Cell Unit 2 - Protein Structure

Front 1

Protein definition: a series of _____ linked by _____ bonds (aka _____ bonds)

Back 1

Amino acids

Covalent/peptide bonds

Formed by dehydration (bond formed btw COO and NH3; O from COOand H2 from NH3 leaves); There will be a free amino end and free carboxyl end on ends of polypeptide chain

Front 2

The _________ of a protein determines its form an function

Back 2

Linear sequence

Front 3

List the four structures of protein categorization

Back 3

Primary

Secondary

Tertiary

Quaternary

Front 4

Define the primary structure

Back 4

Linear sequence of amino acids

Can be determined using experimental techniques

Front 5

The peptide bond is a special type of _____ bond that can be broken with _______

Back 5

Covalent

Strong acid or base @ high temperature

Front 6

List the 3 characteristics of a peptide bond

Back 6

1. Lack of rotation around the N-C=O bond (acts like a double bond). There is rotation around the C--alpha bonds (carbon next to the carbon in the peptide bond)

2. Trans configuration (due to bulky R groups)

3. Uncharged but polar (peptide bonds neither accept nor accept protons @ pH 2-12; H-bond involved)

Front 7

Formation of a peptide bond involves a ____ reaction

Back 7

Dehydration

Front 8

Read peptides from free_____ group on the left to the free ____ group on the right

Back 8

Amino

Carboxyl

Front 9

How would you read a peptide composed of:

Valine-glycine-leucine

Back 9

valyl-glycyl-leucine

Front 10

What are the 3 steps of determining the amino acid composition of a polypeptide?

Back 10

1. Acid hydrolysis (strong acid, 110C, 24 H)

2. Cation exchange chromatography (neg AA bind to positive column; wash out with incr ionic/pH solutions)

3. Quantitative analysis (heat separated AA with ninhydrin; spectroscopically measure the resulting purple color) - to get CONCENTRATION of each type of AA for relative composition

Front 11

Edman's reagent:

1. What is the chemical

2. What does it cleave

3. What is it for

3. Limitations?

Back 11

1. Phenylisothiocyanate

2. N-terminus amino acid

3. Sequencing polypeptide from N-terminus

4. Only for polypeptides with 100 or less AA; otherwise inaccurate

Front 12

Name and describe two-step process of sequencing polypeptides via fragmentation (AAs over 100)

Back 12

1. Enzymatic - Trypsin: digestive pancreatic anzyme; cleaves carbonyl end of lysine and arginine

2. Chemical - Cyanogen bromide: cleaves at carbonyl end of Methionine (Met)

<<Chocolate Baked Mousse>>

LAM - lysine arginine methionine

Overlap fragments to sequence

Front 13

How else can you figure out primary structure?

Back 13

DNA Sequencing - look at nucleotides

-3 nucleotides = a codon;

-Each codon will correspond to an amino acid

Front 14

Define multimeric proteins

Back 14

Protein with more than one polypeptide

Front 15

How do you separate multimeric proteins into individual polypeptides?

Back 15

Denaturing agents

Front 16

Denaturing agents disrupt ______ bonds; 3 examples are _____

Back 16

Non-covalent

1. Urea

2. Guanidine HCl

3. Performic acid (breaks S-S bonds)

Front 17

Define and list structures (3) of secondary structures of proteins

Back 17

Regular, 3D arrangements found within a protein as adjacent amino acids interaction.

1. Alpha helices

2. Beta sheets

3. Beta bends

Front 18

a-Helix is a ____ structure with its R groups extending (in/out)wards.

There are ____ amino acids per turn

Back 18

Spiral

Outwards

3.6

Front 19

Compare and contrast KERATIN v. HEOMGLOBIN

Back 19

Keratin (100% a-helix, rigid bc S-S bonds)

Hemoglobin (80% a-helix, globular and flexible)

Front 20

a-Helix hydrogen bonds:

1. What do they connect?

2. Are they weak or strong?

Back 20

1. Carbonly of one AA + NH of another AA 4 residues ahead.

2. Weak individually, but strong collectively (most contributing bond type in secondary structure)

Front 21

List nine AA that disrupt a-helix

Back 21

BULKY OR CHARGED AAs:

Proline (bulky imino group)

Charged amino acids (Glutamate, Histidine, Lysine, Arginine, Aspartate)

Tryptophan (bulky R group)

Valine and Isoleucine (b-Carbon branching)

Partially Gregarious Homer Licked Ancient Archie's Then Vibrant Igloo

Front 22

What is the appearance of b-sheets?

Back 22

Pleated

Front 23

Can beta sheets have more than one polypeptides? What about alpha helices?

Back 23

Yes

No

Front 24

Hydrogen bonding in b-sheets (2)

Back 24

All peptide components engaged in H-bonding

Perpendicular in b-sheets

Front 25

What are the two forms of b-sheets?

Back 25

Antiparallel - H bonds form in opposite directions

Parallel - H bonds form in same direction

Front 26

What is an amyloid protein?

Disease association?

Back 26

Fibrous protein composed of b-sheets

Twisted b-sheet amyloid proteins accumulate to cause Alzheimer's disease (identical to silk fibrils)

Front 27

Beta bends:

1. ______ direction of polypeptide chain

2. What is its shape?

3. Consists of _____ AA, usually ___ and ___

4. What does it usually connect?

Back 27

1. Reverses

2. Compact, globular

3. 4, Proline or Glycine

4. Successive strands of antiparallel b-sheets

Front 28

What are non-repetitive structures?

Back 28

Parts of globular protein that isn't a-heilces or b-sheets

Loops and coils

Not random, but not as regular as a-helices or b-sheets

Front 29

Define and list 4 examples of supersecondary structures

Back 29

Formed by packing the R groups of adjacent secondary structures.

1. B-a-B unit

2. Greek key

3. B-meander

4. B- barrel

Front 30

Tertiary structure:

1. _____ + _____ = _____ (functioning unit of 3D structure)

2. 3D structure determined by_____

Back 30

1. Secondary structures + motifs = domains

2. AA sequence

Front 31

Domains:

1. Fundamental ___ and ___ unit

2. Core of domain composed of ___

3. Each domain is structurally ___

Back 31

1. Functional and structural

2. Supersecondary structures

3. Independent

Front 32

List the 4 stabilizing interactions

Back 32

1. Disulfide bonds (most stabilizing interaction in tertiary structure)

2. Hydrophobic interactions

3. Hydrogen bonding

4. Ionic interactions

Front 33

Disulfide bonds:

1. What does it bond

2. What chemical can (reduce/oxidize)s it?

Back 33

1. Covalently link the -SH groups on cysteine molecules (cysteine residue)

3. B-mercaptl ethanol REDUCES S-S bonds

Front 34

Hydrophobic interactions:

1. What does it involve?

2. Where is it (outside/inside) protein?

Back 34

1. Non-polar R groups

2. Inside if protein in hydrophilic environment; outside if protein in hydrophobic environment.

Front 35

Hydrogen bonding:

1. What does it involve

2. What does it do for the overall protein (other than stabilize)

Back 35

1. -OH or -NH containing R groups + carboxyl/carbonyl groups of other AA

2. Helps solubilize protein in aqueous solutions

Front 36

Ionic interactions:

1. What does it bond

Back 36

1. Neg and pos charged R groups to stabilize protein

Front 37

Chaperons:

1. What does it do

2. What is it also known as

3. How does it do what it does?

Back 37

1. Aid folding of proteins during translation

2. Pcb proteins - polypeptide chain binding proteins

3. Reads signals on polypeptides itself for how to fold it

Front 38

Quaternary structure:

1. Polypeptides subunits are arranged and held together by ______ interactions

2. Do subunits work together or independently?

3. Nomenclature?

Back 38

1. Non-covalent

2. Either or

3. Dimeric, trimeric, or multimeric.

Front 39

Define denaturation & 6 denaturing agents.

Do proteins fold back to native state after denaturation?

Back 39

Unfolding and disorganizing of a protein's structure.

1. Urea

2. Heat

3. Mechanical mixing

4. Strong acids + bases

5. Detergents

6. Heavy metal ions (Pb, Hg)

Rarely

Front 40

Prion molecules contain _____ instead of _____ and cause normal proteins to do the same

Back 40

beta sheets instead of alpha helices

Gave you a "B" instead of an "A"

*Happens exponentially because infected protein dissociates in two and infects 2 more proteins

Front 41

What (4) diseases does the prion protein cause?

Back 41

1. TSEs (transmissible spongiform encephalopathies)

2. Creutzfeldt-Jakob disease

3. Scrapie (sheep)

4. Mad cow disease (bovine spongiform encephalopathy)