Goldfarb D. Biophysics DeMYSTiFied

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192 Biophysics DemystifieD

do not absorb wavelengths in the green area of the spectrum. Since the green light

is not absorbed, it is reflected; this accounts for the green color of most plants.

Cell Life Cycle

At the beginning of this chapter we noted that all cells come from preexisting

cells through the process of cell division. The phases of cell growth and cell

division make up what is known as the cell cycle. There are two main phases to

–

FIgure 8-14 • Chlorophyll a: space filling model (left) and structural formula with bound

magnesium ion (right).

chapter 8 The cell 193

the cell cycle, each of which is broken up into subphases. The two main phases

of the cell cycle are interphase and cell division. See Fig. 8-15.

There is a third phase, called quiescent, where the cell has essentially left

the cycle and entered into a resting phase where the cell continues to utilize

energy to do work, but has stopped dividing. The quiescent or resting phase

is abbreviated G

The interphase of the cell cycle is where the cell puts most of its energy into

growth and DNA replication. Interphase is broken up into three subphases: G

S, and G

. During G

and G

the cell grows. Protein synthesis is very active dur-

ing G

and G

, and the enzymes built from this protein synthesis go on to cata-

lyze other reactions that digest carbohydrates for energy and manufacture lipids

and other structures needed for cell growth. In between G

and G

is the

S-phase when DNA replication takes place. During the S-phase, protein syn-

thesis is for the most part limited to those proteins that are needed for DNA

replication. For example, the enzymes involved in replication and, in eukary-

otes, the structural proteins that make up histones for the packaging of chro-

matin. See Fig. 8-16.

After the G

phase, the cell enters the cell division phase, also called the mitosis

or M-phase. Mitosis itself is broken into several subphases. In the first stage of

mitosis, called prophase, the chromatin condenses into visible chromosomes.

(Remember from earlier in this chapter that sometimes DNA is spread out in a

Cell cycle

Interphase: Cell growth

and DNA replication

Cell division: mitosis

FIgure 8-15 • The two parts of the cell

cycle, interphase and cell division.

194 Biophysics DemystifieD

spaghetti-like structure called chromatin. At other times the cell organizes indi-

vidual DNA molecules into tightly packed chromosomes.) In the metaphase of

mitosis, the chromosomes line up in pairs. A portion of the cytoskeleton known

as the mitotic spindle begins pulling the paired chromosomes apart, so that each

daughter cell will have its own set of chromosomes. After the chromosomes have

separated, they begin decondensing back into chromatin. In the final phase of

mitosis, called cytokinesis, the cell membrane pinches in toward the center of the

cell and divides the cell in two. See Fig. 8-16.

Anaphase

Metaphase

Mitotic spindle

FIgure 8-16 • Cell cycle. (Courtesy of David O. Morgan, The Cell Cycle: Principles of Control, New Science Press.)

still struggling

This chapter is largely descriptive. The main point is to learn some vocabulary

and to gain some understanding of the context for the biophysical studies that

we will learn about in the rest of the book. Do not feel that you have to have all

of the terms in this chapter memorized. As you encounter some of these terms

later in the book, use this chapter as a reference as needed, or refer to the glos-

sary in the back of the book.

chapter 8 The cell 195

Quiz

Refer to the text in this chapter if necessary. Answers are in the back of the

book.

1. Which of the following is not true about cells?

The cell is the basic unit of life.

cells are surrounded by a phospholipid bilayer membrane.

C. Prokaryotes always have nucleic acids.

D. Eukaryotes are always multicellular organisms.

2. Which of the following statements are true?

S1. Eukaryotes are typically larger that prokaryotes.

S2. Eukaryotes divide more rapidly than prokaryotes.

S3. Eukaryotes compartmentalize various functions into membrane-bound

organelles.

S4. Eukaryotes adapt more quickly to drastic changes in their environment.

A. S1 and S3

B. s2 and s4

C. S1 and S4

s2 and s3

E. S1, S3, and S4

3. What are receptors?

Antenna-like projections from the cell that receive radio signals.

Membrane proteins that receive other cells.

C. Molecules on the surface of the cell membrane that signal specific outside molecules to

come and bind to the membrane.

D. Molecules on the surface of the cell membrane that bind specific outside molecules,

thereby signaling the cell to do something.

4. What are the Golgi apparatus and the ER?

A. The Golgi apparatus is a device used to study cellular function, and the ER is a reticulating

structure found within the cell.

They are both membranous organelles.

C. The Golgi apparatus stores vesicles, and the ER stores ribosomes.

D. The Golgi apparatus is a species of eukaryote, and the ER is a species of prokaryote.

5. What do ribosomes do for the cell?

Process DNA

Generate polypeptides

C. Distinguish between the smooth and rough ER

D. synthesize lipids

196 Biophysics DemystifieD

6. What are the two main parts of the cell cycle?

A. The handle bars and pedals

B. interphase and outerphase

C. Growth and division

expansion and contraction

E. Separation and division

7. Microtubules are part of what structure?

A. Tubulin

B. Mitochondria

c. Bones

D. Cytoskeleton

e. capillaries

8. What does the nucleus of the cell contain?

Protons and neutrons

The nuclear envelope and DNA lamina

C. DNA and histones

D. DNA and ribosomes

9. What are chloroplasts?

A. Mitochondria

B. photosynthetic proteins

C. Plant organelles responsible for photosynthesis

Green leafy plants

10. What do mitochondria contain?

A. DNA

B. Folded membranes

C. ATP

A and B

e. B and c

F. A and C

A, B, and C

197

In Chap. 7 you learned some basics of protein structure and function. In this

chapter we will delve a little deeper into the physics and biophysical chemistry

involved. Proteins, in order to function properly, need to fold up into a specific

shape. Therefore, much of protein biophysics is concerned with gaining a deep

understanding for the physics of protein folding and protein conformational

changes.

CHAPTer OBJeCTIVeS

In this chapter, you will

Learn about protein structure and its relationship to protein function.

•

study the forces and factors that stabilize protein structures.

•

Learn how membrane protein folding differs from cytoplasmic protein folding.

•

Learn ways to analyze peptide bond angles.

•

Learn the two most common protein secondary structures: the alpha helix and

•

the beta sheet.

Quar

De Broglie’s photon

sin

Electr yclosity

lec

ty closit

Relativist

Ong

chapter

Protein Biophysics

198 Biophysics DemystifieD

Protein Folding

When a protein is folded into its correct shape, it is said to be in its native state.

The native state can include one or a small number of conformations that are

involved in the natural functioning of the protein. When a protein is unfolded,

so that it is no longer in its native state, we say that it is denatured.

Experimentally, we can expose proteins to denaturing agents, such as heat,

changes in pH, or exposure to certain chemicals. Denaturing agents destabilize the

protein’s higher-order structure (i.e., quaternary, tertiary, and/or secondary struc-

ture) causing the polypeptide chain to unfold. Frying an egg makes the clear part

of the egg become hard and white, because the protein in the egg white, albumen,

becomes denatured. Frying an egg is irreversible, because the peptide chains from

neighboring albumen molecules become entangled in one another. However,

under carefully controlled experimental conditions, it is possible to avoid entangl-

ing of the denatured chains (e.g., by keeping the protein concentration low and

using a gentle chemical denaturing agent). In such a case denaturing is reversible.

We can remove the denaturing agent and allow the protein to fold back into its

native state. In this way we can experimentally reproduce the folding and unfold-

ing of a protein in order to study the physics of protein folding.

Protein folding is, for the most part, an example of self-assembly. Self assembly

means that the forces driving the molecules to assemble in the appropriate con-

figuration or quaternary structure are inherent in the molecules themselves, and in

their interactions with solvent molecules (such as water and small ions in solution).

Only molecules that are part of the final structure are involved. Solvent molecules

such as water and small ions in solution are part of the final structure in that they

remain associated with the folded protein (or other self-assembled structure) form-

ing hydrogen bonds and other interactions that contribute to stabilizing the

structure.

Not all protein folding is self-assembly. Many proteins do require assistance

from other molecules, called folding moderators or chaperones, in order to achieve

their native state. In some cases the folding moderators (often proteins them-

selves) catalyze a step in the folding process that would otherwise occur very

slowly. In other cases a folding moderator may temporarily bind to the peptide

chain and bring certain parts of the molecule closer together or may provide a

sequestered environment that fosters the protein’s native state.

Proteins are polymers of amino acids. There are 20 major amino acids com-

monly found in proteins. Other amino acids are also found in proteins (many of

which are slight variations of the major 20), but these 20 are by far the most

common. Table 9-1 lists the 20 major amino acids and some of their properties.

chapter 9 protein Biophysics 199

TABLE 9-1 the 20 major amino acids most commonly found in proteins are typically classified into the fol-

lowing three groups: nonpolar (hydrophobic), uncharged polar (hydrophilic), and charged (some-

times called charged polar) (hydrophilic). Among the charged amino acids there are those that are

acidic (release protons and carry a negative charge) and those that are basic (absorb protons and

carry a positive charge). (courtesy of Biochemistry Demystified.)

Name Abbreviation(s) Unique Features Structure

Nonpolar, hydrophobic side chains—found in protein interiors

Glycine Gly, G • Smallest

• R is a single proton

• Flexible

• Neuroinhibitor

• Role in biosynthesis of many

compounds, such as purines

COO

−

Alanine Ala, A • Methane

•

-Keto homologue is

pyruvate

• Role in nitrogen transport

from tissues to the liver

COO

−

Valine Val, V • Butyl group

• Branched chain amino acid

found in high concentration

in muscles

COO

−

Leucine Leu, L • Branched chain amino acid

found in high concentration

in muscles

COO

−

Isoleucine Ile, I • Isomer of leucine

• Branched chain amino acid

found in high concentration

in muscles

COO

−

200 Biophysics D emystifieD

TABLE 9-1 the 20 major amino acids most commonly found in proteins are typically classified into the fol-

lowing three groups: nonpolar (hydrophobic), uncharged polar (hydrophilic), and charged (some-

times called charged polar) (hydrophilic). Among the charged amino acids there are those that are

acidic (release protons and carry a negative charge) and those that are basic (absorb protons and

carry a positive charge). (courtesy of Biochemistry Demystified.) (Continued)

Name Abbreviation(s) Unique Features Structure

Nonpolar, hydrophobic side chains—found in protein interiors

Methionine Met, M • One of two amino acids

containing sulfur

• Contains a sulfur as an

ester

• Sulfur easily oxidized

• As

S-adenosyl-L-

methionine (SAM),

a methyl donor in many

bioreactions

COO

−

Proline Pro, P •

-Carbon forms a ring

containing primary amine

• Inflexible

• Forms kinks in secondary

structures

COO

−

Phenylalanine Phe, F • Alanine plus a phenyl

• Converted to tyrosine,

which is, in turn,

converted to

L-dopa

• Interferes with the

production of serotonin

COO

−

Tryptophan Trp, W • Bulky, aromatic side

chains

• Indole group

• Precursor for serotonin

and niacin

COO

−

chapter 9 protein Biophysics 201

TABLE 9-1 the 20 major amino acids most commonly found in proteins are typically classified into the fol-

lowing three groups: nonpolar (hydrophobic), uncharged polar (hydrophilic), and charged (some-

times called charged polar) (hydrophilic). Among the charged amino acids there are those that are

acidic (release protons and carry a negative charge) and those that are basic (absorb protons and

carry a positive charge). (courtesy of Biochemistry Demystified.) (Continued)

Name Abbreviation(s) Unique Features Structure

Uncharged polar side chains—metabolically active and located on the exterior of proteins

Serine Ser, S • Hydroxyl group

• Found at the active site

of enzymes

• Aids in glycoprotein

formation

COO

−

Threonine Thr, T • Methyl and hydroxyl

group

• Found at the active site of

enzymes

• Aids in glycoprotein

formation

COO

−

Asparagine Asn, N • Methyl group and

carboxyl group with a

highly polar uncharged

amine that readily forms

hydrogen bonds

• Found at the ends of

alpha helices and beta

sheets

• Aids in formation of

glycoproteins

• Input to urea cycle

•

-Keto homologue is

oxaloacetate

COO

−

Glutamine Gln, Q • Two methyl groups and

carboxyl group with a

highly polar uncharged

amine

• Forms isopeptide linkages

• Central role as nitrogen

donor in synthesis of

nonessential amino acids

• Provides nitrogen

transport to the liver

COO

−