Biologically Important Molecules Flashcards
(113 cards)
1
Q
Function of proteins as a biological macromolecule
A
enzymes, hormones, receptors, channels, transporters, antibodies, and support structures inside and outside cells
2
Q
Composition and sequence of proteins
A
20 different amino acids linked together in polymers
◦ their sequence is what makes each protein unique
3
Q
Structure of amino acids
A
◦ 𝛼-amino group
◦ Hydrogen
◦ variable R-group
◦ 𝛼-carboxyl group
◦ tetrahedral alpha-carbon
4
Q
Two types of covalent bonds between amino acids in proteins
A
◦ peptide bonds
◦ disulfide bridges
5
Q
Function of a peptide bond
A
◦ Link amino acids together in polypeptide chains ◦Formed between the carboxyl group of one amino acid and the 𝛼-amino group of another amino acid with the loss of H2O
6
Q
Function of a disulfide bridge
A
Bridge between cysteine R-groups
7
Q
What are polypeptides?
A
Formed by linking amino acids together in peptide bonds
8
Q
What is the backbone of the polypeptide chain
A
◦ Forms a N-C-C-N-C-C pattern
9
Q
What is an individual amino acid called?
A
A residue (when it is part of a polypeptide chain)
10
Q
What is the order of synthesis of an amino acid?
A
◦ The amino (NH2) terminus is the first end make during poylpeptide synthesis
◦ The carboxyl terminus is made last
◦ Therefore, the amino-terminal residue is always written first
11
Q
Proteolysis
A
Hydrolysis of a protein by another protein
(also called proteolytic cleavage)
12
Q
Protease
A
The protein that cleaves (cuts) the peptide bond between two proteins
(also called proteolytic enzyme)
13
Q
Function of proteolytic cleavage
A
A specific means of cleaving peptide bonds
◦Many enzymes only cleave the peptide bond adjacent to a specific amino acid
14
Q
Cysteine
A
◦ An amino acid with a reactive thiol (sulfhydryl, SH) in its side chain
◦ Can form a disulfide bond
15
Q
What is a disulfide bond?
A
◦ The bond formed between two cysteine amino acids as the thiol of one cysteine reacts with the thiol of another cysteine to produce a covalent sulfur-sulfur bond
16
Q
True or False:
The cysteines forming a disulfide bond have to be on the same polypeptide chain
A
False; The cysteines can be located in the same or different polypeptide chain(s)
17
Q
Function of disulfide bridges
A
◦ Play an important role in stabilizing tertiary protein structure (for protein folding)
18
Q
What is a cysteine residue called once its becomes disulfide-bonded to another cysteine redisue?
A
Now called cystine (not cysteine)
19
Q
A
20
Q
What does a protein require to function properly?
A
It has to be folded into its unique 3D structure
21
Q
Why might a protein be non-functional?
A
If;
◦ Improperly folded
◦ Denatured
22
Q
How many levels of protein folding are there that contribute to their final 3D structure?
A
Four levels
(primary, secondary, tertiary, quaternary)
23
Q
What does denaturation refer too?
A
The disruption of a protein’s shape w/out breaking peptide bonds
24
Q
How can proteins be denatured?
A
◦ urea (which distrupts hydrogen-bonding interactions)
◦ extreme pH values
◦ extreme temperatures
◦ changes in salt concentration (tonicity)
25
What does primary structure refer too?
The amino acid sequence
26
What does secondary structure refer too?
Hydrogen bonds b/w backbond groups
27
What does tertiary structure refer too?
Hydrophobic/hydrophilic interactions
28
What does quaternary structure refer too?
Various bonds b/w seperate chains
29
Describe the primary level of protein structure
◦ The linear ordering of amino acid residues bonded together in a polypeptide chain
30
What is primary structure also refered too as?
Sequence
31
What bond determines the primary structure?
The peptide bond
◦ b/c this is the bond that links one amino acid to the next in a polypeptide
32
Describe the secondary level of protein structure
◦The initial folding of a polypeptide chain into shapes stabilized by hydrogen bonds b/w backbone NH and CO groups
33
What are the two most common motifs found in secondary structure of a protein?
◦ 𝛼-helix
◦ β-pleated sheet
34
What is an 𝛼-helix?
◦ Tightly coiled, right-handed spiral
◦ Stabilized by hydrogen bonds b/w the backbone carboxyl oxygen bonding to the backbone amide hydrogen (that is four residues away)
◦ This repeating pattern creates a helical structure, with 3.6 amino acid residues per turn
35
What are the two types of β-pleated sheets?
◦ parallel β-pleated sheet
◦ anti-parallel β-pleated sheet
36
What are parallel β-pleated sheets?
◦ Has adjacent polypeptide strands running in the same direction
◦ Stabilized by hydrogen bonds b/w the backbone carboxyl oxygen bonding to the backbone amide hydrogen
37
What are anti-parallel β-pleated sheets?
◦ Has adjacent polypeptide strands running in opposite directions
◦ Stabilized by hydrogen bonds b/w the backbone carboxyl oxygen bonding to the backbone amide hydrogen
38
Describe the tertiary level of protein structure
◦ Concerns interactions b/w amino acid residues located more distantly from each other in the polypeptide chain
◦ The folding of secondary structures (𝛼-helixes
and β-pleated sheets) into higher order tertiary structures -> which is driven by interactions of R-groups with each other and with the solvent (H2O)
◦ Hydrophobic R-groups tend to fold into the interior of the protein, away from the solvent, and hydrophilic R-groups tend to be exposed to water on the surface of the protein
◦ Under the right conditions, the forces driving hydrophobic avoidance of water and hydrogen bonding will fold a polypeptide spontaneously into the lowest energy correct conformation
39
What are examples of a tertiary structure?
◦ van der Waals interactions b/w two Phe R-groups located far apart on a polypeptide
◦ covalent disulfide bonds b/w cysteine residues located far apart on a polypeptide (forms a disulfide bridge)
40
Describe the quaternary level of protein structure
◦ describes interactions b/w polypeptide subunits (the arrangement of subunits in a multisubunit complex)
◦ these interactions are key for protein function
41
What is a subunit?
A single polypeptide chain that is part of a large complex containing many subunits (a multisubunit complex)
42
What forces stabilize quaternary structure?
◦ non-covalent interactions
◦ van der Waals forces
◦ hydrogen bonds
◦ disulfide bonds
◦ electrostatic interactions
43
What bond is not involved in quaternary structure?
The peptide bond b/c it defines sequence (primary structure)
44
What is the difference between a disulfide bridge involved in quaternary structure and one involved in tertiary structure?
◦ Quaternary disulfides are bonds that form b/w chains that aren't linked by peptide bonds
◦ Tertiary disulfides are bonds that form b/w residues in the same polypeptide
45
What is oxidation in regards to carbohydrates?
The breaking down of carbohydrates into CO2
(oxidation is also known as burning or combustion)
46
What is released by oxidation of carbohydrates?
◦ This process releases large amounts of energy -> this is why carbohydrates often serve as the principle energy source for cellular metabolism
47
What forms the building block of wood or cotton?
glucose in the form of the polymer cellulose
48
What is a monosaccharide?
A single carbohydrate unit (also known as a simple sugar)
49
What is the general chemical formulat for a monosaccharide?
C(n)H(2n)O(n)
50
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What is a disaccharide?
Two monosaccharides bonded together
52
What is an oligosaccharide?
3 to 10 monosaccharides bonded together
53
What is a polysaccharide?
10 + monosaccharides bonded together
54
Glycosidic linkage
◦ The bond b/w two sugar molecules
◦ It is a covalent bond formed in the dehydtation reaction that requires enzymatic catalysis
55
What are examples of commpn disaccharides?
◦ sucrose
◦ lactose
◦ maltose
cellobiose
56
Glycogen
serves an an energy storage carbohydrate in animals and is composed of thousands of glucose unites
57
Starch
very similar to glycogen (branching just slightly differs) and serves as an energy storage carbohydrate in plants
58
What is cellulose?
A polymer of cellobiose (cellbiose does not exist freely in nature - only exists in its polymerized cellulose form)
◦ wood and cotton are made of cellulose
59
How do glycosidic bonds impact the shape of carbohydrates?
They allow the polymer to assume a long, straight, fibrous shape
60
What are lipids
◦ Oily, fatty substances
◦ Known to be hydrophobic
61
3 physiological roles of lipids
1. In adipose cells, triglycerides (fats) store energy
2. In cellular membranes, phospholipids create a barrier between the intracellular and extracellular environments
3. Cholesterol ius a special lipid that functions as the building block for the hydrophobic steriod hormones
62
What makes a substance hydrophilic?
If it is polar
◦ ie. B/c H2O is very polar and polar substances dissolve well in water, they are known as hydrophilic
◦ A synonym of hydrophilic is lipophobic (lipid-fearing)
63
What makes a substance hydrophobic?
◦ carbon-carbon bonds and carbon-hydrogen bonds are non-polar and therefore do not dissolve in water, so they are hydrophobic
◦ A synonym of hydrophobic is lipophilic (lipid-loving)
64
What are fatty acids composed of?
long unsubstituted alkanes that end in a carboxylic acid
◦ The chain is usually 14-18 carbons long
◦ Only even numbered faqtty acids are made in human cells as they are synthesized two carbons at a time
65
What is a saturated fatty acid?
A fatty acid a single bond b/w a carbon-carbon
◦ It is said to be saturated with hydrogen b/c every carbon in the chain is covalently bound to the max number of hydrogens
66
What is an unsaturated fatty acid?
Fatty acids with one or more double bonds in the tail
◦ These double bonds are almost always 'Z' or 'cis'
67
How does the shape of an unsaturated fatty acid differ from that ofd a saturated fatty acid?
An unsaturated fatty acid is bent or kinked at the cis-double bond
68
If fatty acids are mixed into water, how are they likely to associate with each other?
The long hydrophobic chains will interact with each other to minimize contact with water, exposing the charged carboxyl group to the aqueous environment
69
What structure does free fatty acids form when in an aqueous solution?
They form a structure called a micelle
◦ where of force of 'hydrophobic interaction' drives the tails into the center of the micelle
70
Triacylglycerols (Tg)
◦ The storage form of fatty acid is fat -> stored in fat cells as an energy source
◦ It is necessary to store fatty acids in the relatively inert form of fat b/c free fatty acids are reactive chemicals
◦ The technical name for fat is triacylglycerol or triglyceride
71
Composition of triglyceride
◦ 3 fatty acids esterified to a glycerol molecule
72
Formula of glycerol
◦ 3 carbon triol
◦ HOCH2-CHOH-CH2OH
◦ The 3 hydroxyl groups can be esterified to fatty acids
73
What are lipases
Enzymes that hydrolyze fats
74
True or false
Carbohydrates are the most efficient energy storage molecule
False; fats are more efficient energy storage molecules for two reasons, packing and energy content
75
Importance of the packing of fat storage molecules
◦ The hydrophobicity of fat allows for fat to be packed together much more closely that carbohydrates
◦ Conversely, carbohydrates carry a great amount of water-of-solvation (water molecules hydrogen bonded to their hydroxyl groups)
76
Importance of the energy content of fat storage molecules
All packing considerations aside, fat molecules store much more energy than carbohydrates
◦ Regardless of what you dissolve it in, fat has more energy carbon-for-carbon, than a carbohydrate
77
Membrane lipids are...
phospholipids derived from diacylglycerol phosphate or DG-P
78
What structure do phospholipids form in an aqueous environment?
Form a lipid bilayer in order to minimize their interactions with water
◦ Hydrophobic interactions drive the formation of the bilayer and stabilize it by van der Waals forced between the tails
79
Would a saturated or an unsaturated fatty acid residue have more van der Waals interactions w/ neighbouring alkyl chains in a bilayer membrane?
The bend shape of the unsaturated fatty acids means that it doesn't fit well and has less contact with neighbouring groups to form van der Waals interactions
◦ Phospholipids composed of saturated fatty acids make the membrane more solid
80
Do single bonds or double bonds in a phospholipid fatty acids increase or decrease membrane fluidity?
Double bonds (unsaturation) increase membrane fluidity b/c unsaturation prevents the membrane from solidifying by distrupting the orderly packing of the hydrophobic lipid tails
◦ The right amout of fluidity is essential for function
81
What is the impact of decreasing the lenght of fatty acid tails on membrane fluidity?
Increases fluidity
82
What compound helps modulate membrane fluidity
The steriod cholesterol -> known as a membrane antifreeze
83
Why is cholesterol known as a membrane antifreeze?
b/c at low temperatures, it increases fluidity in the samw was as kinks in fatty acid tails, but at high temperatures it attenuates (reduces) membrane fluidity
-> therefore cholesterol keeps fluidity at an optimal level
84
What are the structural determinants of membrane fluidity?
1. Degree of saturation
2. Tail length
3. Amount of cholesterol
85
What is a terpene
A member of a broad class of compounds built from iosprene units (C5H8) with a general formula of (C5H8)n
86
What is the shape of a terpene?
They can be linear or cyclic - and are classified by the number of isoprene units they contain
87
What are monoterpenes?
Consist of two isoprene units
88
What are sesquiterpenes?
Consist of three isoprene units
89
What are diterpenes?
Consist of four isorene units
90
What is squalene?
A triterprene (made of six isoprene units) and an important compound as it is biosynthetically utilized in the manufacture of steroids
◦ It is also a component of earwax
91
What are functionalized-terpenes?
◦ Known as terpeniods
◦ Natural and synthetically derived species that are built from an isoprene skeleton and functionalized with other elements (O, N, S, etc)
92
What is an example of a terpeniod?
Vitamin A
93
Structure of steriods
All teriods have the basic tetracyclic ring system, based on the structure of cholesterol
94
Steroid cholesterol is an important component of what?
The lipid bilayer
95
How is cholesterol obtained and synthesized?
It is obtained fromthe diet and synthesized in the liver
96
How are lipoproteins formed?
Cholesterol that is carried in the blood packaged with fats and proteins to form lipoproteins
97
What are steriod hormones made from?
Cholesterol
98
What are two examples of steriod hormones?
1. Testosterone (an androgen or male sex hormone)
2. Estradiol (an estrogen or female sex hormone)
99
What type of acid is phosphoric acid?
An inorganic acid (it does not contain carbon)
100
How many protons does phosphoric acid have the potential to donate?
3 (H3PO4)
-> the three H
101
What are the pKa's for the three acid dissociation equilibria?
2.1
7.2
12.4
102
What form does phosphoric acid exist in at physiological pH?
At a pH of 7, phosphic acid is significantly dissociated, existing largely in anionic form
103
What is phosphate also known as?
An orthophosphate
104
How are pyrophosphate formed?
w/ two orthophosphates bound together via an anhydride linkage, and the P-O-P bond in pyrophosphate is an example of a high-energy phosphate bond b/c the hydrolysis of pyrophosphate is extremely favourable
105
What is an anhydride linkage?
A chemical bond where two acyl groups (RC=O) are linked together by a single oxygen atom (O)
106
Why fo phosphate anhydride bonds store so much energy?
1. When phosphates are linked together, their negative charges repel each other strongly
2. Ortho phosphate has more resonance forms and thus a lower free engery than linked phosphates
3. Orthophosphate has a more favourable interaction with the biological solvent (water) than linked phosphates
107
What image should be in my mind about linked phosphates?
That linked phosphates act like compressed springs, just waiting to fly open and provide energy for an enzyme to catalyse a reaction
108
What are nucleotides the building blocks of?
DNA & RNA
109
What components do each nucleotide contain?
◦ Ribose (or deoxyribose) sugar group
◦ Purine or pyrimidine base joined to carbon number 1 of the ribose ring
◦ 1, 2, or 3 phosphate units joined to carbon 5 of the ribose ring
110
What is the main role of the nucleotide ATP
Adenosine triphosphate plays a main role in cellular metabolism and is also an RNA precursor
111
Function of ATP
ATP is the universal short-term energy storage molecule
112
How is energy stored in ATP
Energy extracted from the oxidation of food is immediately stored in the phosphoanhydride bonds of ATP
113
How is energy from ATP used?
◦ Involved in powering cellular processes
◦ Used to synthesize glucose or fats (both are longer-term energy storage molecules)
◦ Used from bacteria to humans
-Viruses can carry ATP with them outside the host cell, but viruses cannot make their own ATP
