Biochemistry Exam 2
distinguish the two forms of the DNA double helix
*A-form*: in low humidity -seen in double-stranded RNA and in DNA-RNA hybrids --the oxygen atom at carbon 2' (in ribonucleotides) imposes steric constraints *B-form*: in high humidity DNA in cells is mostly B form A-form is short and fat; B-form is long and lean
describe the actions of DNA pol I-V:
*DNA pol I*: DNA repair, DNA replication (removes RNA primers from lagging strand by 5' exonuclease activity!!) *DNA pol II, IV, V*: DNA repair *DNA pol III*: genomic DNA replication
optimal wavelength for DNA absorption? protein?
*DNA* -> 260 nm *protein* -> 280 nm
how is the R state stabilized if all of the noncovalent interactions are broken?
Fe-O2 bonds stabilize the R state (they are STRONG)
describe site-directed mutagenesis by M13 phage as a cloning vector
M13 is a single-strand DNA phage that replicates via a double-stranded DNA replicative intermediate
Describe manipulation of gel electrophoresis:
Manipulation of the structural state *native gel*: molecule's structure is preserved (stays condensed -> smaller) *denature gel*: molecule's structure is destroyed either by SDS (for proteins) or urea (for nucleic acids) -can cause to outcomes: --1) the molecule stretches out and becomes larger --2) the molecule breaks into smaller pieces if it was originally a di-, tri-, or polymer) Manipulation of the oxidative state *reducing gel*: disulfide bonds are destroyed by the reducing agent -separates a big clunky protein into smaller pieces -examples: DTT and BME gels *nonreducing gel*: disulfide bonds are preserved
how is Mg2+ involved in DNA polymerase activity?
Mg2+ ions coordinate the substrates and stabilize the transition state in the nucleophilic attack of the 3'-OH of the primer and the a-phosphate of the nucleotide -in this way the daughter strand is synthesized in the 5'->3' direction
what are the hypervariable CDR loops in an antibody?
the antigen binding site is hypervariable and comprises the *complementarity-determining regions* of the antibody amino acid sequence; they're located at the ends of the antibody variable regions where the antigen binds to the antibody, there can be charge-charge interactions, hydrophobic interactions, hydrogen bonding, etc.
when it comes to the Hill equation, the higher the Hill constant...
the more the graph looks like an S
which parts of hemoglobin are evolutionarily invariant?
the overall globin fold surrounding the heme ring and the two critical His residues (and most residues involving contacts between alpha and beta chains)
the most normal double-helix is B form, but describe A form:
the pitch of the A-form helix is 24.6 angstroms; thus the A-form is a shorter, wider structure than the B-form one turn in A-form DNA requires 11 bp to complete forms in dehydrated random-sequence DNA stronger tendency for certain sequences (e.g., *alternating GC pairs, high GC content*, e.g. binding site for the transcription factor Sp1) only structure formed by dsRNA RNA-DNA hybrids formed during replication, transcription
(T/F) DNA that is denatured by heat will return to its native state upon cooling
TRUE but it HAS to be cooled *slowly* rapid cooling creates a population of single-stranded random coils
the high binding specificity of antibodies make them ideal for:
delivering drugs to specific locations in the body
deoxyhemoglobin is to the ____ state as oxyhemoglobin is to the ____ state
deoxy -> T state oxy -> R state
northern blotting
detections of a specific RNA sequence -by a radioactive DNA probe -the DNA probe has a sequence that will base-pair(hybridize) with the RNA you want to analyze
southern blotting
detects DNA! -by a radioactive DNA probe -the DNA probe has a sequence that will base-pair with the DNA sequence you want to analyze before the probe is added, you separate by gel electrophoresis
western blotting
detects proteins! -also called immunoblotting: identifies immunoreactive proteins in a complex mixture -proteins are resolved by electrophoresis then transferred to a membrane filter where they are treated with an antibody raised against specific targets -the presence of the bound antibody is detected in the Western blot
how do you find P50 on a graph?
draw a line from the 0.50 Yo2 mark on the y-axis; then draw a line down from where that line intersects with the binding curve -this Po2 value is your P50
why is crystal diffraction the most accurate method for showing the 3D structure of proteins?
due to the regularity of the pattern shown
explain how to use the Sanger method by reading a gel:
gel shows the 5'->3' reading of the NEWLY synthesized strand!!! -if gel reads from bottom to top 5' CACC 3' then we can INFER that the analyzed/template strand was 5' GGTG 3' (to get analyzed strand, read from top to bottom and know it should be complimentary to what the gel shows)
Describe the Meselson-Stahl experiment
growth in media containing N15 as the sole N source gives DNA of density 1.724 g/mL growth of E. coli in standard medium gives DNA of density 1.710 g/mL after transfer of dense bacteria (1.724) to light medium for one generation, all of the DNA had intermediate density (1.717 g/mL which = 0.5 (1.724 + 1.710) as shown by CsCl density equilibrium centrifugation succeeding generations cultured in light medium show both the hybrid and the light DNA SHOWS SEMICONSERVATIVE
what is heme?
heme is an iron prophyrin (a conjugated tetrapyrrole ring system) -in heme, Fe2+ is bound to protoporphyrin IX -heme us synthesized separately from the globins myoglobin and hemoglobin without heme is called an *apoprotein*; with heme is called a *holoprotein* **oxygen binds at the heme Fe2+!! -Fe2+ has six coordinating positions: 4 are N's of heme, one is O2, and the sixth is the *proximal histidine* residue of the globin protein --the *distal His* stabilizes the bound O2 via H-bonding (Mb and Hb with O2 bound are called oxyhemoglobin and oxymyoglobin; without O2 bound, deoxy-)
the stability of the DNA double helix is due to
hydrogen bonds between base pairs and base-pair stacking interactions
where would DNA quadruplexes exist?
in telomeres, the protective structures at the end of linear DNA molecules
read about cloning a dna fragment into a plasmid vector
in the book but shown on slide 67 ch 4
tRNA molecules have extensive regions of _______
intramolecular complementarity
describe Z-DNA
left-handed helix -induced by special chemical environment or by force in A and B DNA helices, all nucleotides are in anti orientation -in the left-handed Z DNA helix, *pyrimidines are anti* and *purines are syn*
describe sickle-cell disease
mutation in hemoglobin; the abnormal erythrocytes block circulation in capillaries and lyse due to their fragility, causing anemia heterozygotes with half mutant and half normal Hb are asymptomatic except when oxygen-stressed
difference between nucleosides and nucleotides
nucleosides have no phosphate group (only sugar and nitrogenous base connected by a *glycosidic bond*) nucleotides have a phosphate group at the 5' carbon
describe ribose and deoxyribose sugars and the bonds they form
numbering on the sugars begins from the carbon connected to the two O atoms, or hemiacetal group (carbon 1 attaches to the nitrogenous base through a *glycosidic bond*) carbon 3 (3'OH) bonds to the 5' phosphate group of the following nucleotide through a *phosphodiester bond*
after replication, each daughter cell receives:
one parental strand and one newly synthesized strand (semiconservative)
describe the main points of the electrophoresis slide thrown into the supercoiling section
particles that are negatively charged (DNA) will migrate toward the anode (the positively charged terminal) the distance that they travel depends on their charge but also their size (larger migrate slower) -this mean if DNA is supercoiled it will travel further/faster
basic components of DNA/RNA:
phosphate group, sugar (ribose or deoxyribose), and a nitrogenous base (A,G,C,T/U)
ethidium bromide (EtBr) is a fluorescent molecule with a planar structure. the flat molecule intercalates, or fits directly between two adjacent base pairs in a double helix. in doing so, it unwinds the double helix by 26 degrees for each ethidium molecule bound. if EtBr was added to relaxed, closed circular DNA, would you expect positive or negative supercoiling to occur?
positive supercoiling it relaxes the relaxed DNA wherever it lands, therefore it tightens the DNA everywhere else
describe the problems of single restriction enzymes
problems of single enzyme digestion and ligation -plasmid self-linking -direction of integrated gene -self-linking of integrated gene
why is DNA more stable in the presence of salt?
salt decreases phosphate backbone repulsion salt has a positive charge so it neutralizes the phosphate backbone
describe triple-stranded DNA structures
self-complementarity within a single DNA molecule creates a triple-stranded structure and an unpaired single strand (picture on slide 58 ch 4)
DNA replication is _____
semiconservative each strand of the parent molecule acts as a template for a new, complementary strand
antibody-antigen interactions are mediated by:
shape and charge complementarity
describe the creation of recombinant DNA *in vitro*
take DNA sequences from different sources and use restriction enzymes (the most important tool in molecular biology) to cleave them; the recognition sites for these restriction enzymes are around 4-8 base pairs and many of them are palindromic -the cleavage is complimentary on the two sources because they're cut by the same enzyme, so it creates "sticky ends" and DNA ligase sticks them together examples of a sticky end restriction enzyme: *EcoRI, BamHI, HindIII, NotI*
how does oxygen binding at the heme group induce the conformational change from the T state to the R state?
the *Perutz mechanism*: when O2 binds, it pulls the Fe2+ ion into the plane of the heme, causing steric strain between the flattened heme and the proximal His (F8) and Val (FG5); this strain is relieved by a change in conformations of both His F8 and Val FG5 -*the F helix is drawn toward the heme*
if given an SDS-page gel and a native page gel, which should you consider when judging the size of polypeptide chains?
the SDS-page gel because we're looking at the size of subunits, not the whole protein
early evidence that DNA is the carrier of genetic information?
Avery and his colleagues showed that nonpathogenic pneumococci could be made pathogenic by the transfer of DNA from a pathogenic strain
(T/F) artificial DNA synthesis is OPPOSITE direction as natural synthesis
TRUE bases added to the 5' end
very basic difference between DNA and RNA
*DNA* is used to store genomic information while *RNA* is used and then broken down -DNA is more stable then RNA because the vicinal -OH groups (2' and 3') in RNA make it more susceptible to hydrolysis -the 2'-OH in RNA makes it impossible for RNA to take B-form structure due to steric hindrance --the 2'-OH also makes RNA more flexible
describe the restriction sites for EcoRI, BamHI, HindIII, NotI
*EcoRI*: 5' G AATTC 3' 3' CTTAA G 5' *BamHI*: 5' G GATCC 3' 3' CCTAG G 5' *HindIII*: 5' A AGCTT 3' 3' TTCGA A 5' *NotI*: 5' GC GGCCGC 3' 3' CGCCGG CG 5'
describe the models for allosteric transitions in hemoglobin:
*KNF model*: Binding of O2 at one subunit changes conformation at that subunit, facilitating transition at*adjacent* subunits in the same molecule; mixed tetramers with low- and high-O2 binding affinity subunits are allowed *MWC model*: Hb exists in two states: T (tense; lower O2 binding affinity) and R (relaxed); O2 binding perturbs the T<->R equilibrium toward the R state, and O2 release favors the T state; mixed tetramers are NOT allowed in this model -this model is more generally accepted
what are Po2 and Yo2?
*Po2* is the partial pressure of oxygen (proportional to concentration) -P50 is a constant that reflects the binding affinity of myoglobin to oxygen --the smaller the P50, the higher the affinity to oxygen!!! --the larger the P50, the lower the affinity to oxygen *Yo2* is the fraction of sites occupied =sites occupied/total sites available =Po2/(P50 + Po2) where P50 is Po2 at half saturation
nomenclature for bases, nucleosides, and nucleotides
*adenine* nucleoside: adenosine nucleotide: adenosine 5'-monophosphate *guanine* nucleoside: guanosine nucleotide: guanosine 5'-monophosphate *cytosine* nucleoside: cytidine nucleotide: cytidine 5'-monophosphate *uracil* nucleoside: uridine nucleotide:uridine 5'-monophosphate *thymine* nucleoside: deoxythymidine nucleotide: deoxythymidine 5'-monophosphate **if any of the bases are present in DNA, they become deoxyadenosine, etc
differentiate homotropic allosteric effectors and heterotropic allosteric effectors
*homotropic* bind at the active site, whereas *heterotropic* bind at other sites on the protein in the case of hemoglobin, O2 is a positive homotropic effector because its binding to heme increases the binding affinity of O2 to other hemes in the tetramer -H+, CO2, and 2,3-bisphosphoglycerate (2,3-BPG) are negative heterotropic effectors; binding of one or more of these effectors decreases the binding affinity of O2 to hemoglobin --this stabilizes the T state and promotes greater O2 delivery/release to tissues
differentiate between a hyperbolic binding curve and a sigmoidal binding curve:
*hyperbolic binding curve*: transport protein is very efficient at binding oxygen but very inefficient at unloading it OR transport protein is very efficient at unloading oxygen but very inefficient at binding it *sigmoidal binding curve*: transport protein is efficient in both binding and unloading oxygen because it can switch between higher and lower affinity states (strong in the lungs and week in the capillaries)
differentiate between allosteric effectors in the lungs and capillaries:
*lungs*: binding of O2 favors the *R state*; releases BPG, CO2, and H+ *capillaries*: binding of BPG, CO2, and H+ favors the *T state*; releases O2
what are myoglobin and hemoglobin?
*myoglobin*: a monomeric heme protein that binds and releases O2 in tissues -about 2mg of myoglobin per gram of human muscle tissue is required for efficient delivery of O2 to mitochondria -deep-diving mammals have 10-30 fold more myoglobin; this capacity for oxygen storage permits long periods underwater between breathes *hemoglobin*: a tetrameric heme protein that transports O2 from lungs or gills to peripheral tissues and returns CO2 to lungs or gills for exhalation -hemoglobin is transported in the vasculature of red blood cells
differentiate between oxygen resource qualities and oxygen destination qualities:
*oxygen resource*: high in O2 low in BPG, CO2, and H+ Need upload O2 Therefore, higher affinity to O2 or decreased P50 *oxygen destination*: low in O2 high in BPG, CO2, and H+ need unload of O2 Therefore, lower affinity to O2 or increased P50 **H+ concentration or pH is related to CO2 because dissolving CO2 makes solution more acidic
describe how to represent the primary, secondary, and tertiary structure of nucleic acids
*primary*: sequence of nucleotides different representations: -ACGTT (5' end always to the left if not explicitly given) -pApCpGpTpT-OH -pApCpGpTpT (-OH is assumed) *secondary*: 3D arrangement of nucleotide residues with respect to one another; short-term folding interactions such as the double helix *tertiary*: longer range 3D interactions; superhelical forms: over and underwinding, cruciforms
how is absorbance ratio of 260/280 used to distinguish protein from DNA?
*protein* 260/280= ~0.5 *DNA* 260/280= ~1.8-2.0
DNA denaturation is promoted by
-electrostatic repulsion (phosphate group negative charge) between chains (charge neutralized to some extent by positively charged molecules) -high entropic factor (denatured = entropically favored) -alkali -heat helix-coil transition is *cooperative*: early structural changes promote later ones, and "melting" of the helical structure occurs over a small temperature range
nucleotide functions
1. Adenosine: autacoid (act like local hormones) 2. Coenzyme components: NAD+, NADP+; FMN and FAD -coenzymes are nonprotein components of an enzyme that provide a chemical functionality not provided by the protein (often vitamins or contain vitamins) -NAD+/NADH and NADP+/NADPH carry out hydride transfer reactions 3. Regulatory molecules: cAMP and cGMP -cAMP functions: --signals the effects of hormones (like adrenaline, glucagon) --activates protein kinases-- regulate glycogen and lipid metabolism --activates ion channels --regulates cyclic nucleotide-binding proteins --regulation of gene expression in prokaryotes 4. Provide energy for reactions: ATP-> ADP + Pi -the phosphoric anhydride bonds present in ATP are a source of chemical energy -ATP is central to energy metabolism -GTP drives protein synthesis -CTP drives lipid synthesis -UTP drives carbohydrate metabolism 5. Substrates for making DNA and RNA: all NTPs and dNTPs
SDS-page is a denature gel that can be run at reducing or non-reducing conditions; describe the model about how a protein is coated by SDS:
1. the native structure or shape of the protein does NOT matter; all proteins have a rod shape in the presence of SDS 2. the charges carried by the protein does NOT matter that much; the negative charge of SDS will dominate 3. **only thing that matters is how long the peptides are (i.e., the molecule weight)
describe the common protein folding motif that both myoglobin and hemoglobin are built on:
2 alpha heme groups, 2 beta heme groups
the ____ on thymine labels it as a special kind of uracil
5-methyl group
base pairing and Chargaff's rules:
A always pairs with T/U forming *two H-bonds* G always pairs with C forming *three H-bonds* Chargaff's rule: mole percent of A = T and G = C
before DNA replication can take place, the DNA strands must be separated at regions called forks. replication begins at one or more fixed sites called replication origins; why are replication origins more often A-T rich sequences?
A-T base pairing only uses 2 hydrogen bonds rather than the 3 hydrogen bonds found in G-C pairing; weaker and easier to break
Describe the Hershey-Chase experiment
Batch 1: phages grown with radioactive sulfur (35 S) Batch 2: phages grown with radioactive phosphorous (32 P) 1: mix radioactively labeled phages with bacteria. The phages infect the bacterial cells 2: agitate in a blender to separate phages outside the bacteria from the cells and their contents 3: centrifuge the mixture so bacteria form a pellet at the bottom of the test tube 4: measure the radioactivity in the pellet and the liquid in the first experiment, all radioactivity was in the liquid where cells were originally suspended In the second experiment, radioactivity was in the bacteria Since radioactivity was in the bacteria, the genetic information was contained in the DNA and not the protein
what's happening during hyperventilation
CO2 levels decrease, and this favors the R state and reduces O2 release in tissues; treat by breathing into a paper bag to reintroduce exhaled CO2 and increase its concentration in plasma
why does DNA contain thymine?
Cytosine spontaneously deaminates to form uracil • Repair enzymes recognize these "mutations" and replace these Us with Cs • But how would the repair enzymes distinguish natural U from mutant U? • Nature solves this dilemma by using thymine (5-methyl-U) in place of uracil in DNA
DNA duplex is ______ favored while denatured DNA is ______ favored
DNA duplex: *enthalpy* favored denatured: *entropy* favored
DNA is a ____ molecule and the human genome contains:
DNA is a linear molecule (a polymer) and the human genome contains three billion bases; when stretched out, the length of all the DNA from one human is 2 meters
describe the activity of DNA polymerase I
DNA polymerase I requires DNA template (guider), an RNA or DNA primer (starting point), and dNTPs (energy and building blocks) has *polymerase activity*, *3'-exonuclease and 5'-exonuclease activity* -can remove what's in front of it and go backwards to fix mistakes
which is the major replicative DNA polymerase in bacteria?
DNA polymerase III
explain DNA polymerase reaction in replication:
DNA polymerase catalyzes the nucleophilic attack by the 3'-OH at the primer terminus upon the a-phosphate of the incoming dNTP that is base paired with the template -this forms a new phosphodiester bond and releases pyrophosphate
protein A has an exposed hydrophobic patch that interacts with protein B. on protein B's surface, which of the following amino acids can be found on the protein A-binding site? a. Glu b. Ser c. Arg d. Ile e. Gln
Ile because it is non-polar and therefore also hydrophobic
describe creating supercoiled DNA
L = T + W L: linking number; number of times one strand crosses the other; L can only be changed by breaking DNA strand; only applicable to circular DNA (bacterial) T: twist; number of turns -generated because DNA wants to keep the same number of bp per turn when the stress increases W: writhe; number of super-helical turns L = T + W is constant so long as no DNA strand is broken superhelicity of DNA is defined in terms of sigma, the superhelix density sigma = delta L/Lnaught where Lnaught is the linking number for DNA in he relaxed state and delta L is the change in linking number caused by supercoiling
elaborate on denaturing gels:
SDS (sodium dodecyl sulfate) can interact with the hydrophobic regions of a *protein* to unfold it -forms hydrophobic-hydrophobic interactions Urea and Guandinium chloride work similarly to denature *nucleic acids* -HOWEVER, Guanidinium cannot be used as a denaturant for electrophoresis because of its charge and high working concentration !!!
(T/F) most mutations occur in somatic cells and are not carried forth to the next generation
TRUE
(T/F) carbon monoxide (CO) binds to myoglobin better than O2
TRUE -distal His does NOT make hydrogen bond with CO --however, it prefers oxygen b/c it can form an H-bond with oxygen, so the stronger binding of CO isn't as problematic as it seems --if oxygen is not present, VERY problematic
(T/F) alkaline hydrolysis of RNA proceeds through a cyclic intermediate not possible in DNA
TRUE the structure involves the the phosphate group bonded to the 3'-OH to unbind from its nucleotide and swing around and make a second bond to the 2'-OH group alkaline hydrolysis yields a mixture of nucleoside 2' and 3'-monophosphate
what is a palindromic DNA sequence?
a symmetrical sequence that can form a hairpin or cruciform conformation example: GAATTC
X-ray diffraction model requires:
a uniform pattern in structure -regular structure aligned in a repeated pattern with the same directionality throughout shows the 3D structure of proteins
each nucleotide in DNA or RNA has a net charge of _____ at physiological pH (pH 7.4) meaning...
about -1 meaning the base amino group is unprotonated
name the purines
adenine and guanine two-ring structures dont forget to memorize the structures!
describe adenosine's physiological activity
adenosine functions as an autacoid, or local hormone -influences blood vessel dilation, muscle contraction, neurotransmitter release, fat metabolism -adenosine is also a sleep regulator (promotes eventful sleepiness) --**caffeine promotes wakefulness by blocking the binding of adenosine to its neuronal receptors (possible because the two are so structurally similar! also the reason that caffeine is addictive)
Describe antibodies:
antibodies (immunoglobulin protein) recognize specific epitopes on antigens -the binding of the two epitopes by each antibody can form a cross-linked network which precipitates as an aggregate structure -antigen binding site is located at the upper ends of the two forks -enzymatic cleavage happens at the hinge region where the fork occurs --when cleavage occurs, the two forks regions become *Fab fragments* (each containing a light chain and part of the heavy chain) and the bottom unit (both heavy units) becomes the *Fc fragment* --each Fab fragment has one antigen binding site --the Fc fragment has no antigen binding site **the immuoglobulin fold is composed of *two antiparallel beta sheets stacked face to face* -this motif occurs 12 times in an IgG molecule (antibody)
describe the Bohr effect
as pH drops (e.g., during period of high metabolic demand), H+ binding to Hb favors the T state; thus P50 and O2 delivery increases this makes biological sense because metabolism usually needs oxygen and generates CO2, making cellular environment more acidic (low pH)
how do topoisomerases affect electrophoresis?
as the relaxation by topoisomerase increases, the less distance the molecule travels
What is the hyperchromic effect?
at 260 nm, native DNA absorbs less light than denatured DNA -denatured DNA has *higher absorbance* --this can be used to follow DNA denaturation
in bacteria (prokaryotic), replication initiates from a fixed origin and proceeds ________; compare to eukaryotic:
bi-directionally eukaryotic replication utilizes multiple replication origins, but it also proceeds bidirectionally; forms replication bubbles
describe the effects of allosteric effectors:
bind their target proteins and promote a conformational change that modulates the functional properties of the protein (e.g., increase/decrease O2 binding affinity in hemoglobin, or increase/decrease the activity of an enzyme)
describe allostery or allosteric regulation:
binding event on one site of a protein or protein complex affects the binding event in a distal and distinct site
how do SDS-page, DTT, and DME gels work?
by breaking disulfide bonds
a mixture of nucleotides can be separated using electrophoresis or ion-exchange chromatography by:
choosing a pH so that different nucleotides have different net charges
analysis of O2 binding to Hb or Mb can be followed by:
color change -oxygen presents = bright red -oxygen absent = venous purple
evolutionary relationships are defined by...
considering rates of mutation in genomes and differences in amino acid sequences for homologous proteins for example, there are 25 amino acid differences between human and sperm whale myoglobins, suggesting that the two species diverged about 100 million years ago
describe the steps of polymerase chain reaction (PCR); how does the polymerase not denature at high temperatures?
cycle 1: yields 2 molecules 1) denaturation: heat briefly to separate DNA strands (*98 C*) 2) annealing: cool to allow primers to form hydrogen bonds with ends of target sequence (*55 C*) 3) extension: DNA polymerase adds nucleotides to the 3'end of each primer (*65-72 C*) cycle 2: yields 4 molecules cycle 3: yields 8 molecules (2 molecules match target sequence) **each cycle doubles the number of molecules! polymerase does not denature because it derived from thermophilic bacteria (thermophiles)
name the pyrimidines
cytosine, thymine, uracil one-ring structures don't forget to memorize the structures!
describe the transition of hemoglobin from the T to the R state
there is a 15 degree rotation upon switching from the T to R state the central channel becomes more narrow when hemoglobin switches from T->R (think of those sliding disc things where when its pulled all the way tight theres an opening you can put your arm through; when its opened up there is no opening) -2,3-BPG binds in the cleft that opens in the T state and perturbs the T<->R equilibrium in favor of the T state (resulting in greater O2 delivery) the overall conformational changes are a result of local structural changes -key noncovalent intersubunit interactions are disrupted during the transition --way more interactions in the T state (salt bridges and H-bonds) between alpha-beta and beta-beta interfaces --all of these interactions are broken in the R state --***this unfavorable enthalpy loss is compensated by favorable O2-heme binding interactions
what is the first process in the readout of information encoded in DNA?
transcription (the production of an RNA transcript)
describe DNA's double helix structure
~10.4 base pairs/turn, some bases are tilted slightly, DNA helix is sometimes slightly bent 36 degree angle between stacked base pairs the rise of the helix = 0.34 angstroms; this is the distance between successive base pairs (twice the van der waal's thickness of a planar ring)