Biochemistry Exam 1 (Ch 1-4)

What are the two suggestions of origin of early organic molecules?

1) UV radiation from sun or lightening discharge caused molecules of primordial atmosphere to react and form simple organic compounds 2) Hydrothermal vents may have provided conditions suitable for formation of amino acids and other small organic molecules from simple compounds present in sea water

2 makor forms of isomer in organic molecules

1) chiral carbon: sp3 hybridized carbon with 4 different single-bonded atoms 2) geometric isomers: cis/trans about double bond, amide group, etc

the overall strategy for seq any polymer of nonidentical units

1) cleave polymer into fragments small enough to be fullly seq 2) determine the seq of residue in each fragment 3) determine the order of the fragments in the original polymer by aligning fragments that contain overlapping seq

how is DNA read/written

5' to 3' (left to right) which is considered the coding direction -polymerases adds nucletotides in the 5' to 3' direction

An enzyme from the human immunodefi ciency virus (HIV, which causes AIDS) can synthesize DNA from an RNA template. Explain how this enzyme activity contradicts Crick's central dogma

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

Purines

Adenine and Guanine

What are the four most abundant elements in the human body?

Carbon, Oxygen, Hydrogen, & Nitrogen

What elements account for 97% of dry wt in the human body?

Carbon. Oxygen, Hydrogen, Nitrogen, Calcium, Phosphorous, & Sulfur

name the nucleotide in picture

Guanosine 5′-diphosphate

(c) Would HEPES or Tris be a better buff er at pH 7.5?

HEPES

biologically active a.a.

a.a. derivatives and a.a. can function as hormones and regulatory molecules -require unique R groups

Triprotic basic A.A. pKa trend

basic form protonates to Zwitterion -> +1 -> +2

DNA carries genetic information in what form?

its seqeunce of nucelotides

Macromolecules

large polymers -give complex end products

Entropy

measure of disorder in a system -going against entropy = unfavorable rxn (not gonna work) -when an isolated/closed system is open it will follow the direction of entropy (particles will move twds low concentration to reach equilibrium)

According to molecular sequence data, to which prokaryotic group are eukaryotes more closely related?

more similiar to Archaea than to eubacteria

isoelectric point (pI)

pH at which a molecule carries no net electric charge pI a.a. = (1/2)(pKi + pKj) Ki and Kj = dissociation constants of the two ionizations involving the neutral species

buffers

resist pH change -pKa ± 1 is the pH buffer range

nucleoside

sugar + base

Osmotic pressure

the pressure that would have to be applied to equalize flow of water across the membrane in both directions -a colligative property: physical property that depends on the concentration of dissolved substances

proton jumping

the rapid movement of a proton among hydrogen-bonded water molecules -conduction/abstraction of protons from a distance -responsible for acid-base rxns fast speed in aq solution

organisms are nonequilibrium, open systems which means

they exchange matter and energy with their surroundings

why does the cell look at the ADP: ATP ratio

to determine production, depletion, or storage (of DNA?)

T or F: structure dictates function

true

When cytosine is treated with bisulfite, the amino group is replaced with a carbonyl group. Identify the resulting base.

uracil

pyrimidines

Cytosine and Thymine

chain-terminator method

DNA polymerase generates DNA fragments that are randomly terminated. the identities of the terminator nucleotides of successive fragment reveal the original DNA seq -sequencing uses four reaction vessels each with a template/primer and four dNTPs and one chain of terminating ddNTP -the concetration are adjusted so that EACH position of the ddNTP terminates a chain -seperation by size gives the seq; shortest gives beginning of seq -good to seq small samples -tagged with fluorescents so wavelength activated determines which nuceltoide is added ddNTP os a nucleotide structure where the ribose is missing the 2' OH and 3' OH which will terminate the chain becaise polymerase needs a free 3'OH

Osmosis

Diffusion of water through a selectively permeable membrane -net movement of solvent across membrane from low solute concentrations (high solvent) to high solute concentration (low solvent)

1st law of thermodynamics

Energy cannot be created or destroyed -it must be conserved so it can take different forms

What is the earliest known fossil evidence of life ~3.5 BYA?

Filamentous Bacterial Cell MIcrofossil

Rank the water solubility of the following compounds: picture a-e

From most soluble (most polar) to least soluble (least polar): c, b, e, a, d.

Over time, the glutamine residues of polypeptides are susceptible to deamidation, a reaction in which the amide group is replaced by a carboxylate group. What amino acid is produced when glutamine is deamidated?

Glutamate

Identify the amino acids that differ from each other by a single methyl or methylene group.

Gly and Ala, Ser and Thr; Val, Leu and Ile; Asn and Gln; Asp and Glu

water dissociates to form

H+ and OH- ions (protons and hydroxide ions) -dissociation constant of 10^-14 -ionization constant: Kw= [H+][OH-]

Structure of water

H2O -polar (dipole) -can form hydrogen bonds -very small molecules which allows it to fit and bond with other molecules -104.5° responsible for water characteristics and abilities; deviation from 109.5° tetrahedral due to O lone pair repulsion; -pseudo symmetry: 4 by 4 symmetry: electrons pushing stonger than H

uncharged polar a.a.

-have hydroxyl, amide, or thiol groups -Serine, Threonine (R-Hydroxyl group), Asparagine, Glutamine (amide groups), Tryosine (phenolic group), Cysteine(thiol group)

Diprotic A.A. pKa trend

-have no ionizable side chains; 2 ionizable groups -the pI is the pH that the switterion is predominate and is calculated by the equation where the pK values are of the neighboring species (where 2 predominate) -pH titration curves show two buffering region, one centered on pKa of the acid and the second centered on pKa of the ammonium -all show similiar behavior

amino acid naming

-have three letter abbreviations and one letter -polymers of a.a. of less than 50 a.a are called peptide -peptide are indentified by number of a.a residues (AYDG is tetrapeptide) -named from N terminus to C terminus (picture: alanyl-tyrosyl-aspartyl-glycine

5'ADP-1'Glucose

-important for starch storage in plants; precursor to starch production -starch synthesis proceeds by repeated addition of glucose units donated by ADP-glucose -conserving energy by binding glucose to growing starch molecule

ice vs liquid water

-in ice water molecules are h-bonded in crystalline array; each molecule is tetrahedrally bonded by 4 nearest neighbors via H-bonds so forms 6 member rings; requires more space; water expands on freezing so less dense than liquid to allow spreading -in liq water H-bonds rapidly break and reform in irregular networks; melting water collapses tetrahedral structure; pseudo order stuctures bc water wants to join other water molecules & move freely while keeping order (H-bonds)

translation

-in translation the linear seq of nucleotides in mRNA is translated to a seq of amino acids in the gene product. -the mRNA is organized into codons: a linear seq of 3 nucleotides (total= 4^3) -the has an AUG start site that also incorporates methionine (N-formyl-Met for prokaryotes) and 3 codonds. Each codon becomes an amino acid -the other 60 codon are assigned to the 20 common amino acids in proteins -each step of translation, formation of the mRNA-ribosome complex, binding tRNA and movement is powered by GTP hydrolysis. -Translation occurs at the ribosome (rRNA + protein) ; it is the site of protein synthesis -it uses a mRNA with a specific codon seq, tRNA that carry its assigned amino acid & an anticodon antiparallel and complementary to its codon, and a ribosome -from the start sitem a.a.-tRNA with anticodon complementary to next codon binds to its codon, the protein chain is transferred to that amino acid, and the ribosome moves to the next codon

what are the attractive forces acting on biological molecules

-ionic interaction -Van der walls -hydrogen bonds

Solvation

-ions surrounded by one or more concentric shells of orientated solvent molecules -polar and ionic substances can dissolve in water -water is a very efficient solvent; "universal solvent" -"like dissolves like" -water cages atoms to separate other compounds & move things around -solubility of polar & ionic substance are enhanced when they carry functional groups that can H-bond

DNA polymerase I

-is used by cells to replicate cellular DNA by parental strand seperation and new strand synthesis -is used experinentally for polymerae chain reaction (PCR) for amplification and DNS sequencing -binds to a template/primer, dNTP's complementary to the next open position on the template, and forms the 3' to 5' phosphodiester bond in the 5' to 3' direction, reading the template in the 3' to 5' direction -a controled rxn that is based on the availability of an open 3'OH

Gel Electrophoresis Apparatus

-it is used for seperation of DNA fragments -DNA sizing uses horizontal agarose gel electrophoresis -molecules of constant mass/charge move through the gel matrix in an electric field based on their size; smaller move farther than larger fragments bc they can move more rapid so their size effects their velocity -visualization (fluoroscent dyes) shows bands, each of different size -DNA is sized based on the number of base paors (bp or kbp) relative to standars -to purify DNA: cut pice of gel then filter to seperatre it

chromosomes in eukaryotes

-linear DNA is associated with protein and can be highly condensed into chromosomes -each chromosome has a homologous pair (similiar in seq) -human have a total of 46 chromosomes

metabolic pathways

-mechanisms for synthesizing the required compounds from simpler but more abundant precursors -evolved to synthesizes molecules and generate energy

modified a.a. side chains

-modification of an a.a. after the polypeptide chain has been synthesized produces unusual a.a. -side chains can be covalently modified -modificiations are often essential to the function

Colony (in situ) Hybridization

-most commonly used -process to screen for presence of desired gene -colonies are placed on master plate -transferred to nitrocellulose filter -treat with NaOH to lyse the cells and seperate into single strans and binds to nitrocellulose -anneal labeled probe which is a short segment of DNA who seq is complimentary to a portion of the DNA seq of interest autoradiograph and blackeing identfies colonies detected by probe

Hydrogen Bonding

-noncovalent -spontaneous -can form and break rapidly -stonger than typical Van der Walls interaction b/c "sharing" spontaneous interaction -one H2O molecule contains 2 donor hydrogens and 2 lone pair "acceptors" so it can participate in a max of 4 H-bonds -Hydrogen bonds with any electronegative atom holding a hydrogen

eukaryotes are characterized by

-nucleus -numerous membrane bound organelles -more complex -multicellular some unicellular

Identify the hydrogen bond donor and acceptor groups in asparagine

Hydrogen bond donors: α-amino group, amide nitrogen. Hydrogen bond acceptors: α-carboxylate group, amide carbonyl

Which reactions tend to be characterized by an increase in entropy: condensation or hydrolysis reactions?

Hydrolysis reactions tend to occur with an increase in entropy, because the highly ordered polymer is broken down into separate units.

dipolar amino acids

-the form show is the correct state of ionization at pH 7 -amino acids are either diprotic or triprotic if the R group is ionizable -amino acid can act as a base or acid -dipolar ions or zwitterions bear charged groups of opposite polarity (neutal) -more soluble in polar solvents -the ionic properties of the side chains influence the physical and chemical properties of the free amino acid and amino acids in proteins

prokaryotes

-the simplest cells -most numerous and widespread -3 common shapes: spirilla (helically coiled), Bacillus (rod), Cocci (sphere) -size range 1-10 microns -externally organize rather than internally -relatively simple structures mostly unicellular

Recombinant DNA Construction

-the vector is prepared by cleaving the plasmid vector and the target gene on BOTH ends with the same unique restiction enxyme that give sticky ends -the two DNAs are anneled using antiparallel complementary of the overhangs -DNA ligase is used to seal the gaps of the sugar-phosphate backbone (require ATP)

Restriction Endonucleases

-they cleave at specific recognition sites (sites that have not been modified by methylation); looking for base structure in major groove; cuts N.A. from the inside -they can leave an overhang or -leave blunt ends -EcoR1 and EcoRV seqs are palindromic, meaning they read identically in 5' to 3' (same fwd or backward) -enzymes are bilateral to read both helix of major groove in DNA -Bacteria has it so it doesn't cut itself: specific seq that have impacted bacteria so its their defense mechanism -a) cleavage at staggered position will leave a "sticky strand" flap -b) cleavage at symmetry will leave blunt ends

DNA fingerprinting

-used to find differences in genomes bc uses areas where repeats are known -measure length -determine genetic similarity

Pyrosequencing

-uses good cameras to take pics when nucletoide is added so no need for termination -fluorescent tags -reading as its being made -can take multiples to deternube any errors -better to seq for an entire genome 1) DNA segments attached to glass plates & amplified to form cluster of identical DNA molcs 2) add solution of 4dNTPs that are linked to fluorescent tags -the fluro groups are excited by laser & identified by color using a camera

RNA structure

-usually single stranded -double stranded does exist but it is not DNA -may form intermolecular base pairs

Schematic Representation: Shorthand of Nucelic Acid

-vertical line is sugar -base at top as in glycosidic bond -top OH is 2'; mid position is 3'; bottom is 5' -P is phosphodiester bond

Variation of spontaneity using ΔG = ΔH - TΔS

-ΔG = spontaneous process 1) -ΔH & +ΔS = spontaneous (exergonic/exothermic) @ all temps 2) -ΔH & -ΔS = spontaneous @ temps below T=ΔH/ΔS 3) +ΔH & +ΔS = spontaneous @ temps above T=ΔH/ΔS 4) +ΔH & -ΔS = nonspontaneous (endergonic)

Purines attach to the ribose at which Nitrogen?

9N

enthalpically favored

=exothermic = -ΔH

# of H-bonds in complimentary base pairing

A-T = 2 H-bonds G-C = 3 H-bonds -H-bonds bw bases maintain uniform width so the diameter of DNA is uniform -antiparallel 180 degree rotation bw bp

Identify the circles functional groups & linkages in the compound below (picture)

A: thiol group B: carbonyl group C: amide linkage D: phosphoanhydride linkage E: phosphoryl group F: hydroxyl group

5' ADP

Adenosine diphosphate -phosphate added to 5'C -2 phosphate groups -Adenine base is planer within structure

Name the following nucleotide (picture)

Adenosine-3′,5′-cyclic monophosphate (cyclic AMP)

Aliphatic Non-polar A.A.

Alanine, Valine, Leucine, Isoleucine, Methionine, Proline

Rapidly growing Burkholderia bacteria normally produce ammonia as a waste product. The accumulation of ammonia kills mutant bacteria that are unable to also produce oxalic acid. Explain how the normal Burkholderia cells are able to avoid death.

Ammonia (NH3) is a base, so as it accumulates, the pH increases. Oxalic acid (Table 2-4) releases protons to restore the pH to near neutral. Mutant cells that cannot produce the acid cannot neutralize the ammonia and die when the pH rises too high

Which of the functional groups in the Table give a molecule a positive charge? Which give a negative charge?

An amino or imino group can give a positive charge. A carboxylate or phosphoryl group give a negative charge.

Glutamate, a 5-carbon amino acid, is the precursor of three other amino acids that contain a 5-carbon chain. Identify these amino acids.

Arginine, glutamine, and proline

charged acidic a.a.

Aspartic acid & Glutamic acid are negatively charged above pH 3 aka aspartate and glutamate -the conjugate base form has a net negative charge -acidic proteins are rich in the negatively charged a.a. side chains -have acidic pI

A diploid organism with a 45,000-kb haploid genome contains 21% G residues. Calculate the number of A, C, G, and T residues in the DNA of each cell in this organism.

Since the haploid genome contains 21% G, it must contain 21% C (because G = C) and 58% A + T (or 29% A and 29% T, because A = T). Each cell is diploid, containing 90,000 kb or 9 × 10^7 bases. Therefore, A = T = (0.29)(9 × 10^7) = 2.61 × 10^7 bases. C = G = (0.21)(9 × 10^7) = 1.89 × 10^7 bases

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

The DNA contains 40 bases in all. Since G = C, there are 7 cytosine residues. The remainder (40 - 14 = 26) must be adenine and thymine. Since A = T, there are 13 adenine residues. There are no uracil residues (U is a component of RNA but not DNA).

condensation reaction

a chemical reaction in which two or more molecules combine by loss of water

a spontaneous rxn is determined by

a negative change in free energy (decrease in free energy)

β-Galactosidase

a selection marker - it cleave X-gal (colorless) to form a blue product -E. Coli that have transformed by unmodified pUC18 plasmid form blue colonies which shows the segment of DNA was not inserted

where is heridatory information encoded?

sequence of bases since each strand can act as a template for synthesis of new strand

Thermodynamics

study of change in energy

(a) Would phosphoric acid or succinic acid be a better buff er at pH 5?

succinic acid

Central Dogma of Molecular Biology

the nucelotide seq of DNA is transcribed into the nucleotide seq of mRNA, which is then translated into a protein. a seq of amino acids -function id to carry information -formulated by Crick in 1958

pKa

value where acid & base are equal -if the pH is lower than the pKa = less acid dissociated so acid still in form -low pKa = more likely to donate = acid -high pKa = more likely to accept = base

For the reaction A → B at 298 K, the change in enthalpy is −7 kJ · mol−1 and the change in entropy is −25 J · K−1 · mol−1. Is the reaction spontaneous? If not, should the temperature be increased or decreased to make the reaction spontaneous?

ΔG = ΔH − TΔS ΔG =−7000J·mol−1−(298 K)(−25 J·K−1·mol−1) ΔG=−7000+7450J·mol−1=450J·mol−1 The reaction is not spontaneous because ΔG > 0. The temperature must be decreased in order to decrease the value of the TΔS term.

biochemist standard state

ΔG°' -temp @ 25°C -pressure @ 1atm -pH @ 7.0 = H+ set to 10^-7 (bc standard 1M = pH 0) -if rxn doesn't include H+, H2O, or an ionizable species then ΔG°' = ΔG

Calculate ΔG°′ for the reaction A + B ⇌ C + D at 25°C when the equilibrium concentrations are [A] = 10 μM, [B] = 15 μM, [C] = 3 μM, and [D] = 5 μM. Is the reaction exergonic or endergonic under standard conditions?

ΔG°′ is positive, the reaction is endergonic under standard conditions.

Would the modified nucleoside described in Question 23 be able to participate in standard Watson-Crick base pairing?

Methylation at N6 leaves one amino hydrogen atom available to participate in hydrogen bonding, so the modifi ed residue would be able to participate in standard base pairing with T or U residues.

Can a process occur if the entropy of the system decreases and the enthalpy increases?

No. When the change in enthalpy is positive and the change in entropy is negative, the free energy change for the process is greater than zero, which makes the process unfavorable

Aromatic Non-Polar A.A

Phenylalanine & Tryptophan

major biological polymers

Protein: amino acid monomers Nucleic Acid: nucleotides monomers Polysaccharide: monosaccharide monomers -lipids are polymers of acetyl unit monomers

Chiral carbon stereochemistry

R/S: atoms are priotized by mass, and with the smallest in the back, the rotation of the top 3 give R if clockwise and S if counterclockwise -D/L: based on Fisher Projections

Determine the net charge of the predominant form of Asp at (a) pH 1.0, (b) pH 3.0, (c) pH 6.0, and (d) pH 11.0.

(a) +1; (b) 0; (c) -1; (d) -2.

Determine the net charge of the predominant form of Arg at (a) pH 1.0, (b) pH 5.0, (c) pH 10.5, and (d) pH 13.5.

(a) +2; (b) +1; (c) 0; (d) -1.

Using the data in Table 3-2, identify restriction enzymes that (a) produce blunt ends; (b) recognize and cleave the same sequence (called isoschizomers); (c) produce identical sticky ends

(a) AluI, EcoRV, HaeIII, PvuII; (b) HpaII and MspI; (c) BamHI and BglII; HpaII and TaqI; SalI and XhoI

Identify the potential hydrogen bond donors and acceptors in the following molecules: (picture a)

(a) Donors: NH1, NH2 at C2, NH9; acceptors: N3, O at C6, N7

question on picture

(a) Glutamate; (b) aspartate

Where would the following substances partition in water containing palmitic acid micelles? (a) H3C—(CH2)11—COO−, (b) H3C—(CH2)11— CH3

(a) Micelle, with the polar carboxylate group on the surface; (b) in the interior of the micelle.

Consider a reaction with ΔH = 15 kJ and ΔS = 50 J · K−1. Is the reaction spontaneous (a) at 10°C

(a) T = 273 + 10 = 283 K ΔG = ΔH − TΔS ΔG = 15 kJ − (283 K)(0.05 kJ·K−1) = 15 − 14.15 kJ = 0.85 kJ ΔG is greater than zero, so the reaction is not spontaneous.

22. (a) What is the net charge at neutral pH of a tripeptide containing only alanine? (b) How does the total number of negative and positive charges change following hydrolysis of the tripeptide?

(a) The net charge is zero (the N-terminus is positively charged and the C-terminus is negatively charged). (b) The tripeptide has one positive and one negative charge. Hydrolysis increases the total number of charges to 6: one positively charged ammonium group and one negatively charged carboxylate group for each of the three alanines.

25. Draw the peptide ATLDAK. (a) Calculate its approximate pI. (b) What is its net charge at pH 7.0?

(a) The pK's of the ionizable side chains (Table 4-1) are 3.90 (Asp) and 10.54 (Lys); assume that the C-terminal Lys carboxyl group has a pK of 3.5 and the N-terminal Ala amino group has a pK of 8.0 (Section 4-1D). The pI is approximately midway between the pK's of the two ionizations involving the neutral species (the pK of Asp and the N-terminal pK): pI ≈ (1/2) (3.90 + 8.0) ≈ 5.95 (b) The net charge at pH 7.0 is 0 (as drawn above)

A red blood cell has an internal salt concentration of ∼150 mM. The cell is placed in a beaker of 500 mM salt. (a) Assuming the cell membrane is permeable to water but not to ions, describe what will happen to the cell in terms of osmosis. (b) If the membrane were permeable to ions, in which direction would solutes diff use: into or out of the cell?

(a) Water will move out of the cell by osmosis, from an area of high concentration (low solute concentration) to an area of low concentration (high solute concentration). (b) Salt ions would undergo a net movement by diff usion from the surrounding solution (high salt concentration) into the cell (low salt concentration).

Where would the following substances partition in water containing palmitic acid micelles? (a) +H3N—CH2—COO−, (b) +H3N—(CH2)11— COO−.

(a) Water; (b) water.

Indicate whether the following familiar objects are chiral or nonchiral: (a) a glove; (b) a tennis ball; (c) a screw; (d) this page; (e) a snowfl ake; (f) a spiral staircase; and (g) a shoe.

(a) chiral; (b) nonchiral; (c) chiral; (d) chiral; (e) nonchiral; (f) chiral; (g) chiral.

Amphiphilic molecules

-have both hydrophilic and hydrophobic groups -form micelles (spheres) or bilayers by hiding there hydrophobic groups and exposing their hydrophilic groups to water

why is Cysteine unique

-has a thiol group that can form disulfide bonds with other cysteine within a protein or bw proteins; through oxidation of 2 thiol groups -the loss of 2 electron to O2 allows formation of S-S bond -the dimer is called cystine

23. Calculate the pI of (a) Ala, (b) His, and (c) Glu

(a) pI = (2.35 + 9.87)/2 = 6.11 (b) pI = (6.04 + 9.33)/2 = 7.68 (c) pI = (2.10 + 4.07)/2 = 3.08

Identify the potential hydrogen bond donors and acceptors in the following molecules: picture b

(b) Donors: NH+, NH2 at C4; acceptors: O at C2, N3.

Consider a reaction with ΔH = 15 kJ and ΔS = 50 J · K−1. Is the reaction spontaneous (b) at 80°C?

(b) T = 273 + 80 = 353 K ΔG = ΔH − TΔS ΔG = 15 kJ −(353 K)(0.05 kJ·K−1) = 15 − 17.65 kJ = −2.65 kJ ΔG is less than zero, so the reaction is spontaneous.

Identify the potential hydrogen bond donors and acceptors in the following molecules: picture c

(c) Donors: NH+ 3 group, OH group; acceptors: COO− group, OH group.

titration curve of polyprotic acid

-has multiple slopes (stair) = multiple pKa values, one for each ionization step sharp incline slopes mean it has gone beyond buffer capacity and shows a 10 fold difference

Intramolecular complimentary

(reciprocal pairing) -gives rise to more complex molecules assemblies with an even greater range of functional possibilities -stored info is a sequence of bits -basis for transcribing DNA and RNA and translation (RNA--> protein)

The 20 standard amino acids are called α-amino acids. Certain β-amino acids are found in nature. Draw the structure of β-alanine (3-amino-n-propionate).

+H3N—CH2—CH2—COO-

entropically favored

+ΔS

what is the best shorthand

-AUCG -where the left hand base nucleotide is 5'

Fisher Convention

-D/L system -the carbon chain is drawn with vetical lines with the most oxidized carbon at top given the lowest number -based on priority of oxidation -if the highest priority project left = L; if right = D -have the meaning shown in the geometric drawing -defines a.a steroechemistry

Semiconservative DNA replication

-DNA must be replicated with high fidelity (precision & accuracy) so that each daughter cells is genetically identical -Watson Crick recognized that their structure of B-DNA could be replicated by strand seperation, followed by synthesis of new strands antiparallel and complimentary to each "template" strand -each daughter cell has once complete strand of parental DNA and one of new DNA -Experimentally DNA is denatured by heat, base, and chaotropic agents that break the structure of water (urea, HCl) by interrupting the DNA interaction (pull apart)

Charged Basic A.A

-Lysine, Arginine, Histidine -weak acid form is a positive charge -basic proteins are rich in the positively charged A.A. side chains -basic a.a. have basic pI

Restriction Digest Electrophoretogram

-RFLP: compare restriction bw restriction enzymes in organisms -used in agriculture to compare plants -sizes of various fragments can be determined by comparing their electronphoretic mobilities to the mobilities of fragments of known size

Triprotic acidic A.A. pKa trend

-a.a. with 3 ionizable R groups -first class are acidic amino acids -start as +1 form->0->-1->-2

what is the major stabilizing force in DNA

-base stacking and base pair H-bonding

alpha amino acids

-called this since both the amino group and acid group are bound to the alpha carbon -19 of the 20 amino acids with R not equal to H are chiral, with nature selecting the L-stereochemistry for all 19 -amino acid chains can be numbered with the carboxyl being C1

Condensation of 2 a.a.

-condensation (eliminate water) of two a.a., one contributing the acid and the second contributing the amine, yields a peptide linked by an amide aka peptide bond -every linear peptide has an amino (N) and carboxyl (C) termini. -each aa is a residue and residues are numbered from the N terminus to C terminus; residues are named by droppig the -ine and replacing with -yl -the residues at each end participate in one peptide bond -the backbone is N-Calpha-Co -N-Calpha-CO

importance of membranes

-create complexity -have proteins, lipids, etc -allow stuff in and out

Hydrothermal vents

-deep thermal vents -high pressure -bacteria & life forms surviving around the vents allowed a different picture of how life formed -complex series of oxidation-reduction rxns

spontaneous process

-delta G (free energy)

DNA structure

-double helix -double stranded with two linear strands -two antiparallel polynucleotide strands wind around each other -interacting via H-bonds bw bases in opposite strands -2 strands are complimentary -bases stack parallel to the axis, forming a hydrophobic interior -backbone is exterior facing the environment and is HIGHLY negatively charged so that things that interact are positively charged

DNA seq using nonspecific enzymes

-early sequencing 1)generate small fragments 2) nucleotide composition is determined by partial digestion with an enzyme that selectively removed nucleotides from one end or another -tedious and time consuming

DNA seq data

-employs the chain-terminator method -identifies each DNA fragment as it exits the bottom of a capillary electrophoresis tube so the seq data takes the form of a series of peaks -convienant data & is repeated to minimize errors -can seq multiple segments

Transgenic Organisms

-express diff genomic makeup -expressing a gene from another organism

Cloning with Bacteriophage λ

-good for cloning large seq of DNA

General Trends in pKa's of A.A.

-pKa's of the alpha carboxyl groups are all near 2.0; this is significantly lower than aliphatic carboxylic acids (pKa~4) because of the charge stabilizing effects of the alpha-ammonium -the pKa's of the alpha-ammonium groups are near 9.5 about 1 pH unit lower than the aliphatic amines due to the electron withdrawing effects of the alpha-carboxylate -the pKa;s of the side chains with Asp and Gly are closer to that for aliphatic acids with pKa;s of 3.9 and 4.0 -the pKa's of the basic amino acids are close to simple functional groups: His imidazolium (pKa 6), Lys ammonium (pKa 10.5), and Arg guanidinium (pKa 12.5) -the pKa's of the neutral uncharged AA's Cys and Tyr are close to the functional groups at 8.4 and 10.5

Nucleotide structure

-pentose sugar -nitrogenous bases attach at 1'C -phosphate groups attach at 5'C or 3'C. However, 5' is more common bc it allowd the phosphates to bind 3'OH

2'Deoxyribose

-pentose sugar in deoxyribonucletotides or deoxynucleotides -missing hydroxyl group at 2C

ribose

-pentose sugar in ribonucleotides -has hydroxyl group at 2C

which bonds link nucleotide residues in DNA & RNA (sugar-phosphate backbone)

-phosphodiester bonds -phosphate esterfied to 2 ribose units

Plasmid pUC18

-plasmids aka cloning vectors are small circular dsDNA molcs with: 1) numerous useful endonuclease cleavage sites for inserting the selected gene 2) origin of replication (OriC) so the plasmid is replicated with host DNA 3) DNA inser with gene of choice and promter that can be activated 4) selection gene; usually bacterial resistance for prokaryote cloning vehicles

Nucleic Acid

-polymer of nucleotides=monomer -nucleotides are connected by 3' & 5' phosphodiester bonds -polymers are linear -polymers have a free 5' end and a free 3' end -chains of nucleotides whose phosphate bridge the 3' and 5' of neighboring riboses -acidic = polyanions

Intramolecular replication

-polymers replicate via complimentary matches by directing assembly of new molecules from smaller complimentary units -permits one member of a pair to determine identity and orientation of other member

Difference between primed and unprimed numbers

-primed numbers refers to atoms on pentose sugar -unprimed numbers refert to atoms of nitrogenous base

Compartmentalization

-promote efficiency in polymerization by maintaining high local concentrations of reactants that otherwise diffuse; substance can more readily react -allows for complexity -protection

Site-directed Mutagenesis

-proteins can be mutated for SAR studies using mismatched primers -the mismatched primers still anneal correctly to the target if the complimentarity is sufficient -extension by DNA pol then completes mutagenic DA -can determine effects of altering an amino acid on a protein

X-ray Diffraction Photograph of DNA

-provided evidence that DNA is helical -Crick analysed 1) DNA is helical 2) planer aromatic bases form a stack that is parallel to the fiber axis -very difficult -pictured really close = farther apart in DNA fiber

Tautomeric Forms

-readily interconverted isomers that differentiate in Hydrogen conformation (positions) -the oxo forms of T, G, & U are in equilibrium with the enol lactim) forms -the equlibrium strongly favors the oxo form. which is mainly seen in organism's DNA or RNA -the lactim forms can introduce mutation in DNA seq if not corrected -position of Hydrogen has a huge impact on how it H-bonds: complimentary base pairing (donor or acceptor)

Virulent Pneumococci

-scientist initially though proteins were the hereditary info but when they eliminate proteins it had no effect -then they denatured DNA and begin studying the importance of hereditary info -exp showed that DNA extracted from a virulent strain of bacterium Dipolococcus pneumonia was the substance that transformed a nonpathogenic strain to a virulent strain

major groove

-semi-exposes the DNA interior -allows proteins, etc. to read the DNA so they most structurally fit -interaction area (H-bond area) -major and minor grooves result from asysymetric sugar distrubution

Maize and Teosinte

-sequencing differences reveal evolutionary change -they share majority of genome with very few different genes (proteins) -the regulation of the genes is what really differs

enzymes increase the rates of thermodynamically favorable rxns by

-serving as a catalysts -can change the rate but don't make an unfavorable rxn favorable

titration curves of Weak Acids

-single slope -midpoint is where pH=pKa (uniform concentration of acid and base) -below pKa = protonated form -above pKa= deprotonated form= loss all protons= fully dissociated

Stem-loop structure

-single stranded DNA and RNA can be self-complimentary -self-complimentary RNA (base pairing occurring intramolecularly: H-bonds) can form loops and stem structures which when the loops interact give RNA a complex secondary 3D shape -palindromic seq of dsDNA give cruciform shapes with each chain forming a stem and loop -provide protection in eukaryotes -can serve as regulatory sites

Dialysis

-solutes diffuse across a semipermeable membrane from regions of high concentration to low concentrations -results in an increase of entropy = thermodynamically favorable -takes time and limits the efficiency of molecules and pathways

Nitrogenous Bases

-stuctural derivatives on the purine and pyrimidine ring structures -planer, aromatic, hetericyclic molecules

L configuration amino acids

-the ammonium (NH3+) is left -the chiral 19 common amino acids are all L at the alpha carbon

Transcription

-the dsDNA is transcribed to ssRNA -RNA polymerase uses the polarity of the transcription start site to differentiate the template strand from the coding strand -the coding strand has a seq identical to the transcribed RNA (with U RNA)

Polymerase Chain Reaction (PCR)

1) heat to denature target DNA 2) cool to allow primers to anneal to target sequence 3) intermediate temp for elongation -DNA is amplified by PCR -COmponents: DNA with target gene and primer, one for each strand; thermostable DNA polymerase; buffer with Mg+2, and all 4dNTPs -done in multiple cycles -takes advantage of polymerae -both 5' ends have seq specific primers -exponential growth

Watson-Crick Model of DNA

1) two polynucleotide chains wound around a single axis creating a double helix 2) the two strands are antiparallel & both form right-handed helices; one strand runs 5' to 3' while the other is 3' to 5' 3) bases occupy the core of the helix with a sugar-phosphate strand on the outside (minimize the repulsions bw the charged phosphate) forming major and minor grooves that create an unequal width 4) bases are H-bonded to each other with A to T and G to C (typical Watson-Crick bp)

Pyrimidines attach to the ribose at which Nitrogen?

1N

26. The protein insulin consists of two polypeptides termed the A and B chains. Insulins from different organisms have been isolated and sequenced. Human and duck insulins have the same amino acid sequence with the exception of six amino acid residues, as shown below. Is the pI of human insulin lower than or higher than that of duck insulin? Amino acid residue A8 A9 A10 B1 B2 B27 Human Thr Ser Ile Phe Val Thr Duck Glu Asn Pro Ala Ala Ser

26. At position A8, duck insulin has a Glu residue, whereas human insulin has a Thr residue. Since Glu is negatively charged at physiological pH and Thr is neutral, human insulin has a higher pI than duck insulin. (The other amino acids that diff er between the proteins do not aff ect the pI because they are uncharged.)

sugar-phosphate backbone

3' OH bound to 5' Phosphate -is soluble

The pK value for N1 of adenine is 3.64, whereas the pK value for N1 of guanine is 9.50. Explain this diff erence.

The energy of N1 in a purine ring is lowest when it is in its uncharged trivalent form. Thus, protonated and therefore tetravalent and positively charged N1 in adenine readily gives up its proton to water (has a low pK value) to yield its uncharged trivalent form. In contrast, the trivalent N1 of neutral guanine resists donating its proton to water (has a high pK value) to yield a divalent and therefore negatively charged ion.

Patients with kidney failure frequently develop metabolic acidosis. If such patients undergo dialysis, the dialysate includes sodium bicarbonate at a concentration higher than that of the blood. Explain why this would benefi t the patient.

The high concentration of bicarbonate in the dialysate means that some bicarbonate will diff use from the dialysate across the dialysis membrane into the patient's blood, where it will combine with and neutralize excess protons.

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

The high pH tends to eliminate the hydrogen-bonding protons between bases, making it easier to separate the strands of DNA

Many foods must be refrigerated to prevent spoiling (microbial growth). Explain why honey (which is ∼82% carbohydrate by weight) resists microbial growth even at room temperature.

The high solute concentration of honey tends to draw water out of microorganisms by osmosis, thereby preventing their growth

How many different amino acids could theoretically be encoded by nucleic acids containing four different nucleotides if (a) each nucleotide coded for one amino acid; (b) consecutive sequences of two nucleotides coded for one amino acid; (c) consecutive sequences of three nucleotides coded for one amino acid; (d) consecutive sequences of four nucleotides coded for one amino acid?

The number of possible sequences of four different nucleotides is 4^n where n is the number of nucleotides in the sequence. Therefore, (a) 4^1 = 4, (b) 4^2 = 16, (c) 4^3 = 64, and (d) 4^4 = 256.

Estimate the isoelectric point of a Ser-His dipeptide. Explain why this value is only an estimate.

The relevant ionizable groups for the neutral species are the His side chain (pKR = 6.04) and the Ser amino group (pK2 = 9.21). pI = (6.04 + 9.21)/2 = 7.62 This value is only an estimate because the pK values of ionizable groups in free amino acids are not the same as the pK values of the groups in amino acid residues.

Calculate the number of possible pentapeptides that contain one residue each of Ala, Gly, His, Lys, and Val.

The first residue can be one of the five residues, the second one of the remaining four, etc. N = 5 × 4 × 3 × 2 × 1 = 120

Use your answer to Problem 27 to determine the relative pK values of N3 in cytosine and in uracil.

Unprotonated N3 in cytosine and protonated N3 in uracil are both trivalent. Consequently, cytosine has a has a lower pK value than uracil.

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

Water molecules move from inside the dialysis bag to the surrounding seawater by osmosis. Ions from the seawater diff use into the dialy sis bag. At equilibrium, the compositions of the solutions inside and outside the dialysis bag are identical. If the membrane were soluteimpermeable, essentially all the water would leave the dialysis bag.

Label the following statements true or false: (a) A reaction is said to be spontaneous when it can proceed in either the forward or reverse direction. (b) A spontaneous process always happens very quickly. (c) A nonspontaneous reaction will proceed spontaneously in the reverse direction. (d) A spontaneous process can occur with a large decrease in entropy.

a) fasle: spontaneous only occurs in one direction b) false: thermodynamics does not specify rate of rxn c) true d) true: spontaneous as long as ΔS > ΔH/T

base

accepts protons -the strongest base to stably exist in aq solution is oH-

DNA contains which bases?

adenine, guanine, cytosine, thymine

RNA contains which bases?

adenine, guanine, cytosine, uracil

5'ATP

adenosine triphosphate -Adenine base is thermodynamically stable -3 phosphates -3'ATP exists -the enrgy currency of cell bc it can remove the gamma phosphate and release a lot of energy (energy carrier)

(b) Would ammonia or piperidine be a better buff er at pH 9?

ammonia

Bacteriophage λ

an alternative cloning vector

how is free energy change determines

by change in enthalpy and change in entropy

Why are elements important for life?

can create building blocks from high discharge rxns

organic compounds

carbon containing

what drives the spontaneous process of water during melting and sublimation

change in enthalpy is positive

hydrolysis rxn

chemical reaction that breaks a molecule apart, usually by adding H2O

Does entropy increase or decrease in the following processes? N2 + 3 H2 → 2 NH3

decreases

acid

donates protons -all biological acids = weak acids = partially ionize in aq solution (K<1) -the stronger the acid the lower the pKa -strong acids= rapidly transfer protons to H2O (K>1) -the strongest acid to stably exist in aq solution is H3O+

Enthalpy

equivalent to heat

whats the importance of the 3'OH

essential for generation of polymer chain. Polymerase always uses the open 3' OH to bind the phosphate

hydrophobic effect

explains the exclusion of nonpolar molecules as a way to maximize the entropy of water molecules -water creates a bubble (cage) so it is not pushing away hydrophilic groups b/c they still interact but prefers to group with other water molecules -water can still form the same # of H-bonds but gives up some rotational & translational freedom -nonpolar substance aggregate (clump) in water to minimize surface area and are stabilized by the hydrophobic effect

which amino acid does not have a chiral center

glycine

H ow does the entropy of ice at −5°C diff er, if at all, from its entropy at −50°C?

ice has less entropy at the lower temperature

why is the carboxylic acid-amine rxn important

important for peptide bonds (protein formation)

Does entropy increase or decrease in the following processes? (look at picture c)

increases

Does entropy increase or decrease in the following processes? H2N-CO-NH2 + H2O -> CO2 + 2NH3

increases

bulk of nucleotides in DNA or RNA function as

information storage and transfer of info

Which has greater entropy, liquid water at 0°C or ice at 0°C?

liquid

what must the rate of condensation of simple compounds be to form a stable polymer

must be greater than rate of hydrolysis

Does entropy increase or decrease in the following processes? (look at picture d)

no change

Are viruses living?

no, because they cannot reproduce outside host cell

how many chromosomes in prokaryotes

one single but circular strand of DNA

pH relates to pKa

pH is above the pKa start losing hydrogens (deprotonate) so -1 form -pH below pKa protonated form so +1 form -pKa = pH gives 0 or -1 charge (50/50)

pH

pH= -log[H+] -the higher the pH the lower the H+ concentration: indirectly proportional -solutions that differ ny 1 pH unit differ in [H+] by a factor of 10 acidic less than 7 baseic greater than 7 neutral = 7