Biochemistry Flashcards

Terms Definitions
Butenol
Prop-
Three Carbons
Ion
charged particle
Hydrophobic
Repels waterex: lipids
 
 
 
Lipids
fats, oils, waxes
*steroids: cholesterol*
1 glycerol + 3 fatty acidsstructure = phospholipids
saturated: all single bonds (-)- bad fat; solid at room temp
unsaturated: some doubles (=)- good fat; liquid at room temp
Example of a protein
DNA
hereditary information in cells
Neutron
an electrically neutral particle within the nucleus of the atom
Maltose
Maltose (Disaccharide Carbohydrate) - Glucose + Glucose (malt sugar)
Ribozymes
RNA that behave like enzymes.
rRNA
Ribosomal RNA
-part of the ribosome
-MOST abundant ~80% of total RNA
Stage clips
holds slide in place
polysaccharide
three or more monosaccharides linked by covalent bonds
what is BAC
bacterial artificial chromosomes. versions of E. coli F factor. inserts are as long as 300 kb. selectable markers. helicase to facilitate DNA replication. 3 loci for accurate positioning of low copy number plasmids to daughter cells.
Myoglobin
A monomeric protein that facilitates the diffusion of oxygen in vertebrates
Chaperones
Proteins that bind newly synthesized polypeptides & assist in proper folding
 
Increases rate of correct folding and prevents incorrect folding
Binds unassembled protein subunits, prevents incorrect aggregation
25,000
Number of biochemical reactions known to have a specific enzyme for enhancement
mRNA
messenger RNA
-encode the amino acids that make protein
Dependent variable
the results of an experiment
pH
the scale used to measure the concentration of Hydrogen ions
0- most acidic
7- distilled water
14- most alcaline
carbohydrates are composed of a _:_:_ ratio of carbon to hydrogen to oxygen
1,2,1
is the geiger counter qualitative or quantitative
qualitative.
Amino Acid
Amino Acid - Subunit of Proteins.
Basic R groups
Histidine (His, H)
Lysine (Lys, K)
Arginine (Arg, R)
 
Uncompetitive Inhibition
This plots as a parallel line
Esters
R-C-O-R (With an Oxygen double bonded to the Carbon)Formation of bonds by dehydration synthesisCombination of an acid with an alcohol
Differentiation
cells are specialized to do certain jobs
bacteria
One of five Kingdoms of organisms, having no complex, membrane-bound organelles or nucleus, and distinct from the Archaea.
induced fit
enzymes and substrate shift and modify themselves slightly to accommodate each other
in the enzyme lab, the enzyme was present in the ____
liver
With small protein MWs should you have a higher or lower % of arylamide
higher
What are nucleic acids?(DNA & RNA)
polymers of nucleotides
Primary structure
The linear sequence of amino acid residues in a protein
Regulatory Enzymes
The reaction product of one enzyme reaction becomes the substrate for the next
km=[S]
This equation is only true when Vmax is equal to 1/2Vo
Fine adjustment knob (Fine focus)
focus in small amounts
activation energy
minimum amount of energy required to convert a normal stable molecule into a reactive molecule
what are the levels of cAMP like in the presence of glucose
low
ethidium bromide
can be used to visualize DNA or proteinsIntercatalating agent used as fluorescent tag.
What type of R group is almost always the 1t amino acid in a polypeptide chain
Methionine
km
If a reaction is using more than one substrate, this is different for each substrate.
Lipids are made of ?
3 fatty acids and glycerol
Lipids
fats and oils
contain C, H, O (H and O greater than 2:1)
nonpolar
store energy
form cell membranes
insulates body
steroids
cushions organs
how does iptg induce expression
by binding to the lac repressor
Nucleotide excision repair is what?
 
what are the steps
NER repairs bulky adducts (thymine dimers) and damage not recognized by DNA glycosylases
 
Steps:
1) multienzyme complex scans DNA dbl helix
2) NUCLEASE cleaves phosph backbone on both sides
3) helicase unwinds area w/lesion
4) gap is repair by DNA poly and DNA ligase
V0= Vmax[S]/ km + [S]
This is the Michaelis Menten equation
equilibrium
The state of a system in which no net change occurs.
1) What causes hypoferremia?
 
2) What does hypoferremia limit?
 
3) During this situation what is not released?
 
4) In chronic situations what can Hypoferremia causes?
1) In acute infection IL-6 triggers liver to release hepcidin
 
2) limits bacterial growth and hydroxyl radical form. b/c low Fe
 
3) Fe is not released from macrophage for distribution to bone marrow for Hb syn
 
4) hypoferremia can result in ANEMIA
Cis conformation is less favorable due to 
steric inteference of alpha-carbon SIDE CHAINS
4 Forces that stabilize the double helix
Stacking interactions (Van der waals)
Hydrogen bonds
Hydrophobic effects
Charge-Charge
what does maintaining copy number depend on?
frequency of initiation of plasmid DNA synthesis
What is the structure of the 5' cap?
 
What is its role in mRNA's?
m7G==7 methyl guanosine
 
its role is to stabilize the mRNA molecule and binds a CBC protein to aid in export of mRNA to cytosol
also helps align mRNA on ribosome during translation
Hydrogen bond is MOST stable 
When the H atoms and the 2 electronegative atoms are aligned or nearly in line. Hydrogen bonds are highly directional
what are the functions of kinases
to transfer gamma phosphate of ATP to 5'-OH in DNA or RNA
TFIID binds what in Eukaryotic initiation?
 
TFIIH contains what activity and does what?
TFIID binds 1st via the TBP subunit w/TATA box
 
TFIIH contains helicase activity to unwind DNA & also is a kinase that phosphorylates RNA poly
Non-ionic detergent Triton X-100 and lipids
Mixed Micelle is composed of these two components.
What happens when RNA polymerase encounters a terminator sequence in DNA template?
it is transcribed into RNA and the RNA then forms hairpin which stops RNA poly and it dissociates
 
"once dissociated it rebinds w/sigma forming holoenzyme"
What is Ferritin and what does it as as?
intracellular Fe storage mol acting as buffer for Fe
If IRP binds to IRE at the 3' end it will?
stabilize mRNA resulting in increased protein translation
Propenone
But-
Four Carbons
Monomers
small molecules
Base
used for support
 
 
 
Enzymes
proteins at tertiary structure
induced-fit model, NOT lock-and-key
competitive inhibition: replaces substrate at active site
non-competitive: allosteric, feedback, operons
Hydrogen bonds
between base pairs
Nonpolar
no attraction to electrons
Lactose
Lactose (Disaccharide Carbohydrate) - Glucose + Galactose (milk sugar)
Allosteric Enzymes
Function through reversible, non-covalent binding of a modulator molecule
Ketone Group
R-CO-RSlightly PolarSoluble in waterCommon in SugarsOxygen is NEVER bonded on a primary Carbon.
Condenser
Diaphragm, controls amount of light
disaccharide
two monomers linked by dehydration synthesis
hydrophilic
"water loving," pertains to polar (charged) molecules that do not dissolve in water
Stringent
(referes to replicon) Plamsid encoded protein required for initiation of synthesis. Cannon be amplified by decreased protein synthesis.
Tertiary structure
The three-dimensional conformation of a protein
Linus Pauling
Proposed alpha-helix and beta-sheets as types of structures in proteins
Elements in a carbohydrate
C= carbonH=hydrogenO= oxygen
Sulfhydryl Group
R-SHorR-S-HCommon in Proteins, where it forms covalent bonds between polypeptides.Amino Acids with a Radical group that contains sulfur=Cystene Methionine
Glycogen
animal starch, how animals store excess carbohydrates
Antibodies
proteins made specifically to attack anything that is foriegn
Proton
a subatomic particle with a positive charge
give examples of saturated fats.
1. lard2. butter
Electroporation use what conditions
2500 v 6 ms
what is base-excision repair?
 
what recognizes and cleaves bond btwn base and deoxyribose?
 
what is this damaged bas called?
 
What removes sugar-phosphate backbone leaving gap
 
what fills and seals gap
single damaged base
 
DNA glycoslase
 
Apurinic or apyrimidinic site
 
AP endonuclease
 
DNA polym and DNA ligase
Alcohol R groups
Serine (Ser, S)
Threonine (Thr, T)
E.C. 6: Ligation (joining) of 2 molecules with hydrolysis of increased energy bond (condensation coupled to ATP hydrolysis)
Ligase
Amino Group
R-NH2Common in Nitrogen BasesPart of each Amino AcidWeak base in water, where it accepts a +
Surface tension
caused by asymmetries in the intermolecular forces between surface molecules
cytoskeleton
A filamentous network within a cell that provides structure to the cytoplasm.
purine
one of the two families of nitrogenous bases found in nucleotides
A- Adenine
G- Guanine
plants store energy in the form of what polysaccharide?
starch
what types of cells express the proteins
tuner cells
DNA is written in which direction?
5' to 3'
Ion product of water 
Kw = [H+][OH-]
 
Kw= 1.0X10^-14 M^2
Protein Kinase
How does a phosphate group get added?
Matter
anything that has mass and takes up space
Catabolism
reaction in which a large molecule is broken into two smaller molecules and energy is released
prokaryote
A historical term used for any species now classed in the Bacteria or Archaea, often used to contrast these with eukaryotes.
What is formed when lacZ alpha and omega come together?
beta galactosidase
1) What is apotransferrin?
 
2) What does apotransferrin do?
 
3) Where does this apotransferrin transport Fe to?
1) empty transferrin
 
2) binds Fe3+ at enterocyte or from internal stores 
 
3) transports Fe to all growing cells
Hydrogen donor
Atom to which H is more tightly associated. O-H, N-H
Steady State Assumption
The initial velocity of a reaction reflects a steady state where ES is constant or ES formation is equal to ES breakdown
Amino acids are joined together by the process of
Dehydration synthesis
what is another name for the R group
side group
What does chloramphenicol act on
it inhibits the peptidly transferase on 70s ribosomes. causes decrease protein synthesis and decreased hot DNA synthesis
What initiates elongation in eukaryotes?
 
What does elongation induce?
kinase phoshporylating the RNA polym causing conformational change so it releases itself
 
supercoiling
k-1 [ES] + k2[ES]
Equation for the rate of product breakdown
what is the building block for carbohydrates?
sugar monosaccharide, or simple sugar
If IRP binds 5' IRE then?
prevents translocation of mRNA so decreased protein syn
For a solution pH ABOVE the pKa
The UNPROTONATED form predominates (B)
besides containing carbon and hydrogen organic compounds are characterized by
usually but not always containing oxygen.covalent bond between atoms
What is kanamycins mode of action
IT binds 3 ribosomal proteins and specific bases in 30s ribosomal units. Its an aminoglycoside antibiotic. Polycations diffuse through porin channels in outrer membranes of gram-negative bacteria. Engergy driven transport via negative membrane potential into cytoplasm. They decrease protein synthesis and increase transcriptional errors
1) Can DNA polymerase initiate syn of primer de novo?
 
2) what enzyme is required to generate primer?
 
3) What primer is syn that is used for extension by DNA polym?
1) no
 
2) primase
 
3) RNA primer which provides 3' OH for extension
COO, NH2, aromatic OH, histidyl groups, R-OH, S
6 groups that can act as nucleophiles
what are the components of PCR reaction
1. buffer(containing Mg++) to keep ph consistant.2. Template DNA3. 2 primers to flank the copy to be replicated.4. dNTPS5. taq polymerase
What does export ready mRNA mean?
 
What does it have to have?
export ready mRNA is capable to go from nucleus to cytoplasm **selective**
 
1-CAP binding complex
2-RNA export factors
3-snRNPs absent
They shake apart because they are held together by weak interactions.
Why are high MW less stable?
1) what does topoisomerase 1 do? Does it require ATP?
 
2) Type II topoisomerase works how? Does it require ATP?
1) Type I creat transient single stranded break in DNA
 
2) Type II transiently breaks double stranded breaks in DNA
1) What has to happen to form heme?
 
2) What is heme controlled by?
 
3) What is the rate-limiting step and what two isoenzymes is there?
1) Fe must be inserted into the porphyrin ring to form heme
 
2) syn of heme is controlled by [Fe] & [heme]
 
3) rate limiting step is syn of enzyme of ALA-S,
ALA-S1-cytochrome syn
ALA-S2-hemoglobin syn
What does it mean for SNPs to have extremely tight association btwn given allele and the SNPs surrounding it?
if a SNP is associated w/given allele, there is an extremely high probability that the presence of the SNP indicates the presence of that allele
C6H12O6
glucose
ion
charged atom
Organic Compounds
contains carbon
Elastin
Stretchy proteinPrecursor: Tropoelastin with fibrillin scaffoldingLungs, large arteries, elastic ligaments, vocal cords, ligamenta flava (connect vertebrae --> relaxed and stretched conformations)Rich in proline and glycine, nonglycosylated formsBroken down by elastase, which is normally inhibited by alpha1-antitrypsinMarfans (fibrillin defect) and Emphysema (alpha1 antitrypsin deficiency)
DNA ligase =
seals
Digoxin
Inihibit Na/K+ pump
energy
capacity to cause change
Losartan
AII receptor blockerdecreases BP
AA precursor to histamine
His
Biotin deficiency -->
dermatitis, enteritis
Citrate shuttle
SYtrate = Synthesis
Carbohydrates
consist of hydrogen, oxygen, carbon
molecule
smallest unit of most compounds
tRNA structure
75-90 ntSecondary structure: cloverleaf form, anticodon end is opposite 3' aminoacyl end.CCA at 3' end with base, covalently bound
Compound that inhibits ATP/ADP translocase
atractyloside
insulin
activates protein phosphatases which can dephosphorylate ACC and activate it in the fed state.
Hunter's syndrome:inheritanceenzymeaccumulated substratefindings
XRiduronate sulfataseheparan sulfate, dermatan sulfatemild Hurler's + aggressive behavior, no corneal clouding
Complete beta-oxidation of a 12-carbon fatty acid produces ___ molecules of acetyl-CoA.a. 2b. 4c. 6d. 12
C
FAP
FAP = Familial ADENOMATOUS POLYPOSIS
ribose
a white, crystalline, water-soluble, slightly sweet solid, C5H10O5, a pentose sugar obtained by the hydrolysis of RNA.
polar molecule
asymmetrical (eg H2O); strong attractions exist between polar molecules; so usually exists as solid/liquid @ room temp
Isomers
Organic compounds with the same chemical formula but different structural formulas. Isomers have different properties. Three types: structural, geometric, and enantiomers (mirror images). Ex. three isomers of C6H12O6 = glucose, galactose, and fructose.
~440 kDa glycoprotein of the extracellular matrix that binds to integrins, collagen, fibrin, and syndecans. Solube form of this protein is a major protein component of blood plasma (300 μg/ml) and is produced by hepatocytes
fribronectin
Type II collagen
Cartilage (including hyaline), vitreous body, nucleus pulposus
Sphingolipidoses defect
Tay Sachs
(Hereditary defect in lysosomal enzymes that degrade sphingolipids)
Deamination of aspartate yields what?
oxaloacetic acid
Other fate of citrate

converted to FA's
TAG
phospholipids


converted to cholesterol
hormones
bile salts
secretin
peptide hormone produced by other intestinal cellsin the pancreas to release bicarbonate solution  neutralize pH for enzyme activity
Pyruvate Dehydrogenase
Transforms pyruvate into acetyl-CoA (used in the citric acid cycle to carry out cellular respiration). Links the glycolysis metabolic pathway to the citric acid cycle and releasing energy via FADH2.Def = low energy, lactate buildup, lactic acidosis in newborns: severe lethargy, poor feeding, tachypnea, death
Chemoautotroph
an autotroph who tranforms evergy from chemicals into chemical bond energy
sucrase
hydrolyzes sucrose into glucose and fructose
Dominant negative mutation =
heterozygote makes nonfunctional/altered protein that prevents normal gene product from functioning
Mutations result in unrestrained growth
Labile cells
2. Inhibits FERROCHELATASE *Protoporphyrin + Fe2+ --> Heme*CO-PRO-PORPHYRIN buildup
Acute Intermittent Porphyria
glucose
a sugar, C6H12O6, having several optically different forms, the common dextrorotatory form
cellulose
an inert carbohydrate, (C6H10O5)n, the chief constituent of the cell walls of plants and of wood, cotton, hemp, paper, etc.
Nucleic Acids
very large and complex organic molecules that store and transfer important information in the cell
amphipathic molecule
has both polar (hydrophilic) and nonpolar (hydrophobic) regions
hydrocarbons
organic molecules that are composed of only carbon and hydrogen
enzyme
regulates the rate of a chemical reaction
organic
term used to describe molecules that contain both carbon and hydrogen
Fermentation
in anaerobic conditions NAD+ cannot be regenerated through the oxidation of pyruvate and NADH
 
in animal tissues - fermentation of pyruvate to lactate
in microorganisms - fermentation of pyruvate to ethanol
Purines
A GGuanine has a ketoneamino acids necessary for purine synthesis: Glycine, Aspartate, Glutamine
SCID
Can be caused by deficiency of adenosine deaminase (ADA) -- excessive ATP and dATP which inhibits ribonucleotide reductase and prevents DNA synthesis; B and T cell deficiency -- recurrent infections
Inhibition of Xanthine Oxidase
e.g. ALLopurinol (hypoxanthine analog)-outcompetes hypoxanthine for binding site---hydroxylation occurs and the result compound, alloxanthine has an even higher affinity to XO and blocks production of uric acidHypoxanthine and Xanthine tend to accumulate-can be ridden off easier b/c they are water-soluble by the kidneys
What is present in human erythrocyte membranes in much larger amounts than in rat liver membranes?
Sphingomyelin
Mechanism of ubiquinylation
ubiquitin activated by ATP
ubiquitin adenylated by ubiquitin activating enzyme E1
E1 tranfer ubiquitin to own cysteine residues
ubiquitin transferred to Cys residue in ubiquitin conjugating enzyme E2
ubiquitin protein ligase E3 tranfer ubiquitin to Lys residue on on target protein: histone
ubiquitin pushes apart chromatin via steric hinderance
If you get 4 ubiquitins, you degrade the histones.
Ratio of babies born with birth defect
3/100
nucleotide
ribulose 5-P--> ribose 5-P is an isomerization that is involved with what type of metabolism
Thymidylate synthase
Thymine, a methylated analog of uracil.____ ____ methylates deoxy uridylate (dUMP) to Thymidylate (TMP). Facilitates the identification of DNA damage for repairMethyl donor is N5,N10-methylene tetrahydrofolate Loses both its methylene group and a hydride ion  oxidized to dihydrofolate. Tetrahydrofolate regenerated by dihydrofolate reductase with the use of NADPH as the reductant
Osteogenesis imperfecta =
AD disorder, abnormal collagen synthesis at triple helix step --> multiple fractures, blue sclera, bad teeth, hearing loss
metabolism
the total of all chemical reactions in an organism
Under aerobic conditions in the body, pyruvate is converted to:a. lactateb. acetyl- CoAc. ethanold. acetaldehyde
B
VitD overdose -->
hypercalcemia, loss appetite, stupor, seen in SARCOIDOSIS!
(recall: macs make active D3)
condensation synthesis is also known as
dehydration synthesis
Serotonin --> Melatonin*Turkey nap
Niacin --> NAD+/NADP+*Requires B6
"Scalding coffee"*KyphoSCOLIOSIS*Cafe au lait spots
Tumors: PALON*Pheos*All tumors (inc. skin fibromas)*Lisch nodules (pigmented iris hamartomas)*Optic gliomas*Neural tumors
polymer
a compound of high molecular weight derived either by the addition of many smaller molecules, as polyethylene, or by the condensation of many smaller molecules with the elimination of water, alcohol, or the like, as nylon.
SPONCH
the 6 most abundant elements in living things
Carboxylic Acid
-an organic acid characterized by one or more carboxyl groups
-COOH
steroids
lipids that consist of 4 fused rings. eg: cholesterol, testosterone, estradiol. some steroids are hormones. cholesterol functions in animal plasma membranes.
quaternary structure
The particular shape of a complex, aggregate protein, defined by the characteristic three-dimensional arrangement of its constituent subunits, each a polypeptide.
inorganic
a type of molecule that does not contain both carbon and hydrogen but can contain any other combination of elements
Bilayer Fluidity
Fluidity is controlled by fatty acid composition and cholesterol
 
depending on temperature, membranes can exist as a gel like solid or a more liquid like state called a liquid crystal some areas are ordered and some are not
 
the sharpness of the transition between gel and liquid crystal depends on
-fatty acid chain length
-degree of saturation
-cholesterol content (in animals only)
 
Southern blot
DNA sample electrophoresed on a gel transferred to filterfilter soaked in denaturantfilter exposed to labeled DNA probe that recognizes and anneals to its complementary strandresults in double stranded labeled piece of DNA which can be visualized when filter is exposed to film
Hemoglobin C
Mutation of Glu to LysMild chronic anemia
which factors must fall off in order for the 60S subunit to bind with the 40S subunit?
eIF2-GDP
Name naturally occuring uncouplers
UCP 1 (thermogenin)
UCP 2
UCP 3
Define mosaic
Individual who has more than one genetically distinct cell lines in his/her body
action of erythromyocin
bind 50S subunit and inhibit translocation
Malonyl CoA
inhibits CAT-I so that when FA synthesis is in progress, the product cannot be transported for oxidation.
AST
what is the marker for 24-36 hours after MI?
H1 ties nucleosomes together in a ___-nm string.
30 nm
reductionism
a complex phenomenon such as life can be eventually understood by analyzing its simplest components
What metal ions are present in the cytochromes of the ETS aid in the passage of electrons down the chain?a. Cr+++ and Ca++b. Fe++ and Fe+++c. Zn and Zn++d. Na+ and Mg++
B
VitC deficiency -->
scurvy: swollen gums, bruising, poor wound healing
Degradation of TG's circulating in chylomicrons and VLDLs
Hepatic TG lipase
cholesterol
a sterol, C27H46O, that occurs in all animal tissues, esp. in the brain, spinal cord, and adipose tissue, functioning chiefly as a protective agent in the skin and myelin sheaths of nerve cells, a detoxifier in the bloodstream, and as a precursor of many
strong vs weak acid
strong acid ionizes completely--one arrow, weak acid does not ionize completely, have only partial ionization and a reversible reaction
allosteric activator
binds to the enzyme and induces the enzyme's active form
Kilocalorie
Energy needed to raise 1 kg of water 1ºC
tissue specific metabolism of glucose
 
muscle
-converts chemical energy to mechanical energy
 
-mostly catabolic tissue - burns glucose and fat for energy
 
-limited anabolic potential - stores glucose in glycogen, makes tissue specific proteins
Golgi apparatus roles (6)
1. distributes proteins and lipids from ER to plasma membrane, lysosomes, and secretory vesicles2. modifies N-oligosaccharides on asparagine3. Adds O-oligosaccharides to serine and threonine residues4. adds mannose-6-P to specific lysosomal proteins -->targets protein to lysosome (I-cell disease)5. proteoglycan assembly from core proteins6. sulfation of sugars in proteoglycans and of selected tyrosine on proteins
DNA polymerase I excises RNA primer with __ -> __ exonuclease.
5' -> 3'
Process of diagnostic microarrays
remove tumor tissue
make labeled tumor cDNA or cRNA

add to DNA microarray
each "minislide" in the microarray reperesents a specific sequence found at a target gene (know due to human genome project)
comparatively analyze gene expression
find the molecular signature that will signify good or bad prognosis
Where do eukaryotes receive exonuclease activity from?
Unlike prokaryotes using DNA polymerase, this one has separate enzymes throughout the body to assist in proofreading.
Function of SWI/SNF
using ATP, push away nucleosomes to expose DNA sequences
Methalonyl CoA+ Succinyl CoA
In the biosynthesis of Nonessential Amino acids the two end products formed by Valine are?
energy of activation
energy difference between that of the reactants and a high-energy intermediate that occurs during the formation of product
450. What couples the citric acid cycle and the urea cycle?
The aspartate-argininosuccinate shunt
What is CTP?
Product of ACTase reaction, serves to inhibit it. - when bound, enzyme is in T-state - interacts with regulatory chain, not catalytic chain
What is the test to detect B12 deficiency?
Schilling test
Mitochondrial inheritance patterns
All offspring of affected females may show signs of disease
Enter your front text here.
Enter your back text here.
heat of vaporization (water)
evaporating water requires a LOT of heat (evaporation of sweat cools body surface)
With what microdeletion is Williams syndrome associated?
long arm of chromosome 7
Type IV Hyperlipoproteinemia (Familial hypertriglyceridemia)
AD; Hepatic overproduction of VLDL; increased TGs in blood beginning at puberty; inc coronary artery disease and peripheral vascular disease; Standing chylomicron test: turbid infranate
When regulating protein synthesis, the cell can phosphorylate ______ to deactivate it and thus stop overall protein synthesis.
eIF-2 (eukaryotic initiation factor 2)
calorie value within a gram of carbohydrate
4 kcal/gram of carb
Compare the number of origins of replication sites in prokaryotes and eukaryotes.
prokaryotes- one
eukaryotes- many
ALL THESE ORIGINS ARE SEQUENCE SPECIFIC!!!!!
Example of post-transcriptional RNA editing- apolipoprtoein
apoB48 found in intestines (form chylomicrons)
apoB100 found in liver (LDL/lipid trafficking)
3-L-Hydroxyacyl CoA dehydrogenase
converts OH to a keto group producing NADH which gives 3 ATP in ETC
What disease makes urine turn black on standing and makes connective tissue dark? May have arthralgias but otherwise benign condition.
Alkaptonuria, deficiency of homogentisic acid oxidase in degradative pathway of Tyrosine
There is one uncommon base that is used especially in tRNA. What is it's name(s)
Inosine aka hypoxanthine
What are 3 autosomal trisomies?
1) Down's (21)
2) Edwards (18)
3) Patau's (13)
Pyruvate = Acetyl CoAAlpha-KG = Succinyl CoA
TCA cycle: Products and energy
On what chromosome is the gene associated with Lisch nodules, skeletal disorders, and optic pathway gliomas found?
long arm of chromosome 17
n DNA mismatch repair in E.Coli, a protein-protein interface between Mut H and Mut S is thought to be achieved by a protein termed ______
Mut L(Mut L Links)
How do uncouplers work?
they prevent a lot of the hydrogen produced by ETC from going through complex, and it basically disipates the gradient so that energy can be used as heat
allowing ATP production
Other fates of succinyl CoA
can be converted to heme
can be produced from propionyl CoA
Role of SCAP (SCREB cleavage activating protein)
SCAP bind cholesterol
in presence of cholesterol, SCAP binds SCREBP
this causes them to stay in the ER (SCREB cannot be cut, so now we cant make our TF)
DNA repair defects:Xeroderma pigmentosum ~ ___Ataxia-telangiectasia ~ ___Bloom's syndrome ~ ___Fanconi's anemia ~ ___
XP ~ UV lightAT ~ xrayBS ~ radiationFA ~ crosslinking agents
Why is it called the 3' end?
the last phosphodiester bond (hydroxyl) on the last nucleotide is connected to Carbon 3
What does adenylate kinase do?
It catalyzes the transfer of terminal phosphate group from ATP onto an NMP
Aberrant METHYLATION, expression of FMR1*Chromosome becomes fragile*Triplet repeat: CGG*Expansion in females
2nd most common cause of genetic mental retardation (DS = #1)
Cholera toxin and EHEC toxin
Permanently activate Gs -- inc cAMP -- secretory diarrhea
Name the difference between a blunt end and sticky end
blunt end- cut evening and symettrically
sticky end- cuts so there is an overhang
Effect of mutation on p53 structure
turns into a tetramer that is functionally inactive
Fate of LDL in liver
LDL binds to LDL receptors (IDL could bind as well due to its apoB100)
forms endosome
esterfy LDL and decrease pH (use pump), leading to its separation from its receptorone endosome w/receptor goes back to membrane
another endosome with LDL fuses with lysosome will be broken down via degradative enzymesrelease phospholipids
convert cholesterol esters back to cholesterol and FA;s
degrade apoB100 to AA's that can be recycled in cell protein population
548. How long does your protein supply last?
nasty cannibal.2 weeks if you're lucky
What do you find with Down's syndrome?
1) mental retardation
2) flat face
3) simian crease
4) heavy epicanthal folds
5) duodenal atresia
6) septum primum ASD
7) inc. risk ALL
Loads AA onto the appropriate tRNA
Uses 2 phosphate bonds (ATP --> AMP)
In E. Coli, pyrimidine dimers that are to be repaired through excision repair are recognized by a complex known as
uvrABC(ultra violet repair, a big complex)
Where NAD and NADP function and the mobile group of the reaction
function at active site of dehydrogenaes
mobile group- hydride ion
TF that must be present for RNA polymerase to bind in eukaryotic transcription
TF IIA
TF IIB
TF IID
TF IIE
TF IIF
438. Where is urea made?
In the urea cycle in the cytosol of liver cells
How is energy trapped to form ATP using protons?
the protons that were vectorally pumped are returned to the matrix through a pore in the ATP-synthase complex
The Omega 3 FA's DHA and EPA have also been shown to be important for
normal brain development and function
Steps of alpha keto acid dehydrogenase rxn
add alpha keto acid to TPP in decarboxylase
carbon dioxide leaves decarboxylase-TPP complex
the RC=O group binds to lipoic acid in trasnferase complex
CoA-SH pick up R=CO, causing two H's to come back to lipoic acid in transferase

dihydrolipoyl dehydrogenase picks of hydride ions via FAD as its coenzyme
this will reform the ringed structure of the lipoic acid within transferase
to regenerate FAD in dihydrolipoyl dehydrogenase, NAD will pick up the hydrides from FADH2
386. What are the four functions of nucleotides?
1. Precursors for RNA and DNA2. Energy (i.e. ATP)3. Signaling Molecules (cAMP)4. Phosphate donors for protein modification
Tendency for alleles at linked loci to occur TOGETHER more often than would be expected by chance
Measured in a populationMay vary by population
Rxn cat. by amino acyl tRNA synthetase
AA + ATP + tRNA + H2O → aminoacyl-tRNA + AMP + 2P
Fate of coenzyme in rxn if it is a prosthetic group
prosthetic group does not leave the active site
Polyneuropathy
Pink urine
carboxyl
O=C-OH carboxyl (acid)
Coenzyme of niacin
NAD
NADP
Reductase
(oxidoreductases...common name) Electron transfer between any 2 compounds.
Proteins
most complex biological macromolecules
made up of C,H,O,N, and S
subunits-amino acids 8 essential- which are joined by peptide bonds
a chain is called polypeptide
a proteinis one or more polypeptide chains working together to perform a particular function or functions
chitin
polysaccharide; exoskeleton of insects
PRPP
-activated form of ribose-5-phosphate-used in both purine & pyrimidine biosynthesis but in different ways*PRPP- activates amidophosphoriribosyl transferase and thus its consumption in the de novo pathway
FA degredation
is mitochondrialDegradation intermediates carried by CoA
C-II apolipoprotein
COFACTOR for LPL
Increases intracellular Ca2+ indirectly --> Contractility
Collagen
Goodpastures
Antibodies against basement membrane of pulmonary and GBM capillaries (those basement membranes look like some good pastures)Basement Membranes = type IV collagen
Function of vitamin D
calcium homeostasis
angiotensin II
increased conversion of corticosterone to aldosterone in the zona glomerulosa
565. What is ghrelin?
Appetite stimulant
W
Writhing number
# of supercoils present
-right handed supercoil is negative
left handed is positive
Common causes:*Fava beans*TB drugs*Sulfonamides, primaquine
Fructose intolerance
starch
a white, tasteless, solid carbohydrate, (C6H10O5)n, occurring in the form of minute granules in the seeds, tubers, and other parts of plants, and forming an important constituent of rice, corn, wheat, beans, potatoes, and many other vegetable foods.
COX (cyclooxygenase) initiates the ___ pathway
cyclic
Substrate
the substance an enzyme acts upon
organic chemistry
the study of carbon compounds
MONOSACCHARIDES
a simple sugar glucose, fructose, galactose
antiporters
2 molecules cross membrane in different directions out of cell
 
1 molecule with concentration gradient, 1 against
 
Achondroplasia
ADcell signaling defect of fibroblast growth factor receptor 3dwarfism, short limbs, with normal trunk and headassociated with advanced paternal age
Methylene THF
-deliver methyl group (Thymidilate synthae) rxn to form DHF (oxidized)-serves as reducing agent (aldehyde to alcohol)
Structure of ATP synthase
transmembrane

contents

F1- the head
3 alpha (do not move)
3 beta (do not move)- have binding units for synthesis of ATP
gamma (shaft in btw alpha, beta)
delta
epsilon


F0- the body
a protein (proton pump)
b2 protein

c protein (8-10 proteins that make up a circle)
in the center of each c protein is Asp
acts as a rodor
binds to epsilon and gamma units and spins with c as the rotor



alpha, beta, delta, b2, a subunits anchored to inner mitochondrial matrix
Missense mutations
mutation of single nucleotide, altering code in triplet sequence, making it code for a different AA (ex: sicke cell)
B48
consists of lipoprotein CM and carriers cholesterol esters
enzyme
a biomolecule that catalyzes a chemical reaction
glycosaminoglycans (GAGs)
Polysaccharides that contain amino groups or modified amino groups. Most are repeating disaccharidesCommon in extracellular structures of organisms i.e, cartilage, vitreal humor of eye, synovial fluid.
VitD deficiency -->
rickets, osteomalacia, hypocalcemic tetany
BidirectionalThings which sample (islet), reabsorb (kidney) or produce (liver) glucose
B islet cellsLiverKidney
Gluconeogenesis
OAA --> PEP circumvents the irreversible glycolytic step of PEP --> Pyruvate
glycerol
a colorless, odorless, syrupy, sweet liquid, C3H8O3, usually obtained by the saponification of natural fats and oils: used for sweetening and preserving food, in the manufacture of cosmetics, perfumes, inks, and certain glues and cements, as a solvent and
pI
isolectric point, pH where the molecule exists in a neutral state
reactants
the starting materials in a chemical reaction
Hydrogen Shell
Sphere of water molecules around dissolved ions in a solution
Radioisotopes
isotopes that have unstable nuclei and undergo radioactive decay
Fructose 2,6 Bisphosphate
fructose 2,6 bisphosphate is synthesized from fructose 6 phosphate
-when fructose 6 phosphate abundant fructose 2,6 bisphosphate increases
 
Fructose 2,6 bisphosphate binding to PFK increases affinity for fructose 6 phosphate and decreases inhibitory effects of ATP
 
net effect is to increase glycolysis when glucose is abundant
Transition
substituting purine for purine or pyr for pyr
Carcinoid syndrome
serotonin increased -- diarrhea and flushingleads to increased tryptophan metobolism and therefore pellagra (B3 def)
Acetylation of histones leads to their activation or deactivation?
activation
Most common secondary structures
alpha helix
beta confirmation
random coils
Define Kwashiorkor syndrome
protein deficiency with sufficient calloric intake (protruding abdomen)
Symptoms/signs of Xeroderma pigmentosa
multiple skin cancers
corneal scarring
cAMP pathway
pathway activates protein kinase which phosphorylates HSL, activating it.
liver specific
LDH type 4 is ____ specific
Glucagon turns glycogen synthase ___, glycogen phosphorylase ___.
OFF, ON
What is Coulomb's law?
E=k(q1q2)/r2DE: forceD: dielectric constant
T/FKetone bodies are formed when the concentration of acetyl-CoA in the cytoplasm is very high.
F
Reverse Transcription:
(cap) eukaryotic mRNA (polyA tail) ---> RNA-DNA hybrid --> single stranded DNA --> double stranded DNA
DC VeGaN*Progressively squishier
Desmin --> MuscleCytokeratin --> Epithelial cells
energy rich
containing great amounts of energy; chemical bonds
Transport proteins
transport materials into and out of cells
neutrons
the particles of the nucleus that have no charge
Molarity
The number of moles of solute per liter of solution
FAtty acid
a hydrocarbon chain with a carboxyl group at one end
What is another name for glucose-6-phosphatase deficiency?
von Gierke disease
tRNA wobble
3rd nt position of codondue to degeneracy (redundancy) of genetic code
NDP Kinase
-can extract the phosphate from any NTP and transfer it to the substrate NDP -catalyze ATP conversion to ADP & NTP-P-produced by the reaction: NDP + NDP Kinase-P to yield NTP & NDP kinase
Nucleotides are linked by:
3' - 5' phosphodiesterase bond
Function of DHA in body
brain development
normal function of membranes of rods and cones of eye
Cause of polyploidy
two sperm fertilize one egg
sperm fertilize diploid egg
Location of pentose phosphate pathway
cytosolic cells of liver
Intrahepatic
in this type of jaundice you would have a problem in the liver, genetic errors, and conjugating enzymes in liver are not mature. There is a problem with the hepatocytes and AST and ALT are increased
telomerase
contains a protein that acts as a reverse transcriptase, and a short piece of RNA that acts as a template
503. What is the top of the hierarchy?
Hypothalamus
What are hydrogen bonds?
electrostatic interactions between H donors and H acceptors
One turn of the Krebs cycle produces ______ molecules of CO2.a. 2b. 3c. 4d. 5
A
Where do endonucleases cleave?
Catalyze hydrolysis of phosphodiester backbone of DNA: bond between 3' oxygen atom and phosphate group.
Uniparental disomy
Offspring receives 2 copies of a chromosome from 1 parent and no copies from the other
Things which don't need insulin for glucose uptake
BRICK Layer
biological macromolecules - importance of carbon??
commonly found in living things
-carbohydrates
-lipids
-proteins
-nucleic acids
DNA
unsaturated fat
have at least one double bond formed by the removal of H atoms in the carbon skeleton. generally from plants, liquid @ room temp, good dietary fats.
CONDITIONS THAT CAUSE DENATURATION OF PROTEIN
extremes of pH, heat
On what chromosome is the WT-1 gene located?
chromosome 11
Cystic Fibrosis
Defect in CFTR CL- ATPase in lungs, pancreas, intestines, skinIncreased salt in sweat and increased viscosity of mucusFTT, malabsorption, recurrent pseudomonas infections
A strategy of detecting mutations through hybridization requires __________
allele-specific oligonucleotide probes (ASOs)
Location of ETC, ATP synthase
integral proteins of inner mitochondrial membrane
Mechanism of strand break repair
single strand via ligase

double strand (more complex)
double strand rejoining
homologous recombination (chromosome crossing over)
structrue of transferrin receptor mRNA
IRE's in untranslated region
IRE's bind to aconitase to stabilize structure WITHOUT effecting translation
acyl CoA dehydrogenase
β-carbon of the acyl group is oxidized by ___ ___ ____FADH2 is produced which yields 2 ATP in electron transport
Describe the general solubility properties of proteins.
Three major categories:
§  Fibrous and insoluble: i.e. collagen, elastin, and a-keratin
§  Globular and soluble: i.e. albumin and hemoglobin
§  Fibrous and soluble: i.e. fibrinogen
508. What are the master regulatory glands?Two glands...
1. Hypothalamus2. Pituitary
You can Dx muscular dystrophies with inc. ___ and a muscle biopsy.
Creatine Phosphokinase (CPK)
Type I Topoisomerase
Type IA: strand passage mechanism with 3'-phosphotyrosine enzyme-DNA intermediate
Type IB: controlled rotation mechanism with 3'-phosphotyrosine enzyme-DNA intermediate
Type IB:
Major pentose phosphate pathway enzymes (2)
1. G6PD --> NADPH*RATE LIMITING
nucleic acid
any of a group of long, linear macromolecules, either DNA or various types of RNA, that carry genetic information directing all cellular functions: composed of linked nucleotides.
additional letters on prostaglandin script designate:
variation in ring structure and substituents
polar covalent bond
a covalent bond in which electrons are not shared equally
What disease is associated with Auer rods?
acute myelogenous leukemia (AML)
A single point mutation can alter the splicing activity of an mRNA (knocking out splice sites or adding them in) by activating ________.
cryptic splice sites.
What is the most common sterol? Which membrane is it almost exclusively found in?
cholesterol; plasma membrane
Mechanism of reaction of chymotrypsin
aromatic AA bind into pocket
enzyme folds to bring Ser, His, Asp close together
hydrogen from OH on Ser attacks N on imidazole ring of His
leads to attack of H on N in His on beta carboxyl group in Asp
oxygen free radical remaining on Ser attacks carbonyl group on peptide bond, leadin to its hydrolysis
Step six of TCA
succinate oxidized to produce FpH2 and fumarate

via succinate dehydrogenase/complex II
What AGA and AGG code for in the mitochondria?
TERMINATION codons
pyridoxal phosphate; Hemin
The synthesis of ALA catalayzed by ALA synthase requires what enzyme? what is the inhibitor?
486. What do eicosanoids cause?Three things...
1. Smooth muscle contraction2. Inflammation3. Blood clotting
heat of vaporization
amount of heat required to change to gas (vapor)
Ex. of Receptor Tyrosine Kinase
Growth hormone receptor, and insulin receptor
The captain was a TYRant (tyrosine)
Congenital deficiency of HOMOGENTISIC ACID OXIDASE
hydrogen bond
a type of chemical bond in which a hydrogen atom that has a covalent link with one of the electronegative atoms F, N, O forms an electrostatic link with another electronegative atom in the same or another molecule.
Beta oxidation is controlled by
the availability of FFA and malonyl CoA
In DNA mismatch repair in E.Coli, the mismatched bases are recognized by a protein termed ______
Mut S(Mut S SenSeS)
Usefulness of methylation of cytosine in cancer diagnostics

treat isolated DNA with sodium bisulfide → spontaneous deamination of cytosine to uradine
if cytosine is methylated, no rxn occurs

use two different probes that are two different colors
one is G (binds with cytosine)
one is A (binds with urasine)

PCR

send through computer to look for different genes linked to cancer
if hypermethylation of certain genes (ex: tumor suppressor genes hypermethylated means poor prognosis)
What is the best way to determine that new mutations are the cause of a disease?
adequate family history
Citrate, Succinyl Coa, NADH
citrate synthase in the step of Acetyl Coa--> citrate is inhibited by
Pyruvate dehydrogenase is activated by exercise which inc. 3 things:
1) inc. NAD/NADH ratio2) inc. ADP3) inc. calcium
beta oxidation yield
one QH2, one NADH and one acetyl Co A
Relationship of pathologies and sweat
Cystic fibrosis - sweat with NaCl concentration higher than normal. Involves most of the glandular epithelia of the body

Schizophrenic patients - peculiar body odor. Have trans-3-methyl 2-hexenoic acid in their sweat.
Eicosanoids & Essential Fatty Acids act on:
cell surface receptors and have a hydrophilic component
DNA polymerase III has __ -> __ synthesis and profreads with __ -> __ exonuclease.
5' -> 3'3' -> 5'
Active site of elastase
contains Cys and His
H on SH group of Cys involved in H attack on His N
How riboswitches form and their importance?
high guanine content will lead to terminator secondary structure
low guanine content, leads to turning on transcription
If we have the end product of transcription, it will bind within the specific pocket of the riboswitch, preventing transcription.
What is the purpose of the Cori cycle?
allows muscle to function anaerobically (net 2 ATP); muscle glucose --> pyruvate --> lactate which goes to Liver and is made into glucose again
What is a class II topoisomerase?
it cuts both backbones and passes through another part of DNA
What 2 things can cause biotin deficiency?
- eat raw eggs
- antibiotic use
ice floats (because, why ecologically important)
because it is LESS dense than water. it insulates the liquid below it. also causes spring overturn.
Where are plasmalogens found and what makes them different?
Found in heart and brainContains an a,B unsaturated ether instead of ester at C1
General rxn mechanism for transamination
takes a donor alpha amino acid and an acceptor alpha keto glutaric AA
donor AA binds to pyridoxal phosphate in aminotransferase
acceptor alpha keto glutaric acid comes in and picks up the amino group to form Glu
FREELY REVERSIBLE (if I need to make/remove it, YES I CAN!!!!)
Secretory pathway of secrection from the cell
secreted proteins enter ER as they are synthesized by ribosome
protein exit ER in vesicle
protein travel through cisternae of Golgi
exit via secretory vesicle
fuse with cell membrane, and spill contents
519. What is phosphocreatine?Two things
1. A storage form of ATP in the muscles2. Able to generate ATP quickly
Which form of Hb has low affinity for O2? Which has high affinity?
T/taut = low
R/relaxed = high
How does the structure of Hb change when oxygen binds?
pulls ferrous back into plane of porphyrin ring
this move F helices of beta subunit, causing confirmational change 
salt linkages between 2,3 BPG and the two beta subunits break
this allows subunits to move in relation to each other, as it is in a more relaxed state
Mechanism of action of Beta subunit of DNA Pol. III
forms a ring and has highly electrostatic interactions with DNA backbone to allow polymerase to move
1) what base pairs with A?2) what base pairs with G?
1) T or U (in RNA)2) C
What is the danger in a mutation that changes AA at the subunit interface?
These subunits must move between tight and loose confirmations, so if a mutation occurs, it could cause oxygen to bind tighter or looser.
431. Where does the NH4 go?Where does the carbon skeleton go?
NH4 goes to urea cycleCarbon goes to glycolysis or citric acid cycle
436. How is excess ammonia in the form of alanine and glutamine transported for disposal?
1. Alanine is a carrier for NH4 and the carbon skeleton of pyruvate from the skeletal muscle to the liver2. NH4 is excreted and pyruvate is used to produce glucose which is returned to the muscles
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