Biochemistry Flashcards
what is the function of cholesterol on the cell membrane
cholesterol influences cell membrane rigidity by adding structure and integrity, which served to make the membrane less fluid,
decreasing cholesterol would make phospholipids pack less efficiently at high temps and making the membrane fluid and leaky.
what are the breakdown products of lipids ?
- the breakdown products of lipids are acetyl coA, malonyl co-a and glycerol.
what is the function of leptin, orexigenic peptides, and ghrelin
Leptin- suppresses appetite
Orexgenic stimulates appetite
Ghrelin stimulates appetite
what is an enzyme without its cofactor called
-apoenzyme
what is the function cofactors and coenzymes?
- small molecules that aid in the catalysis, often by binding to the enzymes active site
Name the 2 ways cholesterol is made
- de novo synthesis
- or derive cholesterol from LDL or HDL
- De novo synthesis, is cholesterol made within the body, not by diet, happens in the liver
- it is driven by acetyl coA and ATP
Describe a Non-competitive Inhibitor,
- Vmax reduced
- Km unaffected
what are the fat soluble vitamins, and where does the majority of fat digestion occur
ADEK
in the duodenum of the small intestine, they need pancreatice lipases
what are the two biggest factors that contribute to melting point ?
a) molecular size
b) intermolecular forces
double blonds or unsaturation would cause bends in the molecule and create a lower melting point
fully saturated, long larger fatty acid chains have higher melting points
how are conjugated proteins formed
proteins are covalently attached to the prosthetic groups to form conjugated proteins
what is the polycistronic mRNA
polycistronic mRNA- mRNA contains code for multiple proteins, and have multiple termination sequences. Since there are multiple stop codons, menans coding for multiple protiens
During low levels of oxygen which enzyme can be elevated?
Lactate Dehydrogenase, is active under anaerobic conditions, if oxygen cannot unbind hemoglobin , tissues would be under anaerobic conditions
- so then fermentation is favored,
- lactate dehydrogenase is a necessary enzyme in regenerating NAD+ for glycolysis
what is the function of transferrins, and describe the affinity relationship
- transport ions from outside the cell to inside the cell via acidic endosome
- transferrins to have a high affinity towards iron outside the cell(where iron is being collected)
-lower affinity towards iron in the new acidic environment (where iron is being delivered)
- the functional ability also will change when the pH changes as well
describe the difference between beta amylase and alpha amylase
Beta is more precise, and cleaves at the acetyl end of the polysaccharide to produce maltose
- beta can digest amylose, but cannot digest amylopectin, because of the 1,6 glycosidic branches
- alpha amylase cuts polysacchraides randomly to yeild shorter polysacchrisdes,
what does NMR Spectroscopy do?
- NMR is used in determining protein structure
describe affinity chromatography
- this method uses bound receptor and ligant to bind to protein of interest
how are beta glycosidic linkages formed? Structurally how are they made
- formed when the hydroxyl group is used to attach to the next monosaccharide to the parent carb chain.
- only cellulose is comprised of beta 1,4 linkages
- galactose has beta 1,4 glucose linkages, and it is called AKA lactose
- it has beta anomers joining their respective carbohydrate monomers
what type of carbohydrates are made from alpha linkages?
-starches formed by alpha linked glucose monomers
- fructose is a monosaccharide
- maltose is a disaccharide with alpha- glycosidic linkages
Competitive inhibition vs Noncompetitive vs uncompetitive
Competitive Inhibition- Km increased, Vmax unaffected.
Non competitive- Km reduced, Vmax reduced
Noncompetitive inhibition- Km unaffected, Vmax reduced
what is the relationship between dissociation constant and affinity
They are inversely related to the affinity
Difference between enhancer and promoter
Promoter- region is responsible for the initiation of transcription for a specific gene
Enhancer- where activators bind, and increase the transcription of a specific gene. Increases the rate of transcription.
cpG sites where are they located and what is their function
- located in the promoter regions of genes, that play roles in silencing, during X-inactivation
what is the function of hemoglobin?
Needed to transfer oxygen from blood to tissues
what type of cells do GLUT 4 receptors affect
Glut 4 in adipose tissue and muscle respond to glucose in the blood.
The rate of glucose transport is increased by insulin
Liver uses what type of glucose transporter
Glut-2
Break down what a glycerophospholipid is
A phospholipid that contains two fatty acid chains, a glycerol backbone, and phosphate group
what kind of glucose subunits is cellulose made of?
Beta 1,4 linked glucose subunits
what kind of subunits is amylose made of
alpha 1,4 linked glucose subunits
what is gel electrophoresis used for?
Technique used to separate macromolecules by charge and by size
what is southern blotting?
used to probe the presence of specific DNA sequences after they have been separated, it is not a separation technique
usually used in conjunction with Gel electrophoresis.
name the ketogenic amino acid
leucine
Describe Van Der Waals Interactions
result of rapid polarization and counter polarization of electron clouds of a molecule that form short lived dipole moments
- basically the stacking interactions DNA base pairs have
what mechanism is used for nucleotide synthesis?
Pentose Phosphate Pathway , it provides the raw products for nucleotide synthesis,
Such as ribose 5 phosphate
What processes does Growth hormone increase and decrease ?
GH promotes lipolysis in adipocytes
-Gluconeogenesis in the liver
-inhibiting Glycogenesis in the liver
- also stimulates IGF-1, that goes on stimulate protein building in muscles and osteoblast and chondrocyte activity to promote bone growth.
Describe how Erythrocytes get energy to function?
- Red blood cells lack mitochondria, thus they use anaerobic metabolism of glucose for their energy source
What kind of reactions does ligase carry out
- joining two large molecules by establishing a new chemical bond
- Esterification
Describe what transferase do?
- catalyze the movement of functional groups between molecules, this reaction is more of a synthesis between two large molecules
what kind of stabilizing bonds do primary, secondary, tertiary, quat use ?
primary structure - linear sequence od AA; peptide(amide) bonds
secondary structure- local structure determined by near by AA; alpha helix, beta pleated sheets; hydrogen bonds
tertiary Stru- 3D shapes of protein; hydrophobic interactions, acid-base salt bridges, disulfide links
Stabilizing bonds= van der waals, H-bonds, Ionic Bonds, Covalent bonds
Quaternary Structure- interaction between seperate subunits of a multisubunit protiein
Stablizing bonds same as tertiary
what are the 2 types of proteoglycans
- Conjugated proteins
-glycoproteins
What are proteoglycans?
- a molecule with a core protein, and one or more covalently attached polysaccharides
- found in connective tissues, surface and cells, and ECM
What do oxidoreductases do ? and what cofactors do they generally need?
Oxidoreduc catalyze oxi- red reactions, transfer of electrons between biological molecules.
Their cofactor is often NAD+ or NADP+
Enzymes in which oxygen is the final electron acceptor often include oxidase in their names.
- They are able to take a hydrogen from their cofactor to form reduced products or catalyze the reverse reaction to form oxidized products.
what is the function of transferase
- movement of a functional group form one molecule to another.
what enzyme does E3 of the PDH complex require
FAD is an intermediate requried for the reaction to be complete. FAD is first used to oxidize lipoic acid, and is then reduced to FADH2, which is later oxidized by NAD+ to make FAD.
- does not usually show up in net reaction when written.
what enzyme does E3 of the PDH complex require
FAD is an intermediate requried for the reaction to be complete. FAD is first used to oxidize lipoic acid, and is then reduced to FADH2, which is later oxidized by NAD+ to make FAD.
- does not usually show up in net reaction when written.
what are zwitterions?
Molecules that are electrically neutral, but have both positive and negative charges.
what are constitutional isomers?
- have the same molecular formula, but different structure
what is amphipathic and give is a few examples
- amphipathic means the molecule will have both a non-polar region, which is hydrophobic and a polar region, which is hydrophilic
- cholesterol
- triacylglycerol
- Soap
-glycerophospholipid
(long fatty chains, but then you have a polar head)
amphipathic lipids spontaneously organize themselves so that hydrophobic portions groups internally from water known as micelles.
Glut 4 is in what 2 kinds of cells in the body ?
Skeletal muscle cells
adipocytes
what is the deprotonated form of aspartic acid? and explain the relevance
deprotonated form of aspartic acid is aspartate
at physiological pH, aspartic acid amino terminus will be fully protonated, carbony deprotonated, and side chain will be deprotonated making it a net -1 charge
the polarity makes it favorable in aqueous solutions.
it is also the reason why acidic residues can buffer solutions
the ability for it to be able to accept a hydrogen without changing the pH of the solution.
what is the function of gap junctions, desmosomes and hemidesmosomes
gap junctions- in cell communication and allow for rapid exchange of ions and other small molecules between adjacent cells.
desmosomes- responsible for cell to cell adhesion. but do not function in connecting epithelial tissue to underlying structure.
hemidesmosomes- primary function is to attach epithelial cells to underlying structures, including basement membrane or the dermis.
what is the function of acetyl co A carboxylase
- enzyme that adds co2 to acetyl Co-A to form malonyl-coA that is a required step for fatty acid synthesis which happens in teh cytoplasm.
what kind of amino acids can be detected on UV-visible spec
- aa with presence of aromatic groups.
-tyrosine and tryptophan
what kind of amino acids can be detected on UV-visible spec
- aa with presence of aromatic groups.
-tyrosine and tryptophan
what is the nernst equilibrium/equation ?
- membrane potential , no net flux of that particular ion from one side of membrane to the other.
- rate of influx and efflux is the same/
what are 2 forms of lipoproteins that are richest in triacylglycerols
Chylomicrons= transport dietary fats and cholesterol to other tissues, produced in small intestine.
VLDL= used to transport triacylglycerols to other tissues, produced in liver
what part of the brain makes epinephrine
adrenal medulla makes 90 percent of the epi in the body.
Epi needs a thyroid hormone to have significant effect on metabolism.
- thyroid hormone increases the # of epi receptors on target cells.
what does the adrenal cortex produce
- aldosterone
- cortisol
posterior pituitary secretes what hormones
- ADH
- oxytocin
what is the function of a chylomicron and where is it made
formed in the liver
function primarily to transport dietary fats to other cells
what is the function of a chylomicron and where is it made
formed in the liver
function primarily to transport dietary fats to other cells
in Edman’s degradation what does the N terminal do and why
- a nucleophilic attack by the N-terminal nitrogen because the lone pair of electrons on the nitrogen on ammonia makes it an ideal nucleophile.
What does insulin stimulate?
- promotes glycolysis
- stimulates PFK-2
- those things help get glucose out of the blood
What do GLUT 2 receptors do
Glut2 transporters will only bind to glucose at high concentrations
Lower the Kd means what in terms of affinity?
Lower the kD means stronger binding affinity, and lesser tendency to to dissociate
what molecules indicate that the krebs cycle is producing sufficient energy and it is time to allosterically inhibit enzymes
those molecules are
ATP
Citrate, succinyl coA
NADH
NADH decreases the activity of all 3 regulated steps of krebs cycle
Protein primary structure is stabilized by
covalent peptide bonds
protein primary structure is represented by amino acid sequence
secondary structure is stabilized by
the local arrangement of the peptide backbone and is stabilized by hydrogen bonds
alpha helices and beta-pleated sheets
tertiary structure is
3d overall shape of single polypeptide chain
driven by hydrophobic interactions and is stabilized by noncovalent interactions like (H bonds, interactions) involving the side chains of the amino acids within the single polypeptide
describe quaternary structure
intermolecular interactions that results in multiple polypeptides coming together to form a single functional protein.
quaternary is stabilized by similar forces like hydrophobic interactions, H bonds, Electrostatic interactions
what are negative and positive controls
negative controls are experimental conditions in which change is not expected
positive control is where change is always expected to be observed
Difference between myoglobin and hemoglobin
Both are oxygen carriers:
Hemoglobin: found in RBCs, composed of 4 subunits that can each bind to an O2, exhibits cooperatively w/ subsequent binding of oxygen to each subunit (which is why the affinity curve is sigmoidal)
Myoglobin: found in muscle cells, monomeric (and therefore can only bind to one oxygen), does not show cooperatively, binds to oxygen much more tightly than hemoglobin.
This is important because hemoglobin is able to effectively offload the oxygen as it reaches muscle tissues.
what is the cori cycle
process of carrying lactate from muscle to the liver
Then taking the lactate converting it back to glucose, so then it can be in the muscles
It connects gluconeogenesis and glycolysis
what happens in size exclusion chromatography
separates molecules by size
Smaller molecules move slower, larger move faster
opposite of gel electrophoreisis
