Chapter 4

Question 1

Bind to DNA, switch genes on or off

Answer 1

Receptor protiens

Question 2

Covalent bonds from amino group to carboxyl group

Answer 2

Peptide bonds

Question 3

Carboxyl group on one end of polypeptide chain

Answer 3

C- terminus

Question 4

Amino group on one end of polypeptide chain

Answer 4

N- terminus

Question 5

Gives amino acid unique properties. Not involved in peptide bonds

Answer 5

Side chains

Question 6

What forces determines polypeptides folded shape?

Answer 6

Hydrogen bonds, electrostatic attraction, van der waals

Question 7

Conformation

Answer 7

Final folded shape. Minimizes free energy

Question 8

Denaturing

Answer 8

Unfold protein by using solvent to disrupt noncovalent bonds

Question 9

Denaturing

Answer 9

Unfold protein by using solvent to disrupt noncovalent bonds

Question 10

Help finish protein folding. Bind using ATP and hydrolysis.

Answer 10

Chaperone Protein

Question 11

Alpha helix

Answer 11

Twisted protein with stabilizing hydrogen bonds between H-N and C=O groups every 4th amino acid unique

Question 12

Beta Sheet

Answer 12

Anti parallel or parallel flat, rigid structure with hydrogen bonds. Code for many proteins

Question 13

Coiled Coil

Answer 13

2/3 alpha helices wrapped within eachother with many non polar (hydrophobic) side chains on one side of helix

Question 14

Clumped, misfolded proteins form long, stable fibers which contribute to neurodegenerative diseases

Answer 14

Amyloid Structures

Question 15

Convert properly folded proteins to disease causing conformations

Answer 15

Prions

Question 16

Structures

Answer 16

Primary- amino acid sequence
Secondary- local folding patterns (a helix/b sheet)
Tertiary- fully folded 3-D structure
Quaternary- larger protein with multiple chains and noncovalent bonds

Question 17

Chain segment folds into compact, stable structure. Carries out specific function

Answer 17

Protein Domain

Question 18

Usually short region of large protein between domains. Flex/bend

Answer 18

Unstructured sequences

Question 19

Protein family

Answer 19

Proteins with similar amino acid sequence or 3D structure.

Question 20

Protein region that used noncovalent bonds to interact with other molecules

Answer 20

Binding site

Question 21

Subunit

Answer 21

Each individual chain that composes a larger protein.

Question 22

2 identical folded chains form symmetric complex, 2 subunits

Answer 22

Dimer

Question 23

Join 2 amino acids or separate chains within a protein. Stabilize extracellular proteins

Answer 23

Covalent cross linkage

Question 24

Disulfide bonds

Answer 24

Covalent cross linkage between sulfhydryl groups on cystine side chains

Question 25

4 Protein shapes

Answer 25

Filament Sheets Microtubules Spheres

Question 26

Globular

Answer 26

Chain folded into compact rounded shape

Question 27

Fibrous

Answer 27

Elingated, rod, cylinder 3D structure Quaternary

Question 28

Anything bound to a protein

Answer 28

Ligand

Question 29

Antibodies

Answer 29

Immunoglobulin protein binds to foreign material. Y- shaped with 2 identical antigen binding sites.

Question 30

What are antibodies comprised of

Answer 30

B lymphocytes which can come from lab animals.

Question 31

Antibodies target is a

Answer 31

Antigen

Question 32

Enzyme

Answer 32

Catalyzes chemical reaction, chemically alter ligands

Question 33

Molecule enzyme acts in to catalyze/function

Answer 33

Substrate

Question 34

Vmax

Answer 34

Max number of substrate molecules an enzyme can convert per sec

Question 35

Michaelis constant

Answer 35

Enzyme concentration for half of V max. Measures how tightly substrate is bound via noncovalent interactions. high=weak, low=strong

Question 36

Antibiotic enzyme that catalyses hydrolysis and minimizes G free energy

Answer 36

Lysozyme

Question 37

Transient structure formed during chemical reaction. Neither substrate nor product. Highest free energy

Answer 37

Transition state

Question 38

Small molecule bound to enzyme to assist catalyzing

Answer 38

Coenzyme

Question 39

Prevents enzyme from acting, suppresses

Answer 39

Negative regulation

Question 40

Stimulates enzyme activity

Answer 40

Positive regulation

Question 41

Allosteric

Answer 41

Protein with multiple conformations depending on ligand bound to alternate site (not catalytic)

Question 42

Phosphorylation

Answer 42

Covalent addition of phosphate group to side chain.

Question 43

Kinase

Answer 43

Catalyzes addition of phosphate group by transferring it’s terminal phosphate to hydroxyl group on side chain.

Question 44

Phosphatase

Answer 44

Enzyme catalyzes removal of phosphate group.

Question 45

Acetylation

Answer 45

Additional if acetyl group to side chain. Covalent modification

Question 46

GTP binding protein

Answer 46

Signaling protein controlled by GTP or GDP. Controlled by phosphate group. GTP- active, GDP- inactive

Question 47

Protein uses energy from hydrolysis to propel itself. Powers intracellular forces

Answer 47

Motor protein

Question 48

Protein machine

Answer 48

Multiple proteins operating together to perform a complex activity

Question 49

Scaffold protein

Answer 49

Has binding sites for other macromolecules and positions them for max efficiency

Question 50

Chromatography

Answer 50

Separates based off size, charge, or ability to bind to specific chemical groups. Can isolate target protein

Question 51

Electrophoresis

Answer 51

Separates by charge/size. Can isolate target protein

Question 52

Mass spectrometry

Answer 52

Process determines exact mass of each molecule in mixture. Results reflect primary structure

Question 53

X-ray crystallography

Answer 53

Uses X-rays passing through crystalline array of protein to determine 3D structure. Gold standard.

Question 54

Nuclear Magnetic Resonance

Answer 54

Determines 3D shape and structure Used for smaller proteins

Question 55

Cryoelectron Microscopy

Answer 55

Used to determine 3D structure Liquid ethane to freeze macromolecule Used for larger proteins (integral membrane)

Question 56

Calculate number of possible amino acid sequences

Answer 56

20^x X= number of amino acids in chain

Question 57

More stable protein has more or less free energy

Answer 57

Less

Question 58

Antibody with 4 polypeptide chains would have how many bands

Answer 58

2