Bio Chem Midterm 1

Blood pH is maintained at

7.4

EcoRi

AATTC

Nontransformed bacteria cannot grow in the presence of

ampicilin because they lack the amp gene carried by the plasmid

When a buffer is subjected to a low temperature as low as 4 dc, less heat is available for ______ and this the equilibrium shifts towards more of associated tris. H+ concentration decreases and the pH value increases.

dissociation

SH =

thiol group

------ CHAPTER 3---

---- CHAPTER 3-----

------- Chapter 2 back of the book problems ---------

------- Chapter 2 back of the book problems ---------

phosphoanhydride group also called diphosphate ester group

2 PO3- groups connected in between by another oxygen

To calculate equilibrium concentrations of Q and R=

25= 50 +x/ 50 - x 50 +x = 25(50-x) 50 +x= 1250 - 25x 26x= 1200 x= 46.15 [Q] 50 -46.15= 3.85 uM [R] 50 + 46.15= 96.15uM

How many different amino acids could theoretrically be encoded by nucleic acids containing four different nucleotides if each nucleotide coded for one amino acid.

4^n is the number of nucleotides in the sequence. a) 4^1 -=4 b) 4^2 = 16

when you're naming anything its always going

5 Prime

Guanine is one of the purine bases among the nucleotides in

DNA and RNA

Free energy equation Delta G= Delta H - T*DeltaS where Delta H is the change in the enthalpy for the reaction in J Delta S is the change in entropy in J*K T is the temperature in K problem with delta H = 15 kJ delta S= 50 J*K T= 10 C

Delta H is 15*1000 15000 S = 50 J*k stays the same because already in Joules T= 10 +273 (because kelvin) =283 K delta G=

True or False? A spontaneous process always happens very quickly

False, the rate of the reaction is determined by the reaction mechanisms and catalysts not the amount of energy needed to run the reaction. A spontaneous reaction could take a very long time to run.

True or False? A reaction is said to be spontaneous when it can proceed in either the forward or reverse reaction

False. A reaction is only spontaneous in one direction, its reverse is non spontaneous or the products would be able to return to the reactants under similar conditions and net reaction would be very small.

at 10 degrees Celcius the keq for a reaction is 100. At 30 degrees celcius the keq = 10. Does the enthalpy increase or decrease during the reaction?

Keq 1: T1 = 10 dC =273 +10 =283 K Keq 2: T2= 30dC =273+30 =303 K Vant Hoff's equation: Keq= -DeltaH/R *(1/T) + deltaS/R thus, ln K1= -DeltaH(1/T1) + deltaS/R ln K2 = - deltaH(1/T2) + deltaS/R ln K1/k2= -delta H/R(1/T1-1/T2)

When writing the equation for the dissociation for the two protons for the chemical formula above remember we just talked about COOH dissociating first so the H COOH dissociates first. then a second equation comes in and NH3 goes to

Nh2

Problem 10 Chapter 2 please explain

Problem 10 Chapter 2 please explain

A segment of DNA containing 20 base pairs includes 7 guanine residues. How many adenine residues are in this segment? How many uracil residues are in the segment?

The DNA contains totally 40 bases as a the total number of base pairs is 20. The number of Guanine residues (G) = 7 A + T = 40 - (G + C) =26 since A = T, there are a total of 13 Adenine residues. Uracul residues will not be present in the segment as uracil nucleotide is not a componenet of DNA. THis is present in RNA instead of thymine.

Explain why increasing the NaCl concentration increases the temperature at which the two strands of DNA "melt" apart

There are more Na+ ions to shield the negatively charged DNA backbones, thus reducing electrostatic repulsions and requiring more energy to separate the strands which means a higher temperature. Thus, increasing the DNA's melting temperature, the two strands of DNA melt apart at higher temperatures.

True or False? A non spontaneous reaction will proceed spontaneously in the reverse direction

True a nonspontaneous rxn is endergonic and rerquires an input on free enrgy. since the reverse reaction is opposite it will be exergonic and will release free erergy making it spontaneous.

True or False? A spontaneous process can occur with a large decrease in entropy.

True, a spontaneous rxn can occur with a large decrease in entropy if the reaction is highly exothermic. (enthalpy is very negative) and the temperature is low. This results in a negative free energy and the low temp helps to slow down the molecules so they will favorably collide and fuse resulting in a decrease in entropy. this reaction must also release energy and become more stable (negative enthalpy) or the reaction will be unfavorable.

Potential Hydrogen bond acceptor groups are those like

a double bonded O that can make an OH bond or N bond with a lone pair that can make a bond with a hydrogen. the Nitrogens that do not have an H bonded to them already notice that the nitrogens that do already have a Hydrogen bonded to them are good hydrogen bond donor groups.

An enzyme from the human immunodeficiency virus can synthesize DNA from an RNA template. Explain how this enzyme activity contradicts Crick's central dogma.

according to central dogma, DNA serves as a template from RNA synthesis. The HIV enzyme called reverse transcriptase works in reverse by synthesizing DNA from an RNA template.

Adenosine monophosphate does what?

acts as a secondary messenger and participates in many intracellular signal transduction pathways. It activates protein kinases and is responsible for regulating the effects of the hormones, glucagon and adrenaline.

Hydrogen bond acceptors:

are those groups or atoms carrying a partial negative charge on them. Hence, attracting partially positive H atoms. they also contain a lone pair of electrons!

Hydrogen bond donors:

are those groves which can donate a positively charged H+ atoms or H+ ions.

potential hydrogen bond donor groups

are usually groups containing a nitrogen since they have that lone pair.

Which proton would you expect to dissociate at a lower pH? the proton of the carboxylic acid group or the ammonium group? Cl-H3N+CH2COOH

at a lower pH the carboxylic acid group is more likely to dissociate into H+ and its conjugate base. However, ammonium dissociates into H+ and ammonia, at a lower pH it will shift toward the formation of the ammonium ion. Its pK value is 9.25 where as the pK value for COOH is 2.3 which is much lower.

Why is the cell membrane not an absolute barrier b/w the cytoplasm and external environment?

b/c it needs to react with its environment. needs to keep required nutrients and maintain appropriate concentrations. the membrane needs to be semipermeable and allow nutrients in and wastes out.

Explain why the strands of a DNA molecule can be separated more easily at pH >11

because the high pH eliminates hydrogen bonds between bases making it easier to separate the strands of DNA. and the concentration of the hydroxide ions is higher.

why is the genomic library larger than a cDNA library for a given organism?

cDNA only the DNA sequences that are trascribed into mRNA genomic library contains DNA sequences corresponding to all the organisms DNA including all genes and non transcribed sequences.

In DNA in a double helical structure guanine pairs with

cytoseine by forming three hydrogen bonds between them .

Describe what happens when a dialysis bag containing pure water is suspended in a beaker of sea water. What would happen if the dialysis membrane were permeable to water but not to the solute?

dialysis bag made up of a semi permeable membrane, allowing water molecules and small solutes to pass through. when 2 solutions of the same solvent are separated by a membrane the solvent molecules move from an area of high concentraion to an area of low concentraion. (osmosis) this is the same trend for solutes if the membrane is permeable to solutes.

why Do cDNA libraries derivedfrom different cell types within the same organism differ from each other

different cell types express different sets of genes.

if the cell membrane were permeable to the salt ions then the solutes (ions) will

diffuse from the beaker from high concentraion into the cell (low concentration) until equilibrium is attained.

if you are trying to find the Keq and are given delta G and temperature you need to use anti natural log which is

e^(-deltaG/(R*T))

H2NCONH2 + H20 -> CO2 + 2NH3

entropy increases here

keq= 25 Q-> R the reaction will proceed to generate more r. since equal concentrations of Q AND r are mixed the reaction will proceed towards generation of R (25 times of [Q] to achieve

equilibrium.

Lowering the temperature for a negative delta H will favor or not favor?

favor

go over #17 on chapter one back of the book problems

go over #17 on chapter one back of the book problems

1M NaCl -> 0.5 M NaCl

here the number of molecules decreases since the molarity is decreased to half of its value. Since the number of molecules decreases, meaning that there is more space in the system allowing the molecules to move freely and hence show more randomness in the system. Meaning that the entropy will increase.

solubility of water

highly polar - least polar.

explain why honey resists microbial growth even at room temperature

honey has a high source of carbohydrates which also means it has high concentrated media of microbes. When honey comes in contact with microbial cells water moves out of the cells into honey by osmosis. this causes loss of water from the cells leading to shrinkage inactivation of metabolism growth and death.

A primer

is a strand of short nucleic acid sequences (generally about 10 base pairs) that serves as a starting point for DNA synthesis. It is required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA.

NH3 is a basic compound and can diffuse through the hydrophobic lipid membrane of kidney cells. NH4+ being a charged molecule is acidid and lipid INSOLUBLE. so it CANNOT easily diffuse through the membrane so this means that NH4+

is transported through the membrane via ion channels or by co-transporters.

Tautomers

isomers that differ only in the placement of the hydrogens this applies to the purine and pyrimidine bases of nucleic acids.

where would the following substances show partition in water containing plamitic acid micelles? H3C-(CH2)11-COO-

it will show partition in micelles due to the presence of non polar groups (CH2)11-CH3

+H3N-CH2-COO- where will it show partition to water?

it will show partition to water due to its polar nature owing to the presence of the hydrogen bond donors (NH3+) and acceptors (COO-)

Kinases are enzymes that can transfer only one of the phosphoryl groups from the three groups present in a nucleotide triphosphate.

kinases can only add phosphoryl groups one at a time to a new nucleotide.

ice has ____ entropy at lower temperatures meaning that there is less kinetic energy and less movement of the molecules. The small amount of movement within the crystal structure create4s disorder and at lower temperature they are held more tightly together.

less entropy

if you have more carbons surrounding the oxygen then it is harder for the oxygen to grab that hydrogen because there is a lot of things protecting it.

less polar

which has a greater entropy? ice or liquid water

liquid water because it has more disorder and is not in crystal form so it has a higher entropy.

amphiphilic molecules when added to aqueous solution, form globules of several molecules together. In these globules the hydrophobic groups are present in the central portion away from the solvent and hydrophilic groups are arranged at the surface facing the aqueous solution. Such globules are called as

micelles.

too many primers has

no effect

If the value of delta G is greater than zero the rection is

non spontaneous

Helicase comes in

opens up DNA double helix primer comes in and attaches to the three 3' end of the DNA if you have a 3 prime to five prime strand. the primer adds the opposite way think of a square and make it 5 to 3 prime so the polymerase can attach to the primer and attach

A weak acid works best as a buffer when

pH=pK

A weak acid is useful as a buffer within the pH range of

pK +- 1.

PO42-

phosphoryl group

Indicate the ionic species of ammonia that predominates at pH 4, 8 and 11..

pk =9.25 when a pH of a solutuion containign ammonia is less than the pK the value is log ([NH3]/[NH4+]) is less than zero. therefore the concentration of the acid (denom) is greater than that of the base (num) the reaction proceeeds toward the acid. pH at 4&8 the predom species is NH4+ but at 11 it is NH3+ ph= pk + log ([base]/[acid])

PCR TEMPERATURES ARE IMPORTANT

polymerase denaturing the DNA template DNA. at 98 decrees celc it has to melt so it has to be a high temperature. primers attach to each side of the DNA at 55 degrees. annealing means primer at each side last step it is terminated using a restriction enzyme and terminates at 75 degrees.

ph > pka

proton absent, donates protons

ph<pka

proton present, accepts protons

When bag is suspended in sea water...

pure water will move from bag into beaker, and small sized solutes such as ions will diffuse into the bag. this process of osmosis takes place until there is equilibrium between the solutions in the bag and beaker. concentrations of both solutions will then both be EQUAL

to favor reaction 2, with a positive delta H should the temperature be raised or lowered?

raised.

to find the equilibrium ration =

ratio = 1/ keq

If there are too few primers then the DNA will not

replicate

chain terminator uses a polymerase dntp and ddntp ddntp has no H to donate dntp has one hydrogen ddntp is the one that terminates

replication of DNA

to prepare a buffer for protein purification, the buffer solution should be prepared and pH adjusted at the _______ ______ rather than equilibriating it later at the required temperature

same temperature.

Primers

short polynucleotides they start everything.

A diploid organism with 45,000 kb haploid genome contains 21% G residues. calculate the number of A, C, G and T

since G is 21% we know that C must also contain 21%. so... A+T= 100 -(G+C) A+T= 100-(21+21) 100 - 42= A+T A+T = 58% so A &T = 29 % since A = T

if the value of delta G is less than zero the reaction is

spontaneous

When the reaction A + B -> C is at equilibrium the concentrations of the reactants are as follows: [A] = 2 mM [B] = 3 mM [C] = 9mM what is the standard free energy change for the reaction?

standard free energy change is given by ΔfG˚ = −RT ln K; K is the equilibrium constant. Keq= [equilibrium concentration of products]/[equilibrium concentration of reactants] so... -RT ln [C]/[A][B] -8.314 x 298 x ln (9/(2*3)) the temperature here is assumed to be 25 degrees celcius or 298 K -1.003 Kj mol

zig zag ends

sticky ends merge another DNA into it

blunt ends

straight ends cannot connect into anything else

too few primers are present in the outcome of a chain terminator sequence procedure

the amount of DNA synthesis would decrease and the resulting gel bands would appear faint

in patients with kidney failure, metabolic acidosis occurs frequently. In dialysis there is a high concentration of bicarbonte in the blood. by osmosis bicarbonate ions from the dialysate to the blood. the bicarbonate ions combine with the extra H+ ions present in the blood to form carbonic acid.

the concrentration of H+ decreases and the pH of blood increases which is required to treat metabolic acidosis

if the value for enthalpy has a negative sign for the reaction this means that

the enthalpy for the reaction decreases.

N2 + 3H2 -> 2NH3 does entropy increase or decrease in this process?

the individual molecules show free random motion wherein the energy of the atoms gets spread out while in a single structure the energy does not spread randomly. Entropy decreases here.

solubility in water depends on

the presence of polar and non polar groups. Polar groups readily DISSOLVE in water either due to the formation of hydrogen bonds or with water molecules and or ionization in water. Non polar groups do not dissolve in water and aggregate the surface of water.

dialysis is commonly used for

the purification of protein samples

If the standard free energy change under standard condition is greater than zero then...

the reaction is non spontaneous and will be endergonic at standard conditions.

explain why water forms nearly spherical droplets on the surface of a freshly waved car. Why doesn't water bead on a clean windshield?

the wax on the car froms a hydrophobic surface. As water is polar in nature, it tries to minimize its interaction with the wax by forming droplets in the form of spheres, which have the lowest surface area by volume. Water doesnt bead on a clean windshield because it is a polar or hydrophilic or polar surface. As water is polar in nature, it can interact with the polar glass, and allows it to expand on the surface instead of beading. The clean wind shield is hydrophilic!!!

if the dialysis membrane was only permeable to wter but not to the solutes,

then all pure water will move from bag to the beaker. which makes it impossible to achieve equilbirum.

occasionally a C-H group can form a hydrogen bond. Why would such a group be more likely to be a hydrogen donor group when the C is next to the N?

this happens only when the C is next to the N atom. The N atom has a lone pair of electrons which can form a bond with a proton and get protonated. This means N now bears a charge. When C-H is next to a protonated atom, the positive charge on N atom attracts C atom towards inself. This leads to the formation of the partial negative charge on the C atom and a partial positive charge on the H atom. Thus, the H atom is now likely to be donated for the formation of the hydrogen bond.

H3C-(CH2)11-CH3

this will also show partition in micelles at the central position facing AWAY from the water due to its non polar nature.

if the cell membrane is permeable to only water but not to ions the water will move from high concentraion to low concentraion, the process of osmosis occurs until the salt concentration inside and out of the cell is almost equal.

this will cause the cell to shrink due to the loss of water

Describe the outcome of a chain terminator sequencing procedure in which too little ddNTP is added or too much ddNTP is added

too little is added: newly synthesize chains would be terminated less frequently so the bands representing trunctuated fragments on the sequencing gel would appear faint. too little added: less frequently too much added: occuring more frequently

when cytosine is treated with bisulfite, the amino group is replaced with a carbonyl group which is then turned into

uracil.

NH4 + <- NH3 + H+

value of log ([NH3]/[NH4+]) the concentration of the denominator is higher than that of the numerator. Hence, the species will predominate at 7.4 is NH4+. So where the concentration is higher is where the species will predominate.

pI is the isoelectric pH at which the net charge of the acid is equal to

zero