Bartling SG Flashcards
Glycine
Non-polar, aliphatic AA
Alanine
Non-polar, aliphatic AA
Valine
Non-polar, aliphatic AA
Isoleucine
Non-polar, aliphatic AA
Phenylalanine
Non-polar, aromatic AA
Tyrosine
Non-polar, aromatic AA
Tryptophan
Non-polar, aromatic AA
threonine
UNCHARGED, POLAR AA
Serine
UNCHARGED, POLAR AA
Asparagine
UNCHARGED, POLAR AA
Glutamine
UNCHARGED, POLAR AA
Aspartic Acid
ACIDIC AA
Glutamic Acid
ACIDIC AA
Histidine
BASIC AA
Lysine
BASIC AA
Arginine
BASIC AA
Cysteine
SULFER CONTAINING AA
Methionine
SULFER CONTAINING AA
Proline
CYLIC AA
does not form conventional peptide bond
Proline
aliphatic sidechain w/ no functional groups
Proline
alpha amino group bonded to side chain
Proline
sidechain covalently bonds to amide N (eliminating H bond possibility)
Proline
the AA exists as a dipolar molecule having both + & - charges
zwitterion
in a zwitterion which group is deprotonated, having a - charge
alpha carboxyl group
in a zwitterion which group is protonated, having a + charge
alpha amino group
which AA doesn’t has an asymmetry center and therefore isn’t optically active?
glycine
at least one center of asymmetry makes most AA’s what?
optically active
AA sequence, linear polymers linked by peptide bonds is what type protein structure
Primary
Local folded structures, maintained by H bond networks what type of protein structure
Secondary
H bonds between backbone amide NH and C=O groups stabilize
Alpha Helices
Alpha helices and Beta sheets
Secondary
backbone of polypeptide is extended into zigzag, polypeptide chains arranged side by side
Beta Sheets
3D structure
Tertiary Structure
disulfide bonds
Tertiary Structure
salt bridges
Tertiary Structure
hydrophobic interactions
Tertiary Structure
structure of more than one subunit together
Quaternary Structure
pH which a molecule has no net charge, isoelectric point
PI
widely used to calculate the isoelectric point of proteins
Henderson-Hasselbach
carboxyl group accepts a proton and becomes uncharged, overall charge on molecule is positive +
Ionization state at low pH
amino group loses its proton and becomes uncharged, overall charge on molecule is negative-
Ionization state at high pH
bond formed between alpha-carboxyl of one AA and the alpha-amino group of another
Peptide
what is removed in the process of linking AA’s together
H2O
2 AA’s linked
Dipeptide
3-10 AA’s
Oligopeptide
11-99 AA’s
Polypeptide
100 or more AA’s
Protein
Abnormal metabolic condition leading to excess levels of homocysteine
HOMOCYSTEINURIA
result of Homocysteinuria
downward dislocation of lens, long limbs, mental retardation, seizures
converts sulfite to sulfate
sulfate oxidase
alternative metabolic pathways for sulfite are used leading to formation of s-sulfocysyeine
sulfate oxidase deficiency
no disulfide bonding in connective tissue
sulfate oxidase deficiency
lens dislocation, associated w/ mutations in the fibrillin gene
Marfan syndrome
Green teeth in children is a result of
hyperbilirubinemia
precipitation of proteins occurs at high salt concentrations
Salting out
which separation method uses salting in and salting out?
Solubility
absorption chromatography is what type of separation method
polarity
to purify and concentrate biomolecules based on chemical or physical differences
Chromatography
paper chromatography is what type of separation method
polarity
reverse-phase chromatography is what type of separation method
polarity
hydrophobic interactions are used for what type of separation method
polarity
adjust solution just below point of solubility of protein of interest for separation
solubility method
Larger molecules flow faster through column, first fractions consist of large and begin to collect smaller in later stages
Size exclusion chromatography
increased polarity increases rate at which molecules move through the column
gel filtration chromatography
uses beads to separate proteins based on charge
Ion exchange chromatography
binds protein w + charge, carboxymehtylcellulose
Cation Exchanger
DEAE cellulose, binds protein w -
Anion Exchanger
bind antibody/antigen to protein resin
AFFINITY CHROMATOGHRAPY
specific interaction of substrate with a ligand & purifies neatly pure product in a single step
AFFINITY CHROMATOGHRAPY
Typical affinity chromatography interaction
antibody - antigen pairs
migration of ions in an electric field depending on molecule charge (q) and frictional coefficient (f)
electrophoresis
Separates proteins on basis of their pI
iloelectric focusing (IEF)
protein that is in a pH region below its pI (+) will migrate towards the cathode until it stops at its pI; vice versa for protein that is in a pH region above pI (-)
iloelectric focusing (IEF)
number of sterioisomers
2^n
chiral variations change what properties
chemical, physical and, physiological
of the 8 D-aldohexoses which 3 are found significantly in body
glucose, mannose, galactose
single sugars: starch, cellulose, glycogen
Homoglycan
More than one sugar: gums, mucopolysaccharides
Heterogylcan
most common storage polysaccharide in plants
Starch
animal equivalent to starch
glycogen
stored in muscle and liver cells as high MW granules
glycogen
hydrolyzed by amylases and glycogen phosphorylase
glycogen
glucosamine is what?
amino sugar
why has glucose been selected by evolution for the base sugar of blood?
inertness/ not reactiveness
relatively un-reactive
glucose
what is the most abundant carbohydrate in nature
Cellulose
extractable by non polar solvents
lipids
fats, waxes, sterols, mono-di-glycerides, phospholipids
lipids
originate from ketoacyl and isoprene groups
lipids
simplest form of lipids
fatty acids
found primarily in plasma
fatty acids
solid storage form of lipids
triglycerides
primarily found in adipose tissue
triglycerides
major class of membrane lipids in a cell
phospholipids
largely determined by the length and degree of unsaturation of the hydrocarbon chain
physical properties of fatty acids
Carboxylic acids with a long aliphatic chain
fatty acid
what decreases with increasing length of a fatty acid chain?
solubility in water
what makes a kink in the linear structure of fatty acids?
cis double bonds
the most stable arrangement is very close packing of the side chains
saturated lipids
the carboxylic end of a fatty acid is ____ making it ____
Polar, Moderately water soluble
Fatty acids are esterified to glycerol to form?
triglycerides
What molecule is central to both carbohydrate and fat metabolism?
Acetyl-coA
Used as STORAGE FUEL
Triacylglyerols
______ has more energy present, are more “reduced” than cabs and not hydrated by water than ____
Fatty acids, polysaccharides
polar lipids derived from phosphatidic acid (1,2-diacyl-glycerol-3-phosphate)
phospholipids
long chain amino alcohol that does not has a glycerol backbone
Sphingolipids
Found largely in the outer face of plasma membranes
Sphingolipids
Involved as cell surface recognition sites
Sphingolipids
how to fatty acids bond to the Sphingolipids, which is unlike the bonding in glycerol?
amine linkage
sulfuric acid ester of galactocebroside
SULFATIDES
brain lipids, present in low levels in liver, lung, kidney, spleen, skeletal muscle, and heart
SULFATIDES
cell to cell regonition, hormone receptors
GANGLIOSIDES
complex glycosphingolipid
GANGLIOSIDES
responsible for inflammation in asthma an bronchitis and anaphylaxis
LEUKOTRIENES
also found in lung, spleen, brain, and heart
Leuktoreines
particles found in plasma that transport lipids including cholesterol
Lipoproteins
what does the liver repackages cholesterol into?
Lipoproteins
what takes lipids from small intestine into lymph cells
Chylomicrons
what are proteins with covalently attached lipids?
lipid-linked proteins
what are the three types of lipid-linked proteins
Prenylated proteins
Fatty acylated proteins
GPI linked proteins
What molecule is central to both carbohydrate and fat metabolism?
Acetyl-CoA
what is determined in part by the type of sugars located on head groups
Blood groups
what is esterified to glycerol to form Triglycerides?
Fatty Acids
what enzyme breaks down dietary fats into smaller molecules called fatty acids and glycerol
Lipase
do lipids or carbohydrates yield more energy?
Lipids
diffusion that uses no energy and molecules move from high concentration to low
Simple diffusion
small hydrophobic molecules cross the cell membrane by
simple diffusion
i.e. lipids O2 CO2
Movement of specific molecules down a concentration gradient, passing through the membrane via a specific carrier protein
Facilitated Diffusion
if the carrier protein of facilitated diffusion ever open all the way through?
No
is energy used in facilitated diffusion?
No
what types of molecules diffuse using a carrier protein
polar, hydrophilic molecules
the greater the difference in concentration on either side of a membrane does what to the rate of diffusion?
increases
diffusion is faster at higher or lower temperatures?
higher, more genetic energy
does increases surface area increase rate of diffusion?
yes
non polar or polar molecules diffuse faster?
non-polar
large molecules diffuse ..
slowly
uses ATP to drive molecules across the cell membrane
Active transport
Moves molecules against concentration gradient
Active transport
uses ATP dependent ion pumps
Primary active transport
passive transport of water moving freely in and out of the cell
osmosis
use electrochemical gradient of Na+ or H+ ions, or a membrane potential produced by primary active transport processes (sugars, aa)
secondary active transport
types of secondary transport
Uniport
Symport
Antiport
transport of a single solute
Uniport
2 different ions/molecules being transported at the same time but in opposite directions
antiport
caries two dissimilar solutes/substrates and transports them together
symport
GLUT1 glucose carrier in plasma membranes
Secondary active (uniport)
Glucose-NA
secondary active (symport)
Lactose permease
secondary active (H+ symport)
The energy value of fuels (calorie content) is calculated for the complete oxidation of the fuel
fuel/ calorie relationship
more reduced fuels (need more oxidizing) have …
higher calorie/g
Fats cals/g
9
alcohol cals/g
7
carbs cals/g
4
proteins cals/g
4
an estimate of how many calories you’d burn if you were to do nothing but rest for 24 hours
Basal Metabolic Rate (BMR)
represents the minimum amount of energy needed to keep your body functioning, including breathing and keeping your heart beating
Basal Metabolic Rate (BMR)
what percent of energy from food is converted into ATP?
40%
what percent of energy from food is lost as heat?
60%
what accounts for most of BMR
heat production by mitochondria
the maximal amount of energy that can be obtained from a reaction at constant temperature and pressure
Gibb’s free energy
free energy content of the final state minus the free energy content of the initial state
Gibb’s free energy
spontaneous, favorable rxn
Neg. Delta G
non-spontatious, unfavorable rxn
Pos. Delta G
how does ATP drive “uphill” rxns
when hydrolyzed ATP yield large neg delta G, allows unfavorable rxn to occur
for the reverse of Hydrolyzing glucose-6-phosphate into glucose and pyruvate to occur what must it be coupled with?
hydrolysis of ATP to ADP
how is the outer membrane of mitochondria different from the inner
outer: very permeable to ions & proteins
inner: impermeable to most things w/o carrier protein
what membrane of mitochondria contains components of oxidative phosphorylation (process of coupling oxidation of reduced nucleotide coenzymes to synthesis of ATP)
inner membrane
3 main Coenzymes
NAD+
FAD
FMD
Coenzymes NAD+ is used in what complex?
Complex I
Coenzymes FAD is used in what complex
complexes II, III, IV
coenzymes FMD is used in what complex
complex I
found in mito and ER, proteins that contain large heme groups but are not involved in oxygen transport
Cytochromes
inhibits respiration via proton channel of ATP synthase
Oligomycin
Shuttles e-‘s from complex III to complex IV
cytochrome C
how many cytochrome C molecules are required from reducing O2 to H2O in complex VI
4 b/c it only carries 1 e-
found in mito and ER, proteins that contain large heme groups but are not involved in oxygen transport
cytochromes
inhibit the coupling between the electron transport and phosphorylation reactions and thus inhibit ATP synthesis without affecting the respiratory chain and ATP synthase
uncoupler
bind to Hgb and inhibit oxygen transport, electron transport, and production of ATP
Mitochondrial Poisons
cells respond to this by switching to anaerobic metabolism, resulting in lactic acidosis and eventually death
Mitochondrial Poisons
what type of poising in CN or CO
Mitochondrial Poisons
what is a triglyceride
storage and transport form of lipids
where is triglyceride found?
adipose tissue
what is triglyceride made of
glycerol back bone & fatty acids
where isn’t triglyceride stored?
RBC’s & Brain
where is triglyceride stored?
liver, muscles, and tissues
how are lipids metabolized in the liver?
Acetyl-CoA → Ketone bodies (ketogenesis)
how are lipids metabolized in muscles?
TCA cycle oxidative phosphorylation for ATP production
triglycerides are broken down with
lipase
how are fats transported
chylomicrons
what regulated the speed at which triglycerides are hydrolyzed in adipose tissue?
hormones
where does beta oxidation occur?
mitochondria
what is a long chain fatty acid?
between 12-20 carbons?
where are long chain fatty acids metabolized?
mitochondria
how are long chain fatty acids metabolized?
carnitine cycle
How is glucose metabolism linked to lipid synthesis
Pentose phosphate pathway
what does Pentose phosphate pathway provide?
NADPH
process by which acetyl-coa is converted to fatty acids?
Lipogenesis
how many steps is Lipogenesis
2
the formation of malonyl-CoA from acetyl-CoA by acetyl-CoA carboxylase is what step of Lipogenesis
stage 1
the elongation of the fatty acid chain in two-carbon increments by fatty acid synthase is what step of Lipogenesis
stage 2
Triacylglycerol synthesis in liver
Glycerol kinase + phosphate
Triacylglycerol synthesis in fat cells
Dihydroxyacetone phosphate
what makes G3P
Dihydroxyacetone phosphate and Glycerol kinase + phosphate
Lipoprotein lipase is produced by?
Adipocytes
what does Lipoprotein lipase promote?
glycolysis (glucose uptake)
what does Lipoprotein lipase increase the synthesis of?
Triacylglycerol
what directs fat metabolism towards synthesis and storage ?
insulin
what does eating stimulate the production of?
insulin
Protein solubility increases due to shielding of protein charges
salting in, solubility purification
Protein solubility decreases with increasing ionic strength, competition for molecules
salting out, solubility purification
affinity chromatography that is ligand specific and is a single step process
Biorecognition
What are some ways to characterize proteins by separation methods
Size, charge, pH, pI
intermediate in the citric acid cycle used by cells to produce energy in the form of adenosine triphosphate (ATP) from food.
Fumerate
