1.3 Proteins

Question 1

α-helix

Answer 1

definition: a prevalent type of protein secondary structure
description: a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O
stabilized by: hydrogen bond between CO and NH groups of the main chain to stabilize.
formed by: formed by hydrogen bonds within protein strands

Question 2

β-pleated sheet

Answer 2

definition: series of anti-parallel chains of covalently-linked amino acids, with adjacent chains linked by hydrogen bonds.
description: The regular folding of each amino acid chain leads to a regular pleated pattern across chains.
stabilized by:
formed by: formed by hydrogen bonds between protein strands

Question 3

•Amino acid

Answer 3

monomeric units that are teh buildingblokcs of protein; that are capable of existing in ionized and unionized forms 
composed of: 
1. amino group 
2. alpha carbon 
3. r-group side chain 
4. hydrogen atom 
5. carboxyl group

Question 4

C-terminus

Answer 4

the end of the peptide chain aka the 5’ end of the chain

Question 5

Chaperones

Answer 5

a protein that assists the folding/assembly of other proteins.

Question 6

Condensation reaction

Answer 6

Monomers polymerize through condensation reactions

Question 7

Denaturation

Answer 7

Definition: structural change in a protein (caused by either pH or temp) that results in the loss (usually permanent) of its biological properties

Because the way a protein folds determines its function, any change or abrogation of the tertiary structure will alter its activity

• —>temp
  1. High levels of thermal energy may disrupt the hydrogen bonds that hold the protein together
  2. As these bonds are broken, the protein will begin to unfold and lose its capacity to function as intended
  3. Temperatures at which proteins denature may vary, but most human proteins function optimally at body temperature (~37ºC)

Question 8

Dimer

Answer 8

a macromolecular complex formed by two protein monomers

Question 9

Disulfide bonds

Answer 9

an S-S bond, or disulfide bridge, is a covalent bond derived from two thiol groups

Question 10

Folding

Answer 10

the process by which a protein structure assumes its functional shape or conformation

Question 11

Hydrolysis

Answer 11

these reactions involve the breaking of polymers into individual monomers by splitting water

Question 12

Macromolecule

Answer 12

a very large molecule, such as a protein

Question 13

Monomer

Answer 13

these subunits polymerize thru condensation reactions

Question 14

Oligopeptide

Answer 14

a short peptide chain used to refer to peptides with less than 20–25 amino acid residues.

Question 15

Peptide bond

Answer 15

The carboxyl group of one amino-acid reacts with the amino group of another to form this type of bond

Question 16

Polymer

Answer 16

3 classes of macromolecules are ____

which are composed of repeating subunits called monomers that are covalently bonded together

Question 17

Polymerization

Answer 17

process in which relatively small molecules, called monomers, combine chemically to produce a very large chainlike or network molecule, called a polymer.

Question 18

Polypeptide

Answer 18

a chain of many amino acids

Question 19

Primary structure•

Answer 19

the unique sequence of amino acids residues in a protein

description: amino acid monomers are joined, forming polypeptide chains
stabilized by: peptide bonds

Question 20

Protein•

Answer 20

are long polymers containing many freely rotating binds which allow for tremendouse confirmational flexibilty
monomer: amino acid
bond type: peptide bond

Question 21

Quaternary structure•

Answer 21

the overall 3d shaped formed from 2 or more polypeptide chains (subunits)
description: 2 or more polypeptides assmeble to form larger protein molecules
stabilized by: h-bonds, ionic interactions, hydrophobic interactions, disulfide brdiges

Question 22

R-group•

Answer 22

a side chain specific to each amino acid that confers particular chemical properties to tha

Question 23

Residue

Answer 23

Any of the monomers comprising a polymer

Question 24

Secondary structure•

Answer 24

the localized fooding of a polypeptide chain into regualr structures (alpha helices and beta-pleated sheets)
description: polypeptide chains may form a-helices or B-pleated sheets
stabilized by: h-bonds between components of the peptide backbone results in secondary structure

Question 25

Side-chain

Answer 25

a chemical group attached to the main chain or backbone of a molecule, such as a protein

Question 26

Tertiary structure•

Answer 26

the overal 3d sturcture of single polypeetide chain, resulting form multiple interactiosn amongst teh amisno acid side chians and the peptide backbone

description: polypeeptide fold, forming specific shapes
stabilized by: h-bonds; disulfide bridges; hydrophobic interaction

Question 27

Tetramer

Answer 27

protein with a quaternary structure of four subunits (tetrameric).

Question 28

trimer

Answer 28

A structure composed of three identical or similar units

Question 29

Sketch the basic structure of an amino acid

Answer 29

Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom.

Question 30

Explain why proteins are essential to cell function by giving examples of their function.

Answer 30

1. Digestive enzyme–> Break down nutrients in food into small pieces that can be readily absorbed
   ex: Amylase, lipase, pepsin
2. Transport–>Carry substances throughout the body in blood or lymph
   ex: Hemoglobin
3. Structure—>Build different structures, like the cytoskeleton
   ex: Actin, tubulin, keratin
4. Hormone signaling—>Build different structures, like the cytoskeleton
   ex: Insulin, glucagon
5. Defense—>Protect the body from foreign pathogens
   ex: Antibodies
6. Contraction—>Carry out muscle contraction
   ex: Myosin
7. Storage–> Provide food for the early development of the embryo or the seedling
   ex: Legume storage proteins, egg white (albumin)

Question 31

•Describe two ways that protein folding can be regulated.

Answer 31

chaperones help proteins fold when they become trapped in an incorrectly folded state.

Question 32

.•Explain how and why proteins are properly folded

Answer 32

chaperones help proteins fold when they are first formed

Question 33

Explain the four levels of protein structure, and give examples of each.

Answer 33

1. Primary
2. Secondary
3. Tertiary
4. Quarentary

Question 34

Explain how amino acid monomers polymerize to form proteins

Answer 34

Monomers polymerize through condensation reactions. Monomers are released from a polymer by hydrolysis reactions.

Question 35

Describe why and how the side chains affect the function and structure of each amino acid.

Answer 35

The gene, or sequence of DNA, ultimately determines the unique sequence of amino acids in each peptide chain. A change in the nucleotide sequence of the gene’s coding region may lead to a different amino acid being added to the growing polypeptide chain, causing a change in protein structure and therefore function.

Question 36

nucleic acid

Answer 36

monomer: nucleotide

bond type: phosphodiester bond

Question 37

complex carbohydrate

Answer 37

monomer: monosaccharide

bond type: glycolic linkage

Question 38

N terminus

Answer 38

the beginning of the peptide chain aka the 3’ end of the chain

Question 39

Why are beta-pleated sheets more stable than alpha-helices?

Answer 39

Unlike the α helix, the ß sheet is formed by hydrogen bonds between protein strands, rather than within a strand. … Antiparallel ß sheets are slightly more stable than parallel ß sheets because the hydrogen bonding pattern is more optimal.

Question 40

how do change in the temperature result in changes in the tertiary structure of proteins?

Answer 40

1. High levels of thermal energy may disrupt the hydrogen bonds that hold the protein together
2. As these bonds are broken, the protein will begin to unfold and lose its capacity to function as intended
3. Temperatures at which proteins denature may vary, but most human proteins function optimally at body temperature (~37ºC)

Question 41

how do changes in the pH result in changes in the tertiary structure of proteins?

Answer 41

1. Amino acids are zwitterions, neutral molecules possessing both negatively (COO–) and positively (NH3+) charged regions
2. Changing the pH will alter the charge of the protein, which in turn will alter protein solubility and overall shape
3. All proteins have an optimal pH which is dependent on the environment in which it functions (e.g. stomach proteins require an acidic environment to operate, whereas blood proteins function best at a neutral pH)