Amino Acids, Amino Acids, Chembio exam 1

Enthalpy

Enthalpy (abbreviated H, with units of J · mol−1) is taken to be equivalent to the heat content of the system

Entropy

Entropy (abbreviated S, with units of J · K−1 · mol−1) is a measure of how the energy is dispersed within that system. Entropy can therefore be considered to be a measure of the system's disorder or randomness, because the more ways a system's components can be arranged, the more dispersed its energy.

How does the entropy change when glucose undergoes combustion?

Entropy increases since the total number of products is greater than the total number of reactants.

Which statement best describes the model of "induced fit"?

Enzyme-substrate binding induces a conformational change in the enzyme, such that the binding site better conforms to the shape of the substrate.

Eukaryotic cells

Eukaryotic cells are usually larger than prokaryotic cells and contain a nucleus and other membrane-bounded cellular compartments (such as mitochondria, chloroplasts, and endoplasmic reticulum). Eukaryotes may be unicellular or multicellular. This group (also called the eukarya) includes microscopic organisms as well as familiar macroscopic plants and animals

What is true about the figures?

Figure 1 represents a spontaneous reaction while Figure 2 does not.

Central Dogma

First, a portion of the DNA, a gene, is transcribed to produce a complementary strand of RNA; then the RNA is translated into protein. This paradigm, known as the central dogma of molecular biology, was formulated by Francis Crick.

Free energy G

Free energy has two components: enthalpy and entropy G=H−TS

Orphan gene

Genes that appear to lack counterparts in other species are known as orphan genes. The RNA or protein products of many genes have not yet been isolated or otherwise identified.

Homologous

Genes with similar functions in different species tend to have similar sequences; such genes are said to be homologous. Even an inexact match can still indicate a protein's functional category, such as enzyme or hormone receptor, although its exact role in the cell may not be obvious.

The specificity pocket of a hypothetical serine protease contains the side chain shown here. This enzyme most likely catalyzes hydrolysis of what peptide bond?

Glu—Ser

Which of the 20 standard amino acids is not optically active (chiral) and why?

Glycine, because its side chain is a hydrogen atom.

Lyases

Group elimination to form double bonds

A portion of the evolutionary tree for a flu virus is shown here. Different strains are identified by an H followed by a number.a. Identify two pairs of closely related flu strains.b. Which strain(s) is(are) most closely related to strain H3?

H15 and H7 are closely related; while H3 is closely related to both H4 and H14.

Why does heat inactivate enzymes?

Heat disrupts the weak, non-covalent interactions that determine protein 3-D structure.

Hydrolases

Hydrolysis reactions

Radioactively labeled [14C]-proline is incorporated into collagen in cultured fibroblasts. The radioactivity is detected in the collagen protein. But collagen synthesized in the presence of [14C]-hydroxyproline is not radiolabeled. Explain why.

Hydroxyproline is not a standard amino acid and is formed by post-translational modifications.

Linkage in DNA

In a nucleic acid, the linkage between nucleotides is called a phosphodiester bond because a single phosphate group forms ester bonds to both C5′ and C3′.

quarternary structure

In a protein that consists of more than one polypeptide chain, the quaternary structure refers to the spatial arrangement of all the chains.

Covalent Catalysis

In covalent catalysis, the second major chemical reaction mechanism used by enzymes, a covalent bond forms between the catalyst and the substrate during formation of the transition state.

Deoxyhemoglobin (T)

In deoxyhemoglobin (hemoglobin without any bound O2), the heme Fe ion has five ligands, so the porphyrin ring is somewhat dome-shaped and the Fe lies about 0.6 Å out of the plane of the porphyrin ring

protein chromatography

In size-exclusion chromatography (also called gel filtration chromatography), the stationary phase consists of tiny beads with pores of a characteristic size. If a solution containing proteins of different sizes is applied to the top of the column, the proteins will move through the column as fluid drips out the bottom. Larger proteins will be excluded from the spaces inside the beads and will pass through the column faster than smaller proteins, which will spend time inside the beads. The proteins gradually become separated and can be recovered by collecting the solution that exits the column

Acid-Base Catalysis

Many enzyme mechanisms include acid-base catalysis, in which a proton is transferred between the enzyme and the substrate. This mechanism of catalysis can be further divided into acid catalysis and base catalysis. Some enzymes use one or the other; many use both.

Metal Ion Ca

Metal ion catalysis occurs when metal ions participate in enzymatic reactions by mediating oxidation-reduction reactions, as mentioned earlier, or by promoting the reactivity of other groups in the enzyme's active site through electrostatic effects.

Myoglobin

Myoglobin is a relatively small protein with a compact shape about 44 × 44 × 25 Å (Fig. 5.1a). Myoglobin lacks β structure entirely, and all but 32 of its 153 amino acids are part of eight α helices, which range in length from 7 to 26 residues and are labeled A through H (Fig. 5.1b). Hemoglobin is a tetrameric protein whose four subunits each resemble myoglobin.

Alanine, Ala, A

Non-polar aliphatic

Glycine, Gly, G

Non-polar aliphatic

Isoleucine, Ile, I

Non-polar aliphatic

Leucine, Leu, L

Non-polar aliphatic

Proline, Pro, P

Non-polar aliphatic

Valine, Val, V

Non-polar aliphatic

Phenylalanine, Phe, F

Non-polar aliphatic aromatic

Two samples of double-stranded DNA have been prepared. Nucleotide analysis reveals that sample 1 is found to be 21% A, while sample 2 is 26% G. Knowing this, which of the following statements is true?

Sample 2 will melt at a lower temperature than Sample 1.

Which amino acid side chains may participate as a nucleophile?

Ser Tyr Cys Lys His

Carbohydrates

Simple carbohydrates (also called monosaccharides or just sugars) have the formula (CH2O)n, where n is ≥ 3.

In studying the structure of a new enzyme, you find that side chains of Phe, Leu, and Ile are directed into the active site. Which of the following can logically be proposed on the basis of this observation?

Some groups on the substrate are likely to be hydrophobic.

Which yields more free energy when completely oxidized, stearate or α-linolenate?

Stearate yields more energy than α-linolenate when completely oxidized to CO2. This is due to the fact that 17 of the 18 carbons of stearate are fully reduced and α-linolenate contains three double bonds, which are already partly oxidized.

Whats an explanation for the frequent appearance of His side chains in enzyme active sites?

The His side chain is able to act as both an acid and a base under physiological conditions.

Ligase

a DNA ligase (an enzyme that forms new phosphodiester bonds between adjacent nucleotide residues). DNA ligases that act on blunt-ended DNA segments are also available.

A domain is:

a folded segment of polypeptide with a separate hydrophobic core.

RNase A is a digestive enzyme secreted by the pancreas into the small intestine, where it hydrolyzes RNA into its component nucleotides. The optimum pH for RNAse A is about 6, and the pK values of the two histidines that serve as catalytic residues are 5.4 and 6.4. The first step of the mechanism is shown. Does ribonuclease proceed via acid-base catalysis, covalent catalysis, metal ion catalysis or some combination of these strategies?

acid-base catalysis

There are three basic kinds of chemical catalytic mechanisms used by enzymes

acid-base catalysis, covalent catalysis, and metal ion catalysis.

Which cytoskeletal proteins are constructed from globular protein subunits?

actin filaments and microtubules

In a motor protein, ATP is used to

alter the conformation of the protein.

The molecule shown here contains a(an)

amide linkage

A zymogen is

an inactive precursor of an enzyme.

Which type of polymer is commonly used for energy storage?

carbohydrates

To which of the four classes of biomolecules do the following compounds belong?

carbohydrates nucleotides amino acids lipids

dielectric constant

dielectric constant, which is a measure of a solvent's ability to diminish the electrostatic attractions between dissolved ions

Exothermic reaction

exothermic reactions are accompanied by the release of heat to the surroundings (Hfinal−Hinitial=ΔH<0)

alpha carbon

formally called α-amino acids because the amino and carboxylate (acid) groups are both attached to a central carbon atom known as the α carbon (abbreviated Cα).

The oxyanion hole in chymotrypsin

helps stabilize the reaction's transition state.

In sickle cell hemoglobin, a Glu replaces a Val, resulting in a structural change in

hemoglobin

MTX and DHF share

2 identical hydrogen bond donors.

Which of the lines labelled 1-4 represent possible free energy levels for X if the reaction were catalyzed by an enzyme?

2,3

Which structure(s) contain(s) a phosphoanhydride bond?

2,4

Which structure(s) contain(s) ribose?

2,4,6

A well-studied bacteriophage has 97,004 bases in its complete genome. There are 24,182 G residues in the genome. Calculate the number of C, A, and T residues.

24,182 C residues; 24,320 A residues; 24,320 T residues

Synthetic biologists at the Scripps Institute expanded the genetic repertoire by adding two new bases into living bacterial cells. The two bases are named d5SICS and dNaM, and they base-pair with one another. How many different codons are possible in nucleic acids containing six different nucleotides if a codon consists of a consecutive sequence of three nucleotides?

6³ = 216 codons

Nucleotide

A five-carbon sugar, a nitrogen-containing ring, and one or more phosphate groups are the components of nucleotides. adenine, cytosine, guanine, thymine, or uracil (abbreviated A, C, G, T, and U).

four major types of biomolecules

Amino acids, carbohydrates, nucleotides, lipids

Genome

An organism's complete set of genetic information is called its genome. A genome may comprise several hundred to perhaps 35,000 genes.

Diploid

humans and many other organisms are diploid (having two sets of genetic information, one from each parent), so that each human cell contains roughly 6 billion base pairs of DNA.

An enzyme that carries out metal ion catalysis

includes a cofactor.

Kinesin is known as a processive motor because

it remains attached to its track after each reaction cycle.

native structure

its most stable tertiary structure (its native structure

An enzyme accelerates a chemical reaction by

making it easier for reactants to reach the transition state.

misfolding

misfolding of proteins can lead to a variety of diseases such as parkinsons, mad cow etc. Normally, the chaperones that help new proteins to fold can also help misfolded proteins to refold. If the protein cannot be salvaged in this way, it is usually degraded to its component amino acids.

A spontaneous chemical reaction

occurs with a decrease in free energy.

His 57 in chymotrypsin's active-site functions

only as an acid-base catalyst.

To separate a polynucleotide into individual nucleotides, what type of bond must be broken?

phosphodiester bond

Polyssacharides

polysaccharides perform essential cell functions by serving as fuel-storage molecules and by providing structural support. Ex glucose

Nonpolar molecules separate from water because

separation maximizes the entropy of water molecules.

Intermediate filaments are difficult to disassemble because

the are built from coiled coils.

Three of the 20 amino acids that are incorporated into proteins are aromatic. They are:

tyrosine, phenylalanine, and tryptophan

list of interactions from weakest to strongest

van der Waals interactions, hydrogen bonds, ionic interactions

An enzyme's specificity refers to

what substrates the enzyme acts on.

Spontaneous

ΔG is less than zero for a spontaneous process

Which of the following represents the overall free energy change of the catalyzed reaction?

∆G

Which of the molecules shown in the figure is a nucleoside?

1

Which structure(s) is/are or contain(s) a nucleotide?

1,2,4

polymerase chain reaction

A much more efficient technique for amplifying a particular DNA sequence was developed by Kary Mullis in 1985: the polymerase chain reaction (PCR). PCR takes advantage of the enzyme DNA polymerase, which catalyzes the polymerization of nucleotides in the order determined by their base-pairing with a single-stranded DNA template. But because DNA polymerase cannot begin a new nucleotide strand (it can only extend a preexisting chain), a short single-stranded primer that base pairs with the template strand is added to the mixture. This means that the polymerase copies only what it is "told" to copy.

Base pair extra info

A short single-stranded polymer of nucleotides is usually called an oligonucleotide (oligo is Greek for "few"). In a cell, nucleotides are polymerized by the action of enzymes known as polymerases. The phosphodiester bonds linking nucleotide residues can be hydrolyzed by the action of nucleases. An exonuclease removes a residue from the end of a polynucleotide chain, whereas an endonuclease cleaves at some other point along the chain. Polymerases and nucleases are usually specific for either DNA or RNA

beta sheet

A single β sheet may contain from 2 to more than 12 polypeptide strands, with an average of 6 strands, and each strand has an average length of 6 residues. In a β sheet, the amino acid side chains extend from both faces

The myosin head contains an enzyme activity for the hydrolysis of

ATP

cooperative binding

Apparently, hemoglobin's four heme groups are not independent but communicate with each other in order to work in a unified fashion. This is known as cooperative binding behavior. In fact, the fourth O2 taken up by hemoglobin binds with about 100 times greater affinity than the first. Hemoglobin's relatively low oxygen affinity and its cooperative binding behavior are the keys to its physiological function

What functional group does Asn have that Cys does not? What functional group does Cys have that Asn does not?

Asn has an amido group and Cys has sulfhydryl group.

Which amino acid side chains may participate in proton transfer?

Asp Glu His Lys Cys Tyr

Transfer RNA (tRNA)

At the ribosome, small molecules called transfer RNA (tRNA), which carry amino acids, recognize sequential sets of three bases (known as codons) in the mRNA through complementary base-pairing. The ribosome covalently links the amino acids carried by successive tRNAs to form a protein.

BPG

BPG binds in the central cavity of hemoglobin, but only in the T (deoxy) state. The five negative charges in BPG interact with positively charged groups in deoxyhemoglobin; in oxyhemoglobin, these cationic groups have moved and the central cavity is too narrow to accommodate BPG. Thus, the presence of BPG stabilizes the deoxy conformation of hemoglobin. Without BPG, hemoglobin would bind O2 too tightly to release it to cells. In fact, hemoglobin stripped of its BPG in vitro exhibits very strong O2 affinity, even at low pO2

restriction enzymes

Bacteria produce DNA-cleaving enzymes known as restriction endonucleases (or restriction enzymes) that catalyze the breakage of phosphodiester bonds at specific nucleotide sequences.

the following interactions is primarily responsible for stabilizing the double-helical structure of DNA

Base-stacking interactions between adjacent bases.

Amyloid fibers are primarily characterized by

Beta sheets

List the elements found in biological molecules.

Biological molecules primarily contain H, C, N, O, P, and S.

Ligases

Bond formation coupled with ATP hydrolysis

Which substance is least soluble in water? CH3CH2OH Ca2+ NH3 CH3CH2CH3

CH3CH2CH3

The protease from the human immunodeficiency virus (HIV) is a target of the drugs used to treat HIV/AIDS. The protease has a mechanism similar to that of renin, except that renin consists of a single protein with two catalytic Asp residues, whereas the HIV protease consists of two identical subunits, each of which contributes an Asp residue. Is this an example of convergent or divergent evolution?

Convergent evolution, since the protein structures are different.

Which of the following diseases has been linked to protein misfolding?

Creutzfeldt-Jakob Disease

RNA is susceptible to base catalysis in which the hydroxide ion abstracts a proton from the 2' OH group and then the resulting 2' O- nucleophilically attacks the 5' phosphate. Is DNA susceptible to base hydrolysis?

DNA is less prone to base hydrolysis due the lack of 2' OH group.

disulfide bonds

Disulfide bonds (a type of covalent bond, shown in Section 4.1) can form within and between polypeptide chains. Experiments show that even when the cysteine residues of certain proteins are chemically blocked, the proteins may still fold and function normally. This suggests that disulfide bonds are not essential for stabilizing these proteins. In fact, disulfides are rare in intracellular proteins, since the cytoplasm is a reducing environment. They are more plentiful in proteins that are secreted to an extracellular (oxidizing) environment

Proteins

Each protein consists of one or more polypeptides, which are chains of polymerized amino acids.

What intermolecular interactions are likely to form between the two amino acid side chains shown in the protein diagram below?

In the diagram, the two amino acids can form a London dispersion interaction, a type van der Waals force

What are the strongest intermolecular interactions that likely form between the two amino acid side chains shown in the protein diagram?

In the diagram, the two amino acids can form a hydrogen bond.

What are the strongest intermolecular interactions that likely form between the two amino acid side chains shown in the protein diagram?

In the diagram, the two amino acids can form an ion pair.

Denature and renature

In the laboratory, proteins can be denatured by adding highly soluble substances such as salts or urea (NH2─CO─NH2). Large amounts of these solutes interfere with the structure of the solvent water, thereby attenuating the hydrophobic effect and causing the protein to unfold. When the solutes are removed, the proteins renature.

peptide bond

In the peptide bond that links successive amino acids in a polypeptide chain, the electrons are somewhat delocalized so that the peptide bond has two resonance forms: The polypeptide backbone can still rotate around the N─Cα and Cα─C bonds, although rotation is somewhat limited.

The complete genome of a virus contains 1578 T residues, 1180 G residues, 1609 A residues, and 1132 C residues. What can you conclude about the structure of the viral genome, given this information?

In this genome, the DNA is single stranded, where the trend in base abundance follows A > T > G > C.

Isomerases

Isomerization reactions

A compound present in many foods has the formula C44H86O8NP. To which class of molecules does this compound belong?

It is a lipid (it is actually lecithin) since it is mostly C and H; also, there is too little O to be a carbohydrate, too little N to be a protein, and too little P to be a nucleic acid.

DNA nucleotides

Nucleic acids are polymers of nucleotides Each nucleotide of DNA includes a nitrogen-containing base. The bases adenine (A) and guanine (G) are known as purines because they resemble the organic compound purine. The bases cytosine (C) and thymine (T) are known as pyrimidines because they resemble the organic compound pyrimidine

What are the structural components of the biological molecules called nucleotides?

Nucleotides consist of a five-carbon sugar, a nitrogenous ring, and one or more phosphoryl groups linked covalently together.

Hemoglobin's oxygen-binding curve is sigmoidal because

O2 binding shifts hemoglobin to a high-affinity conformation.

How do eukaryotic and prokaryotic cells differ?

Only eukaryotic cells have a nucleus.

Oxidation fact

Oxidation does not readily take place when the heme is part of a protein such as myoglobin or hemoglobin. Oxygen binding to myoglobin depends on the oxygen concentration

Oxidoreductases

Oxidation-reduction reactions

Cysteine, Cys, C

Polar Neutral

Methionine, Met, M

Polar Neutral, hydrophobic

Aspartate, Asp, D

Polar acidic, negative charge

Glutamate, Glu, E

Polar acidic, negative charge

Tryptophan, Trp, W

Polar aromatic

Tyrosine, Tyr, Y

Polar aromatic, partial hydrophilic

Arginine, Arg, R

Polar basic, positive charge

Histidine, His, H

Polar basic, positive charge

Lysine, Lys, K

Polar basic, positive charge

Asparagine, Asn, N

Polar neutral

Glutamine, Gln, Q

Polar neutral

Serine, Ser, S

Polar neutral

Threonine, Thr, T

Polar neutral

Polymerization

Polymerization involves the phosphate and sugar groups of the nucleotides, which become linked by phosphodiester bonds.

Polymers

Polymers of amino acids are called polypeptides or proteins (20) Polymers of nucleotides are termed polynucleotides or nucleic acids, better known as DNA and RNA. (4) Polysaccharides usually contain only one or a few different types of monosaccharide residues, so even though a cell may synthesize dozens of different kinds of monosaccharides, most of its polysaccharides are homogeneous polymers.

Prokaryote

Prokaryotes are small unicellular organisms that lack a discrete nucleus and usually contain no internal membrane systems. (Bacteria and archaea)

Functions of Biopolymers

Proteins- carry out metabolic reactions,support cellular structures, store energy

Reduction

Reduction, the gain of electrons, is accomplished by the addition of hydrogen or the removal of oxygen

RNA

Ribonucleic acid (RNA) contains the pyrimidine uracil (U) rather than thymine

Myoglobin

The myoglobin structure lacked the simplicity and symmetry of a molecule such as DNA and was more irregular and complex than expected

Stop codons

The ORF ends with one of the three "stop" codons: DNA coding sequences of TAA, TAG, or TGA, which correspond to the three mRNA stop codons

If a Lys residue that interacts with 2,3-bisphosphoglycerate (BPG) in the central cavity of hemoglobin is changed to a Ser residue, how would this affect hemoglobin behaviour?

The T state would be less stable.

Which of the following explains why drinking a carbonated soda does not lead to a decrease in blood pH?

The bicarbonate buffer system resists radical changes in pH upon addition of small amounts of acid or base.

tertiary structure

The complete three-dimensional conformation of the polypeptide, including its backbone atoms and all its side chains, is the polypeptide's tertiary structure

secondary structure

The conformation of the polypeptide backbone (exclusive of the side chains) is known as secondary structure

Vector

The cutting-and-pasting process allows a desired DNA segment to be incorporated into a carrier DNA molecule called a vector, leaving an unbroken, fully base-paired recombinant DNA molecule

Ends of DNA

The end of the polymer that bears a phosphate group attached to C5′ is known as the 5′ end, and the end that bears a free OH group at C3′ is the 3′ end. By convention, the base sequence in a polynucleotide is read from the 5′ end (on the left) to the 3′ end (on the right).

What is the primary driving force in the formation of protein tertiary structure?

The exclusion of non-polar substances from aqueous solution.

heme

The fully functional myoglobin molecule contains a polypeptide chain plus the iron-containing porphyrin derivative known as heme (shown below). The heme is a type of prosthetic group, an organic compound that allows a protein to carry out some function that the polypeptide alone cannot perform—in this case, binding oxygen.

Oxygen binds cooperatively to hemoglobin

The hemoglobin in red blood cells, like myoglobin, binds O2 reversibly, but it does not exhibit the simple behavior of myoglobin. A plot of fractional saturation (Y) versus pO2 for hemoglobin is sigmoidal (S-shaped) rather than hyperbolic (Fig. 5.7). Furthermore, hemoglobin's overall oxygen affinity is lower than that of myoglobin: Hemoglobin is half-saturated at an oxygen pressure of 26 torr (p50 = 26 torr), whereas myoglobin is half-saturated at 2.8 torr.

quartinary structure

The individual chains, called subunits, may all be identical, in which case the protein is known as a homodimer, homotrimer, homotetramer, and so on (homo- means "the same"). If the chains are not all identical, the prefix hetero- is used. The spatial arrangement of these polypeptides is known as the protein's quaternary structure.

Using Table 3.2 as a guide, estimate the melting temperature of the DNA from an organism whose genome contains equal amounts of all four nucleotides. To what temperature would you have to cool the DNA to allow it to reanneal?

The melting point would be approximately 90°C and the annealing temperature would be 65-70°C.

The difference in free energy between the substrate and product of a reaction catalyzed by Enzyme A is negative and small. What conclusions can be drawn about this reaction?

The reaction is spontaneous and its speed is unknown from these data.

Bohr effect

The reduction of hemoglobin's oxygen-binding affinity when the pH decreases is known as the Bohr effect. The Bohr effect plays an important role in O2 transport in vivo. Tissues release CO2 as they consume O2 in respiration. The dissolved CO2 enters red blood cells, where it is rapidly converted to bicarbonate (HCO3−) by the action of the enzyme carbonic anhydrase

primary structure

The sequence of amino acids in a polypeptide is called the protein's primary structure. There are as many as four levels of structure in a protein

Naming amino acids

The three-letter code is usually the first three letters of the amino acid's name. The one-letter code is derived as follows: If only one amino acid begins with a particular letter, that letter is used: C = cysteine, H = histidine, I = isoleucine, M = methionine, S = serine, and V = valine. If more than one amino acid begins with a particular letter, the letter is assigned to the most abundant amino acid: A = alanine, G = glycine, L = leucine, P = proline, and T = threonine. Most of the others are phonetically suggestive: D = aspartate ("asparDate"), F = phenylalanine ("Fenylalanine"), N = asparagine ("asparagiNe"), R = arginine ("aRginine"), W = tryptophan ("tWyptophan"), and Y = tyrosine ("tYrosine"). The rest are assigned as follows: E = glutamate (near D, aspartate), K = lysine, and Q = glutamine (near N, asparagine). The carbon atoms of amino acids are sometimes assigned Greek letters, beginning with Cα, the carbon to which the R group is attached. Thus, glutamate has a γ-carboxylate group, and lysine has an ε-amino group.

Messenger RNA

The transcribed RNA is known as messenger RNA (mRNA) because it carries the same genetic message as the gene. The mRNA is translated by a ribosome, a cellular particle consisting of protein and ribosomal RNA (rRNA).

Flurofamide is a potent inhibitor of urease, an enzyme that catalyzes the conversion of urea to CO2 and NH3 (shown below). What does this tell you about the transition states for the reaction?

The transition state involves tetrahedral intermediates.

Conformational stages

The two conformational states of hemoglobin are formally known as T (for "tense") and R (for "relaxed"). The T state corresponds to deoxyhemoglobin, and the R state corresponds to oxyhemoglobin. Deoxyhemoglobin is reluctant to bind the first O2 molecule because the protein is in the deoxy (T) conformation, which is unfavorable for O2 binding (the Fe atom lies out of the heme plane).

Alpha helix twist

The α helix was first identified through model-building studies carried out by Linus Pauling. In this type of secondary structure, the polypeptide backbone twists in a right-handed helix (the DNA helix is also right-handed). There are 3.6 residues per turn of the helix, and for every turn, the helix rises 5.4 Å along its axis. Most α helices are about 12 residues long.

CRISPR/Cas9

These RNAs then bind to a nuclease called Cas9 (for CRISPR-associated) and guide it to complementary DNA sequences, which presumably represent bacteriophages trying to infect the cell. The Cas9 nuclease cleaves both strands of this DNA, destroying the incoming bacteriophage. Without the CRISPR RNA guide, Cas9 cannot cleave DNA, but it will cleave whatever DNA is complementary to the guide RNA.

Lipids

These compounds cannot be described by a single structural formula since they are a diverse collection of molecules. However, they all tend to be poorly soluble in water because the bulk of their structure is hydrocarbon-like. Ex cholesterol

globular proteins

This enzyme is a globular protein (fibrous proteins, in contrast, are usually highly elongated. Globular proteins typically contain at least two layers of secondary structure. This means that the protein has definite surface and core regions. On the protein's surface, some backbone and side-chain groups are exposed to the solvent; in the core, these groups are sequestered from the solvent. In other words, the protein comprises a hydrophilic surface and a hydrophobic core.

Beta sheet structure

This type of secondary structure consists of aligned strands of polypeptide whose hydrogen-bonding requirements are met by bonding between neighboring strands. The strands of a β sheet can be arranged in two ways (Fig. 4.7): In a parallel β sheet, neighboring chains run in the same direction; in an antiparallel β sheet, neighboring chains run in opposite directions. Each residue forms two hydrogen bonds with a neighboring strand, so all hydrogen-bonding requirements are met.

Transferases

Transfer of functional groups

Enzyme

Virtually all metabolic processes occur with the aid of catalysts called enzymes, most of which are proteins (a catalyst greatly increases the rate of a reaction without itself undergoing any net change).

Oxyhemoglobin (R]

When O2 binds to produce oxyhemoglobin, the Fe—now with six ligands—moves into the center of the porphyrin plane. This movement of the Fe ion pulls His F8 farther toward the heme group, and this in turn drags the entire F helix so that it moves as much as 1 Å. The F helix cannot move in this manner unless the entire protein alters its conformation, culminating in the rotation of one αβ unit relative to the other.

How alpha helix and beta sheets are made

the first stages of protein folding can be described as a "hydrophobic collape," when nopolar groups are forced out of contact with water. Once the hydrophobic core of the protein begins to take shape, the hydrogen bonding responsible for regular secondary structure can occur, and other structures and side chains jostle themselves into their final positions in the tertiary structure. certain small proteins can be repeatedly denatured and renatured, but in the cell, protein folding is more complicated and may require the assistance of other proteins. Some of these are known as molecular chaperones and are described in more detail in Section 22.4. The pathway to full functionality may require additional steps beyond polypeptide folding. Some proteins contain several polypeptide chains, which must fold individually before assembling. In addition, many proteins undergo post-translational processing before reaching their mature forms. Depending on the protein, this might mean removal of some amino acid residues or the covalent attachment of another group such as a lipid, carbohydrate, or phosphate group

Haploid

the haploid state, equivalent to one set of genetic instructions

pH

the hydrogen ion concentration is expressed as a pH: pH=−log [H+]

dissociation constant

the ionization of water can be described by a dissociation constant, K, which is equivalent to the concentrations of the reaction products divided by the concentration of un-ionized water: K=[H+][OH−][H2O]

regular secondary structure

the polypeptide backbone often assumes a repeating conformation, known as regular secondary structure, such as an α helix or a β sheet.

Enzymes are classified according to

the type of reaction they catalyze.

amino acids

they contain an amino group (─NH2) and a carboxylic acid group (─COOH). Under physiological conditions, these groups are actually ionized to ─NH3+ and ─COO−. a side chain or R group—that may also contain N, O, or S;

Myoglobin, α globin, and β globin have similar structures because

they evolved from a common ancestor.