Chapter 4: Protein Structure and Function Flashcards
(85 cards)
1
Q
______ are the main building blocks from which cells are assembles, and they constitute most of the cell’s dry mass.
A
Proteins
2
Q
What are the functions of enzymes?
A
Catalyze covalent bond breakage or formation
3
Q
What does alcohol dehydrogenase do?
A
Makes the alcohol in wine
4
Q
What is the function of pepsin?
A
To degrade dietary proteins in the stomach
5
Q
What is the enzyme that helps convert carbon dioxide into sugars in plants?
A
Ribulose bisphosphate Carboxylase
6
Q
What does protein kinase do?
A
Adds a phosphate group to a protein molecule
7
Q
What is the function of structural proteins?
A
To provide mechanical support to cells and tissues
8
Q
What are some examples of structural proteins?
A
- collagen and elastin
- tubulin
- actin
- keratin
9
Q
What is the function of transport proteins?
A
To carry small molecules or ions
10
Q
What are the names of the motor proteins?
A
Myosin
Kinesin
Dynein
11
Q
Name the motor protein in skeletal muscle cells provides the motive force for humans to move
A
Myosin
12
Q
Name the motor protein that interacts with microtubules to move organelles around the cell
A
Kinesin
13
Q
What does Dynein do?
A
enables eukaryotic cilia and flagella to beat
14
Q
How is iron stored in the liver?
A
By binding to the small protein ferritin
15
Q
What are some examples of signal proteins?
A
insulin, it controls glucose levels in the blood.
netrin, attracts axons to specific locations.
16
Q
Name the function of receptor proteins
A
Detect signals and transmit them to the cell’s response machinery
17
Q
What does rhodopsin do?
A
detects light in the retina
18
Q
What are transcription regulators?
A
They are proteins that function by binding to DNA to switch genes on or off
19
Q
What is an example of a transcription regulator in bacteria
A
The Lac repressor in bacteria silences the genes for the enzymes that degrade the sugar lactose
20
Q
What are a few examples of special purpose proteins?
A
- antifreeze proteins found in the arctic and antarctic fishes to protect their blood against freezing
- monellin, a protein found in an african plant, has an intensely sweet taste
21
Q
What are the most structurally complex and functionally sophisticated molecules known?
A
PROTEINS
22
Q
T/F the shape of a protein is specified by its amino acid sequence
A
True
23
Q
Amino acids are linked together by _______ bonds.
A
peptide
24
Q
What is the N-terminus?
A
the amino side of a polypeptide chain
25
What is the C-terminus?
The carboxyl side of the amino acid
26
What is the part of the amino acid that is not involved in forming peptide bonds?
side chains
27
Name the negatively charged amino acids
```
Aspartic acid (Asp)
Glutamic acid (Glu)
```
28
Name the positively charged amino acids
Arginine (Arg)
Lysine (Lys)
Histidine (His)
29
Name the uncharged polar Amino acids
```
Asparagine (Asn)
Glutamine (Gln)
Serine (Ser)
Threonine (Thr)
Tyrosine (Tyr)
```
30
What are the three types of noncovalent bonds that help fold proteins?
- Hydrogen Bonds
- Electrostatic attractions
- Van der Waals attractions
31
What is the fourth weak interaction that determines the shape of proteins?
The hydrophobic force
32
Which side chains tend to cluster in the interior of the folded protein?
The nonpolar (hydrophobic) side chains—which belong to amino acids such as phenylalanine, leucine, valine, and tryptophan
33
Which side chains tend to cluster in the exterior of the folded protein?
polar side chains—such as those belonging to arginine, glutamine, and histidine
34
T/F Proteins form into a conformation of lowest energy
True, Proteins will adopt the structure in which free energy is minimized
35
Define conformation:
The final folded structure adopted by any polypeptide chain.
36
The folding process is _______ _______ as it releases heat and increases the disorder of the universe
Energetically favorable
37
What is it called when the protein that is formed unfolds?
Denaturation
38
What is it called when the denatured protein reforms?
Renaturation
39
Can a protein fold back into its formation after denaturation without help?
Yes
40
Which proteins assist protein folding in the cell?
Chaperone proteins
41
How can single polypeptide chains fold without the risk of forming aggregates in the crowded conditions of the cytoplasm?
Isolation chambers
42
What is the size range of proteins?
30 amino acids - more than 10,000
43
What are the two most common folding patterns?
a helix and b sheet
44
In an a helix a hydrogen bond is made between every ___ amino acid.
fourth
45
what is handedness?
whether a helix is right or left handed (which way it twists
46
what is a coiled coil?
when 2 or 3 a helices will wrap around one another to form a structure
47
T/F B sheets form rigid structures at the core of many proteins
True
48
What are the two types of beta sheets?
paralell
| antiparallel
49
What are the properties of beta sheets?
tensile strength,
| basis of amyloid structures --> stacked together in long rows like the teeth of a zipper
50
T/F misfolded proteins can form amyloid structures that cause prion diseases
True
51
Name the levels of organization of proteins:
1. primary structure
2. secondary structure.
3. tertiary structure
4. quaternary structure
52
What are the serine proteases?
a family of protein-cleaving (proteolytic) enzymes that includes the digestive enzymes chymotrypsin, trypsin, and elastase, as well as several proteases involved in blood clotting. When any two of these enzymes are compared, portions of their amino acid sequences are found to be nearly the same.
53
globular proteins:
proteins in which the polypeptide chain folds up into a compact shape like a ball with an irregular surface
54
enzymes tend to be ____ proteins
globular
55
Fibrous proteins:
- these proteins generally have a relatively simple, elongated three-dimensional structure
- have roles in the cell that require them to span a large distance
56
Define intermediate filaments:
a component of the cytoskeleton that gives cells mechanical strength
57
Fibrous proteins are especially abundant ________ the cell.
outside
58
What is the most abundant fibrous extracellular protein?
Collagen
59
What is the most common covalent cross links in proteins?
Sulfur-sulfur bonds. These disulfide bonds act as an atomic staple to reinforce the proteins most favored conformation.
60
What is a lysozyme?
| How does this enzyme relate to covalent cross links?
an enzyme in tears, saliva, and other secretions that can disrupt bacterial cell walls—retains its antibacterial activity for a long time because it is stabilized by such disulfide cross-links
61
Why don't disulfide bonds generally form in the cell cytosol?
There is a high concentration of reducing agents that convert these bonds back to cysteine-SH groups. Proteins also rarely require these reinforcements in the calm intracellular environment.
62
T/F all proteins bind to other molecules
true
63
Any substance that is bound by a protein is referred to as a _______
ligand
64
T/F the binding of a protein to another molecule is highly selective
true
65
Define antibodies:
immunoglobulin proteins produced by the immune system in response to foreign molecules, especially those on the surface of an invading microorganism.
(y shaped molecules with 2 antigen binding sites)
66
Define antigen:
An antibody recognizes its target molecule
67
B lymphocytes (cells) produce ______
antibodies
68
what is the complex to which molecules bind?
an enzyme-substrate complex
69
What are the 10 enzyme classes?
1. hydrolase
2. nuclease
3. protease
4. ligase
5. isomerase
6. polymerase
7. kinase
8. phosphatase
9. oxido-reductase
10. ATPase
70
```
Name the enzyme class for the following function:
General term for enzymes that catalyze a hydrolytic cleavage reaction
```
hydrolase
71
```
Name the enzyme class for the following function:
Breaks down nucleic acids by hydrolyzing bonds between nucleotides
```
Nuclease
72
```
Name the enzyme class for the following function:
Breaks down proteins by hydrolyzing peptide bonds between amino acids
```
Protease
73
```
Name the enzyme class for the following function:
Joins two molecules together; DNA ligase joins two DNA strands together end-to-end
```
Ligase
74
```
Name the enzyme class for the following function:
Catalyzes the rearrangement of bonds within a single molecule
```
Isomerase
75
```
Name the enzyme class for the following function:
Catalyzes polymerization reactions such as the synthesis of DNA and RNA
```
Polymerase
76
```
Name the enzyme class for the following function:
Catalyzes the addition of phosphate groups to molecules. Protein kinases are an important group of kinases that attach phosphate groups to proteins
```
Kinase
77
```
Name the enzyme class for the following function:
Catalyzes the hydrolytic removal of a phosphate group from a molecule
```
Phosphotase
78
```
Name the enzyme class for the following function:
General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced. Enzymes of this type are often called oxidases, reductases, or dehydrogenases
```
Oxido-reductase
79
```
Name the enzyme class for the following function:
Hydrolyzes ATP. Many proteins have an energy-harnessing ATPase activity as part of their function, including motor proteins such as myosin (discussed in Chapter 17) and membrane transport proteins such as the Na+ pump (discussed in Chapter 12)
```
ATPase
80
where does catalysis take place?
On the proteins active site (binding site on the surface)
81
T/F Allosteric enzymes have two or more binding sites that influences on another
true
82
define allosteric in relation to proteins:
a protein can adopt two or more slightly different conformations, and their activity can be regulated by a shift from on to another
83
Reversible ______ ______
controls the activity of many types of proteins in eukaryotic cells.
84
phosphorylation is catalyzed by a _____ _____
protein kinase
85
dephosphorylation is catalyzed by a _____ ______
protein kinase
