Biochemistry - FFM1 Flashcards
Overview of Biochemistry for FFM1
1
Q
Define:
Catabolism in term of metabolism
A
The metabolic pathway of breaking down large macromolecules into smaller units/monomers (Fats/Lipids —> Fatty Acids)
2
Q
Define:
Anabolism in term of metabolism
A
The metabolic pathway of building up larger molecules from smaller monomer units (Nucleotides —> Nucleic Acids, DNA/RNA)
3
Q
Examples of metabolites
A
Glucose
ATP
Hormones
Neurotransmitters
Electrolytes
Cations/Anions
Xenobiotics
4
Q
What is:
Xenobiotic
A
Any chemical substance foreign to organism
5
Q
Example of Xenobiotics?
A
Drugs
Environmental pollutants
Food additives
6
Q
What are the monomers that, when put together, for lipids
A
Fatty Acids
7
Q
What are the monomers that, when put together, form polysaccharides
A
Carbohydrates/Sugars
8
Q
Types of Disease processes associated with biochemical processes?
A
Congenital/Inherited diseases
Metabolic Disorders
Vitamin Deficiencies
Cancer
Alzheimer’s
Cushing Syndrome
CV Diseases
9
Q
Functionality of Biomolecules?
(5)
A
Enzymatic
Structural
Movement/Transportation
Information Carrying
Compartmentalization
10
Q
Where are macromolecules assembled at within the cells?
A
Ribosomes
Membranes
Chromosomes
Starch/Glycogen
11
Q
List of most common metabolic pathways?
A
Glycolysis
TCA/Citric Acid Cycle
Oxidative Phosphorylation
12
Q
Other types of metabolic pathways with different products?
A
Glycogenesis
Glycogenolysis
Hexose Monophosphate Shunt
FA Synthesis
FA Degradation
AA catabolism
Urea Cycle
Purine/Pyrimidine Synthesis & catabolism
13
Q
Properties of macromolecules (6)
Lipids, Carbs, NA, Proteins
A
Energy source
Building blocks of the body
Assembly into macromolecule complexes
Structural
Functionality
14
Q
Types of nucleotides
A
RNA
DNA
15
Q
Nucleotide(s) for information storage
A
DNA
16
Q
Nucleotide(s) used to transfer information
A
mRNA
17
Q
Nucleotide(s) used for translation
A
mRNA, rRNA, and tRNA
18
Q
Nucleotide(s) used for catalytic functions
A
Enzymes
19
Q
Nucleotide(s) used for energy transduction
A
ATP
20
Q
Nucleotide(s) used as cofactors for enzymes
A
NADPH+, NADH
21
Q
Overview of Central Dogma of Molecular Bio
A
DNA —> RNA —>Proteins
22
Q
Does this genetic material flow one direction? Why or why not?
A
No - there are RNA viruses that will used reverse transcriptase to create DNA FROM RNA strand; also prions to not use DNA/RNA to cause disease
23
Q
Describe the structure of nucleotides
A
1) Phosphate group on 5’ end
2) A pentose sugar with either a hydroxyl group on 2’ carbon end or hydrogen on 2’ carbon end
3) Nitrogenous base (purine/pyrimidine) attached to 1’ carbon
23
Q
Describe structure of pyrimidine?
A
Single aromatic/benzene ring with Nitrogens located at 1’ and 3’ positions within ring
24
Describe structure of purine?
Double ring structure with pyrimidine structure attached to imidazole ring (pentose ring)
25
Which pyrimidine has an amine group attached at the 4' C?
Cytosine
26
Which pyrimidine has a methyl group attached at the 5' C?
Thymine
27
Which pyrimidine does not have any functional groups attached to it?
Uracil (for RNA)
28
Which nucleotide?
Guanine
29
Which nucleotide
Adenosine
29
Which nucleotide?
Thymine
30
Which nucleotide
Cytosine
30
Which nucleotide
Uracil
31
Type of bond forming backbone of DNA/RNA
Phosphodiester linkage
32
Formation of phosphodiester bonds
Condensation rxn between 5' phosphate group and 3' hydroxyl group; removes water molecule during rxn
33
Does DNA/RNA have polarity?
Why/why not?
Yes - due to formation of phosphodiester bonds between nucleotides
34
Type of bonding between complementary strands of DNA
Hydrogen bonding
35
Explain Chargaff's Rule
A's = # T's
#C's = #G's
All total - equal to 100%
36
Number of bonds between A---T
2 hydrogen/double bonds
(2 Attic Tents
37
Number of bonds between C---G
3 hydrogen/triple bonds
(3 Car Garage)
38
Types of RNA
mRNA
tRNA
siRNA
miRNA
rRNA
39
Functions of Protein
(9)
1) Energy (last source of)
2) Source of AA's for new proteins
3) Enzyme catalysts
4) Structural
5) Receptor signaling
6) Carriers of small molecules
7) Movement (actin)
8) Communication
9) Transportation
40
What codes for proteins
DNA
41
Type of protein structures
1) Primary - AA chain
2) Secondary - alpha helices/beta sheets
3) Tertiary - formed protein of use
4) Quarternary - multiple proteins form together to create function unit (heme)
42
Explain structure of AA
Alpha carbon surrounded by carboxyl group, amino group, a hydrogen, and an R group conveying various functions TO that AA
43
L vs D chirality
Mirror images of one another; they are NOT superimposable though
44
Catagories of AA's, based on R group
Polar/Nonpolar
Charged/Uncharged
Aromatic
(+) or (-) Charge
45
What's my name, sign, 1 letter abbreviation and charge?
Aspartic Acid
Asp
D
Acidic (negative charge due to carboxyl group)
46
What's my name, sign, 1 letter abbreviation and charge?
Glutamic acid
Glu
E
Acidic (negative charge due to carboxyl group)
46
What's my name, sign, 1 letter abbreviation and charge?
Histidine
His
H
Basic (positive charge due to amine group)
47
What's my name, sign, 1 letter abbreviation and charge?
Lysine
Lys
K
Basic (positive charge due to amine group)
48
What's my name, sign, 1 letter abbreviation and charge?
Arginine
Arg
R
Basic (positive charge due to amine group)
49
What's my name, sign, 1 letter abbreviation and charge?
Threonine
Thr
T
Uncharged/Polar
50
What's my name, sign, 1 letter abbreviation and charge?
Cystine
Cys
C
Uncharged/Polar
50
What's my name, sign, 1 letter abbreviation and charge?
Tyrosine
Tyr
Y
Nonpolar/Aromatic
51
What's my name, sign, 1 letter abbreviation and charge?
Asparagine
Asn
N
Uncharged/Polar
52
What's my name, sign, 1 letter abbreviation and charge?
Glycine
Gly
G
Nonpolar/Aliphatic
53
What's my name, sign, 1 letter abbreviation and charge?
Alanine
Ala
A
Nonpolar/Aliphatic
54
What's my name, sign, 1 letter abbreviation and charge?
Valine
Val
V
Nonpolar/Aliphatic
55
What's my name, sign, 1 letter abbreviation and charge?
Leucine
Leu
L
Nonpolar/Aliphatic
56
What's my name, sign, 1 letter abbreviation and charge?
Phenylalanine
Phe
F
Nonpolar/Aromatic
57
What's my name, sign, 1 letter abbreviation and charge?
Isoleucine
Ile
I
Nonpolar/Aliphatic
58
What's my name, sign, 1 letter abbreviation and charge?
Tryptophan
Trp
W
Nonpolar/Aromatic
59
What's my name, sign, 1 letter abbreviation and charge?
Proline
Pro
P
Polar/uncharged
60
What's my name, sign, 1 letter abbreviation and charge?
Methionine
Met
M
Polar/Aliphatic
61
What's my name, sign, 1 letter abbreviation and charge?
Glutamine
Gln
Q
Polar/uncharged
62
What's my name, sign, 1 letter abbreviation and charge?
Serine
Ser
S
Polar/uncharged
63
Nutritionally Essential AA's?
Unable to form ourselves in the body; MUST take in from diet
64
Nutritionally Nonessential AA's
The human body can produce these; we don't need them from diet
65
List of Essential AA's
PVT TIM HALL
Arginine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine
66
List of Nonessential AA's
Alanine
Asparagine
Aspartate
Cysteine
Glutamate
Glutamine
Glycine
Proline
Serine
Tyrosine
67
Best source of energy
Carbohydrates
68
Functions of Glycolipids
- Immune recognition on outside of cell membrane
- Physical barriers
69
Functions of glycoproteins
1) Regulation of folding inside cell membrane
2) Structural proteins
70
Hexose Sugars
Glucose
Galactose
Mannose
Fructose
71
Pentose Sugars
Ribose
Deoxyribose
72
Disaccharides
Sucrose
Lactose
Maltose
73
Sucrose formed from...
Glucose and Fructose
74
Lactose formed from...
Glucose and Galactose
75
Maltose formed from...
2 glucose molecules (D-glucose)
76
Which disaccharide am I?
Maltose
77
Which disaccharide am I?
Lactose (1,4 Link)
78
Which disaccharide am I?
Sucrose (1,2 link)
79
Types of Starch
Amylose
Amylopectin
80
Describe amylose
Liner, non-branched
Connected by 1,4 glycosidic bonds (forms spiral)
81
Describe amylopectin
Glucose storage in plants
Animals can digest
alpha (1,4) glycosidic bonds with branch at alpha (1,6) (forms branches)
82
Glycoproteins
NAC - n-acetyl-glucosamine
GAG - glycosaminoglycan
Glucuronic acid
Iduronic acid
83
Function of Lipids
Energy storage
Compartmentalization
Signaling
Vitamins
84
Define micelle
spherical amphiphilic structures with hydrophobic core and hydrophilic shell; formed from lipids
Polar head group larger than aliphatic HC chains
85
What are functions of lipids?
Signaling molecules
Inflammatory molecules
Issues in metabolic disorders
86
What is an oil?
- Hydrophobic liquid of mostly plant based origin
- Hydrocarbons, trigycerides, pr FA's of varying lengths.
86
Define lipid
- Non-polar, amphipathic molecule (predominately hydrophobic)
- Broad category for fats, waxes and detergents
- Can form micelles, bilayer sheets
87
What is a fat?
- For medicine, triglyceride
- Hydrophobic solid/semisolid substance
88
What is a micelle?
- Single layer of amphipathic molecules that form cyclic structure
- Composed of hydrophobic tails towards the interior; hydrophilic head towards the exterior
89
What is a detergent?
- amphipathic compound acting as surfactants
- form micelles
90
What is a saturated fatty acid (FA)?
One which has long hydrocarbon tail composed of only single bonds - completely saturated with hydrocarbons
91
What is an unsaturated fatty acid (FA)?
- One which has long hydrocarbon tail composed of hydrocarbons with 1 or more cis-double bonds seen
- cis-Double bond allows for bend in the hydrocarbon tail
- mono or poly depending on number of double bonds
92
Why are unsaturated FA and trans-fatty acids similar?
Both have long hydrocarbon tails; trans fatty acid has a double bond but not breaks in the hydrocarbon chain. Structurally similar to one another.
93
2 examples of essential FA's
Linoleic acid
Linolenic
94
Composition of fat
- Glycerol backbone linked with FA chains via ester bond
- Bond is easy to break; allows molecules to be transferred
95
Glycerols with one FA attached
MonoAcylGlycerol
Act as detergent during digestion
96
Glycerol with 2 FA chains attached
DiAcylGlycerol
97
Glycerol with 3 FA's attached
TriAcylGlycerol
98
Types of membrane lipids
1) Glycerolphospholipids
2) Sphyingolipids
3) Cholesterol
4) Others
98
Types of Sphingolipids (2)
Phosphosphingolipid/sphingomyelin
Glycosphingolipids
98
Types of glycerophopholipids (4)
Phosphatidylcholine (PC)
Phosphatidylserine (PS)
Phosphatidylethanolamine (PE)
Phosphatidylinositol (PI)
99
Explain picture
100
Structure of Glycerophospholipids
(Backbone with attachements (sat or unsaturated)
- Glycerol backbone
- 2 FA's - 2' FA is unsaturated, 1' end FA is typicall saturated
- Phosphate attached to glycerol
- Head group attached to phosphate
101
Phosphatidylcholine functions/properties
- Most common
- Required as part of diet
- Part of lung surfactant
- Can contribute to cellular signaling
102
Phosphotidylethanolamine functions/properties
- primary constituent of bacterial membranes
- Constituent of mammalian membranes
- Can contribute to cellular signaling
103
Phosphatidylserine functions/properties
- Found inner leaflet of membrane
- Signal in apoptosis
- Less common
104
Phopshotidylinositol funtions/properties
- Minor constituent in mammals
- Involved in intracellular signaling
- IP3 releases Ca2+
- PIP3 is a signaling molecule
105
Plasmologen function/properties
- Comprise good amount of lipids in membranes/myelin
- Have ether linkage w/ double bond instead of ester linkage
- Synthesized in perioxisomes
106
Cardiolipin functions/properties
- Specialized lipid
- Found in mitochondrial membrane
- Makes mitochondrial membrane more impermeable to ions/regulates ion entry into mitochondria
107
Plasmologens vs DiAcylglycerophospholipids (DAG's)
Too similar - how different?
DAG's have phosphodiester/ester linkage/bond
Plasmologens have a vinyl-ether
108
Enzymes to degrade lipids:
1) Phospholipase A1
2) Phospholipase A2
3) Phospholipase B
4) Phospholipase C
5) Phospholipase D
1) Remove FA from glycerol backbone
2) Remove FA from glycerol backbone
3) Remove FA at either 1/2 positions, use lysophosphatidylcholine as substrate
4) Removes head group between glycerol and phosphate
5) Removes head group after phosphate
109
Importance of phospholipase A2
- Activated through hormone signaling
- Releases arachidonic acid from PI or PC
- Arachidonic acid converted to prostaglandins (inflammation)
110
Importance of Phospholipase C
- Releases IP3
- Generates DAG
- Part of 2nd messenger system of cells
111
Sphingomyelin functions/properties
- Seen in many membranes, predominantly in neuronal/myelin
- Phosphocholine headgroup
- Structure based on serine NOT glycerol
- Bonded by aliphatic/amide bonds
- Role in intracellular communication (outer layer)
112
Functions of glycolipids
Carbohydrate layer on outer membrane of membrane
Provide mechanical integrity to bilayer
Protect bilayer from breaking
113
Cholesterol functions/properties
- Major component of bilayer
- Get from diet or from synthesis of AceCoA
- HIGHLY REGULATED!
- Carried thru body in lipoprotein particles
(chylomicrons, LDL, HDL)
- Allows bilayer to have both rigidity and fluidity at the same time (bilayer too fluid, gives support)
114
Detergent properties
- larger head group than normal ampipathic molecules
115
List of common detergents
Lysophosphatidylcholine
MonoAcylGlycerol
Sodium Dodecyl Sulfate
FA's
116
Lipids found on inner membrane
- PS
- PI
117
Lipids found on outer membrane
Glycolipids
118
Lipids found on outer AND inner membrane
Cholesterol
119
Types of lipid motion within the bilayer
(fastest to slowest)
1) Bond vibrations
2) Gauche-trans isomerization
3) Protrusion
4) Lateral diffusion
5) Undulations
6) Flip-flop (enzymes required to do quickly)
120
Properties of proteins
- most abundant molecule
- most functionally diverse molecule
- AA's joined together by peptide bond
121
Functions of proteins
1) Energy
2) Enzymes
3) Movement
4) Cell signaling
5) Transport
6) Structural integrity
122
Most AA's are in what conformation
L-amino
123
What confers functionality to final protein product
Side chains - allow for bending, folding of protein
124
What is the only AA without chirality
Glycine - no alpha chiral carbon
125
Characteristics of peptide bond
- Does not allow rotation around the bond - double bond quality
- trans configuration - allows steric hindrance to be dispersed among the R groups
- polar, uncharged (no ionization, will contribute to H-bonding - can form 2 H-bonds between peptides)
126
Who's the one exception to formation of other H-bonds with other AA's
Proline - due to cyclic nature and there is no amine group to bond with
127
Levels of protein structure
Primary, Secondary, Tertiary, Quarternary
128
Primary structure properties
Single AA's linked to one another via peptide bonds
The order in which the AA's joined to one another
Stabilized by covalent bonds
129
Secondary structures
Alpha helices
Beta pleated sheets
Beta turns
130
Alpha helices properties
- Form spontaneously
- Rigid rod-like coil
- Side chains pointed outward
- Most stable conformation
- H-bond +/- parallel to axis of helix (4th residue)
- Formation of maximum number of possible H-bonds
131
Beta pleated sheet properties
- 2+ peptide chains arranges anti/parallel to one another
132
Beta turns properties
- most common turn
- Change in direction of chain
- H-bond from main carbonyl O to main chain NH3 residues along chain
133
Common AA's seen in Beta turns
Glycine - smallest R group
Proline - causes kink in peptide chaino
134
Function of Superoxide Dismutase
Catalyzes superoxide free radical (O2-) into O2 or H2O2
- example of Beta barrel structure
135
Mutation in superoxide dismutase causes
Familial Amyotrophic lateral Sclerosis (AML, motor neuron disease)
136
Tertiary Structure Interactions
- H-bonding
- Hydrophobic interations
- van der Waals interactions
- Ionic bonds (albeit rare! - stabilizaton of interior)
- Disulfide bridges
137
Define disulfide bridge
Covalent bond between 2 cysteine residues
Forms cystine residue
138
If one AA in peptide chain is read incorrectly -
Can cause protein to have different shape, functionality, or new unexpected properties
139
Different domains for proteins
1) Ligand-binding site
2) EGF precursor homology domain (epidermal growth factor)
3) O-linked sugar domain
4) Membrane spanning domain
5) Cytoplasmic domain
140
Examples of quarternary structure:
Hemoglobin - 2 alpha and 2 beta chains form
FA Synthase Comples - homodimer
Heptahelical receptor - G protein, heterotrimer
141
Fibrous protein properties
- Cylindrical rods that are long
- Low water solubility
- Structural role
- Large amounts of secondary structures
- N true tertiary structure - secondary/quarternary structures are strong
142
Examples of Fibrous proteins
Collagen
Elastin
Keratin (IF for epithelial cells)
143
Collagen properties
- Most abundant protein in body
- Present in all tissue
- Framework for tissue formation/stucture
- 3 L-handed helices (Gly-X-Y) form large R-handed super helix
- H-bonds stabilize
- X = proline; Y = hydroxyproline, hydroxylysine
144
Why glycine in collagen?
Only R group small enough to allow close proximity of chains to one another
145
Why proline in collagen?
Rigidity to helix due to ring structure (conformationally inflexible)
146
Why hydroxyproline or hydroxylysine in collagen?
Hydroxyproline = involvement with H-bond formation
Hydroxylysine = allows attachment of carbohydrate moieties (glucose and galactose)
147
Types of post translational modifications for proteins
Phosphorylation, Hydroxylation, Carboxylation, Ubiquitininization
148
What roles do these post-translational modifications have
Regulatory - either activate or deactivate activity of protein
149
Henderson-Hasselbalch Equations
Describes relationship between pH to acid and conjugate base
150
Why use Henderson-Hasselbalch?
Estimation of pH of buffer solution
Equilibrium pH in acid-base rxns
Calculate isoelectric point of proteins
151
Buffer point for Acid/Base
- pKa is best buffering point
- +/- 1 from pH: within this range = good buffer.
- Solution doesn't want to change - less pH change is better
152
What is isoelectric point
- pH value where molecule is NET NEUTRAL (net charge = 0)
- pH where proteins net neutral = less soluble, precipitate out of solution
153
How to find net charge of proteins?
- Find acidic/basic AA's.
Acidic = -1
Basic = +1
-
154
