of the peptide bond group are always _________.

Planar

_________ are ether glycerophospholipids in which the alkyl chain on Carbon 1 is unsaturated.

Plasmalogens

Within the promoter, the _________ ________ consensus sequence (TATAAT) is ideal for unwinding while the _____ ___________ consensus sequence (TTGACA) is where the σ-subunit binds.

Pribnow box ; -35 region

A protein structure involving the sequence of amino acids is known as the _________ structure.

Primary

__________ (DnaG) bound to the DnaB helicase carries out this priming function, periodically forming new RNA primers on the lagging strand.

Primase

An oligonucleotide that pairs with the 3'-end of the template molecule to form dsDNA.

Primer

DNA polymerases cannot initiate DNA synthesis de novo - all require a _________ oligonucleotide with a free 3′-OH to build upon

Primer

5'-exonuclease activity plays an important role in _________ _________ during DNA replication

Primer removal

A mixture of Carboxypeptidase A and B cleaves all, but _________.

Pro

Proteins: ________ and ________ are helix breakers.

Pro ; H-Pro

(Eukaryotes / Prokaryotes) have no cholesterol in membrane. Drugs target these cells. Cholesterol protects (eukaryote / prokaryote) cells from cationic antibiotics peptides,

Prokaryotes / Eukaryotes

In (prokaryotes / eukaryotes), a single mRNA may contain the information for synthesis of many proteins, while in (prokaryotes / eukaryotes), a single mRNA codes for just one protein, but structure is composed of introns and exons.

Prokaryotes ; Eukaryotes

Mitochondrial and chloroplast ribosomes are quite similar to ____________ ribosomes, reflecting their ______________ origin.

Prokaryotic

____________ are nucleotide sequences that identify the location of transcription start sites, where transcription begins.

Promoters

Clotting factors are _________.

Proteases

Binds at the A site of both prokaryotic and eukaryotic ribosomes, accepting the peptide chain from the P site, and terminating protein synthesis

Puromycin

_________ inhibits protein synthesis by inhibiting translation.

Puromycin

Aldohexoses prefer the (furanose / pyranose) form while ketohexoses prefer the (furanose / pyranose) form.

Pyranose ; Furanose

A protein structure involving an aggregated tertiary structure with subunits is known as the _________ structure.

Quaternary

Association of 2 or more polypeptide chains (subunits) that already have their own separate tertiary structure. Usually bound by non-covalent attractions of by covalent disulfide (-S-S-) bridges.

Quaternary Structure

The _____ group of an amino acid influences protein structure.

R

Denatured DNA will ____________ to re-form the duplex structure if the denaturing conditions are removed through a process termed __________.

Renature ; Reannealing

Decreased synthesis in response to a metabolite is ____________.

Repression

Each unit of a polymer is called a __________ - 2 = dipeptide - 3 = tripeptide - 12-20 = oligopeptide - Many = polypeptide

Residue

RNA viruses that replicate their RNA via a DNA intermediate are termed _____________.

Retroviruses

The RNA-directed DNA polymerase is called ________ __________.

Reverse transcriptase

Lipid anchoring and de-anchoring is __________ and can control (modulate) signaling pathways.

Reversible

The ______ transcription termination factor is an ATP-dependent helicase.

Rho (ρ)

Within the nucleus, hnRNA forms ________________ ___________ through association with a characteristic set of nuclear proteins.

Ribonucleoprotein particles (RNPs)

____________ are about 2/3 RNA, 1/3 protein.

Ribosomes

___________________ are compact ribonucleoprotein particles found in the cytosol of all cells.

Ribosomes

Segments of RNA that display enzyme activity in the absence of protein.

Ribozymes

Proteins: Alpha helixes are mostly (left / right) handed, but not always.

Right

What are the polar amino acids?

Serine (Ser) Threonine (Thr) Cysteine (Cys) Tyrosine (Tyr) Asparagine (Asp) Glutamine (Gln) Glycine (Gly)

Cyclic nucleotides are _________ _________ and regulators of cellular metabolism and reproduction.

Signal molecules

RNA molecules are typically ________-stranded and thus have six to seven degrees of freedom per nucleotide unit.

Single

Each deoxyribose-phosphate segment of the backbone has _____ degrees of freedom

Six

In the core enzyme, the β subunit dimer "________ ________" forms a ring around DNA

Sliding clamp

The breakdown of ES to form products is assumed to be (slower / faster) than 1) formation of ES and 2) breakdown of ES to re-form E and S

Slower

(Small / Large) Km means tight binding; (low / high) Km means weak binding.

Small ; High

Splicing depends on a unique set of ___________ ___________ __________ _________. Hint: snRNPs, pronounced "snurps"

Small nuclear ribonucleoprotein particles

(Soluble / Insoluble) glycoproteins include immunoglobulins and transport proteins.

Soluble

In eukaryotes, transcription and translation processes are __________ __________: transcription occurs on DNA in the nucleus, and translation occurs on ribosomes in the cytoplasm.

Spatially separated

Ceramides with a phosphate at C1. They are found in neurons.

Sphingomyelins

_________ inhibit HMGCoA reductase, the cholesterol bisynthesis controlling enzyme.

Statins

__________, __________, __________, and __________are the four basic secondary structural elements in RNA

Stems ; Loops ; Bulges ; Junctions

Duplexes partially unwind, and the free, single-stranded end of one duplex begins to base-pair with its nearly complementary single-stranded region along the intact strand in the other duplex. This process is called...

Strand invasion

An aminoglycoside antibiotic - induces mRNA misreading. Resulting mutant proteins slow the rate of bacterial growth

Streptomycin

Specificity of an enzyme is controlled by _________- the unique fit of substrate with enzyme controls the selectivity for substrate and the product yield

Structure

Mild reduction of sugars.

Sugar alcohols

Phosphate esters like ATP are important.

Sugar esters

Aspirine is a _________ _________ that inhibits cyclooxygenase.

Suicide Inhibitor

Circular DNA sometimes has more or less than 10 bp per turn. This is called being in a...

Supercoiled state

In Z DNA, the G goes to (syn / anti) conformation, while C stays (syn / anti), but the whole C nucleoside (base and sugar) flips 180 degrees.

Syn ; Anti

Two homologous DNA duplexes first juxtapose so that their sequences are aligned - a process of chromosome pairing called ___________.

Synapsis

___________ (an RNA-dependent DNA polymerase) maintains telomere length by restoring telomeres at the 3'-ends of chromosomes

Telomerase

__________ are the structures at the ends of eukaryotic chromosomes.

Telomeres

The strand of duplex DNA that is read by RNA polymerase is termed the ___________ _________.

Template strand

Occurs when a stop codon is reached.

Termination

Eukaryotic peptide chain initiation begins with formation of a _________ ________ of eIF-2, GTP and Met-tRNAiMet.

Ternary complex

_________ are polymers of isoprene. Can link head-to-tail or tail-to-head.

Terpenes

A protein structure involving many α helices and β sheets is known as the _________ structure.

Tertiary

3D structure formed when secondary structures (alpha helices and beta sheets) aggregate or fold into more complex arrangements.

Tertiary Structure

What is a unique characteristic of every protein, encoded by the nucleotide sequence of DNA, is read from the amino terminus to the carboxyl terminus, and is thus a form of genetic information?

The Sequence of Amino Acids

Vmax is the ________ _________ _________ of the reaction - but it is NEVER achieved in reality

Theoretical maximal rate

In the core enzyme, the ______ subunit is involved in holoenzyme assembly and ε-subunit stabilization.

Theta (θ)

G and C share _____ H bonds

Three

Stimulates release of TSH* & Prolactin (pituitary).

Thyrotropin Releasing Hormone (TRH, from the Hypothalamus)

The __________ state is stabilized by wrapping around proteins that serve as spools for the DNA "ribbon".

Toroidal

Peptide bonds are usually found in the (cis / trans) conformation.

Trans

Information encoded in a DNA molecule is _________ via synthesis of an RNA molecule.

Transcribed

All three eukaryotic RNA polymerases interact with their promoters via ____________ ___________.

Transcription factors

____________ _____________ are DNA-binding proteins that recognize and accurately initiate transcription at specific promoter sequences

Transcription factors

Animals that have acquired new genetic information as a consequence of introduction of foreign genes are termed __________.

Transgenic

Recent evidence indicates that lipid anchors are quite _________ in nature.

Transient

When one purine or pyrimidine is swapped for another, this mutation is known as a __________.

Transition

The sequence of the RNA molecule is "read" and is _________ into the sequence of amino acids in a protein

Translated

The series of events that return the 70S ribosome:mRNA complex to the starting point in the elongation cycle.

Translocation

_____________ is the enzymatic insertion of a transposon, a mobile segment of DNA.

Transposition

When a purine is swapped with a pyrimidine, or vice versa, this mutation is known as a ________.

Transversion

_________ glucose-alpha-1,1-glucose, is a temperature protectant forinsects (they have hemolymph, not blood), fungi, yeast, bacterial spores, etc.

Trehalose

_________ inhibits cGMP hydrolysis in smooth muscle cells.

Viagra

Why is RNA more unstable than DNA?

Vicinal -OH groups (2' and 3') in RNA make it more susceptible to hydrolysis.

In bacteria, the ___________ ____________ is f-Met-tRNAifMet

initiator tRNA

Determine the amino acid sequence of the following oligopeptide from the experimental data below 1. The amino acid composition is found to be ala, lys, phe, met, cys, trp 2. Treatment with carboxypeptidase results in tryptophan and a peptide 3. CNBr treatment yields a tetrapeptide and a dipeptide 4. Trypsin digestion produces an amino acid and a pentapeptide with met on the amino end 5. Chymotrypsin digestion yields a dipeptide and a tetrapeptide

lys-met-cys-phe-ala-trp

DNA replication starts at _________ in E. coli (DnaA helps helicase to find ________).

ori-C

Termination of transcription occurs only after RNA polymerase has transcribed past a consensus AAUAAA sequence in eukaryotic mRNA.

poly(A) addition site

Three classes of RNA polymerases (I, II and III) transcribe _______, ________ and ________ genes, respectively.

rRNA ; mRNA ; tRNA

The basis of structure and function of ribosomes.

ribosomal RNA (rRNA)

In ________, extensive H-bonding creates four double-helical domains, three capped by loops, one by a stem.

tRNA

The 3'-terminal sequence on __________ is always CCA-3′-OH.

tRNAs

Carries the amino acids for protein synthesis.

transfer RNA (tRNA)

DNA replication yields _____ daughter DNA duplexes identical to the parental DNA molecule.

two

What is the pKa value of the alpha carboxyl group on an amino acid?

≈ 2

What is the pKa value of the alpha amino group on an amino acid?

≈ 9