Biochem Flashcards
How do enzymes change a reaction?
Lowers activation energy and are not changed or consumed during the course of the reaction.
DeltaG remains unchanged.
What do dehydrogenases do?
Catalyze oxidation reduction reactions, not transfer reactions.
What does the Michaelis Menten equation tell us?
Enzymes form enzyme substrate complexes which can either dissociate back into the enzyme and substrate or proceed to form a product
What happens at high concentrations of substrate when the enzyme concentration stays the same?
Reaction rate approaches minimal velocity and is no longer changed by further increases in substrate concentration. This levels off the reaction rate after an initial increase.
What is a holoenzyme?
Biochemically active compound formed by the combination of an enzyme with a coenzyme
What is an apoenzyme?
Enzyme devoid of it’s necessary cofactor and is catalytically inactive
What is a coenzyme?
Non protein compound that is necessary for the functioning of an enzyme
What is a zymoenzyme?
Inactive precursor of an enzyme
What determines an enzymes specificity?
The three dimensional shape of the active site
What is Km?
This is the Michaelis menten constant.
Concentration of substrate which permits the enzyme to achieve half vmax.
What is Vmax?
Reaction rate when enzyme is fully saturated by substrate. All binding sites are being constantly refilled.
Example: vmax is near 100mmol/sec, vmax/2 equals 50mmol/sec. so the substrate concentration giving this rate is 0.5 mM and corresponds to Km.
This is from a chart
At high concentration values of substrate how if the rate of reaction affected?
It will be very close to Vmax if the concentration value is significantly larger than the value of Km.
Competitive inhibitors
Same Vmax and higher Km
Competes for active site
Increasing substrate can overcome this
Creates a X in the Burke plot
Noncompetitive inhibitors
Decreased Vmax and same Km
Binds to free E or ES complex
Increasing substrate can not overcome this
Doesn’t bind at active site
Km unaffected
Vmax reduced
Comes to a point for the Burke plot
Uncompetitive inhibition
Binds to ES complex only. Increasing the substrate favors the inhibition because it creates more ES complexes for it to bind to
Km reduced
Vmax reduced
Parallel lines
What is a lyase?
Responsible for breakdown of a single molecule into two molecules without the addition of water or the transfer of electrons
Often form cyclic compounds or double bonds in the products to accommodate this
What is a ligase?
Enzyme that catalyzes the joining of two large molecules by forming a new chemical bond. Usually with accompanying hydrolysis.
What is a hydrolase?
Use water to break a chemical bond which typically results in dividing a larger molecule to smaller molecules
What is a transferase enzyme?
Class of enzymes that enact the transfer of specific functional groups from one molecule (called the donor) to another (called the acceptor)
Cooperative enzyme
Demonstrates a change in affinity for the substrate depending on how many substrate molecules are bound. 3 substrates bound means higher affinity than 2 or 1 substrates bound.
Example is hemoglobin.
How does the idea temperature for a reaction change with and without an enzyme catalyst?
The rate of reaction generally increases with temperature because of the increased kinetic energy of the reactants but reaches a peak temp because the enzyme denatures. In the absence of an enzyme this peak temperature is generally much hotter.
What is the function of SDS in an SDS page?
SDS solubilizes proteins to give them uniformly negative charges so the separation is based purely on size
How does electrophoresis separate proteins?
By charges. Use a pH that will cause all of the proteins to be positive or negative except for the one you are trying to separate. Want the one you are separating to be a different charge than the others. Don’t want it to be neutral or it won’t separate out. Can be achieved by comparing the PI to the pH of the solution. If PI is lower than the pH charge will be negative. If PI is higher than pH it will be positively charged. If PI equals PH then it is neutral
What are the most prevalent extra cellular proteins?
Keratin, elastin, collagen.
What are the primary cytoskeleton proteins?
Tubulin and actin
What is myosin?
A motor protein
What type of receptors are hormones most likely to act on?
Enzyme linked receptors and G protein coupled receptors.
Not as likely to use ligand gated ion channels because hormones are found in small concentrations but have large effects due to second messaging.
Ligand gated ion channels do not use second messengers
Sodium and potassium are used for
Action potentials and are found in their free states rather than bound to proteins.
Chloride is
Readily excreted by the kidney
Calcium is normally found bound to a protein because
It must be sequestered in the bloodstream and intracellularly because calcium is used for muscle contraction, exocytosis and many other cellular processes that must be tightly regulated
What are characteristics of antibodies?
Label antigens for targeting by other immune cells
Antibodies can cause agglutination by interaction with antigen
Have to heavy chains and two light chains.
DO NOT BIND TO MORE THAN ONE DISTINCT ANTIGEN
What ion channels are responsible for maintaining the resting membrane potential?
Ungated channels.
What are the components of all trimeric G proteins?
Galpha, Gbeta and Ggamma
Gs, Gi and Gq are subtypes of the Galpha subunit of the trimeric G protein and differ depending on the G protein coupled receptors function
Ion-exchange chromatography
Separates ions and polar molecules based on their affinity to the ion exchanged. Works on almost any charger molecule including large proteins, small nucleotides and amino acids.
Doesn’t work when pI is very close
Size exclusion chromatography
Molecular sieve,
Molecules in solution are separated by their size and in some cases molecular weight. Usually applied to large molecules such as proteins
Isoelectric focusing
Electrophoresis technique that separates proteins based on their isoelectric point (pI). The pI is the pH at which a protein has no net charge and does not move in an electric field
Native PAGE
Also known as a CN page. Separates acidic water soluble and membrane proteins in a polyacrylamide gradient gel.
Doesn’t use a charger dye so the electrophoretic mobility of proteins is related to the intrinsic charge of the proteins
Difference between gel and chromatography
Gel can only handle a small volume of protein so chromatography is used to separate larger volumes
How does the gel for isoelectric focusing differ from the gel for traditional electrophoresis?
The gel in isoelectric focusing uses a pH gradient. When a protein it in a region with a pH above its pI it is negatively charged and moves toward the anode. When it is in a pH region below its pI it is positively charged and moves toward the cathode. When the pH equals the pI the migration of the protein is halted.
Anode is positively charged
Cathode is negatively charged
UV spectroscopy
Best used with conjugated systems of double bonds. Things such as aromatic amino acids will be adequate for UV absorption
Affinity chromatography
Protein elites off of an affinity column by binding free ligand.
If the binding is not reversed the free ligand competes with the active site of the enzyme which lowers its activity
Bradford protein assay
Spectroscopic analytical procedure used to measure the concentration of protein in a solution. The reaction is dependent on the amino acid composition of the measured proteins.
The Bradford reagent (is blue) forms a complex with proteins in solution which shifts its absorption maximum from 465 to 595nm. The absorption is proportional to the amount of protein present
What property of protein digesting enzymes allow for a sequence to be determined without fully degrading the protein
Selectivity.
The selective cleavage of proteins by digestive enzymes allow fragments of different lengths with known amino acid endpoints to be created. Allows us to make a basic outline of the amino acid sequence
What developmental stage had the greatest nuclear to cytoplasmic ratio?
Blastula
Morula stage
Early embryo stage consisting of 16 cells (called blastomeres) in a solid ball contained within the zona pellucida
Mulberry
The blastula is formed from this
Blastula
Hollow ball of cells, referred to as blastomeres, surrounding an inner fluid filled cavity called the blastocoel
Zygote
A diploid cell resulting from the fusion of two haploid gametes. A fertilized ovum
What does the ectoderm give rise to?
Gives rise to the integument (epidermis, hair, nails, and the epithelial of the nose, mouth and anal canal, the lens of the eye, nervous system (including the adrenal medulla)
Lungs derived from ectoderm
What does the endoderm give rise to?
Epithelial linings of the digestive and respiratory tracts and parts of the liver, pancreas, thyroid and bladder.
What does the mesoderm arise?
Musculoskeletal systemic, circulatory system, excretory system, the gonads and adrenal cortex.
Cardiac muscle, skeletal muscle, red blood cells, smooth muscle in gut, tubule cell of the kidney
Where does the notochord form from?
The mesoderm.
Forms under the dorsal layer of the ectoderm.
While the neural tube forms from ectoderm, the notochord itself is mesodermal
What does the dorsal ectoderm form into?
Spinal cord and brain.
The influence of a specific group of cells on the differentiation of another group of cells is called
Induction
What is competence?
Refers to ability of a cell to respond to a given inducer but not the influence of the group of organizing cells
What is senescence?
Term for biological aging
What is determination?
Cells commits to a certain developmental pathway and eventually produces a specialized cell
(Cell fates)
Differentiation
Cells becoming specialized as the body develops
Autocrine signaling
Occurs she. A molecule is secreted by a cell and results in an effect on the same cell
Juxtacrine signaling
Occurs between adjacent cells but does not spread by diffusion. Ligand on one cell surface binds to a receptor on the other.
Paracrine signaling
Cell releases a substance that diffuser through the environment resulting in differentiation of a nearby cell
Endocrine signaling
A molecule is secreted that travels via the bloodstream to a very distant target
Telomerase
Synthesizes telomeres to counteract chromosome shortening during mitosis
What is epidermal growth factor?
Protein that stimulates cell growth and differentiation by binding to its receptor EGFR
Sonic hedgehog
Encodes by the SHH gene. Essential for embryonic development. Plays a role in cell growth, cell specialization and normal shaping of the body
Transforming growth factor beta
Cytokine belonging to the transforming growth factor superfamily. Controls cells growth, cell poliferation, cell differentiation and apoptosis
Nonpotent cell
Can’t differentiate
Totipotent cells
Can form all the cell types in the body plus the extra embryonic or placental cells
Pluripotent cells
Can give rise to all of the cell types that make up the body; embryonic stem cells are considered pluripotent
Multipotent cells
Can develop into more than one cell type but are more limited than pluripotent cells; adult stem cells and cord blood stem cells are considered multipotent
Apoptosis
Programmed cell death.
Occurs in multiple locations in order to ensure development of the correct adult structures such as between fingers and toes so we don’t have webbed fingers
Neurulation
Folding process in vertebrate embryos which includes the transformation of the neural plate into the neural tube. The embryo at this stage is termed the neurula
Complete regeneration
New tissue is the same as the lost tissue
Incomplete regeneration
After the necrotic tissue comes fibrosis.
Tissue is replaced by a scar by fibroblasts
What is the correct order of early milestones in embryogenesis?
Morula—->blastula——>gastrula
Teratogens
Any agent that can disturb the development of an embryo or fetus
Fetal circulation
In the umbilical cord there are more arteries than veins.
The foramen ovale is the only shunt that connects two chambers of the heart
The ductus venous is the only shunt that bypasses the liver
Blood flow in the ductus arteriosus is from the pulmonary artery to the aorta
When glucose is in a straight chain formation it:
Is one of a group of 16 stereoisomers
Glucose has 4 chiral centers not five.
The number of stereoisomers possible for a chiral molecule is 2^n where n is the number of chiral carbons
Epimers
Are monosaccharide disatereomers that differ in their configuration about only one carbon. As with all diastereomers they have different chemical and physical properties and their optical activities have no relation to each other
How are enantiomers optical activities related?
Equal but opposite optical activities
Aldonic acids are compounds that
Have been oxidized and have acted as reducing agents
Form after the aldehyde group on a reducing sugar reduces another compound becoming oxidized in the process
The formation of alpha-D-glucopyranose from Beta-D-glucopyranose is called:
Mutarotation which is the inter conversion between anomers of a compound.
Enantiomerization and racemization mean
The same thing as each other, the formation of a mirror image or optically inverted form of a compound
Glycosidation
Is the addition of a sugar to another compound
Why can ketone sugars act as reducing sugars?
Ketose sugars undergo tautomerization, a rearrangement of binds to undergo keto-Enol shifts. This forms an Aldose which allows them to act as reducing sugars
A ketone group alone cannot be
Oxidized
Anomerization
Refers to ring closure of a monosaccharide, creating an anomeric carbon.
Carbonyl carbon becomes anomeric carbon in ring(carbon to the right of the O) then ring works clockwise around ring and down Fischer projection starting with 1 to add substituents. Anomeric carbon is labeled 1
In the ring the substituent on the anomeric carbon can be in either position
What enzyme cleaves polysaccharide chains and yields maltose exclusively?
B-amylase.
Cleaves amylose at the non reducing end of the polymer to yield maltose exclusively
Alpha amylase
Cleaves amylose anywhere along the chain to yield short polysaccharides, maltose and glucose.
Debranching enzyme
Removes oligosaccharides from a branch in glycogen or starches
Glycogen phosphorylase
Yields glucose 1-phosphate
Maltose
Glucose and glucose
Alpha 1,4
Reducing sugar
Lactose
Glucose and glucose
Beta 1,4
Reducing sugar
Sucrose
Glucose and fructose
Beta 1,5
Plant sugar
Non reducing
Why is the alpha anomer of D glucose less likely to form than the B anomer?
The beta anomer undergoes less electron repulsion.
They hydroxyl group in the anomeric carbon of the beta anomer is equatorial thereby creating less steric hindrance than the alpha anomer which has the hydroxyl group of the anomeric carbon in axial position
Wheat two polysaccharides share all of their glycosidic linkage types in common?
Glycogen and amylopectin
Both demonstrate branching structure.
Both use alpha 1,4 and alpha 1,6 linkages
Cellulose
Beta 1,4 linkages
Glucoses together
Amylose
Alpha 1,4 glycosidic bonds
Connecting glucose
What is digestible by humans and is made up of only one type of monosaccharide?
Maltose. Disaccharide)
Alpha 1,4 linkages of glucose.
Cellobiose have same glucose subunits but has B glycosidic linkages which can not be cleaved by the human body
Mutarotation
Hemiacetal ring breaks open spontaneously and then reforms after bond is roared between C-1 and C-2 to produce either an alpha or beta anomer.
Hemiketal
Has an OH group, an OR group and two R groups and are formed from ketones
The cyclic forms of monosaccharides are
Hemiacetals and hemiketals
Glycolipid
Lipid with a carbohydrates attached by a glycosidic covalent bond. Maintains stability of the cell membrane and facilitates cellular recognition which is crucial to immune responses
Phospholipid
Make up cellular membranes
Form lipid bilayers because of their amphipathic nature
Consists of two hydrophobic fatty acid tails and a hyrophillic head consisting of a phosphate group
During saponification
Triacylglycerides undergo ester hydrolysis using a strong base like sodium or potassium hydroxide to form glycerol and fatty acid salts.
This is a cleavage reaction
Albumin
Fatty acids travel through the body bound to serum albumin
What is the structure of a steroid?
Three cyclohexane rings and one cyclopentane ring
Soap bubbles form because fatty acid salts organize into
Micelles
Steroid hormones are hormones that
Are produced in the endocrine glands and travel in the bloodstream to bind high affinity receptors in the nucleus. The hormones receptor binds to DNA, but the hormone itself does not
Why are triacylglycerols used in the human body for energy storage?
The carbon atoms of the fatty acid chains are highly reduced and therefore yield more energy upon oxidation
Fatty acid chains vary in length and saturation
Vitamin A
Fat soluble vitamin
Metabolized to retinal which is important for sight
Vitamin D
Is metabolized to calcitriol which is important for calcium regulation
Vitamin E
Fat soluble
Made up of tocopherols which are biological antioxidants
Vitamin K
Fat soluble
Necessary for the introduction of calcium binding sites such as during the posttranslational modification of prothrombin
Sphingolipids
They can have either a phosphodiester bond and therefore he phospholipids or have a glycosidic linkage and therefore be glycolipids
Not all sphingolipids have sphingolipids backbones
Used in ABO blood typing system
More saturated fatty acids (less double bonds) makes for a
Less fluid solution. This is because they can pack more tightly and form more noncovalent bonds
More double bonds (unsaturated) means more liquidy
Glycerophosphlipids
Are a subset of phospholipids as are sphingomyelins. Contain a glycerol backbone. Have a polar head group, glycerol and two fatty acid tails
Terpenes
Strongly scented molecules that sometimes serve as protective functions
Terpenes are steroid precursors
Made by plants and insects
One terpene unit=two isoprene units
Isoprene has 5 carbons so a 3 terpene unit would have 6 isoprene units which would give it 30 carbons
Cholesterol
A steroid precursor
Precursor for vitamin D
Cholesterol helps with membrane fluidity by stabilizing the membrane in high temps and prevents bunching of phospholipids in low temps to prevent stiffening of the membrane
Prostaglandins
Paracrine or autocrine hormones, not endocrine.
They affect regions close to where they are produced rather than affecting the entire body.
