Exam 1 Flashcards
(123 cards)
1
Q
Elements found in biological systems
A
4 major subsets
- H, C, N, O
- Na, Mg, K, Ca
- P, S, Cl
- B, F, Al, Si, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Br, Mo, Cd, I,W
2
Q
What are amino acids?
A
polymer: polypeptides and proteins Major type of biological molecule They contain -an amino group (NH3) -a carboxylic acid group (COO-) -a side chain (CH3, methyl)
3
Q
What are carbohydrates?
A
Sugars: polymer: polysaccharides
4
Q
What are nucleotides?
A
Found in DNA and RNA: polymer: nucleic acids
They are the building blocks of nucleic acids.
5
Q
What is chirality?
A
“Handedness” comes from the asymmetry of the alpha carbon
A carbon with 4 different substituents is considered to be asymmetric.
6
Q
What are lipids?
A
Fats;store energy
Lipids DO NOT form polymers
7
Q
What formation are all naturally occurring amino acids in humans?
A
L (left) formation
Exception is Glycine
8
Q
Sugars (carbohydrates) can be drawn two different ways
A
Linear and cyclical
9
Q
What is the most important lipids in human health?
A
Cholesterol
It can be easily identified with the 4 ring structure
10
Q
What are the three major kinds of biological polymers?
A
Polypeptides and proteins, nucleic acids, and polysaccharides
11
Q
Amino acid residues are linked by what?
A
Peptide bonds
12
Q
How are polypeptide sequences read?
A
From N terminus to C terminus
13
Q
How do nucleotide residues link?
A
Via phosphodiester bonds.
O
O-P=O
O
14
Q
Where can a glycosidic bond be found?
A
Connecting two sugars; it is a special type of ether bond
It links the Anomeric carbon to another group.
15
Q
What is the function of proteins?
A
Major function- carry out metabolic reactions (enzymes) and support cellular structures (cytoskeleton proteins ie keratin, actin, collagen)
Minor function- store energy (glycogen)
16
Q
What is the function of nucleic acids?
A
Major function- encode information (DNA genetic traits)
Minor function- carry out metabolic reactions and support cellular structures
17
Q
What is the function of polysaccharides?
A
Major function- store energy (glycogen) and support cellular structures (cellulose in plants and trees)
Minor function- encode information
18
Q
Hydrophobic amino acids
A
Have nonpolar R groups
19
Q
Hydrophilic amino acids
A
Have polar R groups. They can be charged or uncharged R groups.
20
Q
What is the most simplest amino acid?
A
Glycine and it does not have chirality because both side chains are the same H group
Gly
G
21
Q
Which are the hydrophobic amino acids?
A
Alanine (Ala, A) Valine (Val, V) Phenylalanine (Phe, F) Tryptophan (Try, W) Leucine (Leu, L) Isoleucine (Iso, I) Methionine (Met, M) Proline (Pro, P)
22
Q
What are the hydrophilic polar, uncharged amino acids?
A
Serine (Ser, S) Threonine (Thr, T) Tyrosine (Tyr, Y) Asparagine (Asn,N) Glutamine (Gln, Q) Cysteine (Cys, C) Histidine (His, H)
23
Q
Which amino acids are hydrophilic polar, positively charged
A
Lysine (Lys, K)
Arginine (Arg, R)
24
Q
Which amino acids are hydrophilic polar, negatively charged?
A
Aspartate (Asp, D)
Glutamate (Glu, E)
25
What are amphipathic molecules that form lipid bilayers in cell walls?
Glycerophospholipids and sphingolipids
26
What are the classification of lipids?
Fatty acids, triacylglycerols, glycerophospholipids, sphingolipids, and isoprenoids
27
What are lipids (fats)?
Biological molecules that ARE soluble in nonpolar solvents and largely soluble in water
28
What bonds dominate lipids?
Long chain Hydrocarbon bonds
29
What is the polar head group on a fatty acid chain?
It is the carboxylic acids
30
What is the nonpolar tail of the long chain?
The hydrocarbon chain
31
Sphingosine and Sphingomyelin do not have what backbone found in glycerophospholipids?
They do not have a glycerol backbone
32
What does a cerebroside have as a head group?
A monosaccharide
33
What does a ganglioside have as a head group?
An oligosaccaride (oligo means more than one; a “gang”)
34
What is cholesterol?
An amphiphilic isoprenoid. It is the metabolic precursor of steroid hormones (estrogen and testosterone)
35
Which vitamins are isoprenoid derivatives?
Fat-soluble vitamins (A, D, E and K)
36
Which amphipathic lipid molecules form a lipid bilayer?
| Triacylglycerols, glycerophospholipids, shingolipids, cholesterol, or glutamic acid?
Glycerophospholipids and sphingolipids
37
What is the simplest aldose?
Glyceraldehyde
38
What is the simplest ketone?
Dihydroxyacetone
39
How do you designate D and L Notation?
Identify the last chiral center in the molecule.
OH on the right=D
OH on the left=L
Most sugars in nature have the D configuration.
40
What are enantiomers?
Non-superimposable mirror images;have different configurations at ALL stereocenters.
41
What are diastereomers?
Non-superimposable non-mirror images, when there are 2 or more chiral carbons. Have different configurations at one or more (but not all) stereocenters.
42
What are epimers?
Special diastereomers that differ from each other in the absolute configuration at only ONE center
43
How do you determine the number of stereoisomers?
2 to the ‘n’ power
44
How does cyclization occur?
When an aldose cyclizes, the hydroxyl group on the 2nd to last carbon undergoes an intramolecular reaction with the carbonyl group of the aldehyde. The product resulting from aldose cyclization is a hemiacetal. The product resulting from ketone cyclization is a hemiketal.
45
Five membered ring that consists of 4 Carbons + 1 Oxygen
Furanose
46
Six membered ring that includes 5 Carbons + 1 Oxygen
Pyranose
47
What is an alpha Anomer?
A chiral carbon on a cyclical sugar with the OH group on the bottom
48
What is a beta Anomer?
A chiral carbon of a cyclical sugar with the OH group on the top
49
What is a glycoside?
A molecule consisting of a sugar linked to another molecule by a glycosidic bond.
50
Phosphorylated sugars
Glyceraldehyde-3-phosphate and fructose-6-phosphate are intermediates in the metabolic pathways for breaking down glucose. (Glycolysis)
51
How are sugars in RNA and DNA numbered?
With primes.
52
DNA and RNA are each furanose. What is the only difference?
In RNA, the 2’ carbon has an OH group and DNA has a H group.
53
What are two examples of monosaccharides derivatives?
Glucosamine (an amino group has replaced an OH substituent)
| Glucuronate (a carboxyl group has replaced the terminal CH2OH)
54
Examples of disaccharides
Lactose and sucrose ->source of metabolic fuel
55
Examples of polysaccharides
Glucose polymers
Starch and glycogen -> fuel-storage
Cellulose ->structural support
56
Other structural polysaccharides
Bacterial polysaccharides form a biofilm (bacterial biofilms)
57
What is the lactose structure?
Beta(1->4) glycosidic bond
~ shape
Galactose + Glucose = Lactose
58
What is the sucrose structure?
Alpha(1->2) glycosidic bond
Makes a U shape
Glucose + Fructose = Sucrose (the most abundant sugar in nature)
59
Glucose polymers
Alpha (1->4) glycosidic bond
U shape
Starch and glycogen are storage forms of glucose
60
What is amylose?
A linear and helical polymer of glucose
61
What is Amylopectin?
A branched polymer of glucose
| Alpha(1->6) glycosidic bond
62
Structure of cellulose
Beta(1->4)
~ shape
Cellulose is composed of glucose
63
Glycoproteins
Oligosaccharide chains are covalently attached to the proteins as N-linked or O-linked oligosaccharides.
Glycoproteins function as protection and as recognition markers (blood groups).
N-linked via Asn (Asparagine); amide group
O-linked via Ser or Thr
64
DNA and RNA are polymers of nucleotides,each of which consists of a:
- purine or pyrimidine base
- deoxyribose or ribose
- phosphate
65
Adenine and guanine are ______ in both ____ and ______.
Purines in both DNA and RNA
A purine has 2 rings.
Adenine has an amine group in the same location where guanine has a double bonded oxygen. Guanine has an amide group in a location that adenine does not any molecules.
66
Pyrimidines found in DNA
Cytosine and thymine
| Pyrimadines is a single ring
67
Pyrimidines found in RNA
Cytosine an uracil
| Uracil is missing the methyl group thymine has
68
NucleoSide =
Base + Sugar
69
NucleoTide =
Base + sugar + phosphate
70
How do nucleotides link?
Via sugar in phosphodiester backbone
| Read sequence of bases from 5’ -> 3’
71
How many bonds do adenine and thymine make?
2 H-bonds
72
How many hydrogen bonds do guanine and cytosine make?
3 and is stronger than A and T
73
What does the stability of a DNA double helix depend on?
It depends mostly on stacking interactions.
74
What does it mean to go from genes to proteins?
Central dogma
| DNA to transcription, RNA to translation to protein
75
True or false
| DNA can denature and re-nature
True
76
What does it mean when water is amphoteric?
It means that water can act as an acid or a base depending on the environment
77
List the strengths of bonds from strongest to weakest
Covalent
Ionic
Hydrogen
van deer Waals
78
What is the hydrophobic effect?
The phenomenon by which nonpolar molecules aggregate to avoid contact with hydrophilic molecules, particularly water.
79
True or false
| Nonpolar molecules tend to aggregate in nonpolar solvents
False
| They tend to aggregate in POLAR solvents
80
Amphiphilic molecules form _______ in ________ solutions
Micelles
| Aqueous
81
On the pH scale, 0 to 7 is considered acidic or basic?
Acidic
82
On the pH scale, what values are basic?
7 to 14
83
What does the pk describe?
An acid’s tendency to ionize
An example is acetic acid
The lower the pka for acids, the higher the strength
84
If the pH is acidic, will the hydrogen ions dissociate quickly or slowly?
Slowly because they do not want to give any up. The opposite is true for basic pH.
85
In pulmonary function, if the blood pH is acidic, what will happen to the carbon dioxide during exhalation?
More gaseous carbon dioxide is lost during exhalation causing a right shift in the chemical reaction. The opposite happens during alkalosis (left shift occurs).
86
What is bicarbonate reabsorption?
When a pH adjustment needs to be done and it is over a long period of time, such as hours to days, the kidneys will excrete and restore the balance.
87
What are amino acid residues?
Amino acids within the peptide bond are called amino acid residues because only the residual atoms remain after the condensation reaction (loss of water)
88
What will happen to the acidic groups amino acid side chain/terminal when pH>pK?
They will be mostly ionized with a -1 charge
89
What will happen to the acidic groups amino acid side chain/terminal when pH < pK?
They will be mostly unionized with a 0 charge
90
What will happen to the basic groups amino acid side chain/terminal when pH > pK?
They are mostly unionized with a 0 charge.
91
What will happen to the basic groups amino acid side chain/terminal when pH < pK?
It will be mostly ionized with a +1 charge
92
What is the isoelectric point, pI?
The pH at which it carries no net charge.
94
How do you find the pI of an acidic amino acid?
Add pKa1 and pKa3 and divide by 2.
95
What are the 4 levels of protein structure?
Primary- the sequence of amino acid residues
Secondary- the spatial arrangement of the polypeptide backbone
Tertiary- three-dimensional structure of an entire polypeptide
Quaternary- spatial arrangement of polypeptide chains in a protein with multiple subunits (not every protein will have one)
96
What are the 2 principal secondary structures?
Alpha helix and Beta sheet
| Both are characterized by hydrogen bonding
97
What is i + 4 pattern of hydrogen bonding?
Stabilized by a characteristic pattern of hydrogen bonding of the carbonyl of one amide(i) to the NH of another amide i +4.
98
How do you find the pI of a basic amino acid?
Add pKa2 and pKa3 and divide by 2.
99
What do protein folding and protein stabilization depend on?
Non covalent forces
100
What happens when misfolded proteins are not immediately refolded or degraded, but instead aggregate?
They are often long insoluble fibers and can lead to disease.
An example is Alzheimer’s.
101
What does myoglobin transport?
O2 throughout the muscles
102
What does hemoglobin transport?
O2 in the blood
103
What are the other functions of proteins?
Immunity- antibodies
Catalysis- enzymes
Regulation of gene expression
104
What is the structure and sequence of myoglobin?
Monomer- 1 polypeptide chain with primary, secondary and tertiary structure
Primarily in muscles
O2 binds to the heme group in a hyperbolic manner
105
What is the structure and sequence of hemoglobin?
Tetramer (alpha2:beta2) 4 individual subunits
Erythrocytes
O2 binds to the heme group in a sigmoidal manner
106
What do the similarities and structure between myoglobin and hemoglobin indicate?
A common evolutionary origin
107
What is a prosthetic group?
Organic molecule bound to protein that aids protein function
108
Myoglobin transports _______ via the _______ in heme.
O2, Fe
109
What role does his residues play?
They play a key role in anchoring both O2 and iron.
110
How are pO2 and O2 saturation related?
They are directly related. If pO2 increases, O2 saturation increases.
111
Myoglobin binds to _____ in a ________ trend.
O2, hyperbolic
112
Does hemoglobin or myoglobin have a quaternary structure?
Hemoglobin does
113
Homologous proteins
Evolving from a common ancestor gene through genetic mutation
114
Invariant residues
- identical in homologous proteins
- essential for structure or function of the protein
- cannot be replaced by other residues
115
Conservative substitution
- when an amino acid can be replaced by another similar amino acid (ie Ile for Leu or Ser for Thr)
- structure or function is conserved
116
Variable residues
- not involved in the structure or function of the protein
| - can be substituted by other dissimilar amino acids (Ile for Ser or Leu for Lys)
117
What is cooperativity?
Binding of O2 to one subunit induces easier binding to other subunits by conformational change.
118
What kind of curve does hemoglobin have?
A sigmoidal curve; sigmoidal data are indicative of cooperativity.
119
Which has a higher affinity of oxygen? Myoglobin or hemoglobin?
Myoglobin does
120
A tense hemoglobin cooperative behavior is _____?
Deoxy (missing oxygen); is not in the site of conformational change
121
A relaxed hemoglobin cooperative behavior is _____?
Oxy (contains oxygen); is in the conformational change site
122
What is the Bohr effect?
The reduction of hemoglobin’s oxygen binding affinity when the pH decreases (more acidic or an increase in hydrogen concentration
123
What is happening biochemically when you breathe?
It allows O2 to unbind from hemoglobin.
124
What decreases hemoglobin’s O2 affinity?
BPG 2,3-bisphosphoglycerate
| BPG binds only to the tense (deoxy) conformation of hemoglobin.
