protein reading gonzalez - weebly

You can’t look at a living organism and not see proteins (FIGURE 2-36). Inside and out, proteins are the chief building blocks of all life. They make up skin and feathers and horns. They make up bones and muscles. In your bloodstream, proteins fi ght invading microorganisms and stop you from bleeding to death from a shaving cut. Proteins control the levels of sugar and other chemicals in your bloodstream and carry oxygen from one place in your body to another. And in just about every cell in every living organism, proteins called enzymes initiate and assist every chemical reaction that occurs.

Although proteins perform several very different types of functions, all are built in the same way and from the same raw materials in all organisms. In the English language, every sentence is made up of words and every word is formed from one or more of the 26 letters of the alphabet. With 26 letters we can write anything, from sonnets to cookbooks to biology textbooks. Proteins, too, are constructed from a

sort of alphabet. Instead of 26 letters there are 20 molecules, known as amino acids. Unique combinations of these 20 amino acids are strung together, like beads on a string, and the resulting protein has a unique structure and chemical behavior.

Let’s look more closely at the structure of the amino acids in the protein alphabet. They all have the same basic two-part structure: one part is the same in all 20 amino acids, and the other part is unique, differing in each of the 20 amino acids.

Proteins contain the same familiar atoms as carbohydrates and lipids—carbon, hydrogen, and oxygen—but differ in an important way: they also contain nitrogen. At the center of every amino acid is a carbon atom, with its four covalent bonds (FIGURE 2-37). One bond attaches the carbon to something called a carboxyl group, which is a carbon bonded to two oxygen atoms. The second bond attaches the central carbon to

62 CHAPTER 2 • CHEMISTRY

Atoms Water Carbohydrates Lipids

5 Proteins are body-building molecules.

2 • 15 ------------------------------------------------- Proteins are versatile macromolecules that serve as building blocks.

Hair and feathers are built from proteins.

63

Proteins Nucleic Acids

a single hydrogen atom. The third bond attaches the central carbon to an amino group, which is a nitrogen atom bonded to three hydrogen atoms. These components—the central carbon with its attached hydrogen atom, carboxyl group, and

FIGURE 2-36 Proteins everywhere! Proteins are the chief building blocks of all organisms.

Amino group Side chain

Carboxyl group

Glycine

Tryptophan

Alanine

SIDE CHAIN EXAMPLES

CH

H HH

C

N

O

O

The side chain is the unique part of each of the 20 amino acids, varying in size, shape, and charge.

AMINO ACIDS

Symbol for amino acid used in this book

FIGURE 2-37 Amino acid structure. Amino acids are made up of an amino group, carboxyl group, and a side chain.

Unique combinations of 20 amino acids give rise to proteins, the chief building blocks of the physical structures that make up all organisms. Proteins perform myriad functions, from assisting chemical reactions to causing blood clotting to building bones to fi ghting microorganisms.

TAKE-HOME MESSAGE 2 • 15

Proteins perform a variety of different functions. They all, however, are built the same way and from the same raw materials in organisms.

STRUCTURALHair, fingernails, feathers, horns, cartilage, tendons

CONTRACTILEAllow muscles to contract, heart to pump, sperm to swim

REGULATORYControl cell activity, constitute some hormones

PROTECTIVEHelp fight invading microorganisms, coagulate blood

TRANSPORTCarry molecules such as oxygenaround your body

PROTEIN DIVERSITY

amino group—are the foundation that identifi es a molecule as an amino acid and, as multiple amino acids are joined together, forms the “backbone” of the protein.

The fourth bond of the central carbon attaches to a functional group or side chain. This side chain is the unique part of each of the 20 amino acids. In the simplest amino acid, glycine, for example, the side chain is simply a hydrogen atom. In other amino acids, the side chain is a single CH3 group or three or four such groups. Most of the side chains include both hydrogen and carbon, and a few include nitrogen or sulfur atoms. The side chain determines an amino acid’s chemical properties, such as whether the amino acid molecule is polar or non-polar.

The atoms present in the plant and animal proteins we eat—especially the nitrogen atoms—are essential to the constant growth, repair, and replacement that take place in our bodies. As we eat protein and break it down into its amino acids through digestion, our bodies are collecting the amino acids needed for various building projects. Proteins also store energy in their bonds and, like carbohydrates and lipids, they can be used to fuel living processes.

The amount of protein we need depends on the extent of the building projects underway at any given time. Most individuals need 40–80 grams of protein per day. Bodybuilders, however, may need 150 grams a day or more to achieve the extensive muscle growth stimulated by their

training; similarly, the protein needs of pregnant or nursing women are very high.

Contrary to the impression you might get from the labels you see on food packaging, all proteins are not created equal (FIGURE 2-38). Every different protein has a different composition of amino acids. And while our bodies can manufacture

certain amino acids as they are needed, many other amino acids must come from our diet. Those that we must get from our diet—about half of the 20 amino acids—are called “essential amino acids.” For this reason, we shouldn’t just speak of needing “x grams of protein per day.” We need to consume all of the essential amino acids every day.

Many foods, containing “complete proteins,” have all of the essential amino acids. Animal products such as milk, eggs, fi sh, chicken, and beef tend to provide complete proteins. Most vegetables, fruits, and grains, on the other hand, more often contain “incomplete proteins,” which do not have all



2 • 16 ------------------------------------------------- Proteins are an essential dietary component.

Traditional dishes in many cultures combine proteins, bringing together all essential amino acids.

FIGURE 2-38 All proteins are not created equal. Some foods have “complete proteins” with all the essential amino acids. Other foods have “incomplete proteins” and we must consume proteins from multiple sources to get all the essential amino acids.

the essential amino acids. If you consume only one type of incomplete protein in your diet, you may be defi cient in one or more of the essential amino acids. But two incomplete proteins that are “complementary proteins,” when eaten together, can provide all the essential amino acids. Traditional dishes in many cultures often include such pairings (see Figure 2-39). Examples are corn and beans in Mexico, rice and lentils in India, and rice and black-eyed peas in the southern United States.

Twenty amino acids make up all the proteins necessary for growth, repair, and replacement of tissue in living organisms. Of these amino acids, eight are essential for humans: they cannot be synthesized by the body so must be consumed in the diet. Complete proteins contain all eight essential amino acids, while incomplete proteins do not.


Food labels indicate an item’s protein content. Why is this insuffi cient for determining whether you are protein defi cient, even if your protein intake exceeds your recommended daily amount?

Q

65


Proteins are formed by linking individual amino acids together with a peptide bond, in which the amino group of one amino acid is bonded to the carboxyl group of another. Two amino acids joined together form a dipeptide and several amino acids joined together form a polypeptide. The sequence of amino acids in the polypeptide chain is called the primary structure of the protein and can be compared to the sequence of letters that spells a specifi c word (FIGURE 2-39).

Amino acids in a polypeptide chain don’t remain in a simple straight line like beads on a string. The chain begins to fold as side chains come together and hydrogen bonds form between various atoms in the chain. The two most common patterns of hydrogen bonding between amino acids cause the chain to either twist in a corkscrew-like shape or form a zigzag folding pattern. This hydrogen bonding between amino acids gives a protein its secondary structure.

The protein eventually folds and bends upon itself, and additional bonds continue to form between atoms in the side chains of amino acids that are near each other. Eventually, the protein folds into a unique and complex

three-dimensional shape called its tertiary structure. The exact form comes about as the secondary structure folds and bends, bringing together amino acids that then form bonds such as hydrogen bonds or covalent sulfur-sulfur bonds (see Figure 2-39).

Some protein molecules have a quaternary structure in which two or more polypeptide chains are held together by bonds between amino acids in the different chains. Hemoglobin, the protein molecule that carries oxygen from the lungs to the cells where it is needed, is made from four polypeptide chains, two “alpha” chains and two “beta” chains.

Some proteins are attached to other types of macromolecules. Lipoproteins, for example, circulate in the bloodstream carrying fats. They are formed when cholesterol and a triglyceride (both lipids) combine with a protein. Glycoproteins are combinations of carbohydrates and proteins. These are found on the surfaces of nearly all animal cells and play a role in helping the immune system to distinguish between your own cells and foreign cells. (We learn more about glycoproteins in the next chapter, which discusses cells.)

Peptide bonds

Amino acids

Hydrogen bonds

PRIMARY STRUCTUREThe sequence of amino acids in a polypeptide chain, similar to the sequence of letters that spell out a specific word

SECONDARY STRUCTUREThe corkscrew-like twists or pleated folds formed by hydrogen bonds between amino acids in the polypeptide chain

TERTIARY STRUCTUREThe complex three-dimensional shape formed by multiple twists and bends in the polypeptide chain based on interactions between the side chains

QUATERNARY STRUCTURETwo or more polypeptide chains bonded together

STRUCTURE OF PROTEINS

2 • 17 ------------------------------------------------- Proteins’ functions are infl uenced by their three-dimensional shape.

FIGURE 2-39 Protein structure. The functions of proteins are infl uenced by their three-dimensional shape.

The overall shape of a protein molecule determines its function—how it behaves and the other molecules it interacts with. For proteins to function properly, they must retain their three-

dimensional shape. When their shapes are deformed, they usually lose their ability to function. We can see proteins deformed when we fry an egg. The heat breaks the hydrogen bonds that give the proteins their shape. The proteins in the clear egg white unfold, losing their secondary and tertiary structure. This disruption of protein folding is called denaturation (FIGURE 2-40).

Almost any extreme environment will denature a protein. Take a raw egg, for instance, and crack it into a dish containing baking soda or rubbing alcohol. Both chemicals are suffi ciently extreme to turn the clear protein opaque white, as in fried egg whites.

Hair is a protein whose shape most of us have modifi ed at one time or another. Styling hair—whether curling or straightening it—involves altering some of the hydrogen

bonds between the amino acids that make up the hair protein, changing its tertiary structure. When your hair gets wet, the water is able to disrupt some of the hydrogen bonds, causing some amino acids in the protein to form hydrogen bonds with the water molecules instead. This enables you to change your hair’s shape—making it straighter or, if you manipulate it around curlers, making it curlier—if you style it while it’s wet. The hair can then hold this shape when it dries as the hydrogen bonds to water are replaced by other hydrogen bonds between amino acids of

the hair protein as the water evaporates. Once your hair gets wet again, however, unless it is combed, brushed, or wrapped in a different style, it will return to its natural shape.

Whether your hair is straight or curly or somewhere in between also depends on your hair protein’s amino acid sequence and the three-dimensional shape it confers (FIGURE 2-41). This amino acid sequence is something you’re born with (that is, it’s genetically determined). The chains are more or less coiled, depending on the extent of covalent and hydrogen bonding between different parts of the coil. Many hair salons make use of the ability to alter covalent bonds to change hair texture semi-permanently. They are able to do this in three simple steps. First, the bonds are broken chemically. Second, the hair is wrapped around curlers to hold the polypeptide chains in a different position. And third, chemicals are put on the hair to create new covalent bonds between parts of the polypeptide chains. The hair thus becomes locked in a new position. (New hair will continue to grow with its genetically determined texture, of course, requiring the procedure to be repeated regularly.)



Extreme environment (heat, pH) disrupts protein

shape and function.

Normal protein Denatured protein

FIGURE 2-40 Denaturation. When proteins are unfolded, they lose their function.

FIGURE 2-41 Curly or straight? Proteins determine it!

The particular amino acid sequence of a protein determines how it folds into a particular three-dimensional shape. This shape determines many of the protein’s features, such as which molecules it will interact with. When a protein’s shape is deformed, the protein usually loses its ability to function.


Egg whites contain a lot of protein. Why does beating them change their texture, making them stiff?

Q

Why is wet hair easier to style than dry hair?

QQ Why do some

people have curly hair and others have straight hair?

67


Protein shape is particularly critical in enzymes, molecules that help initiate and accelerate the chemical reactions in our bodies. Enzymes emerge unchanged—in their original form—when the reaction is complete and thus can be used again and again. Here’s how they work.

Think of an enzyme as a big piece of popcorn. Its tertiary or quaternary structure gives it a complex shape with lots of nooks and crannies. Within one of those nooks is a small area called the “active site” (FIGURE 2-42). Based on the chemical properties of the atoms lining this pocket, the active site provides a place for the participants in a chemical reaction, the reactants or substrate molecules, to nestle briefl y.

Enzymes are very choosy: they bind only with their appropriate substrate molecules, much like a lock that can be opened with only one key (see Figure 2-42). The exposed atoms in the active site have electrical charges that attract rather than repel the substrate molecules, and only the substrate molecules can fi t into the active-site groove.

Once the substrate is bound to the active site, a reaction can take place—and usually does so very quickly. An enzyme can help to bring about the reaction in a variety of ways. These include:

1. Stressing, bending, or stretching critical chemical bonds, increasing the likelihood of their breaking.

2. Directly participating in the reaction, perhaps temporarily sharing one or more electrons with the substrate molecule, thereby giving it chemical features that increase its ability to make or break other bonds.

3. Creating a “micro-habitat” that favors the reaction. For instance, the active site might be a water-free, non-polar environment, or it might have a slightly higher or lower pH than the surrounding fl uid. Both of these slight alterations might increase the likelihood that a particular reaction occurs.

4. Simply orienting or holding substrate molecules in place so that they can be modifi ed.

Sometimes a protein “word” is misspelled—that is, the sequence of amino acids is incorrect. If an enzyme is altered even slightly, the active site may change and the enzyme no longer functions. Slightly modifi ed, non-functioning enzymes

2 • 18 ------------------------------------------------- Enzymes are proteins that initiate and speed up chemical reactions.

GlucoseGalactose

Lactose

Substrate

Active site

Lactase

1 Each enzyme has an active site that is a perfect fit for its substrate.

Enzymes can help to bring about chemical reactions in a variety of ways. The enzyme lactase, for example, breaks down the milk sugar lactose into two simple sugars that can be used for energy.

2 Like a key in a lock, lactose fits in the active site in lactase. The bond between the simple sugars is then broken.

3 The two simple sugars making up lactose are then released.

LACTOSE INTOLERANCEEven a slight alteration to an enzyme's active site can disrupt its functioning. If the enzyme lactase is not built just right, an individual cannot digest milk properly, a condition called lactose intolerance.

ENZYMES FACILITATE CHEMICAL REACTIONS

FIGURE 2.42 Lock and key. Enzymes are very specifi c about which molecules and reactions they will catalyze.

are responsible for a large number of diseases and physiological problems; an example is the inability to break down the amino acid phenylalanine (in a condition known as phenylketonuria).



Without a functioning version of the enzyme lactase, some people are unable to break down the disaccharide lactose in milk.

One protein “misspelling” is responsible for the condition called lactose intolerance. Normally, during digestion, the lactose in milk is broken

down into its component parts, glucose and galactose (see Figure 2-42). These simple sugars are then used for energy. But some people are unable to break the bond linking the two simple sugars because they lack a functioning version of the enzyme lactase that assists in this process. Consequently, the lactose passes through their stomach and small intestine undigested. Then, when it reaches the large intestine, bacteria living there consume the lactose. The problem is that, as they break down the lactose, they produce some carbon dioxide and other gases. These gases are trapped in the intestine and lead to severe discomfort.

These unpleasant symptoms can be avoided by not consuming milk, cheese, yogurt, ice cream, or any other dairy products, but they can also be avoided by taking a pill containing the enzyme lactase. It doesn’t matter how the enzyme gets into your digestive system; as long as it’s there the lactose in the milk can be broken down.

Enzymes are proteins that help initiate and speed up chemical reactions. They aren’t permanently altered in the process, but rather can be used again and again.


Why do some adults get sick when they drink milk?

Q

protein reading gonzalez - weebly

Documents