Biology I Proteins

__________structure describes the alpha-helices and beta-sheets that are formed by hydrogen bonding between backbone atoms located near each other in the polypeptide chain.

Secondary

If you wanted to show a generalized protein in which the focus is on the protein's function rather than its structure, you should use a _________.

Simple shape

If you wanted to show the general shape of a protein, along with some important functional details such as folds and coils, you should use a _________.

Simplified diagram

Why doesn't a skin cell make crystallin protein?

Skin cells have the crystallin gene but do not express it and skin cells do not need crystallin for their function. Crystallin protein has a specific function in lens cells, and skin does not make lenses. It would be wasteful to make protein that is not needed, and the crystallin protein might even have a detrimental effect if it were expressed in skin cells. So even though skin cells have the gene to make crystallin, they do not express that gene.

If you wanted to show the 3-dimensional shape of a protein, including all of the atoms composing it, you should use a _________.

Space-filling model

Which of the three different representations of protein structure is most useful for studying the exterior of the protein?

Spacefill; the spacefill representation shows the space occupied by the protein, hiding the interior, and allowing close examination of the shapes and properties of the exterior of the protein.

The illustration shows several side chain interactions in the tertiary structure of a protein. Which of the following bonds is a result of hydrophobic interactions between two amino acid R-groups?

#3

How do you differentiate the three classifications of amino acids?

- Acidic amino acids have acidic R groups. Their electrically charged R groups make these molecules highly soluble in water. - Basic amino acids have basic R groups. Their electrically charged R groups make these molecules highly soluble in water. - Neutral (neither acidic nor basic) amino acids can be further classified as nonpolar or polar. The neutral nonpolar amino acids have R groups that contain no charged atoms; most of these amino acids are not water soluble. The neutral polar amino acids have R groups that have a dipole moment. The partial charges in their R groups make these molecules generally water soluble.

About how many hemoglobin molecules can be found in a typical red blood cell?

3 X 10^8

How many different kinds of nucleotides does DNA contain?

4: A, C, T, G DNA contains thousands of nucleotides per strand, and two strands wind together to make a DNA double helix. There are only 4 different kinds of nucleotides in DNA: A, C, T, and G.

The R group on glutamic acid is -CH2CH2COOH, which becomes -CH2CH2COO- at pH=7. Classify glutamic acid based on its R group.

Acidic; Glutamic acid can be classified as acidic because its R group contains a carboxylic acid functional group, -COOH.

Which of the three different representations of protein structure is most useful for observing the path of the protein chain from one amino acid to the next?

Backbone; in the backbone view, a line traces the backbone's path directly from one amino acid to the next. Each sharp turn of the line indicates the position of an amino acid along the protein chain.

The R group on arginine is -(CH2)3NHC(NH2)NH, which becomes-(CH2)3NHC(NH2)N+H2 at pH=7. Classify arginine based on its R group.

Basic; Arginine can be identified as basic by the presence of the amino group, -NH2, in its R group, and by the ability of the R group to accept a H+ ion.

You have just sequenced a new protein found in mice and observe that sulfur-containing cysteine residues occur at regular intervals. What is the significance of this finding?

Cysteine residues are involved in disulfide bridges that help form tertiary structure.

As a researcher in a protein lab, you analyze two different proteins for their shape and the amino acids they contain. Your results show that the two proteins have exactly the same numbers and types of amino acids, but they have different shapes. What explains these results?

Each protein has a unique linear sequence of amino acids. In the same way that the same letters can be arranged to make different words with different meanings, the same amino acids can be arranged in different linear sequences to form different proteins with different shapes and functions.

To which functional class of proteins does lysozyme belong?

Enzymatic protein; enzymatic proteins, or enzymes, are chemical agents that selectively speed up chemical reactions without being consumed by the reaction.

What does it mean to say that a gene is expressed?

Information in DNA is used to make a protein. All genes contain information about how to make a protein or other product, but when a gene is expressed the information is actively used.

The R group on alanine is -CH3. Classify alanine based on its R group.

Neutral nonpolar; Alanine can be identified as neutral nonpolar because its R group consists of carbon and hydrogen atoms.

The R group on methionine is -CH2CH2SCH3. Classify methionine based on its R group.

Neutral nonpolar; Methionine can be identified as neutral nonpolar because its R group consists of carbon and hydrogen atoms.

Tertiary structure is NOT directly dependent on _____.

Peptide bonds; peptide bonds link together the amino acids of a protein's primary structure.

What type of bond joins the monomers in a protein's primary structure?

Peptide; the amino acids of a protein are linked by peptide bonds.

__________ structure is the sequence of amino acids in a protein.

Primary

What are the four levels of protein structure?

Protein structure is conceptually divided into four levels, from most basic to higher order: Primary structure describes the order of amino acids in the peptide chain. Secondary structure describes the basic three-dimensional structures, αα-helices and ββ-sheets. Tertiary structure describes how the secondary structures come together to form an individual globular protein. Quaternary structure results from individual proteins coming together to form multi-subunit protein complexes.

__________ structure is the result of two or more protein subunits assembling to form a larger, biologically active protein complex.

Quaternary

How is the tertiary structure of a protein changed when exposed to high or low pH?

The changes in pH disrupt the hydrogen and ionic bonds between side chains.

A tripeptide has ________.

Three amino acids, two peptide bonds

If you wanted to show the 3-dimensional shape of a protein by showing the amino acid side chains and their interactions, you should use a _________.

Wireframe model

Proteins are polymers of _____.

amino acids

What is ovalbumin?

storage protein

What illustrates the secondary structure of a protein?

Alpha helices and beta pleated sheets are characteristic of a protein's secondary structure.

Globular proteins in aqueous environments will adopt a structure in which hydrophobic amino acids will be located towards the center of the protein whereas polar amino acids will be found on the exterior of the protein. What amino acids would most likely be found on the exterior of such a protein?

Any amino acid with polar R-group

The R group on lysine is -CH2CH2CH2CH2NH2, which becomes-CH2CH2CH2CH2N+H3 at pH=7. Classify lysine based on its R group.

Basic; Lysine can be classified as basic by the presence of the amino group, -NH2, in its R group, and by the ability of the R group to accept a H+ ion.

When two amino acid monomers are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can be joined through a _________ reaction. This reaction forms a(n) _________ bond.

Dehydration, peptide; proteins are complex molecules made of many repeating amino acid monomers linked together by covalent peptide bonds. Recognizing amino acids and understanding how they are linked together into polypeptides provides a foundation for understanding the three-dimensional architecture of proteins.

What are amino acids made of?

Every amino acid has a carboxylic acid group, an amino group, an αα-carbon, and an R group. Look at the R group to classify the amino acid. Acidic R groups contain a carboxylic acid functional group, -COOH. Basic R groups contain an amino (not amide) functional group, -NH2, which attracts a proton to form -NH3. Neutral polar R groups are neither acidic nor basic, but they contain a highly electronegative atom such as oxygen, nitrogen, or sulfur. Neutral nonpolar R groups contain mostly carbon and hydrogen (alkyl groups). They may also contain nitrogen or sulfur, but the effect of those atoms is diminished due to the size of the alkyl portion. You should also keep in mind the different behaviors of acids and bases: acids can donate H+ ions; bases can accept H+ ions.

The secondary structure of a protein results from _____.

Hydrogen bonds; electronegative oxygen and nitrogen atoms leave hydrogen atoms with partial positive charges.

The R group on phenylalanine contains an aromatic ring composed entirely of carbon and hydrogen atoms. Classify phenylalanine based on its R group.

Neutral nonpolar; Phenylalanine can be identified as neutral nonpolar because its R group consists of carbon and hydrogen atoms.

The R group on tryptophan is a two-ring system composed almost entirely of hydrogen and carbon atoms. Classify tryptophan based on its R group.

Neutral nonpolar; Tryptophan can be identified as neutral nonpolar because its R group consists of carbon and hydrogen atoms.

The R group on valine is -CH2(CH3)2. Classify valine based on its R group.

Neutral nonpolar; Valine can be identified as neutral nonpolar because its R group consists of carbon and hydrogen atoms.

The R group on asparagine is -CH2CONH2 . Classify asparagine based on its R group.

Neutral polar; Asparagine can be identified as neutral polar by the presence of the electronegative oxygen atom in its R group.

The R group on glutamine is -CH2CH2CONH2. Classify glutamine based on its R group.

Neutral polar; Glutamine can be identified as neutral polar by the presence of the electronegative oxygen atom in its R group.

The R group on serine is -CH2OH. Classify serine based on its R group.

Neutral polar; Serine can be identified as neutral polar by the presence of the electronegative oxygen atom in its R group.

The R group on threonine is -CH(OH)CH3. Classify threonine based on its R group.

Neutral polar; Threonine can be identified as neutral polar by the presence of the electronegative oxygen atom in its R group.

The R group on tyrosine is composed of an aromatic ring with an -OH group. Classify tyrosine based on its R group.

Neutral polar; Tyrosine can be classified as neutral polar by the presence of the electronegative oxygen atom in its R group.

What element is found in proteins that is absent in carbohydrates and lipids?

Nitrogen

What is lysozome?

One of your primary defenses against bacterial infections is lysozyme, a protein found in saliva, tears, and most body fluids. Lysozyme is an enzyme that helps fight off infections by breaking down the tough bacterial cell wall. Like all proteins, lysozyme is composed of amino acids linked together into a long chain called a polypeptide. A polypeptide becomes a functioning protein when it folds into a specific shape that positions critical amino acids so that they can function. Without the correct shape, the protein cannot function properly.

If you wanted to show the 3-dimensional shape of a protein, including the backbone structure, folds, and coils, you should use a _________.

Ribbon model

Which of the three different representations of protein structure is most useful for studying the interior shapes formed by the folds of the protein?

Ribbon; in the ribbon view, a smooth line or string traces the backbone's path, flattening into a ribbon when helix or sheet-like shapes are formed.

__________ structure is achieved when a protein folds into a compact, three-dimensional shape stabilized by interactions between side-chain R groups of amino acids.

Tertiary

Why are positions of amino acids important for proteins?

The position of every amino acid in a protein is determined by the folding pattern of the polypeptide chain. Some amino acids are internal and help to hold the protein's shape. Others are external and provide an opportunity to interact with other molecules. In addition, the position of certain amino acids is absolutely essential for the function of the protein.

What are the classifications of amino acids?

There are 20 amino acids that most commonly occur in proteins. Based on the functional group making up their side chain, or R group, amino acids are classified as acidic, basic, or neutral. The physical and chemical properties of the R group determine the unique characteristics of each amino acid.

Why are enzymes the most important types of proteins found?

They provide a microclimate to make or break covalent bonds; this climate is called the active site. Forcing electrons into shared orbits releases or requires energy but ALWAYS requires an enzyme active site - a little microclimate whereby the sharing of electron pairs can be forced onto a molecule/broken up.

Which of the following are structural proteins? actin and tubulin glycogen and glycerol sucrase and lactase guanine and cytosine chitin and cellulose

actin and tubulin

Which parts of the amino acids X and Y are involved in the formation of a peptide bond? (N-terminus) XY (C-terminus)

carboxyl group of X and amino group of Y

What is NOT a function of proteins?

energy storage

What maintains the secondary structure of a protein?

hydrogen bonds

The covalent addition of a ______________ functional group differentiates the amino acids phenylalanine and tyrosine from each other.

hydroxyl

Which bonds are created during the formation of the primary structure of a protein?

peptide bonds