Biochem Final

Which of the following best describes the structure of a nucleosome (M3)

...150bp of DNA...set of two H2A/H2B and two H3/H4 dimers....

Which curve is Hb at 7.8 if 3 is binding of oxygen to Hb at 7.2 (M2)

2

Which of the following lines represent fetal Hb curve if 3 represents binding of oxygen to maternal Hb (M2)

2

While fatty acids are most often formed by the condensation of ____-carbon units, isoprenoids are assembles from ____-carbon units (M3)

2,5

DNA fragment has 12% A, calculate C (M3)

38%

If curve 3 is normal Hb in presence of 3mM BPG, which curve is Hb at 6mM BPG (M2)

4

The bond energy of an ionic interaction is approximately _____ that of a H bond (M1)

4 Times

Rank the melting points of the fatty acids from highest to lowest (M3)

4>5>2>1>3 (18:0)>(16:0)>trans(18:1)>cis(18:1)>(18:2)

Which of the following is true regarding crystalline proteins? (M2)

A and B are both true. A. The diffractive pattern observed during X-ray exposure to the crystal can be used to calculate the electron density map of the protein B. Many crystallized proteins remain catalytically active

Ion exchange chromatography is commonly used.... (S1) A. Two types of ion exchange chromatography B. Order of Lys, Asp, Leu elute from the carboxymethyl at pH 7. C. What two changes to elute protein more quickly

A. Anion and cation exchange B. Asp, Leu, Lys Lys is positively charged and will elute last due to the attraction to carboxymethyl. Asp is negative and witll elute first, Leu is neutral and will elute after Asp but before Lys C. Increase pH above pI, salt in? (better anser needed

Below is the secondary structure of a protein (S2) A. What is the symmetry B Estimate length of longest alpha helix C. How many residues are involved in the formation of this helix

A. C2 symmetry B. 15 turns x 5.4A(pitch lenght) = length (~85A) C. 15 turns x 3.6 (AA/turn) = ~55AA residues

A. On the graph, draw typical curve for oxygen binding of Mb and another curve for Hb (approporiate p50 values) (S2) B. What is the main difference between Mb and Hb that causes the oxygen binding curve to be so different?

A. Drawing on graph (p50 Mb is ~2.6, p50 Hb is ~28) B. Hb shows positively cooperative behavior, meaning as O2 binds to a subunit, it increases the affinity for O2 at the remaining unbound subunits. Mb shows noncooperative behavior, meaning it can only bind to 1 O2 at a time

A. What are the subunit composition of the fetal and mother Hb (S2) B. Explain in details how a fetus is able to obtain O2 for the mother

A. Fetal = a2y2; Maternal= a2b2 B. The y subunits in Fetal Hb has a Ser residue where the b subunit on the mother has a His residue, needed for BPG binding. lower BPG binding higher O2 affinity in the fetal Hb (more information necessary )

The diagram below shows 4 different lipid linked proteins, name these four and indicate which side is cytosilic (S3)

A. Palmitoylated (cytosol side) B. Mytistoylated C. Prenylated D. GPI-linked (Extracellular side)

Below is Ramachandran plot (S2) A. What information is provided in this plot? What are the labels of the two axes? B. Why is the plotted are mostly empty C. What could the residues be in the lower right quadrant D. Is this DNA binding protein an a,b, or a/b proteins, explain

A. This describes the torsion angles of each residue, and shows which combinations are stereoically accepted or forbidden. Y axis is the psi (Y looking symbol), X axis is phi (theta looking symbol) B. The empty area represents the forbidden phi and psi angles. There are much less stereoically accepted angles than forbidden combinations. C. This could be Gly (mabye something else?) D. a/b, there are many aras ploted in both the alpha and beta regions

Neuron membrane undergoes depolarization then rapid hyperpolarization... (S3) A. Which ion channel is responsible for membrane depolarization (draw permeability on ion on graph) B. Which ion channel is responsible for membrane repolarization (draw permeability on ion on graph)

A. Voltage-gated-Na channel B. Voltage-gated-K channel

Identify the circled functional groups and linkages in the compound below (S1)

A. diphosphoester B. Amide C. Hydroxyl D. Amine

Which of the following DNA sequences is considered palindromic (M3)

AAGCTT

How do you increase the buffering capacity of a pH 6.8 buffer containing phosphate (pKs listed) (M1)

Add more NaH2PO4 and Na2HPO4

Which of the following statements about PCR is true (M3)

All of the above

Nucleosides play a central tole in living organisms because (M3)

All the above

Recombinant DNA technology can be used for (M3)

All the above

Which of the listed enzymes produce identical sticky ends (M3)

BamHI and Bg1II

What can you do with the van't Hoff equation/plot (M1)

Better and needed

Below is the data from five steps used in protein purification (S1) A. Which step in this table has best purity, explain B. Explain why U/ml go up and down during purification C. Explain why Total units consistently decrease during successive steps

Better answer needed

The composition of an aqueous solution is .2M acetic acid + .1M sodium acetate (S1) 1. Calculate the pH of the solution 2. What would the pH be if 2ml of 10M NaOH was added to 1L of this solution 3. By comparison, what would the pH be if the same amount of NaOH were added to 1L of pure water

Better answer needed

The size oh human myoglobin and jellyfish GFP is 17kD and 27kD (S1) A. Plot photoabsorbance at 280nm B. Sketch results of SDS-PAGE C. protein is 100kD, what is your explanation

Better answer needed AB C. The protein has multiple subunits?

Which structure is a uronic acid? (M2)

C (has 1CHO and 6COOH)

Mutations leading to changes that can be inherited by the next generation have to be introduced at the____ level (M3)

DNA

Which of the following conditions guarantees that the reaction is spontaneous? (M1)

Delta H <0; Delta S >0

Which of the carbon atoms represents the anomeric carbon, which is the one that determines if it is D or L? (M2)

E,A

A single amino acid mutation of hemoglobin's B-chain results in sickle cell HbS. The change is from a polar to a non-polar residue which: (M2)

Enhances hydrophobic interactions among HbS tetramers

Which of the following methods will allow you to determine if a substrate used mediated transport (M3)

Evaluate the flux at several different concentrations....

Which of the following interactions are most important in stabilizing protein 3D structure? (M2)

Hydrophobic interactions

The E coli. maltoporin utilizes the greasy slide. Which describes the function of greasy slide (M3)

Hydroxyl groups on glucose......mimicking a screw-like pathway

Which feature allows the KcsA channel to selectively transport K+ (M3)

II, III, IV II. it is attracted to the entrance of the channel via electrostatic interactions III. The selectivity filter involves a narrowing of the channel IV. As K is transported through the channel it interacts with C=O

Which of the following are characteristic of the Na-K-ATPase (M3)

II,IV II. It is covalently modified by phosphorlylation at an Asp residue... IV. It is essential for excitation of nerve cells

A suspension of which of the following is most likely to form a liposome (M3)

III, IV III. glycerophospholipids IV. sphingomyelins

Which of the following segments of integral membrane likely contains the membrane-spanning sequence (M3)

ITLIFFGV.....

Describe how hydrogens are formed in alpha helices and beta sheets. What atoms are involved and where are they located? (S2)

In alpha-helical, the carbonyl O on the nth residue hydrogen bonds with the NH group on the n+4 residue. In beta sheets, hydrogen bonds form between the carbonyl O and the NH group of adjacent strands

Draw the structure of dinucleotide GT (S3)

Insert drawing here

Draw the structure and list function of the following: (S3) A. a phosphatidylserine with 16:1n-6 at C1 and 18:2n-3 at C2 B. a ceramide with an N-acyl 20:4n-6 fatty acid C. Cholesterol

Insert drawing later A. fxn: membrane component B. fxn: precurser to sphingolipids C. fxn: decrease membrane fluidity and precursor to hormones

Which of the following is False about RNA (M3)

It always forms a singe strand that resembles the structure of B-DNA

Which of the transporters listed below differs from the others (M3)

KcsA

Which of the following tripeptides carries a net positive charge at pH 7.0

Leu-Lys-Gly

A fast and common method for determining the concentration of protein in aqueous solution is: (M1)

Measuring light absorption at 280nm

Explain how sickle cell disease provides protection against malaria (S2)

More information needed PF lowers pH in RBC, causing HbS to form filament in Tstate, increase distortion of RBC, due to PF invasion, destroyed by IR

In the intestinal epithelium, glucose enters the cell in symport with ____, which is subsequently ejected by ____ (M3)

Na, Na/K pump

Give the name of the following disaccharide (S2)

O-a-D-galactopyranosyl-(1-6)-B-D-glucopyranose

In bacteria, phospholipids are synthesized: (M3)

On the cytoplasmic face of the cell membranes

Which of the following statements describes one reason that plant oils are generally healthier for human consumption than animal fats (M3)

Plant oils usually contain more unsaturated fatty acids than animal fats

Lactose permease uses a ____ gradient generated ____ to cotransport lactose across the cell membrane (M3)

Proton, via oxidative metabolism

The positive charge on proteins in electroscopy ionization mass spectrometry is the result of: (M1)

Protonated Arg and Lys residues

Describe the secondary and quatenary structures of previous ion channel (voltage-gated-K channel) (S3)

Secondary structure consists of a TM domain with 6 alpha helices (S1-S6). The S4 helix has 5 positevily charged residues, called the voltage sensor. When the membrane potential increases, the S4 helix moves towards the extracellular surface, pulling on the channel for K to pass into the cell for repolarization Quatenary structure: need more information

Which of the following is not a reducing sugar? (M2)

Sucrose

Which of the following about aquaporins is false (M3)

The transport water and hydronium efficiently

Which amino acids is least likely to be found on the surface of a single subunit protein? (M2)

Trp

Which of the following amino acids is likely to be positioned into the active site of an enzyme that binds the following molecule (M1)

Trp,Leu,Ile

Double stranded DNA molecules can be cleaved at specific recognition sites by (M3)

Type II restriction endonucleases

The boiling point of water is 160C higher than the BP of H2S because (M1)

Water molecules are connected to each other by H-bonds

A gene knockout is (M3)

a gene that has been inactivated or removed from an organism

Which polysaccharide is found in a helically coiled conformation? (M2)

a-amylose

Nucleotides play important roles in cell signaling...list 5 nucleotides involved (S3)

cAMP cGMP-AMP cGMP pppGpp c-di-AMP (or c-di-GMP)

Glycosphingolipids with several attached carbohydrates are called: (M3)

gangliosides

Calculate pI of GLDK (S1)

pI = 6.7

Nucleoside triphosphate carry energy in the form of (M3)

phosphoanhydride bones

Which of the following nucleic acids provides the key to decoding genetic information (M3)

tRNA

During which of the following processes are RNA-DNA hybrids observed (M3)

transcription, both prokaryotes and eukaryotes

Which of the following lipids is least polar (M3)

triacylglycerols