Steele 2

Question 1

Common protein properties:

Answer 1

Size
Shape
Charge
Location in the cell

Question 2

Protein Size Characteristics

100 amino acids has MW of?

Answer 2

Protein Size is variable
Typical weight is 20,000-40,000 daltons
Average AA size is 100 daltons
…has MW of 10,000

Question 3

Shapes of proteins

Answer 3

Globular proteins: most dominant

Structural proteins: elongated/fibrous (collagen, elastin, keratin)

Question 4

Human genome encodes approximately _____ proteins

Answer 4

20,000 proteins

Question 5

Charge of proteins can come from

Answer 5

End chains (negative NH4) (positive COOH), negate
Side chains of charged AA
Covalent modifications (phosphorylation, transitory)
Metal ions

Question 6

Zwitterion and example

Answer 6

Molecule that carries two distinct ionizable groups (amino and carboxyl groups)

pH 7 +H3N and -COO net charge 0. Once move to higher/lower pH, it gets deprotonated/protonated so net charge changes and concentration of that goes down.

Question 7

pKa

so if pka of arginine in physiologic pH 7, what form will it take?

Answer 7

pH of solution in which one of the amino acid side chains finds itself balance between the acid/base form

positively charged form because it moves from basic (higher than 7) towards more acidic reaction, 7.

Question 8

Buffering is

Implications?

Answer 8

a molecule that resists changes in pH of a solution at 1 pH unit above and below the pKa for the molecule.

Bad to have dramatic changes in biological solution

Question 9

Buffers tend to stay near what range?

What molecule is not a good buffer? Why? What comes close

Answer 9

pKa range

Proteins sucky buffers because pka are not useful for physiological buffering. Histidine and alpha amino acid groups may be good, but occur too sparsely

Question 10

How is charge distributed in a protein?

Answer 10

Based on environment. Hydrophobic amino acids will be on interior and charged amino acids on surface of protein.

Question 11

Types of Membrane Proteins

Answer 11

Peripheral:associates with surface membrane (no actual touch/penetration
Integral / transmembrane: Actual penetration, can be anchored by lipid anchor

Question 12

Transmembrane proteins

Answer 12

Single and multiple pass
External domain: glycosylation and disulfide bonds
Transmembrane segment: hydrophobic alpha helices
Internal domain: reduced sulfhydryl groups, phosphorylation (transient), no complex carbohydrate on the internal part

Question 13

SH bonds reduced where
Oxidized where
Reduced =
Oxidized =

Answer 13

Reduced at cytoplasmic side
Oxidized at extracellular
Reduced = sulfhydryl
Oxidized = disulfide bonds

Question 14

Types of protein glycosylation:

Answer 14

N-linked: sugar linked to side chain N of asparagine

O-linked:sugar linked to OH group of threonine and serine

Question 15

Elastase

Answer 15

secreted glycoprotein

Question 16

Protein localization must be…

How can problem arise?

Answer 16

synthesized, modified, and localized properly inside or outside of the cell

Perfectly functional, but improperly localized

Question 17

Leri-Weill dyschondrosteosis

Answer 17

SHOX TF mutation. TF stays in cytoplasm instead of nucleus.

Question 18

Nuclear localization signals are mostly

Answer 18

Basic amino acids

Question 19

Protein isolation based on protein

Answer 19

Size
Charge
Hydrophobicity
Binding to molecules

Question 20

Protein isolation methods and based on what property and description!

Answer 20

Ion-exchange chromatography (based on charge)
positively charged protein binds to negatively charged bead. Negatively charged protein flows through

Gel filtration chromatography (based on size)
Sized beads to separate

Absorption chromatography (based on hydrophobicity)

Affinity chromatography (based on interaction with other molecules)
Link to something in matrix. Everything else goes except that.

Question 21

Protein sequence comparisons

Answer 21

Protein of same function in different species have related sequences

Proteins of similar function often have similar sequences

Tertiary structure may be even more conserved than primary sequence

Proteins of similar function but little structural similarity may have been formed by convergent evolution

Question 22

“in silico”

Answer 22

Protein studies / analysis focusing on primary structure of proteins

Question 23

Examples of similar traits

Answer 23

Hemoglobin and myoglobin (identical AA and similar AA)

Globin in human, muscle, and plants have similar / same structure = same ancestor
** 3 distinct proteins have their origins in a single gene that underwent duplication **

Question 24

Ortholog vs Paralog with examples

Answer 24

Ortholog: Protein with similar structure and same function between two different species (human vs bovine ribonuclease)
Paralog: Protein with similar structure but different function between same species (ribonuclease vs angiogenin)

Question 25

Hemoglobin structure is

Answer 25

a tetramer composed of two alpha chains and two beta chains

Question 26

Describe sickle cell anemia Implication:

Answer 26

Single point mutation Glutamic acid at position 6 in the beta chain is changed to a valine (now called HbS instead of HbA in normal adults). Charge changed from negative to hydrophobic causes valine to aggregate near other valine (surface). Stick together and hide and form fibers. Long fibers creates sickle shape (normal is solid). If accumulate enough can lysis and fibers release. Some changes in amino acid can cause zero to deleterious effects

Question 27

Electrophoresis

Answer 27

used to analyze proteins. Can be used to separate proteins based on size, charge, or both Polyacrylamide gel, migrate based on size. Apply electric field. Bigger ones move less quickly than smaller ones.

Question 28

Hemoglobin banding

Answer 28

Normal has one big band Sickle has one Sickle can also have 2, one normal and one sickle Neonates have two

Question 29

Allozymes

Answer 29

Forms of a protein encoded by different alleles of a gene (maternal and paternal alleles)

Question 30

Isozyme

Answer 30

Forms of a protein encoded by different genes but catalyzes the same reaction. 5 copies of one enzyme X, but do it differently

Question 31

Creatine Kinase Clinical significance?

Answer 31

``` Isozymes Quaternary structure 2 subunits CK1 isozyme BB CK2 isozyme MB (heart) CK3 isozyme MM (skeletal) ``` Heart attack leads to increased levels of (CK2) from undetectable levels to detectable levels in bloodstream

Question 32

Cardiac troponin Clinical significance?

Answer 32

Marker for heart attack. It has greater specificity and remains elevated longer following infarction.