Foundations week 1: Proteins

3. Tertiary structures continued... 1. Polypeptides having more than ____ amino acids generally consists of ___ or more domains (more complex requires more domains to help the 3 dimensional structure perform. 2. Amino acids with non-polar side chains (R groups) tend to be located in the _______ of the polypeptide molecule. Why is this? -what is an example of a non-polar amino acid being located on the exterior portion but still interacting with the hydrophobic (internal) non-polar groups? 3. Amino acids with polar side chains (R groups) tend to be located where? Interacting with? 4. ane example,e of a tertiary structure is _____?

1. 200, 2 2. interior where they can hide from water (fats, non-polar groups hate water and water (polar) hates fats). This is where the non-polar groups can interact with each other. -an example is when the non-polar amino acids are located on the exterior surface of the integral protein (spans the cell membrane). This occurs because since the integral protein spans the membrane it has both 1. hydrophilic portions and 2. hydrophobic portions. The amino acids are located on the exterior surface of the integral protein but ONLY within the phospholipid bilayer (not on the EXF). 3. on the exterior surface interacting with water (polar) charged. 4. myoglobin

2. Secondary structure of proteins: -the 2 major secondary structures are? 1. 2. In addition, loops and bends (turns) also form a part of secondary structures (a-helix). Which amino acid/imino acid disrupts the conformation (physical shape) of the α- helix by producing bends within the secondary structure where bends are not suppose to be. A. alanine B. cysteine C. Proline And why? doesn't this amino/imino acid help? Amino acids that do not favor alpha helix of proteins: 1. and why? 2. and why? 3. and why? 2 of these amini/imino aids produce bends which 2 do? 1. 2.

1. a helix 2. B-pleated sheet C. Proline, because the amide N bond (N-H) of proline doesn't contain a Hydrogen H+ ion which is what forms the backbone of the A-helix. and without this hydrogen bond the secondary structure of the a-helix cannot be stabilized as this occurs through hydrogen bonds. 1. Proline (lack of peptide N hydrogen ion that forms bends) 2. glycine (too small) because of its small size, also often induces bends in α -helices 3. charged side chains (Presence of large number of charged R groups or large number of bulky R groups are not favorable for α -helix)

4. Quaternary structure: 1. Quaternary structure refers to the ability of _____ or more polypeptide chains coming together to form a functional ____?

2 or more, proteins

52. Alzheimer disease is characterized by loss of memory and alterations in the mood and behavior. Which one of the following best explains the disease? A. It is caused by the accumulation of amyloid β protein aggregates in the brain B. It is an environmentally produced disease C. It is caused by the alteration in the sequence of amino acids in the polypeptide D. The disease is due to the accumulation of denatured protein in the brain E. The disease is caused by the high exposure to ultraviolet radiation which damages to the brain cells

A

57. Determination of the primary protein structure is accomplished by which of the following techniques? A. Edman's degradation B. Gel filtration C. Paper chromatography D. Polymerase chain reaction E. Mass spectroscopy

A

58. Alzheimer disease is characterized by loss of memory and alterations in the mood and behavior. Which one of the following best explains the disease? A. It is caused by the accumulation of amyloid β protein aggregates in the brain B. It is an environmentally produced disease C. It is caused by the alteration in the sequence of amino acids in the polypeptide D. The disease is due to the accumulation of denatured protein in the brain E. The disease is caused by the high exposure to ultraviolet radiation which damages to the brain cells

A

4. Quaternary structure: an example of a quaternary structure protein is? A. hemoglobin B. myoglobin

A. Hemoglobin (that lies within the polypeptide molecule (protein)

4. Quaternary structure: Denaturation of proteins: 1. all proteins are active within their native ____________ (normal joining of their atoms), its when you lose their nativeness that they then go through ____________? A. denaturation, confirmation B. confirmation, denaturation 2. of the 4 structures that form a protein which of them is destroyed during denaturation and which are saved? A. secondary--> quart but NOT primary B. primary---? tertiary but NOT quart C. tertiary and quart but not primary and secondary Is denaturation mostly reversible or irreversible?

A. confirmation, denaturation (HIGH fever over 105. I 8 degrees Fahrenheit. Hence why you get sweaty when you have a fever as water carriers the polar heat out of the body via perspiration) A. secondary--> quart but NOT primary Irreversible and hence why high fevers are so deadly.

3. Tertiary structures continued... i. Hydrophobic interactions: Hydrophobic Interactions take place between __________ amino acid side chains? A. non-polar B polar ii. Hydrogen bonds: Amino acids containing oxygen-bound hydrogen (OH amino acids), such as in ________ and ____________ can form __________bonds with oxygen of either carboxyl group (COOH) or carbonyl group (C=O) of a peptide bond iii. Ionic interactions: ________ charged groups, such as carboxyl (carboxylate) (COO-) in the side chain of aspartate or glutamate can interact with__________ charged groups such as amino (-NH3+) in the side chain of lysine which form what bonds? A. ionic B. hydrogen

A. nonpolar (like dissolves like) "shoot the tiger OHOUCCCH" OH serine and threonine, Hydrogen bonds negativley, positivley A. ionic

If the two peptide segments are placed in the same direction ( N-terminal to C-terminal), then they are said to be arranged _______ to each other. A. parallel B. anti-parallel If the peptide segments run in opposite directions the b-pleated sheet pattern is? A. antiparallel B. parallel Alternating R-groups project _______ & ______ the plane of the sheet. A. up and down B. across and through

A. parallel A. anti-parallel A. above & below

3. Tertiary structure of proteins: 1. Tertiary structure refers to the ____- dimensional shape of a polypeptide chain (which is beginning to fold into a protein) in which a-helixes an b-pleated sheets interact. A. 2 B. 3 C. 4 2. the term __________ refers to the spatial relationship that every atom within a molecule may take the form of forming the protein. A. cyclical B. arrangement C. confirmation 3. _____ structure determines the tertiary structure as well as the secondary structure. A. primary B. tertiary 4. the 3 dimensional tertiary beginning of folding of proteins also generates _______ (areas owned) within the proteins. A. proteins B. side groups C. domains

B. 3 dimensional C. confirmation A. Primary (have to begin with the primary structure of a protein first and if you don't you get mistakes like sickle cell anemia. C. Domains

Loops & Bends: B-pleated sheet In a typical Protein a sizeable portion of the secondary structures exists as α - helices and β - sheets. On the other hand the remaining portion of the secondary structures form _____, ____, or ______. Turns or bends refer to short sequences of amino acids that join the two units of secondary structure, such as two adjacent strands of β - pleated sheets A. twists, kinks, or bends B. loops, turns or bends A turn involves ______ amino acid residues, in which the first residue is hydrogen-bonded to the ________. a. 1, 1st b. 2, 2nd. c. 3, 3rd d. 4, 4th What 2 amino acids are found in high amounts within these turns and bends but NOT within the a-helix structure that makes up most of the secondary structure of a protein. 1. 2.

B. loops, turns or bends D. 4, 4th.

4. Quaternary structure: In the quaternary structure of a protein each of the polypeptide chains represents a _______(subunit) of the protein and when 2 or more monomers come together they form a single functional protein called a ___________. A. oligomer, monomer B. monomer, oligomer What 3 bonds stabilize the 1. 2. 3. What bond is present in the teritary structure of proteins but not the quarternary?

B. monomer, oligomer (just like a oligosaachride in a polymer of glucose subunits that form disaccharides and then 2 or more are oligosaccharides. 1. H-bonds 2. hydrophobic bonds 3. electrostatic (don't want to move the 4th structure of proteins and keep it stable. Ionic bonds

Domains are the _____ dimensional structural units and functional units of __________.(proteins) found within the tertiary structure. A. 2 dimensional, proteins B. 3 dimensional, proteins

B. tertiary

54. Select the correct statement regarding stabilization of tertiary structure in proteins A. Ionic bonds in the proteins enhances the solubility of the protein B. Methionine, a sulphur containing amino acid is responsible for the covalent bonding in the side chains C. Lysine and aspartate contribute for the ionic interactions in the protein molecule D. There dimensional stabilty of the structure mainly due to the presence of hydrogen bonds A. Hydrogen bonds can be formed between glutamate and aspartate

C

1. Primary structure of Protein: An example of an alteration in the primary sequence of amino acids that forms the protein hemoglobin occurs on which carbon atom of which chain? causing which disease? A. 5th carbon, A chain, B. 4 carbon, B chain C. 6th carbon, beta chain D. 6th carbon, alpha chain

C. 6th carbon, beta chain sickle cell anemia HbS

2. secondary structure of proteins: The peptide Nitrogen (N-H) and peptide carbonyl (C=O) that form the the backbone of the A-helix is made from _______ hydrogen bonds? A. extrachain B. ionic chains C. Intrachain

C. Intrachain

2. Secondary structure of proteins: 1. | Alpha helix (a-helix) | -In a A-Helix the polypeptide chain is coiled around a central axis forming a _____ handed helix. just like DNA. A. left B. inverse C. Right -a-carbon, peptide amide (N-H) terminal, and peptide carbonyl (C=O) C terminal form the ____________ of the right handed helix via ________ bonding. A. backbone, ionic bonding B. front side, hydrogen bonding C. Backbone, hydrogen bonding -the side chains (R) of amino acids located on the R handed helix of the secondary (a-helix) structure radially extend ______? A. (R), inwards (internally) B. (R), outwards (Externally) The a-helix that is apart of the secondary structure of proteins is stabilized by what ___________ bonds? A. ionic B. hydrogen C. covalent

C. Right C. backbone, hydrogen bonding B. side (R) chains, outwards B hydrogen (making it polar)

2. β - Pleated Sheets: The second (hence "beta") recognizable secondary structure in a proteins is not the A-helix but the? A. a-hleix B a-pleated sheet C. b-pleated sheet The amino acid residues of a β- sheet, when viewed , form a _____ or _____ pattern. A. zizag or crossed B. zizag or inverted C. Zizag or pleated Unlike the compact (short, narrow) peptide bonded backbone of the α - helix which is hydrogen bonded, the peptide backbone of the β sheet is highly __________ between 2 sheets. A. flexed, B. compact C. extended -But like the α - helix, β sheets also derive much of their stability from __________ bonds between the carbonyl C=O oxygen and amide ________ of peptide bonds. A. ionic, oxygen B. hydrogen, Nitrogen However, in contrast to the α - helix, these b-pleated sheet hydrogen bonds are formed with ___________ peptide segments between the sheet. A. opposite B. different C. adjacent

C. b-pleated C. Zizag or pleated C. extended (between two sheets) B. Hydrogen, Nitrogen (N-H) plus the C=O carbonyl bonded Oxygen C. Adjacent

53. Select the CORRECT statement regarding protein structure: A. The α-helix can be composed of more than one polypeptide chain B. Secondary structure determines the amino acid sequence in the peptide chain C. Domains are a type of secondary structure D. α-helix is rich in fibrous proteins E. β sheet is stable during the heat treatment

D

55. Which of the following features correctly describes the nature of the peptide bond in polypeptides? A. They release protons in the pH range of 2-12 B. Mainly single bond character C. Occurs between two amino groups D. The peptide bond generally assumes the trans configuration E. C=O and -NH groups of the peptide bonds are nonpolar in nature

D

56. Select the correct statement regarding the characteristics of peptide bond A. Occurs mostly in the cis configuration B. Has double bond in between carbon and nitrogen atoms C. The bond is unstable in the presence of weak acids D. The bond is rigid and planar E. The conventional reading of amino acid sequences in the C-terminal to N- terminal end.

D

Proteins that are made up of two or more (even 4) polypeptide chains are considered what kind of protein structure? A. primary B. secondary C. teritary D. Quart

D. quaternary structure

51. Prion diseases are mainly caused by the changes of structural organisation of proteins. The main structure which is predominant in the infectious prion protein is A. β- Bends B. Tertiary structure C. α-Helix D. Zinc fingure motifs E. β- Sheets

E

3. Tertiary structures are made up of what 3 types of bonds? i. ii. iii. and

I. hydrogen bonds ii. hydrophobic bonds (non-polar) aka lots of CH bonds. iii. ionic bonds (between NH3+ and COO-

1. Primary structure of Protein: -refers to the ________ sequence and total _________ of AA. -is it true that the primary structure is unique to each protein. -the primary structure is decide for by the _____ that uses a codon to code for the specific protein. A. gene B. proton C. chromosome -in a protein/ polypeptide chain that makes up a protein at each end of the polypeptide chain there are 2 free a-(alpha) ends. What are those ends and what names of them? 1. 2.

Linear, # yes , true A. gene 1. a-amiNo group NH3+ N terminal 2. a-Carboxyl group COO- C terminal

1. Primary structure of Protein: When numbering the sequence of amino acids that are linked together by peptide bonds that make up chains of peptide bonds called polypeptides that forms proteins, which terminal to you start with? A. C or B. N terminal which protein contains 153 amino acids? which chain of hemoglobin contains 141 AA and which contains 146 AAs? A. b-hemoglobin chain B. a-hemoglobin chain C. myoglobin Alteration in the primary (linear sequence) of a protein's structure may result in a derangement of its ______ activity? A. life B. biological C. hereditary

N to C 153 AA= myoglobin 141 AA=a-chain hemoglobin B. biological activity

Protein's 4 structures; 1. Primary 2. secondary 3. tertiary 4. quaternary Before continuing off of the top of your head what are the key pieces of these 4 structures.

The linear sequence begins, then begins folding into a and b pleated sheets, to from the 3 dimensional shape of proteins that can now form associations between two or more polypeptide chains to form a PROTEIN. 1. linear sequence of amino acids 2. A helix B related sheets (Alzheimers) 3. 3 dimensional shape. 4. proteins

2. Secondary structure of proteins: -the 2 major secondary structures are? 1. A-hleix 2. ????

a helix b-pleated sheet

2. Secondary structure of proteins: What are 3 examples of proteins rich within the A-helical structure of secondary proteins? 1. 2. 3. and

a-keratin myoglobin (protein) hemoglobin (protein)

A peptide bond is formed when an amino group of one amino acid reacts with a ______ group of another amino acid by a _______ amide linkage. -what is an amide again?

carboxyl group (OH) + H+ from the Amino group covalent amide linkage amide is a derivative of a carboxyl group that replaces the carboxyl group with an amine or ammonia. (NH)

3. Tertiary structures continued... What bonds stabilize the tertiary structure? 1. covalent______ bonds and ______ covalent _________ bonds between the sulfhydryl groups (S-S), which consists of which two amino acids? forming?but which amino acid for the tertiary structure only?

covalent covalent Disulfide bonds: Covalent linkage formed from the sulfhydryl group (-SH) of each of two cysteine residues to form a Cystine residue. A disulfide bond contributes to the stability of the three-dimensional shape of the protein molecule and prevents it from denaturation in ECF compartment (water soluble and cystine is highly insoluble so it needs this)

2. Secondary structure of proteins: - the 2nd structure of proteins refers to the ______________ segments of protein into geometrically ordered units. A. folding of short B. folding of long C. non-folding -The ______ structure determines the secondary structure. A. secondary B. tertiary C. quaternary -the secondary structure of proteins is maintained by ______ bonding. A. ionic B. covalent C. hydrogen

folding of short A. Primary C. hydrogen

General aspects of Proteins: -Proteins act as the major ________ buffer. what is the other buffer? -AA build proteins -20 different amino acids are linked together to form. _______ bonds. What pieces of the amino acid come together to form the peptide bonds? and what kind of reaction occurs during the process?

intracellular , bicarbonato extracellularly peptide carboxyl group (OH) and amino group (H) to give off water forming a dehydration reaction.

On denaturation: - Except _________ structure, other levels of protein structures are destroyed - __________ activity is lost - ____________ is increased - Proteins become ________ soluble

primary biological viscosity (thickness from them being stretched out for their protein structure formation. less