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FFM-1 Spring 2024 > Biochemistry - FFM1 > Flashcards

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)

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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)

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3
Q

Examples of metabolites

A

Glucose
ATP
Hormones
Neurotransmitters
Electrolytes
Cations/Anions
Xenobiotics

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4
Q

What is:
Xenobiotic

A

Any chemical substance foreign to organism

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5
Q

Example of Xenobiotics?

A

Drugs
Environmental pollutants
Food additives

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6
Q

What are the monomers that, when put together, for lipids

A

Fatty Acids

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7
Q

What are the monomers that, when put together, form polysaccharides

A

Carbohydrates/Sugars

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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

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9
Q

Functionality of Biomolecules?
(5)

A

Enzymatic
Structural
Movement/Transportation
Information Carrying
Compartmentalization

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10
Q

Where are macromolecules assembled at within the cells?

A

Ribosomes
Membranes
Chromosomes
Starch/Glycogen

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11
Q

List of most common metabolic pathways?

A

Glycolysis
TCA/Citric Acid Cycle
Oxidative Phosphorylation

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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

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13
Q

Properties of macromolecules (6)
Lipids, Carbs, NA, Proteins

A

Energy source
Building blocks of the body
Assembly into macromolecule complexes
Structural
Functionality

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14
Q

Types of nucleotides

A

RNA
DNA

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15
Q

Nucleotide(s) for information storage

A

DNA

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16
Q

Nucleotide(s) used to transfer information

A

mRNA

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17
Q

Nucleotide(s) used for translation

A

mRNA, rRNA, and tRNA

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18
Q

Nucleotide(s) used for catalytic functions

A

Enzymes

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19
Q

Nucleotide(s) used for energy transduction

A

ATP

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20
Q

Nucleotide(s) used as cofactors for enzymes

A

NADPH+, NADH

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21
Q

Overview of Central Dogma of Molecular Bio

A

DNA —> RNA —>Proteins

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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

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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

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23
Q

Describe structure of pyrimidine?

A

Single aromatic/benzene ring with Nitrogens located at 1’ and 3’ positions within ring

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24
Q

Describe structure of purine?

A

Double ring structure with pyrimidine structure attached to imidazole ring (pentose ring)

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25
Q

Which pyrimidine has an amine group attached at the 4’ C?

A

Cytosine

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26
Q

Which pyrimidine has a methyl group attached at the 5’ C?

A

Thymine

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27
Q

Which pyrimidine does not have any functional groups attached to it?

A

Uracil (for RNA)

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28
Q

Which nucleotide?

A

Guanine

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29
Q

Which nucleotide

A

Adenosine

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29
Q

Which nucleotide?

A

Thymine

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30
Q

Which nucleotide

A

Cytosine

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30
Q

Which nucleotide

A

Uracil

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31
Q

Type of bond forming backbone of DNA/RNA

A

Phosphodiester linkage

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32
Q

Formation of phosphodiester bonds

A

Condensation rxn between 5’ phosphate group and 3’ hydroxyl group; removes water molecule during rxn

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33
Q

Does DNA/RNA have polarity?

Why/why not?

A

Yes - due to formation of phosphodiester bonds between nucleotides

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34
Q

Type of bonding between complementary strands of DNA

A

Hydrogen bonding

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35
Q

Explain Chargaff’s Rule

A

A’s = # T’s
#C’s = #G’s
All total - equal to 100%

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36
Q

Number of bonds between A—T

A

2 hydrogen/double bonds
(2 Attic Tents

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37
Q

Number of bonds between C—G

A

3 hydrogen/triple bonds
(3 Car Garage)

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38
Q

Types of RNA

A

mRNA
tRNA
siRNA
miRNA
rRNA

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39
Q

Functions of Protein
(9)

A

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

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40
Q

What codes for proteins

A

DNA

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41
Q

Type of protein structures

A

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)

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42
Q

Explain structure of AA

A

Alpha carbon surrounded by carboxyl group, amino group, a hydrogen, and an R group conveying various functions TO that AA

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43
Q

L vs D chirality

A

Mirror images of one another; they are NOT superimposable though

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44
Q

Catagories of AA’s, based on R group

A

Polar/Nonpolar
Charged/Uncharged
Aromatic
(+) or (-) Charge

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45
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Aspartic Acid
Asp
D
Acidic (negative charge due to carboxyl group)

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46
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Glutamic acid
Glu
E
Acidic (negative charge due to carboxyl group)

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46
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Histidine
His
H
Basic (positive charge due to amine group)

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47
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Lysine
Lys
K
Basic (positive charge due to amine group)

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48
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Arginine
Arg
R
Basic (positive charge due to amine group)

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49
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Threonine
Thr
T
Uncharged/Polar

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50
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Cystine
Cys
C
Uncharged/Polar

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50
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Tyrosine
Tyr
Y
Nonpolar/Aromatic

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51
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Asparagine
Asn
N
Uncharged/Polar

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52
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Glycine
Gly
G
Nonpolar/Aliphatic

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53
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Alanine
Ala
A
Nonpolar/Aliphatic

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54
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Valine
Val
V
Nonpolar/Aliphatic

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55
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Leucine
Leu
L
Nonpolar/Aliphatic

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56
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Phenylalanine
Phe
F
Nonpolar/Aromatic

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57
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Isoleucine
Ile
I
Nonpolar/Aliphatic

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58
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Tryptophan
Trp
W
Nonpolar/Aromatic

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59
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Proline
Pro
P
Polar/uncharged

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60
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Methionine
Met
M
Polar/Aliphatic

61
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Glutamine
Gln
Q
Polar/uncharged

62
Q

What’s my name, sign, 1 letter abbreviation and charge?

A

Serine
Ser
S
Polar/uncharged

63
Q

Nutritionally Essential AA’s?

A

Unable to form ourselves in the body; MUST take in from diet

64
Q

Nutritionally Nonessential AA’s

A

The human body can produce these; we don’t need them from diet

65
Q

List of Essential AA’s
PVT TIM HALL

A

Arginine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine

66
Q

List of Nonessential AA’s

A

Alanine
Asparagine
Aspartate
Cysteine
Glutamate
Glutamine
Glycine
Proline
Serine
Tyrosine

67
Q

Best source of energy

A

Carbohydrates

68
Q

Functions of Glycolipids

A
  • Immune recognition on outside of cell membrane
  • Physical barriers
69
Q

Functions of glycoproteins

A

1) Regulation of folding inside cell membrane
2) Structural proteins

70
Q

Hexose Sugars

A

Glucose
Galactose
Mannose
Fructose

71
Q

Pentose Sugars

A

Ribose
Deoxyribose

72
Q

Disaccharides

A

Sucrose
Lactose
Maltose

73
Q

Sucrose formed from…

A

Glucose and Fructose

74
Q

Lactose formed from…

A

Glucose and Galactose

75
Q

Maltose formed from…

A

2 glucose molecules (D-glucose)

76
Q

Which disaccharide am I?

A

Maltose

77
Q

Which disaccharide am I?

A

Lactose (1,4 Link)

78
Q

Which disaccharide am I?

A

Sucrose (1,2 link)

79
Q

Types of Starch

A

Amylose
Amylopectin

80
Q

Describe amylose

A

Liner, non-branched
Connected by 1,4 glycosidic bonds (forms spiral)

81
Q

Describe amylopectin

A

Glucose storage in plants
Animals can digest
alpha (1,4) glycosidic bonds with branch at alpha (1,6) (forms branches)

82
Q

Glycoproteins

A

NAC - n-acetyl-glucosamine
GAG - glycosaminoglycan
Glucuronic acid
Iduronic acid

83
Q

Function of Lipids

A

Energy storage
Compartmentalization
Signaling
Vitamins

84
Q

Define micelle

A

spherical amphiphilic structures with hydrophobic core and hydrophilic shell; formed from lipids
Polar head group larger than aliphatic HC chains

85
Q

What are functions of lipids?

A

Signaling molecules
Inflammatory molecules
Issues in metabolic disorders

86
Q

What is an oil?

A
  • Hydrophobic liquid of mostly plant based origin
  • Hydrocarbons, trigycerides, pr FA’s of varying lengths.
86
Q

Define lipid

A
  • Non-polar, amphipathic molecule (predominately hydrophobic)
  • Broad category for fats, waxes and detergents
  • Can form micelles, bilayer sheets
87
Q

What is a fat?

A
  • For medicine, triglyceride
  • Hydrophobic solid/semisolid substance
88
Q

What is a micelle?

A
  • Single layer of amphipathic molecules that form cyclic structure
  • Composed of hydrophobic tails towards the interior; hydrophilic head towards the exterior
89
Q

What is a detergent?

A
  • amphipathic compound acting as surfactants
  • form micelles
90
Q

What is a saturated fatty acid (FA)?

A

One which has long hydrocarbon tail composed of only single bonds - completely saturated with hydrocarbons

91
Q

What is an unsaturated fatty acid (FA)?

A
  • 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
Q

Why are unsaturated FA and trans-fatty acids similar?

A

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
Q

2 examples of essential FA’s

A

Linoleic acid
Linolenic

94
Q

Composition of fat

A
  • Glycerol backbone linked with FA chains via ester bond
  • Bond is easy to break; allows molecules to be transferred
95
Q

Glycerols with one FA attached

A

MonoAcylGlycerol
Act as detergent during digestion

96
Q

Glycerol with 2 FA chains attached

A

DiAcylGlycerol

97
Q

Glycerol with 3 FA’s attached

A

TriAcylGlycerol

98
Q

Types of membrane lipids

A

1) Glycerolphospholipids
2) Sphyingolipids
3) Cholesterol
4) Others

98
Q

Types of Sphingolipids (2)

A

Phosphosphingolipid/sphingomyelin
Glycosphingolipids

98
Q

Types of glycerophopholipids (4)

A

Phosphatidylcholine (PC)
Phosphatidylserine (PS)
Phosphatidylethanolamine (PE)
Phosphatidylinositol (PI)

99
Q

Explain picture

A
100
Q

Structure of Glycerophospholipids
(Backbone with attachements (sat or unsaturated)

A
  • 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
Q

Phosphatidylcholine functions/properties

A
  • Most common
  • Required as part of diet
  • Part of lung surfactant
  • Can contribute to cellular signaling
102
Q

Phosphotidylethanolamine functions/properties

A
  • primary constituent of bacterial membranes
  • Constituent of mammalian membranes
  • Can contribute to cellular signaling
103
Q

Phosphatidylserine functions/properties

A
  • Found inner leaflet of membrane
  • Signal in apoptosis
  • Less common
104
Q

Phopshotidylinositol funtions/properties

A
  • Minor constituent in mammals
  • Involved in intracellular signaling
  • IP3 releases Ca2+
  • PIP3 is a signaling molecule
105
Q

Plasmologen function/properties

A
  • Comprise good amount of lipids in membranes/myelin
  • Have ether linkage w/ double bond instead of ester linkage
  • Synthesized in perioxisomes
106
Q

Cardiolipin functions/properties

A
  • Specialized lipid
  • Found in mitochondrial membrane
  • Makes mitochondrial membrane more impermeable to ions/regulates ion entry into mitochondria
107
Q

Plasmologens vs DiAcylglycerophospholipids (DAG’s)
Too similar - how different?

A

DAG’s have phosphodiester/ester linkage/bond
Plasmologens have a vinyl-ether

108
Q

Enzymes to degrade lipids:
1) Phospholipase A1
2) Phospholipase A2
3) Phospholipase B
4) Phospholipase C
5) Phospholipase D

A

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
Q

Importance of phospholipase A2

A
  • Activated through hormone signaling
  • Releases arachidonic acid from PI or PC
  • Arachidonic acid converted to prostaglandins (inflammation)
110
Q

Importance of Phospholipase C

A
  • Releases IP3
  • Generates DAG
  • Part of 2nd messenger system of cells
111
Q

Sphingomyelin functions/properties

A
  • 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
Q

Functions of glycolipids

A

Carbohydrate layer on outer membrane of membrane
Provide mechanical integrity to bilayer
Protect bilayer from breaking

113
Q

Cholesterol functions/properties

A
  • 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
Q

Detergent properties

A
  • larger head group than normal ampipathic molecules
115
Q

List of common detergents

A

Lysophosphatidylcholine
MonoAcylGlycerol
Sodium Dodecyl Sulfate
FA’s

116
Q

Lipids found on inner membrane

A
  • PS
  • PI
117
Q

Lipids found on outer membrane

A

Glycolipids

118
Q

Lipids found on outer AND inner membrane

A

Cholesterol

119
Q

Types of lipid motion within the bilayer
(fastest to slowest)

A

1) Bond vibrations
2) Gauche-trans isomerization
3) Protrusion
4) Lateral diffusion
5) Undulations
6) Flip-flop (enzymes required to do quickly)

120
Q

Properties of proteins

A
  • most abundant molecule
  • most functionally diverse molecule
  • AA’s joined together by peptide bond
121
Q

Functions of proteins

A

1) Energy
2) Enzymes
3) Movement
4) Cell signaling
5) Transport
6) Structural integrity

122
Q

Most AA’s are in what conformation

A

L-amino

123
Q

What confers functionality to final protein product

A

Side chains - allow for bending, folding of protein

124
Q

What is the only AA without chirality

A

Glycine - no alpha chiral carbon

125
Q

Characteristics of peptide bond

A
  • 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
Q

Who’s the one exception to formation of other H-bonds with other AA’s

A

Proline - due to cyclic nature and there is no amine group to bond with

127
Q

Levels of protein structure

A

Primary, Secondary, Tertiary, Quarternary

128
Q

Primary structure properties

A

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
Q

Secondary structures

A

Alpha helices
Beta pleated sheets
Beta turns

130
Q

Alpha helices properties

A
  • 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
Q

Beta pleated sheet properties

A
  • 2+ peptide chains arranges anti/parallel to one another
132
Q

Beta turns properties

A
  • most common turn
  • Change in direction of chain
  • H-bond from main carbonyl O to main chain NH3 residues along chain
133
Q

Common AA’s seen in Beta turns

A

Glycine - smallest R group
Proline - causes kink in peptide chaino

134
Q

Function of Superoxide Dismutase

A

Catalyzes superoxide free radical (O2-) into O2 or H2O2
- example of Beta barrel structure

135
Q

Mutation in superoxide dismutase causes

A

Familial Amyotrophic lateral Sclerosis (AML, motor neuron disease)

136
Q

Tertiary Structure Interactions

A
  • H-bonding
  • Hydrophobic interations
  • van der Waals interactions
  • Ionic bonds (albeit rare! - stabilizaton of interior)
  • Disulfide bridges
137
Q

Define disulfide bridge

A

Covalent bond between 2 cysteine residues
Forms cystine residue

138
Q

If one AA in peptide chain is read incorrectly -

A

Can cause protein to have different shape, functionality, or new unexpected properties

139
Q

Different domains for proteins

A

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
Q

Examples of quarternary structure:

A

Hemoglobin - 2 alpha and 2 beta chains form
FA Synthase Comples - homodimer
Heptahelical receptor - G protein, heterotrimer

141
Q

Fibrous protein properties

A
  • 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
Q

Examples of Fibrous proteins

A

Collagen
Elastin
Keratin (IF for epithelial cells)

143
Q

Collagen properties

A
  • 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
Q

Why glycine in collagen?

A

Only R group small enough to allow close proximity of chains to one another

145
Q

Why proline in collagen?

A

Rigidity to helix due to ring structure (conformationally inflexible)

146
Q

Why hydroxyproline or hydroxylysine in collagen?

A

Hydroxyproline = involvement with H-bond formation
Hydroxylysine = allows attachment of carbohydrate moieties (glucose and galactose)

147
Q

Types of post translational modifications for proteins

A

Phosphorylation, Hydroxylation, Carboxylation, Ubiquitininization

148
Q

What roles do these post-translational modifications have

A

Regulatory - either activate or deactivate activity of protein

149
Q

Henderson-Hasselbalch Equations

A

Describes relationship between pH to acid and conjugate base

150
Q

Why use Henderson-Hasselbalch?

A

Estimation of pH of buffer solution
Equilibrium pH in acid-base rxns
Calculate isoelectric point of proteins

151
Q

Buffer point for Acid/Base

A
  • 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
Q

What is isoelectric point

A
  • pH value where molecule is NET NEUTRAL (net charge = 0)
  • pH where proteins net neutral = less soluble, precipitate out of solution
153
Q

How to find net charge of proteins?

A
  • Find acidic/basic AA’s.
    Acidic = -1
    Basic = +1
    -
154
Q
A

FFM-1 Spring 2024 (11 decks)

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