EXAM 1 Material Flashcards
(105 cards)
1
Q
Structure of Protein
A
Amino Group (Left) —– Hydrogen Atom (Top) —– R Group / Side Chain (Bottom) —– Carboxyl Group (Right)
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Q
Types of Bonds of Proteins
A
Ionic (Charged R-Groups)
Hydrogen (Polar R-Groups)
None (Non-polar R-Groups)
3
Q
R-Group’s Polarity’s Effect on Solubility
A
Polar (Hydrophilic)
Non-polar (Hydrophobic)
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Q
Name of Protein Polymerization Bond
A
Peptide Bond
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Q
Mechanism of Peptide Bond
A
Carboxyl Tail -> Amine Head (C-N) via CONDENSATION RXN
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Q
Directionality of Protein Chains
A
Amine -> Carboxyl
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Q
Oligo-peptide
A
Small chain of proteins
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Q
Polypeptide
A
Long chain of proteins
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Q
Primary Structure of Proteins
A
Sequence of Amino Acids
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Q
Secondary Structure of Proteins
A
Hydrogen Bonds between Carbonyl Group and Amino Groups
11
Q
Tertiary Structure of Proteins
A
Caused by…
1) Hydrogen Bonding
2) Hydrophobic Interactions
3) Van Der Waals Interactions
4) Covalent Bonding (Disulfide Bonds)
5) Ionic Bonding
Largely determines protein function
12
Q
Quaternary Structure of Proteins
A
Combination of multiple Polypeptide parts
13
Q
Alpha-helix folding
A
Type of secondary structure resulting from a very close bonding of Carbonyl and Amino Groups (4 steps apart)
14
Q
Beta-pleated sheet folding
A
Type of secondary structure resulting from far-apart bonding of Carbonyl and Amino Groups; Segments bend 180 degrees and fold in the same plane
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Q
Molecular Chaperones
A
Help a protein fold correctly
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Q
Prions
A
Misfolded Proteins that cause other proteins to misfold
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Q
Protein Function
A
-Catalysis (Enzymes)
-Structure (Hair/Nails)
-Movement (Motor Proteins)
-Signaling (Glucagon)
-Transport (Hemoglobin)
-Defense (Antibodies)
18
Q
Protein Monomer
A
Peptide
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Q
Nucleic Acid Monomer
A
Nucleotide
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Q
Structure of Nucleic Acids
A
Phosphate Group —– 5-Carbon Sugar —– Nitrogenous Base
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Q
Deoxyribose vs. Ribose
A
2’ Carbon H vs OH
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Q
Nucleic Acid Sugar Labeling
A
Rightmost Carbon is 1’, Clockwise direction
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Q
Nucleic Acid Polymerization
A
3’ Hydroxyl to Phosphate Group via CONDENSATION RXN
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Q
Pyrimidines
A
Thymine, Cytosine, Uracil (Ringed)
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Purines
Adenine, Guanine (Double Ringed)
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Nucleic Acid Directionality
5' -> 3'
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Name of Nucleic Acid Bond
Phosphodiester Linkage
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Nucleic Acid Monomer
dATP/ATP ((Deoxy)adenosine Triphosphate)
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Watson and Crick Experiment
Discovered Double Helix Nature of DNA (X-ray Crystallography)
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RNA Secondary Structure
Bonding of the same strand to itself
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RNA Tertiary Structure
Secondary Structure folds to form 3D structure
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DNA Secondary Structure
Double Helix Shape
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Ribozymes
RNA w/ Catalytic Activity (Ex. Polymerize Amino Acids)
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DNA Tertiary Structure
Compact around histones, or twisted into supercoils
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Monosaccharides
Carbohydrate monomer
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Oligosaccharides
small amount of monosaccharides
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Polysaccharides
many monosaccharides
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Structure of Carbohydrates
Carbonyl Group (C=O) + Several Hydroxyl Groups (-OH) + Multiple C-H Bonds
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Aldose
Sugar w/ Carbonyl at End of Molecule (Glucose, Galactose)
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Ketose
Sugar w/ Carbonyl in middle of Molecule (Ex. Fructose)
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Alpha-Glucose
Glucose w/ Hydroxyl group above
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Beta-Glucose
Glucose w/ Hydroxyl group below
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Carbohydrate Bond Name
Glycosidic Linkage (-O-) via CONDENSATION RXN
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Why can Carbohydrates branch but Proteins and Nucleic Acids can't?
Carbohydrates contain multiple hydroxyl groups, meaning there are multiple linkage sites
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Maltose
Disaccharide of two glucoses
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Lactose
Disaccharide of glucose + galactose
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Glycosidic Linkage Nomenclature
(Type of Bond)-(First carbon #), (Second carbon #)-glycosidic linkage
E.x. Beta-1,4-Glycosidic Linkage
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Starch
Energy storing polysaccharides found in plants made up entirely of alpha-glycosidic linkages
Made up of 2 polymers -> Amylose (Unbranched, only alpha-1,4-glycosidic linkages) + Amylopectin (Branched, contains alpha-1,6-glycosidic linkages)
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On average, how often do starches branch?
1 in 30
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What joins cellulose strands together?
Hydrogen Bonds
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Cellulose
Structural polysaccharides found in plants made up entirely of beta-glucose monomers via beta-1,4-glycosidic linkages s/t each subsequent monomer is FLIPPED
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Glycogen
Animal equivalent of starch, 3x as many branches
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Chitin
Structural polysaccharides found in Fungi made up of N-acetylglucosamine (NAG) joined via beta-1,4-glycosidic linkages s/t each subsequent monomer is FLIPPED
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What joins chitin strands together?
Hydrogen Bonds
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Peptidoglycan
Structural polysaccharides found in Bacteria made up of NAG + N-acetylmuramic acid (NAM) that alternate via beta-1,4-glycosidic linkages
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What joins peptidoglycan strands together?
Amino acids attach to the C-3 carbon of NAM and link to other amino acids on other strands
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Carbohydrate's Purposes
1) Structure (Cellulose)
2) Energy Storage (Starch)
3) Identity (Glycoproteins)
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Glycolipid/Glycoprotein
Lipid/Protein that has been glycosylated
Glycolipid Ex: Blood type markers (A, AB, B, O)
Glycoprotein Ex: Ensures Sperm binds to Egg of same species
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Wassarman Experiment
Placed carbs as the main reason for egg/sperm recognition
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Phosphorylase
Enzyme that breaks down glycogen by hydrolyzing alpha-1,4-glycosidic linkage bonds
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Amylase
Enzyme that breaks down starches by hydrolyzing alpha-1,4-glycosidic linkage bonds
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Plasma membrane
Selective barrier that separates the outside environment from the inside, allowing the chemical rxns of life to occur more efficiently
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Fat Structure
Long hydrocarbon chain (nonpolar) with a glycerol (3-Carbon) backbone joined via an ester linkage (DEHYDRATION RXN)
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Saturated vs. Unsaturated Fatty Acids
All C-C bonds vs. One or more C=C (cis bonds, produce "kinks" in chains)
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What makes nonpolar lipid chains stick together?
Van der Waals Interactions
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Why is butter solid, but something like oil isn't?
Longer, straighter lipid chains = more Van der Waals interactions = more solid substance
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Steroid Structure
Four-ring structure w/ functional groups/chains coming off of them
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Phospholipid
Lipid consisting of a glycerol molecule bonded to a phosphate group and 2 hydrocarbon chains of either isoprenoids (Archaea) or fatty acids (Bacteria/Eukarya)
Polar head -> Nonpolar Tails (Important for Lipid Membranes)
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Micelles
Formed spontaneously by phospholipids; small, ring structures usually formed by single chain hydrocarbon tails
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Liposomes
Artificially generated membrane-bound vesicles
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Lipid Bilayer
Formed spontaneously by phospholipids; Paired, double-layered sheets usually formed by double hydrocarbon tails
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Selective Permeability of Lipid Bilayers
Allow certain substances (small, nonpolar or polar uncharged molecules) to pass through, but rejects others (large, uncharged polar molecules or ions)
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Bond Saturation and Hydrocarbon Chain Length effect on Lipid Bilayers
Greater Bond Saturation = Straighter Tails = Less Kinks = More Van Der Waals Interactions = Less Fluidity
Greater Hydrocarbon Length = More Van der Waals Interactions = Less Fluidity
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Cholesterol Effect on Lipid Bilayers
Greater Cholesterol = Pushes Fatty acids closer together = More Van der Waals Interactions = Less Fluidity
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Temperature effect on Lipid Bilayers
Greater Temp = Slower movement of individual phospholipids = Less Fluidity
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Diffusion
Passive evening out of concentrations (High -> Low) across a membrane
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Osmosis
Water Diffusion
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Fluid-Mosaic Model
Proposed by Singer and Nicolson, replaced previous "sandwich model" (Davson + Danielli) which stated that proteins surrounded the lipid bilayer (argued that proteins could span membrane as well)
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Pit and Mound Graph
Evidence for transmembrane (integral) proteins
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Peripheral Proteins
Proteins on outside of membrane
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Detergent
Small, amphipathic molecules that form micelles
When added to lipid bilayers, cause it to break apart
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Ion Channels
Specialized transmembrane proteins that allow for the passive diffusion of ions across the membrane in response to a gradient
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Gated Channels
Protein channels that are only activated in response to a signal
78
Aquaporin
Protein channel facilitates the faster movement of water across the membrane
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Cystic Fibrosis
Caused by defects in the transmembrane protein CFTR, which regulates Cl- diffusion
Less Cl- outside of cells = No water movement outside cells = sticky mucus consistency
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Carrier Proteins
Proteins that actively transport molecules from one side of the membrane to the other
81
GLUT-1
Primary membrane protein that transports glucose via a conformational change (passive transport) powered by a concentration gradient
82
Active Transport
Transport of molecules AGAINST the gradient
83
Pump
Any membrane protein that uses ATP to power active transport
84
Sodium-Potassium Pump
Type of Protein Pump:
Sodium ions bind to pump -> ATP cleaved into ADP an P (binds to pump) -> Conformational Change -> Sodium ions released -> Potassium ions bind to pump -> Phosphate ion is cleaved -> Conformational Change -> Potassium ions released
3 Na+ for ever 2 K+
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Purpose of Sodium-Potassium Pump
Creates an electrochemical gradient that can be used for energy
86
Secondary Active Transport
ATP not used directly to power transport, but the gradient created by an ATP pump is used instead
87
Phosphatidyl Ethanolamine
Major structural component of biological membranes composed of 2 Fatty acid tails, an ethanolamine molecule (Amino acid), Glycerol backbone (3-Carbon), and a Phosphate group
88
Fatty Acid Nomenclature
(# of Saturated Carbons):(Number of Unsaturated Carbons)
Ex. 16:1 Fatty Acid Tail
89
Sphingomyelin
Type of Lipid found in animal cell membranes that mainly play a structural component
*NOT SYNTHESIZED FROM GLYCEROL*
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