Chapter 19 Proteins and Amino acids

what is the R group of polar amino acids made up of?

groups that interact with water OH, SH, or amide (CONH2)

what is the range of pI values for nonpolar, polar neutral amino acids?

5.1-6.0 pH

what is the range of pI values for polar basic amino acids?

8-11

What is the quaternary protein structure?

A protein structure in which two or more polypeptide chain subunits form an active protein

describe process of naming peptides.

N-terminus and amino acid residues have -yl ending, C-terminus keeps whole name

What happens when an amino acid is placed in a more basic solution than its pI?

Becomes negative ion, losing hydrogen on ammonium end.

Would you expect to find valine and leucine on the outside or the inside of the tertiary structure? Why?

Both valine and leucine have non polar residues and would be found on the non polar inside of the tertiary structure.

what is the R group of polar acidic amino acids made up of?

Carboxylate, COO-, making it negative charged

what is the R group of nonpolar amino acids made up of?

Hydrogen, alkyl or aromatic groups

Generally list the interactions in tertiary protein structure.

Hydrophilic interactions - polar amino acid residues interact with water, being pulled to outer surface of peptide chain Hydrophobic interactions - non polar amino residues pushed towards each other towards center due to hydrophilic interactions which repel them, forms non polar center interiorly Salt bridge - ionic attractions between acidic and basic charges of residues Hydrogen bonds - hydrogen of one residue bonds with hydrogen of N or O of other residue Disulfide bonds - covalent bonds formed from oxidation of two SH groups.

19.27 Two peptides each contain one valine residue and two methionine residues. What are their possible primary structures?

MMV VMM MVM

Describe globular proteins

Spherical and compact, highly soluble. shape attributed to interactions between amino residues

Which proteins carry out the work of cells?

globular proteins, involved in transport, synthesis and metabolism

List the acidic amino acids.

glutamate and aspartate

which amino acid is the lone achiral atom?

glycine

What is the primary structure of a protein?

The specific sequence of the amino acid residues held by peptide bonds in a protein. Basically how you'd name an amino sequence

what kind of secondary structure is collage?

a triple helix

what are the two types of fibrous proteins and where are they found

a-keratin found in hair, skin, wool, nails. b- keratin found in bird feather and reptilian scales, made up of b-pleated sheet structure

Indicate whether the following interactions are responsible for primary, secondary, tertiary, or quaternary protein structures: a. disulfide bonds that form between portions of a protein chain b. peptide bonds that form a chain of amino acids c. hydrogen bonds between the H of a peptide bond and the O of a peptide bond four amino acids away

a. Disulfide bonds are a type of interaction between amino acid residues found in the tertiary and quaternary levels of protein structure. b. The peptide bonds in the sequence of amino acids form the primary level of protein structure. c. The hydrogen bonds between the peptide bonds along the polypeptide chain form the secondary structures of a helix or b-pleated sheet.

What type of interaction would you expect between the residues of each of the following amino acids in a tertiary structure of a protein? a. cysteine and cysteine b. glutamate and lysine c. tyrosine and water

a. Two cysteines, each containing ¬ SH, will form a disulfide bond. b. The interaction of the ¬ COO- in the residue of glutamate and the ¬ NH + in the residue of lysine will form an ionic bond called a salt bridge. c. The residue in tyrosine has an ¬ OH group that is attracted to water by hydrophilic interactions.

identify the secondary structure (a helix, b-pleated sheet, or triple helix) described in each of the following statements: a. a structure that has hydrogen bonds between adjacent polypeptide chains b. three helical polypeptides woven together c. a peptide chain with a coiled or corkscrew shape that is held in place by hydrogen bonds

a. b-pleated sheet b. triple helix c. a helix

19.37 A portion of a polypeptide chain contains the following sequence of amino acids: -Leu-Val-Cys-Asp- a. Which amino acid can form a disulfide bond? b. Which amino acids are likely to be found on the inside of the protein structure? Why? c. Which amino acids would be found on the outside of the protein? Why? d. How does the primary structure of a protein affect its tertiary structure?

a. cysteine b. leucine and valine, they are non polar, hydrophobic, and will be pushed towards each other, towards the internal surface, due to other hydrophilic interactions and its repelling from it. c. cysteine and asparate, both are polar hydrophillic. they interact with water, thus being pulled away towards outer surface d. polarity, functional groups, of amino acids can determine its interactions

19.35 What type of interaction would you expect between the following groups in a tertiary structure? a. cysteine and cysteine b. glutamate and lysine c. serine and aspartate d. leucine and leucine

a. disulfide bonds b. salt bridge c. hydrogen bond d. hydrophobic interaction

19.7 Give the name of the essential amino acid that has the following abbreviation: a. His b. V c. K d. Ile

a. histidine b. valine c. lysine d. isoleucine

which amino acids make up most of collagen?

glycine, proline, alanine

19.39 Indicate whether each of the following statements describes the primary, secondary, tertiary, or quaternary protein structure: a. Residues interact to form disulfide bonds or ionic bonds. b. Peptide bonds join the amino acids in a polypeptide chain. c. Several polypeptides in a b-pleated sheet are held together by hydrogen bonds between adjacent chains. d. Hydrogen bonding between amino acid residues in the same polypeptide gives a coiled shape to the protein.

a. tertiary and quaternary b. primary c. secondary d. secondary (alpha helix)

19.8 Give the name of the essential amino acid that has the following abbreviation: a. Trp b. Met c. F d. W

a. tryptophan b. methionine c. phenylalanine d. tryptophan

which amino acid predominates in hair and which bonds?

abundant in cysteine and disulfide bonds they form

describe the general structure of all amino acids.

all amino acids have a central carbon called the "a" carbon. this carbon is attached to an ammonium ion (+NH3), a carboxylate ion (COO-), a hydrogen, and an R group.

What is the difference in bonding between an alpha helix and a b-pleated sheet?

alpha helix bonds within the peptide b pleated bonds within polypeptide or between adjacent ones.

what are the type of secondary proteins structures?

alpha helix, beta pleated sheets and triple helices

The remaining parts of the amino acids when a peptide bond is formed are referred to as what?

amino acid residues

What are the building blocks of proteins?

amino acids (20 different kinds)

what are essential amino acids and how many amino acids are essential?

amino acids that the body cannot synthesize itself, must be obtained through diet, there are 9

what is the R group of polar basic amino acids made up of?

ammonium group, +NH3

what is the range of pI values for polar acidic amino acids?

around 3.0

in fisher projections of amino acids, where do you draw the R group?

at the bottom.

what types of interactions occur in tertiary protein structures?

attractions and repulsions of amino acid residues within chain

what makes up the backbone of a peptide?

backbone is the repeating sequences of the ammonium group, the a-carbon, and the carboxylate end. pretty much a complete segment

What happens when an amino acid is placed in a more acidic solution than its pI( isoelectric point)?

becomes positive ion. gaining hydrogen on carboxylate end, now forming carboxylic acid

What is a peptide bond?

bond between amino acids, which forms a peptide

what is a neutrally charged amino acid called and when does it occur?

called a zwitterion, occurs at the isoelectric point, which is its specific optimal pH for that amino acid.

how do the interactions of tertiary protein structures affect the overall protein?

causes it to bend and twist, giving its three dimensional shape

complete vs incomplete proteins.

complete proteins have all essential amino acids, meat, eggs, fish, milk, poultry incomplete has a deficiency of one or more essential amino acids, rice, beans, corn, nuts

List peptide names by number of amino acids in peptide.

dipeptide 2 tripeptide 3 tetrapeptide 4 pentapeptide 5 polypeptide 6+

list the basic amino acids

histidine, lysine, arginine

Which attractive force holds secondary structures together in proteins?

hydrogen bonding

19.30 In an a helix, how does bonding occur between the amino acids in the polypeptide chain?

hydrogen bonding occurs between hydrogen of Nitrogen atom of backbone and oxygen of backbone of carbonyl 4 amino acids away

In what form do most biologically active proteins exist.

in quaternary structures, although many do exist active in tertiary.

where are fibrous proteins typically found?

in structural components of cells and tissues.

What is a protein?

large polypeptide consisting of 50 or more amino acids.

How are most of the amino acids that predominate both alpha helix and b-pleated sheet different?

larger amino acids like histidine, leucine, and methionine make up the a-helix smaller amino acids glycine, valine, alanine, and serine tend to make up b-pleated sheets

what is the importance of collagen in the body?

most abundant protein, very rigid, makes up 30% in our body structural component of eyes, cartilage, tendons, skin, cornea of eye, blood vessels and connective tissue

Would hydrophilic amino acids be found on the outside or inside of the myoglobin structure?

on the outside. interactions with H2O cause it to be pulled off center.

19.25 What type of bonding occurs in the primary structure of a protein?

peptide bonding

19.29 What happens to the primary structure of a protein when a protein forms a secondary structure?

primary structure remains unchanged and intact as hydrogen bonds form between carbonyl oxygen atoms and amino hydrogen atoms in the secondary structure.

What is the difference between a tertiary structure and a quaternary structure?

quaternary structure is made up of 2 or more subunits whereas tertiary is only one.

sections of polypeptide with no definite secondary structure are called

random coils

what kinds of interactions take place for quaternary protein structures?

same as for tertiary

what does the isoelectric point refer to?

specific optimal pH for amino acid

what are the different classes of proteins and their function?

structural - provides structural components contractile - makes muscles move transport - carries essential substances throughout body storage - store nutrients hormone - regulate body metabolism and nervous system enzyme - catalyze biochemical reactions in the cells protection - recognize and destroy foreign substances

What are fibrous proteins?

structural proteins, long, thin and fiber-like shape.

give a specific example of the functions of each class of proteins in our body

structural- collagen in tendons and cartilage contractile - actin and myosin moves muscles transport - hemoglobin transports oxygen, lipoproteins transport lipids storage - ferritin stores iron in spleen and liver hormone - insulin regulates blood glucose levels enzyme - trypsin catalyzes hydrolysis of proteins protection - immunoglobulins are proteins that stimulate immune responses

What does the secondary structure of a protein refer to?

structure that forms when amino acids form hydrogen bonds between the atoms in the backbone within a single polypeptide chain or between polypeptide chains

What structural level is represented by the hydrophobic side chains of the amino acid residues at the center of a globular protein?

tertiary structure

The N-terminal amino acid or N-terminus is referred to as

the free ammonium group written on the left

The C-terminal amino acid or C-terminus is referred to as

the free carboxylate ion group on the right

which group of amino acids determines the type of enantiomer it is?

the location of the ammonium group(+NH3) left gives L stereoisomer right side give D stereoisomer

where do the differences of amino acids come from?

their R group

19.26 How can two proteins with exactly the same number and type of amino acids have different primary structures?

they may be arranged in a different order, thus affecting its biologically functional

zwitterions are similar to which organic compound?

to salts, soluble in water and having high melting points

How is the structure of a b-pleated sheet different from that of a triple helix?

triple helix is a result of three helices woven like a braid, b-pleated are not woven tightly together, but rather are zig zags.