MCAT biochemistry
B12
Cyanocobalamin
D/L naming system
D- or L- •Assigned based on the molecule in question's relationship to the enantiomers of glyceraldehyde•All amino acids found in organisms are amino acids (almost)•All sugars found in organisms are sugars (almost)
Pentose is deoxyribose
DNA -OH of ribose replaced with -H
alpha anomer
OH group in the C1 is trans to the CH2OH *it will be axial and down*
isoelectric point
Point at which a compound is electrically neutral.
Respiratory Quotient (RQ)
RQ = CO2(produced)/O2(produced) Normal: 0.8 Range: 0.67-1.3
disulfide bonds
Strong chemical side bonds that can only be broken by chemical solutions
Tautomerization
The rearrangement of bonds within a compound, usually by moving a hydrogen and forming a double bond
B1
Thiamine
Chargaff's Rule
[A]=[T] and [G]=[C], they pair up across from one another forming two strands also called base pairing.
modified standard state
[H+] = 10^-7M and pH = 7 Under these conditions, deltaG° becomes deltaG°' meaning it is standardized to the neutral buffers used in biochemistry
lipid digestion
[digestion] when chyme is present, the duodenum secretes cck (cholecystokinin) hormone into the blood, which stimulates the secretion of pancreatic enzymes and bile and promotes satiety; bile made in the liver emulsifies fat in the small intestine but isn't an enzyme; lipase is an enzyme made in the pancreas that hydrolyzes lipids (also in the small intestine)
Flavin mononucleotide (FMN)
a coenzyme that functions in the transfer of electrons in the electron transport chain
replisome (replication complex)
a complex of DNA polymerase and other enzymes that catalyzes the synthesis of DNA
initiation complex
a complex of protein factors, mRNA, met-tRNA, and the small and large ribosomal subunit which is required to start translation
phosphate ester
a compound formed by reaction of an alcohol with phosphoric acid
lac operon
a gene system whose operator gene and three structural genes control lactose metabolism in E. coli
agarose gel
a jelly-like slab used to separate molecules on the basis of molecular weight
adenosine monophosphate (AMP)
a low-energy compound that results from the removal of two phosphate groups from ATP
Zwitterion
a molecule or ion having separate positively and negatively charged groups.
chiral
a molecule that is not superimposable on its mirror image
Exocytosis
a process by which the contents of a cell vacuole are released to the exterior through fusion of the vacuole membrane with the cell membrane.
Ketose
A carbohydrate whose carbonyl group is a ketone
Fermentation
A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid.
allosteric site
A specific receptor site on some part of an enzyme molecule remote from the active site.
alpha helix
A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure.
noncompetitive inhibitor
A substance that reduces the activity of an enzyme by binding to a location remote from allosteric site, changing its conformation so that it no longer binds to the substrate. Km unchanged Vmax decrease
Complex I (NADH-CoQ oxidoreductase)
- transfers electrons from NADH to coenzyme Q - flavoprotein oxidizes NADH - coenzyme Q becomes CoQH2 - moves four protons to the intermembrane space
Benedict's reagent
-detects presence of reducing sugar -aldehyde group of an aldose is readily oxidized indicated by a red precipitate of Cu2O
Tollen's reagent
-detects presence of reducing sugar -uses Ag(NH3)2+ as oxidizing agent *in a + test, aldehydes reduce Ag+ to metallic silver
absolute configuration
-determined by the 3D arrangement of the groups attached to the chiral carbon
glycogen phosphorylase
-enzyme activated by glycogen that cleaves glucose from the non-reducing end of a glycogen branch by phosphorylation *permits rapid release of glucose from glycogen stores
alditol
-forms when the aldehyde group of an aldose is reduced to an alcohol
active muscle
-fuel source used depends on activity *short-lived (2-7 seconds) = creatine phosphate ADP to ATP. *moderate, high-intensity, continuous = oxidation of glucose and fatty acids *1-3 hours of continuous exercise = muscle glycogen stores depleted and intensity of exercise declines at a rate that can be supported by oxidation of fatty acids
triterpenes
-have 6 isoprene units -can be converted to cholesterol & various steroids
Denature DNA
-heat (near boiling) -salt solution (low ionic strength) -Chemical denaturants (urea/formamide)
Hormone Sensitive Lipase (HSL)
-hydrolyzes triacylglycerols, yielding fatty acids and glycerol -activated by a decrease in insulin levels and an increase in epinephrine and cortisol
number of stereoisomers
2^n where n is the number of chiral centers
Triose
3 carbon sugar
Peptides
Chains of amino acids that can function as neurotransmitters or hormones.
induced fit model
Change in the shape of an enzyme's active site that enhances the fit between the active site and its substrate(s)
Riboflavin (B2)
essential for carbohydrate fat and protein metabolism. Necessary for tissue maintenance. And healthy eyes
Oncogenes
genes that cause cancer by blocking the normal controls on cell reproduction
structural genes of operon
genes that code for proteins
1,3-BPG and PEP
high energy glycolysis intermediates generate ATP via substrate level phosphorylation
Outer Mitochondrial Membrane (OMM)
highly permeable due to large pores
connexons
hold tissues/membranes together; hollow cylinders composed of proteins that span the entire width of the abutting membranes
Ghrelin
hormone secreted by empty stomach; sends "I'm hungry" signals to the brain
Keratins
intermediate filament proteins found in epithelial cells; contribute to the mechanical integrity of the cell and also function as regulatory proteins; the primary protein that makes up hair and nails
Amino acid behavior
ionized groups protonate in low pH and high pH deprotonated greater than pKa = deprotonated less than pKa= protonated
heme
iron-based, pigment part of hemoglobin
isocitrate dehydrogenase
isocitrate to alpha-ketoglutarate inhibited by ATP and NADH activated by ADP and NAD+
Enantiomers
isomers that are identical and mirror images of each other
Diastereoisomers
isomers that are identical but not mirror images
Anomers
isomers that differ at a new asymmetric carbon atom formed on ring closure
Hybridization
joining of complementary base pair sequences can be DNA-DNA or DNA-RNA recognition
cDNA library (complementary DNA)
lack introns and only includes genes expressed in tissue from which mRNA was isolated
lipid absorption
leave chylomicrons then lacteals in small intestine absorb dietary lipids that are not absorbed by the blood capillaries, then re-enter blood steam via thoracic duct
fatty acid synthase (palmitate synthase)
major enzyme complex in fatty acid synthesis found in the cytosol becomes rapidly induced in the liver following a high meal in carbohydrates - because of the elevated insulin levels
steriod hormones
make secondary sex characteristic in pubery. Female (estrogen, Progesterone), Male (testosterone)
Backbone of DNA
made up of alternating sugar and phosphate, bases are attached to the deoxyribose or sugar reads from 5' to 3' complementary join by 3' to 5' phosphodiester bonds
Endocytosis
process by which a cell takes material into the cell by infolding of the cell membrane
enzyme activity and pH
pH effect the ionization of the active site changes in it can lead to denaturation optimal active at 7.4 exceptions stomach pepsin - ph = 2 pancreatic enzymes pH= 8.5
coupled reactions
pairs of chemical reactions in which some of the energy released from the breakdown of one compound is used to create a bond in the formation of another compound
B5
pantothenic acid
chimera
patches of cells, including germ cells, derived from two lineages
integral proteins
penetrate the hydrophobic interior of the lipid bilayer
Glycerophospholipids (phosphoglycerides)
phospholipids that contain a glycerol backbone bonded by ester linkages to two fatty acids and by a phosphodiester linkage to a highly polar head group
vitamin K
phylloquinone (K1) and menaquinones (K2) bloodclotting
emulsification
physical process of breaking up large fat globules into smaller globules, thereby increasing the surface area that enzymes can use to digest the fat
Cellulose
polysaccharide consisting of glucose monomers that reinforces plant-cell walls
Polycrylamide Gel Electrophoresis
positive charge move toward anode
osmotic pressure
pressure that must be applied to prevent osmotic movement across a selectively permeable membrane
where is body protein catalyzed
primarily in muscles and liver
palmitic acid (palmitate)
primary end product of fatty acid synthesis (16:0)
protein level of structure
primary, secondary, tertiary, quaternary
pyruvate dehydrogenase complex regulation
regulated by pyruvate dehydrogenase kinase (respond to high ATP) and pyruvate dehydrogenase phosphatase (respond to high ADP)
aromatic rules
stable ring 1. is cyclic 2. is planar 3. is conjugated 4. has 4n+2, pi electrons
Prokaryote DNA replication
starts from a single point and proceeds in two directions until the entire chromosome is copied
malate formation
step 7: Fumarase = Fumarate → Malate
Oxaloacetate Formed Anew
step 8- catalyzed by malate dehydrogenase
Catecholamines (epinephrine and norepinephrine)
stimulates by sympathetic NS; increases heart rate, blood pressure, blood glucose levels and dilates lung passageways
N-terminus
the end of a polypeptide or protein that has a free amino group
C-terminus
the end of a polypeptide or protein that has a free carboxyl group
Saponification
the ester hydrolysis of triacylglycerols using a strong base
intermembrane space
the fluid filled space between the inner and outer mitochondrial membranes
micelle formation
the free fatty acids, 2 monoacyclglycerol, cholesterol with bile salts all form into micelles
Elute
to extract one material from another, usually by means of a solvent.
Why must pyruvate undergo fermentation for glycolysis to continue?
to replenish NAD+ and produce ATP
Siamese cats and tyrosinase
tyrosinase (enzyme responsible for pigmentation) is mutated - active at cooler temps and inactive at body temp pigmentation only in the cooler lower extremities
Amylopectin
a soluble polysaccharide and highly-branched polymer of glucose found in plants as one of the two components of starch (the other being amylose).
lye
a strong solution of sodium or potassium hydroxide
aldonic acid
a sugar produced by oxidation of an aldose aldehyde group to a carboxylic acid group
Glycogen phosphorylase regulation
activated bu glycogen by phosphorylation in skeletal muscles: activated by AMP/epinephrine and inhibited by ATP
positive control of transcription
activation of transcription; controlled by binding of activator protein when inducer is present
Lysases
add groups to or remove groups from double-bonded substrates
3' polyadenosyl tail (poly-A)
added 3' end of mRNA transcript and protect message against rapid degradation and export mature mRNA from nucleus
DNA methylase
adds a methyl group to cytosine and adenine nucleotides often linked to gene silencing
hexose monophosphate shunt (HMP)
aka PPP, occurs in cytoplasm of most cells, generates NADPH and sugars for biosynthesis (derived from ribulose 5-phosphate, irreversible)
glucogenic amino acids
all except leucine and lysine; can be converted into intermediates that feed into gluconeogenesis
Calorimeter
an insulated device used to measure the absorption or release of heat in chemical or physical processes
arachidonic acid
an omega-6 fatty acid derived from linoleic acid
Holoenzyme
apoenzyme + cofactor
ApoE
apolipoprotein permits uptake of chylomicron remnants and VLDL by the liver
embedded proteins
are associated with only the interior/cytoplasmic or exterior/extracellular surface of the cell
Bradford protein assay
assay to determine the concentration of protein in solution with Coomassie Brilliant Blue Dye protonated form = brown green color deprotonated form = blue
elongation factors
assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used
Hemidesmosomes
attach epithelial cells to the basement membrane
single strand DNA binding proteins
attach to the separated strands to prevent them from closing and degrading
protein catabolism
begins in stomach (pepsin) and continues with pancreactic proteases
cholesteryl ester transfer protein (CETP)
catalyzes the transition of IDL to LDL by transferring cholesteryl esters from HDL
ketogenic amino acids
converted to ketone bodies
Galactose-1-phosphate uridyltransferase
converts galactose 1-phosphate to glucose 1-phosphate
pyruvate dehydrogenase
converts pyruvate to acetyl-CoA. - stimulated by insulin - inhibited by acetyl-CoA
lactate dehydrogenase
converts pyruvate to lactate
pyruvate carboxylase
converts pyruvate to oxaloacetate by adding a carboxyl group to it activated acetyl CoA
Glycogenin
core protein found in the glycogen protein start of glycogenesis
Ketogenesis
creation of ketone bodies when in fasting state
excision endonuclease
cuts and patches helix-deforming lesions such as thymine dimers
Melting DNA
denaturing; added heat breaks H-bond between DNA strands; A-T separates more readily than G-C;
terpenoids/isoprenoids
derivatives of terpenes that have undergone oxygenation or rearrangement of the carbon skeleton
Process of Replication
dna unwinds- helicase breaks hydrogen bonds (unzips- replication forks), works in 5' to 3' direction only, polymerase brings complimentary nucleotide, ligase joins all DNA (OKAZAKI), polymerase proofreads and corrects mistakes
enzyme activity and temperature
double in velocity for ever 10 degrees Celsius until optimal temperature is reached human body optimal temp is 37C/98.6F/310K activity falls sharply after that because proteins start to become denatured
NADPH
electron donor synthesis of fatty acids and cholesterol assist cellular bleach production replenish glutathione
Fructose
fruit sugar
probe DNA
(DNA with known sequence) added to a mixture of target DNA sequences, when it binds to target DNA sequences, it may provide evidence of the presence of a gene of interest
gap junctions
(communicating junctions) provide cytoplasmic channels between adjacent cells
Pyrimidines
(cytosine, thymine, and uracil) have a single six-membered ring
Sesquiterpenes
* sesqui means ½ *contain 3 isoprene units
Watson-Crick Model
*DNA is a double helix w/ 2 linear polynucleotide chains wound together in spiral orientation along a common axis *Antiparallel strands (oriented in opposite directions) *Sugar-phosphate backbone is on the outside of the helix w/ nitrogenous bases on the inside *Adenine always pairs with thymine via 2 H bonds *Guanine always pairs with Cytosine via 3 H bonds *Hydrogen bonds and hydrophobic interactions b/w bases provide stability to the double helix *DNA is a right handed helix (B-DNA) *turns at every 10th base pair
Citric Acid Cycle (Krebs Cycle)
- 2 Pyruvates enter the mitochondrion - releases 2 ATP, 6NADH, and 2 FADH2 for each glucose
Fructokinase
- Traps fructose into the cell - catalyzes fructose into fructose 1-phosphate
alpha-ketoglutarate dehydrogenase complex
- acts similarly to PDH complex - metabolizes alpha-ketoglutarate to form succinyl-CoA - inhibited by ATP, NADH, and succinyl-CoA - activated by ADP and Ca2+
Succinyl CoA and CO2 Formation
- catalyzed by α-Ketoglutarate dehydrogenase complex produce CO2 then produce NADH
glycogen synthase
- creates alpha-1,4 glycosidic links between glucose molecules - activated by insulin in liver and muscle -inhibited by epinephrine and glucagen
glycerol 3-phosphate shuttle
- electrons are transferred from NADH to dihydroxyacetone phosphate (DHAP), forming glycerol 3-phosphate - these electrons can then be transferred to mitochondrial FAD, forming FADH2
malate-aspartate shuttle
- electrons are transferred from NADH to oxaloacetate, forming malate - malate can then cross the inner mitochondrial membrane and transfer electrons to the mitochondrial NAD+, forming NADH
GLUT 2 transporter
- facilitated glucose transport - Km= 15mM - located in liver, kidney, pancreas B cells
GLUT 4 transporter
- facilitated glucose transport, INSULIN dependent - Km=5mM, becomes saturated - located in skeletal/heart muscle, adipocytes
Globosides
- glycosphingolipids - have two or more sugars attached to sphingosine
branching enzyme
- hydrolyze a oligoglucose from one chain and adds it to the growing glycogen as a new branch using and alpha-1,6 glycosidic link
prolonged fasting (starvation)
- levels of glucagon & epinephrine are markedly elevated - increased levels of glucagon relative to insulin result in rapid degradation of glycogen stores in the liver
prostalglandins
- modified fatty acids - induce fever, pain sensation, inflammation
termination of translation
- occurs when the codon in A-site is a stop codon - release factor places a water molecule on the polypeptide chain and thus releases the protein
Dihydrolipoyl transacetylase (E2)
- oxidizes remaining two-carbon molecule using lipoic acid, and transfers the resulting acetyl group to CoA, forming acetyl CoA
Glyceraldehyde-3-phosphate dehydrogenase
- produces NADH which can feed into electron transport chain
Complex III (CoQH2-cytochrome c oxidoreductase)
- transfers electrons from coenzyme Q to cytochrome c - iron is reduced on heme groups from Fe 2+ to Fe 3+ - contribution to the proton motive force via Q cycle - in the Q cycle, 2 electrons are shuttled from CoQH2 to CoQ - moves four protons to the intermembrane space
Complex II (Succinate-CoQ oxidoreductase)
- transfers electrons to coenzyme Q - receives electrons from succinate - oxidizes to FADH2 - FADH2 reoxidized to FAD - coenzyme Q is reduced - no hydrogen pumping occurs
Hill's Coefficient (cooperativity)
- value indicated nature of binding by the molecule - if > 1, positively cooperative binding is occuring - if < 1, negatively cooperative binding is occuring - if = 1, enzyme does not exhbit cooperative binding
amino acid derivative hormones
-derived from 1 or 2 amino acids w/ additional modifications -Include epinephrine, norepinephrine, triiodothyronine, and thyroxine
nucleosides
-a 5 carbon sugar (pentose) linked to a nitrogenous base - formed by covalently linking the base to C-1' of the sugar
transgenic mice
-altered at their germ line by introducing a cloned gene into fertilized ova or into embryonic stem cells -Transgene is a cloned gene that is introduced -If transgene is a disease-producing allele, the transgenic mice are used to study the disease process from early embryonic development through adulthood
reducing sugar
-any monosaccharide w/ a hemiacetal ring (since they can be oxidized, they are considered reducing agents)
size exclusion chromatography
-beads contain tiny pores -small molecules enter the pores & get stuck so they elude later -large molecules don't fit in the pores so they move around taking a shorter path & elude faster
vitamin A
-carotene -unsaturated - important in vision, growth, development, & immune function
peptide bond hydrolysis
-catalyzed by hydrolytic enzymes such as trypsin and chymotrypsin, only cleave at specific points in the peptide chain •break by adding a H atom to the amide nitrogen and an OH group to the carbonyl carbon
Sphingomyelin
-class of sphingolipids and phospholipids (sphingophospholipids) -have either phosphatidylcholine or phosphatidylethanolamine as a head group (contain phosphodiester bond) -its head groups have no charge
genomic libraries
-contain large fragments of DNA - include both coding (exon) and non-coding (intron) regions of DNA
Propionyl-CoA carboxylase
-converts propionyl-CoA to methylmalonyl-CoA -requires biotin (vitamin B7)
regulation of cholesterol synthesis
-increased levels of cholesterol can inhibit further synthesis by a feedback inhibition mechanism -insulin promotes cholesterol synthesis -control over de novo cholesterol synthesis is dependent on regulation of HMG-CoA reductase gene expression in the cell
Terpenes
-metabolic precursors to steroids and other lipid signaling molecules built from isoprene -grouped by # of isoprene units present
Lipid Mobilization
-mobilized from adipocytes by hormone-sensitive lipase -mobilized from lipoproteins by lipoprotein lipase
Phosphofructokinase-2 (PFK-2)
-produces fructose 2,6-bisphosphate (F2,6-BP) that activates PFK-1 - activated by insulin - inhibited by glucagon
vesicle-coating proteins
-proteins that initiate and carry out the process of cell membrane invagination during endocytosis
translocation (elongation)
-ribosome translocated tRNA from A-->P sites and empty tRNA goes from P-->E to be released -requires GTP
Ceramide
-simplest sphingolipid - has a single hydrogen atom as its head group
ion exchange chromatography
-stationary phase is made of either negatively or positively charged beads (attract & bind compounds that have opposite charge) -salt is added to elute proteins stuck to column
3-hydroxy-3-methylglutaryl (HMG) CoA reductase
-the key enzyme in cholesterol biosynthesis -most active in the absence of cholesterol and when stimulated by insulin -cholesterol reduces the activity of HMG-CoA reductase, which is located in the smooth ER
Edman degradation
-used to analyze small proteins - selectively & sequentially removes the N terminal AA of the protein which is analyzed by mass spectroscopy -larger proteins, synthetic reagent can be used
Complex IV (cytochrome c oxidase)
-uses cytochromes and Cu2+ to transfer electrons in the form of hydrdie ions (H-) from cytochrom c to oxygen, forming water -two protons are translocated
affinity chromatography
-uses specific interactions to slow down select molecules -can make use of receptor-ligand, enzyme-substrate, and antigen-antibody interactions
elongation cycle
1. codon recognition 2. peptide bond formation 3. translocation
Reversible inhibition types
1. competitive 2. noncompetitive 3. mixed 4. uncompetitive
insulin increases
1. glucose and triglyceride uptake by fat cells 2. lipoprotein lipase activity - which clears the VLDL and chylomicrons from the liver 3. triglyceride synthesis (lipogenesis) in adipose tissue and the liver from acetyl coA
Steps and proteins involved in DNA replication
1. origin of replication 2. unwinding of DNA double helix (helicase) 3. stabilization of unwound template strand (single-stranded DNA-binding Protein) 4. synthesis of RNA primers (primase) 5. Synthesis of DNA (DNA polymerase) 6. removal of RNA primers 7. replacement RNA with DNA 8. Joining of Okazaki fragments (DNA ligase) 9. removal of positive supercoils ahead of advancing replication forks (DNA Topoisomerases/DNA Gyrase) 10. synthesis of telomeres
insulin decreases
1. triglyceride breakdown/lipolysis in adipose tissue 2. formation of ketone bodies in the liver
Four steps of beta-oxidation
1.oxidation of fatty acid to form a double bond (creates FADH2) 2. hydration of the double bond to form a hydroxyl group (req. H2O) 3. oxidation of the hydroxyl group to form a carbonyl; called a beta-ketoacid (generates NADH) 4. splitting of the beta-ketoacid into a shorter acyl-CoA and acetyl-CoA (req. CoA-SH) -process continues until chain has been shortened to two carbons (for even chained fatty acids)
Michaelis constant (Km)
1/2Vmax -indicates how highly concentrated the substrate must be to speed up the reaction high Km= low affinity low Km= high affinity
Lineweaver-Burk Plot
1/v = (Km/Vmax)(1/[S]) + 1/Vmax
how much down APT produce
30kJ/mol
tetrose
4 carbon sugar
oligopeptide
4-10 amino acids joined together
pentose
5 carbon sugar
Hexose
6 carbon sugar
Recombinant DNA
A DNA molecule made in vitro with segments from different sources.
Southern Blot
A DNA sample is electrophoresed on a gel and then transferred to a filter. The filter is then soaked in a denaturant and subsequently exposed to a labeled DNA probe that recognizes and anneals to its complementary strand. The resulting ds labeled piece of DNA is visualized when the filter is exposed to film.
replication fork
A Y-shaped region on a replicating DNA molecule where new strands are growing.
Sphingosine
A complex alcohol backbone sphingolipids lipids
glycosidic linkage
A covalent bond formed between two monosaccharides by a dehydration reaction.
lactone
A cyclic ester; named according to the number of carbon atoms other than the carbonyl carbon and for the straight-chain form of the compound.
Disaccharide
A double sugar, consisting of two monosaccharides joined by dehydration synthesis. sucrose, lactose, maltose
deoxyribonucleic acid (DNA)
A double-stranded, helical nucleic acid molecule capable of replicating and determining the inherited structure of a cell's proteins.
saturated fatty acid
A fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, thus maximizing the number of hydrogen atoms that can attach to the carbon skeleton.
unsaturated fatty acid
A fatty acid possessing one or more double bonds between the carbons in the hydrocarbon tail. Such bonding reduces the number of hydrogen atoms attached to the carbon skeleton.
furanose
A five-membered ring sugar.
hemiacetal
A functional group that contains a carbon atom bonded to one -OR group, one -OH group, an alkyl chain, and a hydrogen atom.
hemiketal
A functional group that contains a carbon atom bonded to one -OR group, one -OH group, and two alkyl chains
Triacylglycerols (triglycerides)
A glycerol molecule esterified to three fatty acid molecules; the most common form of fat storage in the body Overall nonpolar and hydrophobic Can be seen in oily droplets
glycosidic bond
A glycosidic bond is a covalent bond in which a carbohydrate binds to another group, which could also be a carbohydrate. A glycosidic bond is found between the two glucose molecules in maltose.
operator site of operon
A nontranscribable region of DNA that is capable of binding a repressor protein
amphoteric species
A species capable of reacting as either an acid or base, depending on the nature of the reactants
Leptin
A hormone produced by adipose (fat) cells that acts as a satiety factor in regulating appetite.
spliceosome
A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.
Heterotrimeric G proteins
A large group of proteins consisting of three subunits (α, β, and γ) that can be activated by exchanging bound GDP for GTP, resulting in the liberation of two signaling molecules‚ αGTP and the βγ dimer.
conformational coupling
A less-accepted mechanism of ATP synthase activity in which the protons cause a conformational change that releases ATP from ATP synthase
Body Mass Index (BMI)
A measure of body fat that is the ratio of the weight of the body in kilograms to the square of its height in meters. normal: 18.5-25 overweight: 25-30 obese: over 30
semipermeable membrane
A membrane that allows some molecules to pass through but does not allow other molecules to pass through.
antiport
A membrane transport process that carries one substance in one direction and another in the opposite direction.
symport
A membrane transport process that carries two substances in the same direction across the membrane.
Pentose Phosphate Pathway (PPP)
A metabolic process that produces NADPH and ribose 5-phosphate for nucleotide synthesis.
beta oxidation
A metabolic sequence that breaks fatty acids down to two-carbon fragments that enter the citric acid cycle as acetyl CoA.
Haworth projection
A method for depicting cyclic sugars as planar rings with -OH groups sticking up or down from the plane of the sugar
UV spectroscopy
A method of determining the concentration of protein in an isolate by comparison against a protein standard; relies on the presence of aromatic amino acids Can also be used with nucleic acids and other compounds
Fischer projection
A method of drawing organic molecules in which horizontal lines are coming out of the page (wedges) and vertical lines are going into the page (dashes)
respirometry
A method of measuring metabolism through the consumption of oxygen
Colloid
A mixture containing small, undissolved particles that do not settle out.
Phospholipids
A molecule that is a constituent of the inner bilayer of biological membranes, having a polar, hydrophilic head and a nonpolar, hydrophobic tail.
prosthetic group
A non-protein, but organic, molecule (such as vitamin) that is covalently bound to an enzyme as part of the active site.
Polypeptide
A polymer (chain) of many amino acids linked together by peptide bonds.
Heterosaccharide
A polysaccharide made up of more than one type of monosaccharide
negative feedback
A primary mechanism of homeostasis, whereby a change in a physiological variable that is being monitored triggers a response that counteracts the initial fluctuation.
TATA box
A promoter DNA sequence crucial in forming the transcription initiation complex.
promoter region
A regulatory region a short distance upstream from the 5' end of a transcription start site that acts as the binding site for RNA polymerase. A region of DNA to which RNA polymerase binds in order to initiate transcription.
nucleotide excision repair (G1 and G2 phase)
A repair system that removes and then correctly replaces a damaged segment of DNA using the undamaged strand as a guide.
electron transport chain
A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP.
Glucose
A simple sugar that is an important source of energy.
ribosome binding sites
A site, P site, E site
pyranose
A six-membered ring sugar.
G-protein coupled receptors
A special class of membrane receptors with an associated GTP binding protein; activation of a G protein-coupled receptor involves dissociation and GTP hydrolysis
polymerase chain reaction (PCR)
A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules, and nucleotides. reannealing is an important step!
Chromatography
A technique that is used to separate the components of a mixture based on the tendency of each component to travel or be drawn across the surface of another material.
enzyme-substrate complex
A temporary complex formed when an enzyme binds to its substrate molecule(s).
Messenger RNA (mRNA)
A type of RNA, synthesized from DNA and attached to ribosomes in the cytoplasm; it specifies the primary structure of a protein.
Phagocytosis
A type of endocytosis in which a cell engulfs large particles or whole cells
Pinocytosis
A type of endocytosis in which the cell ingests extracellular fluid and its dissolved solutes.
Cholesterol
A type of fat made by the body from saturated fat; a minor part of fat in foods. maintain fluidity of cell membranes and form steriods
operon
A unit of genetic function common in bacteria and phages, consisting of coordinately regulated clusters of genes with related functions.
ATP hydrolysis
ATP is converted to ADP & phosphate energized myosin heads (removal of phosphate) need energy
Acetyl CoA
Acetyl coenzyme A; the entry compound for the citric acid cycle in cellular respiration, formed from a fragment of pyruvate attached to a coenzyme.
ApoA-1
Activates *LCAT* and found on HDL
allosteric activator
Allosteric activators bind to an enzyme and induce its active form.
Transfer RNA (tRNA)
An RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA
flavin adenine dinucleotide (FAD)
An energy carrier that accepts electrons and feeds them into the electron transport chain
creatine phosphate
An energy storage molecule used by muscle tissue. The phosphate from creatine phosphate can be removed and attached to an ADP to generate ATP quickly.
peptidyl transferase
An enzyme in the ribosome responsible for peptide bond formation during translation. (GTP energy source)
Glucose-6-phosphate dehydrogenase (G6PD)
An enzyme that aids in the proper functioning of red blood cells; its deficiency, a genetic condition, leads to hemolytic anemia. induced by insulin activated by NAD+ and inhibited by NADPH
nuclease
An enzyme that cuts DNA or RNA, either removing one or a few bases or hydrolyzing the DNA or RNA completely into its component nucleotides.
Primase
An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.
Helicase
An enzyme that untwists the double helix of DNA at the replication forks.
zymogen
An inactive precursor of an enzyme, activated by various methods (acid hydrolysis, cleavage by another enzyme, etc.)
mevalonic acid
An intermediate in Steroid biosynthesis that converts to Acetone in metabolic crisis
Cytochromes
An iron-containing protein that is a component of electron transport chains in the mitochondria and chloroplasts of eukaryotic cells and the plasma membranes of prokaryotic cells
repressible system
An operon that requires a repressor to bind to a corepressor before binding to the operator site to stop transcription of the relevant gene; also called a negative control system
inducible system
An operon that requires an inducer to remove a repressor protein from the operator site to begin transcription of the relevant gene; also called a positive control system.
Desmosomes
Anchoring junctions that prevent cells from being pulled apart
cofactors and coenzymes
Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. can be permanently bound to the active site or may bind loosely with the substrate during catalysis
Purines
Bases with a double-ring structure. Adenine and Guanine
beta-oxidation in mitochondria
Beta-oxidation oxidizes and releases (rather than reducing and linking, as in fatty acid synthesis) acetyl-CoA
B7
Biotin
Monoterpenes
C10H6 two isoprene units abundant in essential oils and turpentine
carbonyl carbon
C=O
Polysaccharides
Carbohydrates that are made up of more than two monosaccharides cellulose, starch, glycogen
column chromatography
Chromatography in which the substances to be separated are introduced onto the top of a column packed with an adsorbent (as silica gel or alumina), pass through the column at different rates that depend on the affinity of each substance for the adsorbent and for the solvent or solvent mixture, and are usually collected in solution as they pass from the column at different times
ApoB-48
Chylomicron assembly and secretion by the intestine
Exons
Coding segments of eukaryotic DNA.
transcription factors
Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.
lipid rafts
Collections of similar lipids with or without associated proteins that serve as attachment points for other biomolecules assist in signaling
starches
Complex carbohydrates that are composed of many sugars linked together.
amino acids
Compounds with an amino group on one end and a carboxyl group on the other end.
negative control of transcription
Condition where binding of a repressor protein to a regulatory DNA sequence prevents transcription of a gene or a cluster of genes.
Thiophorase (Succinyl CoA: acetoacetate CoA Transferase)
Converts acetoacetate (ketone bodies) into acetoacetyl CoA, which then gets broken down into acetyl CoA. Only present in tissues outside of the liver.
2,4-dienoyl-CoA reductase
Converts two conjugated couble bonds to one double bond at the 3,4 position to undergo isomerization by enoyl-CoA isomerase, allowing for the oxidation of polyunsaturated fatty acids.
base excision repair
DNA repair that first excises modified bases and then replaces the entire nucleotide
Eukaryote DNA replication
DNA replication occurs at many places at the same time move
Enhacers
DNA sequence that acts as a regulatory element to increase the level of transcription when regulatory proteins, such as transcription activators, bind to it
glucogenic
Describes amino acids that can be converted into intermediates that feed into gluconeogenesis; all amino acids except leucine and lysine
ketogenic
Describes amino acids that can be converted into intermediates that feed into ketogenesis
epimer
Diastereomers that differ at only one chiral center.
Activation of Amino Acid for Protein Synthesis
Each type of amino acid is activated by different aminoacyl-tRNA syntheses that requires two high-energy bonds from AT, implying that the attachment of the amino acid is an energy rich bond.
Tetraterpenes
Eight isoprene units Contain carotenoids group (i.e. beta-carotene and lutein)
DNA polymerase
Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule
RNA polymerase
Enzyme similar to DNA polymerase that binds to DNA and separates the DNA strands during transcription does not undergo proofreading
enzyme specificity
Enzyme specificity is the concept that each enzyme catalyzes only one kind of reaction.
Kinases
Enzymes that catalyze the transfer of phosphate groups from ATP to acceptor molecules.
restriction enzymes (restriction endonucleases)
Enzymes that recognize specific double-stranded DNA sequences (palindromic sequences - the 5'-3' of one strand matches the 5'-3' strand of another in antiparallel fashion)
Heterochromatin
Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.
fatty acyl CoA synthetase
Fatty Acids must be activated before transport into mitochondria by adding CoA
Acetyl-CoA carboxylase (ACC)
Fatty acid synthesis: rate determining enzyme acetyl-CoA -> malonyl-CoA
Collagen
Fibrous protein that gives the skin form and strength trihelical fiber
Intermediate Density Lipoprotein (IDL)
Formed from the degradation of very low density lipoproteins; enables fats and cholesterol to move within the bloodstream
gylcogen
Found in the pancreas; stores glucose (stored sugar for energy source) has many branches allowing more enzyme cleaving
Ketones
Fragments formed by the tissues during incomplete use of fat for energy, and released into the blood.
Glycine
Gly, G, nonpolar tends to not be optically active (achiral)
Substrates for gluconeogenesis
Glycerol, Amino acids, Lactic Acid
Gangliosides
Glycolipids with a head group composed of oligosaccharides with a terminal sialic acid (NANA) molecule.
Cerebrosides
Glycosphingolipids with one sugar
G proteins types
Gs=stimulates adenylate cyclase and increase cAMP Gi=inhibits adenylate cyclase and decrease cAMP Gq=activates phospholipase C
5 histone proteins
H1, H2A, H2B, H3, and H4. (H1 is the only one not in the histone core)
Hypotonic
Having a lower concentration of solute than another solution
insulin effects fat metabolism
Increases fatty acid synthesis in liver. Increases triglyceride synthesis in adipose tissue.
competitive inhibition
Inhibition of an enzyme's ability to catalyze a chemical reaction via a non-reactant molecule that competes with the substrate(s) for access to the active site. Km increases Vmax unchanged
transmembrane proteins
Integral proteins that span the membrane.
molten globule
Intermediate states in the folding of a protein
methylmalonyl CoA mutase
Involved in the oxidation of odd-numbered carbon fatty acids, producing succinyl-CoA for entry into the TCA; requires B12.
catalytic efficiency
Kcat/Km higher = more efficient
ATP synthase
Large protein that uses energy from H+ ions to bind ADP and a phosphate group together to produce ATP
de novo
Latin, meaning "anew." A trial de novo is a completely new trial. Appellate review de novo implies no deference to the trial judge's ruling.
membrane-associated proteins
May act as recognition molecules or enzymes. proteins which are bound through electrostatic interactions with the lipid bilayer, particularly at lipid rafts or to other membrane proteins
tight junctions
Membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid
facilitated diffusion (passive transport)
Movement of specific molecules across cell membranes through protein channels
high energy electron carriers
NADH, NADPH, FADH2, ubiquinone, cytochromes, glutathione
Retinol
Natural form of vitamin A; stimulates cell repair and helps to normalize skin cells by generating new cells.
sodium dodecyl sulfate (SDS)
Negatively-charged detergent used to denature and confer a negative charge to proteins before separation by electrophoresis
B3
Niacin
Introns
Noncoding segments of nucleic acid that lie between coding sequences.
start codon (AUG)
On mRNA, the specific three-nucleotide sequence (AUG) to which an initiator tRNA molecule binds, starting translation of genetic information.
beta sheet
One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.
Alpha-linolenic acid (ALA)
One type of omega-3 fatty acid, polysaturated
citrate synthase
Oxaloacetate + acetyl-CoA --> citrate. Inhibited by citrate, ATP, NADH, and succinyl-CoA (competes with acetyl-coA)
Phosphoenolpyruvate carboxykinase (PEPCK)
Oxaloacetate -> phosphoenolpyruvate Gluconeogenesis, irreversible enzyme In cytosol Requires GTP
pyruvate kinase
PEP to pyruvate activated by 1,6-biphosphate from PFK-1 rxn (feed-forward activation)
secondary structure and proline
Proline will introduce kink in petite chain when found in a-helix more found in a-helices across membrane proline is often found between turns of B-sheet and reside of a-helix
dipeptidase and aminopeptidase
Protein digestion is completed by the small intestinal brush-border enzymes
Apolipoproteins
Protein molecules responsible for the interaction of lipoproteins with cells and the transfer of lipid molecules between lipoproteins; also called apoproteins
catabolite activator protein (CAP)
Protein that functions in catabolite repression. When bound with cAMP, CAP binds to the promoter of certain operons and stimulates transcription.
Chaperones
Proteins that assist in protein folding during posttranslational processing
B6
Pyridoxine
Net Results and ATP Yield from Krebs
Pyruvate Dehydrogenase Complex: 1NADH Citric Acid Cycle: 3NADH, FADH2, GTP ATP Production: 10, 1.5, 1 = 25 Glycolysis Yields another seven molecules of ATP
Pentose is ribose
RNA
small nuclear RNA (snRNA)
RNA molecule of around 200 nucleotides that participates in RNA splicing
enoyl-CoA isomerase
Rearranges cis double bonds at the 3,4 position to trans double bonds at the 2,3 position once enough acetyl-CoA has been liberated to isolate the double bond within the first three carbons (permits beta-oxidation to proceed in monounsaturated fats)
B2
Riboflavin
B-DNA
Right-handed helical structure of DNA that exists when water is abundant; the secondary structure described by Watson and Crick and probably the most common DNA structure in cells.
Z-DNA
Secondary structure of DNA characterized by 12 bases per turn, a left-handed helix, and a sugar-phosphate backbone that zigzags back and forth.
origins of replication
Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.
How does soap work?
Soap works by having a polar end and a nonpolar end which allows the water and oil to interact indirectly by forming colloid
initiator tRNA
Special tRNA that initiates the translation of an mRNA in a ribosome. It always carries the amino acid methionine (AUG).
Citrate formation
Step 1 of citric acid cycle Acetyl-CoA and oxaloacetate undergo a condenstaion reaction to form citryl-CoA
Citrate Isomerized to Isocitrate
Step 2 of Citric Acid Cycle Achiral citrate is isomerized to one of four possible isomers of Isocitrate
alpha-ketoglutarate and CO2 formation
Step 3 and rate limiting step of Citric Acid Cycle Produces first CO2 and first NADH molecule of the cycle Uses isocitrate dehydrogenase
Succinate Formation
Step 5; only time we directly produce ATP in the citric acid cycle (in the form of GTP)
Fumarate formation
Step 6: succinate becomes oxidized to form fumarate takes place in the mitochondrial inner membrane Only step of the cycle that does not occur in the matrix
optical isomers
Stereoisomers that are non-superimposable mirror images of each other
fluid mosaic model
Structural model of the plasma membrane where molecules are free to move sideways within a lipid bilayer.
Nuclear magnetic resonance spectroscopy
Technique used for determining the three-dimensional structure of a protein. It is performed in solution without requiring a protein crystal.
5' cap
The 5' end of a pre-mRNA molecule modified by the addition of a cap of guanine nucleotide.
DNA methylation
The addition of methyl groups (—CH3) to bases of DNA after DNA synthesis; may serve as a long-term control of gene expression. CONDENSE
allosteric effects
The binding of a ligand to one site on a protein molecule in such a way that the properties of another site on the same protein are affected
mismatch repair (G2 phase)
The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides.
peptide bond
The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid
monocistronic
The coding pattern of eukaryotes in which one mRNA molecule codes for only one protein.
polycistronic
The coding pattern of prokaryotes, in which one mRNA may code for multiple proteins.
Jacob-Monod Model
The description of the structure and function of operons in prokaryotes, in which operons have structural genes, an operator site, a promoter site, and a regulator gene
Phosphofructokinase-1 (PFK-1)
The enzyme that catalyzes the phosphorylation of fructose-6-phosphate to form fructose-1-6-bisphosphate in the third step of glycolysis. inhibited by ATP and citrate activated by AMP
substrate-level phosphorylation
The enzyme-catalyzed formation of ATP by direct transfer of a phosphate group to ADP from an intermediate substrate in catabolism.
Hexokinase
The enzymes that catalyzes the phosphorylation of glucose to form glucose-6-phosphate in the first step of glycolysis. inhibited by glucose-6-P low Km
Gluconeogenesis
The formation of glucose from noncarbohydrate sources, such as amino acids.
gene therapy
The insertion of working copies of a gene into the cells of a person with a genetic disorder in an attempt to correct the disorder
Euchromatin
The less condensed form of eukaryotic chromatin that is available for transcription.
leading strand
The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.
active site
The part of an enzyme or antibody where the chemical reaction occurs.
proton-motive force
The potential energy stored in the form of an electrochemical gradient, generated by the pumping of hydrogen ions across biological membranes during chemiosmosis.
Transamination
The process by which an amino group from one amino acid is transferred to a carbon compound to form a new amino acid.
oxidative phosphorylation
The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.
Shine-Dalgarno sequence
The prokaryotic ribosome-binding site on mRNA, found 10 nucleotides 5' to the start codon.
connexins
The proteins that make up gap junctions
Mutarotation
The rapid interconversion between different anomers of a sugar
HMG-CoA synthase
The rate-limiting enzyme of ketogenesis.
Regulation of Oxidative Phosphorylation
The rates of the citric acid cycle and oxidative phosphorylation are very close, because the products of the citric acid cycle feed into the ETC, and therefore oxidative phosphorylation
Esterification
The reaction of an alcohol with a carboxylic acid to produce an ester and water. ester transferred by using ATP to form ADP
Enol
The resonance form of a carbonyl that has a carbon-carbon double bond (ene) and an alcohol (-ol)
gene amplification
The selective synthesis of DNA, which results in multiple copies of a single gene, thereby enhancing expression.
Q cycle
The shuttling of electrons between ubiquinol and ubiquinone in the inner mitochondrial membrane as a part of Complex III's function
lagging strand
The strand that is synthesized in fragments using individual sections called Okazaki fragments opposite direction as parent strand
cooperative binding
The tendency of the protein subunits of hemoglobin to affect each other's oxygen binding such that each bound oxygen molecule increases the likelihood of further oxygen binding.
lock and key theory
Theory of enzyme catalysis stating that the active site's structure is complementary to the structure of the substrate.
vitamin E
Tocopherol, serves as an antioxidant to the body
3-phosphoglycerate kinase
Transfers the high-energy phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate
Dipeptide
Two amino acids bonded together
quanternary structure
Two or more polypeptide chains bonded together in a single protein; hemoglobin is an example of a protein molecule with this structure. allows stability, reduce protein DNA needed to encode protein complex
Stop codons
UAA, UAG, UGA
chemiosmotic coupling
Utilization of the proton-motive force generated by the electron transport chain to drive ATP synthesis in oxidative phosphorylation.
Proofreading by DNA polymerase (s phase)
Verifies accuracy Can back up, excise nucleotide Incorporate correct nucleotide Very efficient but not flawless
apurinic/apyrimidinic (AP) site
abasic site, site on DNA lacking nucleotide
Selectins
allow cells to adhere to carbohydrates on the surfaces of other cells and are most commonly used in the immune system
enzyme cooperativity
allows for an enzyme to become increasingly receptive to additional substrate molecules after a substrate molecule has attached to an active site
peptide bond formation
amide bond formed by amino group attacking carboxyl group and eliminating the OH non-spontaneous process that needs enzymes!
residues
amino acids that are incorporated into a protein
retention time
amount of time a compound spends in stationary phase
acetaldehyde dehydrogenase (ALDH)
an alcohol-metabolizing enzyme found in the liver that converts acetaldehyde to acetate
ApoC-II
an apoprotein that activates lipoprotein lipase
ApoB-100
an apoprotein that permits uptake of LDL by the liver
Glucokinase
an enzyme induced by insulin, adds a phosphate group to a molecule of glucose sound in hepatocyte and beta islet cells high Km
hormone sensitive lipase
an enzyme inside adipose cells that responds to the body's need for fuel by hydrolyzing triglycerides so that their parts (glycerol and fatty acids) escape into the general circulation and thus become available to other cells for fuel. The signals to which this enzyme responds include epinephrine and glucagon, which oppose insulin.
DNA topoisomerase
an enzyme that alleviates DNA supercoiling during DNA replication
lipoprotein lipase
an enzyme that sits on the outside of cells and breaks apart triglycerides, so that their fatty acids can be removed and taken up by the cell
linoleic acid
an essential polyunsaturated fatty acid of the omega-6 family, polysaturated
xray crystallography
an important method used to determine a protein's three-dimensional structure
carrier proteins
bind to molecules and change shape to shuttle them across the membrane
RNA polymerase II
binds to TATA box and begins to transcribes mRNA
Lowry reagent assay
biochemical assay for determining the total level of protein in a solution. The total protein concentration is exhibited by a color change of the sample solution in proportion to protein concentration, which can then be measured using colorimetric techniques.
High-density lipoprotein (HDL)
blood fat that helps transport cholesterol out of the arteries, thereby protecting against heart disease
low-density lipoprotein (LDL)
blood fat that transports cholesterol to organs and tissues; excess amounts result in the accumulation of fatty deposits on artery walls
chemical denaturation
break disulfide bridges, hydrogen bonds, and reducing cystine to cysteine
amino acid catabolism
breakdown of amino acids for use as energy; includes 2 processes: transamination or deamination.
Glycogenolysis
breakdown of glycogen to glucose
HMG-CoA lyase
breaks down HMG CoA into acetoacetate this acetoacetate can be broken down into 3 hydroxybutarate
Reannealed DNA
brought back together when denaturing condition is slowly removed
expression libraries
cDNA library where it only includes genes that are expressed in the tissue from which the mRNA was taken from
Cadherins
calcium-dependent glycoproteins that hold similar cells together
glycoprotein coat
carbohydrates associated with membrane-bound proteins
Zwitterions at intermediate pH
carboxylic acids become deprotonated at neutral pH, forming zwitterions--two charges neutralize each other; molecule that has both positive and negative charge; pH is above pKa of carboxylic acid so it is deprotonated, but pH is below pKa of amine group so, protonated
regulation of body mass
carbs and proteins relatively stable water quickly adjusted by endocrine/kidneys lipids are primary factor in gradual change of body mass over time
occluded state
carrier is not open to either side of the phospholipid bilayer
Hydrolases
catalyze cleavage with the addition of water
Oxidoreductases
catalyze oxidation-reduction reactions that involve the transfer of electrons
Ligases
catalyze the formation of bonds with the input of ATP and the removal of water
Isomerase
catalyzes the rearrangement of bonds within a single molecule
Mutase
catalyzes the shifting of a chemical group from one position to another within a molecule
Nernst Equation
cell in equilibrium has an actual cell potential of 0 and a standard cell potential of not 0 *E = E0 - (RT/nF)lnQ* E0 = (RT/nF)lnK -as temp increases, Ecell decreases -as battery approaches equilibrium, Ecell approaches 0 -E0 is constant
Centromere
central part of chromosome, joining the two sister chromatids composed of heterochromatin and have high G-C content
Glycogen storage disease
characterized by the accumulation or lack of glycogen in one or more tissues due to isoforms of glycogen enzymes most common is Von Gierke's disease
beta amylase
cleaves amylose at the nonreducing end of the polymer the end with the acetal to yield maltose
Aldolase B
cleaves fructose-1-phosphate into glyceraldehyde and DHAP
alpha-amylase
cleaves randomly along the chain to yield shorter polysaccharide chains, maltose, and glucose
isoforms
closely related proteins whose function is similar but whose affinity for ligands differs
Lipoproteins
clusters of lipids associated with proteins that serve as transport vehicles for lipids in the lymph and blood
regulatory gene of operon
codes for repressor protein
fibrous proteins
collagen, elastin, keratin
DNA libraries
collection of clones containing all the DNA fragments from one source (tissue type, cell type, or single individual)
resting muscle
conserves carbohydrates as glycogen and uses free fatty acids for fuel
-ogen suffix and enzymes
contain catalytic domain and regulatory domain
oxidation and reduction of carbohydrates
enables the body to use carbohydrates to yield energy
dihydrolipoyl dehydrogenase
enzyme in the PDH complex used FAD to re oxidize lipioc acid so it is ready to be reduced once more lip -SH-SH +FAD+ --> LipS-S + FADH2 NAD+ oxidizes FADH2 to FAD+ and NADH
Covalently Modified Enzymes
enzymes can be activated or deactivated by phosphorylation or dephosphorylation Can also be modified by covalent attachment of sugar groups (glycosylation)
Epimerase
enzymes that catalyze the conversion of one sugar epimer to another
Mannose
epimer of glucose
Adipocytes
fat cells that make up most of the subcutaneous layer
cardiac muscle
fatty acids fuel the muscle or ketones during prolonged fasting decline in heart muscle results glucose oxidation and beta oxidation falls
Stationary phase of chromatography
filter paper; allows elute
codon recognition
first stage of elongation; tRNAs recognize through their anticodon and bring appropriate amino acid to the A site
protein processing
folding, cleaving, adding sugar groups, targeting for transport
B9
folic acid
lariat of excised introns
form lasso shape then degrade
Glycogenesis
formation of glycogen from glucose 1. glucose-6-P to glucose-1-P (activated by UDP) 2. UDP converted to UTP to form UDP-glucose and pyrophosphate
Acetals
formed when hemiacetals react with alcohol the anomeric hydroxyl group is transformed into a alkoxy group - making alpha and beta acetals with water as the leaving group
diterpenes
four isoprene units ex. vitamin A --> makes retinal (pigment necessary for sight)
counterregulatory hormones
glucagon cortisol epinephrine norepinephrine growth hormone have the opposite effects of insulin
irreversible enzymes of glycolysis
glucokinase/hexokinase PFK1 pyruvate kinase
Glucose-6-phosphatase
glucose 6-phosphate to glucose only in ER if not found in skeletal muscle then glycogen can not be used
Monosaccharides
glucose, fructose, galactose
furanosides
glycosides derived from furanose rings
pyranosides
glycosides derived from pyranose rings
Anti-codon
group of three bases on a tRNA molecule that are complementary to an mRNA codon
antioncogenes
growth inhibiting cancer suppressor genes
allosteric enzymes
have both an active site for substrate binding and an allosteric site for binding of an allosteric effector (activator, inhibitor)
amphipathic
having both a hydrophilic region and a hydrophobic region
protonated
having received and containing an additional H+
Orexin
hunger-triggering hormone secreted by hypothalamus
termination factors
hydrolyzes the completed polypeptide chain from the final tRNA during translation allows tRNA release in P site and A/E subunits release
Glucagon second messenger
increase glycogenolysis, glucogeonesis, ketogenesis, lipolysis. decrease lipogenesis
max velocity of enzyme
increase max velocity by increase
heat denaturation
increases kinetic energy of protein and this affects hydrophobic and hydrophilic interactions cause protein to unfold
operon types
inducible and repressible
uncompetitive inhibition
inhibitor binds only to enzyme-substrate complex locks substrate in enzyme preventing its release (increasing affinity b/w enzyme and substrate so it lowers Km) Lower Km and vmax
mixed inhibition
inhibitor binds to allosteric site in either enzyme or enzyme-substrate complex vmax decreases If inhibitor binds to enzyme, it increases Km (lowers affinity) If inhibitor binds to enzyme-substrate complex, it lowers Km (increases affinity)
irreversable inhibition
inhibitor covalent bonds to side chains in the active site and permanently inactivates the enzyme
inner mitochondrial membrane
innermost membrane of the mitochondria. Oxidative phosphorylation and chemiosmosis take place at the inner mitochondrial membrane, which produces ATP via the flow of protons across the membrane.
postabsorptive (fasting) state
insulin secretion decreases while glucagon and catecholamine secretion increases
non-template synthesis
lipid and carbohydrate synthesis process that does not rely directly on the coding of nucleic acids (unlike protein and nucleic acids synthesis)
micelle
lipid molecules that arrange themselves in a spherical form in aqueous solutions
Steriods
lipids whose structures resemble chicken-wire fence. include cholesterol and sex hormones
nucleic acid prosthetic group
lipoproteins glycoproteins nucleoproteins
very low density lipoproteins (VLDL)
lipoproteins that transport triglycerides and other lipids from the liver to various tissues in the body
RNA polymerase I
located in the nucleolus and synthesizes rRNA
RNA polymerase III
located in the nucleus and synthesizes tRNA and some rRNA
Sphingolipids
long fatty acid chain polar head group backbone=amino alcohol (not glycerol)
Denaturation
loss of normal shape of a protein due to heat or other factor
Adenosine Diphosphate (ADP)
low-energy molecule that can be converted to ATP
urea cycle
mechanism that takes nitrogen across the rumen wall back to the salivary glands in order to preserve nitrogen in the system
Integrins
membrane proteins; they transmit signals between the ECM and cytoskeleton promote cell division, apoptosis, etc
Vitamin D (cholecalciferol)
metabolized to calcitrol in the kidneys and regulates calcium and phosphorus homeostasis in the intestines (increasing calcium and phosphate absorption), promotes bone formation
semiconservative
method of replication that implies that each new strand of DNA is half original and half new
Electrophoresis
method of separating serum proteins by electrical charge
knockout mice
mice in which a gene of interest has been silenced or deleted by genetic engineering
Galactose
milk sugar
Nucleotide
monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base
debranching enzyme
moves a block of oligoglucose from one branch and connects it to the chain using an alpha-1,4 glycosidic link
tissues in which glucose uptake is not affected by insulin
nerve, kidney tubules, intestinal mucosa, red blood cells, beta cells.
outcomes of antibody-antigen binding
neutralizating antigen, opsonization, agglutinating antigen and antibody into large protein complexes
ungated channels
no gates, unregulated, ex. potassium channels
recombinant vector
nucleic acid (vector) with the DNA of interest ligated to it also needs to make sure that this plasmid has antibiotic resistance
alcohol dehydrogenase (ADH)
one of the alcohol-metabolizing enzymes, found in the stomach and the liver, that converts ethanol to acetaldehyde
anomeric carbon
only carbon attached to two oxygens -OH may point up or down
voltage gated channels
open and close in response to changes in membrane potential
ligand-gated channels
open in the presence of a specific binding substance, usually a hormone or neurotransmitter
pyruvate dehydrogenase complex
oxidative decarboxylation, pyruvate oxidized to acetyl-CoA (loses a carbon) uses up CoA, NAD+ reduced to NADH, releases CO2 acetyl-CoA inhibitor
biphosphoglycerate mutase
produces 2,3-biphosphoglycerate (2,3-BPG) from 1,2-BPG in glycolysis
colligative properties
properties that depend on the concentration of solute particles but not on their identity
elastin
protein base similar to collagen that forms elastic tissue
apoprotein
protein component of a lipoprotein
Histones
protein molecules around which DNA is tightly coiled forming chromatin
Apoenzyme
protein portion of an enzyme
secondary structure of protein
protein structure is formed by folding and twisting of amino acid chain
tertiary structure of protein
protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3D structure contain hydrophobic interactions, acid-base/salt bridges, and disulfide bridges
Flippase
protein that facilitates the movement of membrane lipids from one leaflet to the other leaflet of a phospholipid bilayer use energy to flip
histone acetylases
proteins that are involved in chromatin remodeling can be recruited due to transcription factors they acetylate (CH3C=O) lysine residues found on the N terminal of the histone tail region it increases the space between the histones, allowing for better access to DNA for other transcription factors
histone deacetylases
proteins that function to remove the acetyl groups from histones make the chromatin in a more closed conformation overal decreases the gene expression levels of the cell
Nucleosome
proteins with nucleic acid prosthetic groups
Aromatic Heterocycles
purines and pyrimidines are biological __ __
Glucocorticoids
raises blood sugar levels
Carnitine acyltransferase I
rate limiting enzyme of fatty acid oxidation following beta oxidation
Fructose-1,6-bisphosphatase
rate limiting step of glycolysis fructose 1,6-bisphosphate to fructose 6-phosphate activated my ATP and inhibited by AMP/fructose-2,6-phosphate
respiratory control
rates of oxidation phosphorylation and citric acid cycle are very closely linked - the TCA cycle gives the reactants for the ETC O2 and ADP are key regulators O2 limited rate of oxidation phosphorylation decreases concentration of NADH and FADH2 increase - inhibiting the TCA cycle enough O2 - dependent of the availability of ADP ADP and ATP are reciprocally related a lot of ADP - not much ATP a lot of ATP - not much ADP a lot of ADP - need for ATP synthesis ADP activated isocitrate dehydrogenase - increasing the rate of the TCA cycle and thus increasing the production of NADH and FADH2
Substrate
reactant of an enzyme-catalyzed reaction
glycoside formation
reaction between an alcohol and a hemiacetal or hemiketal group on a sugar to yield an alkoxy group dehydration rxn and hydrolysis required to break glycoside bonds
Glutathione
reducing agent that can help reverse radical formation before damage is done to the cell
ketolysis
regenerates acetyl-CoA for use as an energy source in peripheral tissues
R state
relaxes state of an enzyme subunit high affinity state
AP endonuclease
removes the damaged sequence during base excision repair
Motif
repetitive organization of secondary structures
Telomere
repetitive unit (TTAGGG) at the end of a eukaryotic chromosome that prevents them from unraveling from high G-C content can be shortened or replaced by telomerase
Heterocycles
ring structures that contain at least two different elements in the ring
enzyme activity and salinity
salt concentration can change the enzyme activity in vitro increasing concentration can disrupt hydrogen and ionic bonds this can cause partial changes in the conformation of the enzyme also can lead to denaturation
fatty acid oxidation (beta oxidation) of saturated
saturated fatty acids- dehydrogenase to create double bond (produce FADH2), then produce NADH to create ketone, breaks off acetyl-CoA, repeat needs *2 ATP* to initially activate fatty acid need 1 FAD, 1 NAD+ for each 2 C removed produces *1 FADH2, 1 NADH*
peptide bond formation (elongation)
second stage of elongation; peptide bonds form between amino acids that are linked to tRNAs in the P and A sites
DNA cloning
set of procedures that uses living cells to make many identical copies of a DNA fragment
Dihydroxyacetone
simplest ketose
ribonucleic acid (RNA)
single-stranded nucleic acid that contains the sugar ribose
promoter site of operon
site of RNA polymerase binding (similar to promoters in eukaryotes)
liposome
small membrane bounded transport vesicles
initation of translation
small ribosomal subunit binds to a special initiator tRNA (methionine), then binds to mRNA, large ribosomal unit then attach to small ribosomal unit, in the end initiator tRNA is in P site of ribosome, and A and E sites are empty
alternatice splicing
splicing can occur more than one way to produce different products
Structure of glycogen
straight chain of alpha-glucose (1,4-glycosidic bond) with side branches (1,6-glycosidic bond)
paracellular route
substances pass through gaps between the cells
Homosaccharides
sugar composition is the same
deoxy sugars
sugars with a -H replacing an -OH group
Aldoses
sugars with aldehydes as their most oxidized group
isoelectric point for basic amino acids
tend to be high
isoelectric point for acidic amino acids
tend to be low
T state
tense state of a enzyme subunit low affinity state
proteinogenic amino acids
the 20 alpha amino acids encoded by the human genetic code
7-methylguanylate triphosphate cap
the 5' cap added to the end of the hnRNA molecule during RNA processing of eukaryotes during transcription and is recognized by the ribosome as the binding site, and protects the mRNA from degradation in the cytoplasm
beta anomer
the OH group of the C1 cis to the CH2OH group *it will be equatorial and up*
primary structure of protein
the amino acid sequence of the polypeptide chain
histone acetylation
the attachment of acetyl groups (-COCH3) to certain amino acids of histone proteins, the chromatin becomes less compact, and the DNA is accessible for transcription
Proteolysis
the breakdown of proteins or peptides into amino acids by the action of enzymes starts in stomach (pepsin)
Chylomicrons
the class of lipoproteins that transport lipids from the intestinal cells to the rest of the body
Proto-oncogenes
the corresponding normal cellular genes that are responsible for normal cell growth and division
solvation layer
the layer of solvent particles that interacts directly with the surface of a dissolved species
allosteric inhibition
the mechanism for inhibiting enzyme action in which a regulatory molecule binds to a second site (not the active site) and initiates a conformation change in the active site, preventing binding with the substrate
Goldman-Hodgkin-Katz equation
the membrane potential that results from the contribution of all ions that can cross the membrane
phosphoryl group transfers
the overall free energy of the reaction will be determined by taking the sum of the energies of the individual reactions - due to a transfer of phosphate groups from ATP free energy of hydrolysis (transfer of phosphate group to water) ATP + H2O --> ADP + Pi 𝛥G°'= -30kj/mol
heterogeneous nuclear RNA (hnRNA)
the precursor to processed mRNA; converted to mRNA by adding a poly-A tail and 5' cap, and splicing out introns
ketone bodies
the product of the incomplete breakdown of fat when glucose is not available in the cells acetoacetate and 3-hydroxybutyrate
post-translational processing
the protein needs modifications for proper folding chaperones - help in the folding process ex) phosphorylation carboxylation glycosylation prenylation
basal metabolic rate (BMR)
the rate at which the body burns energy when the organism is resting
van't Hoff factor
the ratio of moles of particles in solution to moles of solute dissolved
feedback regulation
the regulation of the activity of an enzyme by one of its products
Deamination
the removal of an amino group from an organism, particularly from an amino acid
Saturation
the state or process that occurs when no more of something can be absorbed, combined with, or added.
coding strand
the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine
Bioenergetics
the study of how energy flows through living organisms
ATP cleavage
the transfer of a high-energy phosphate group from ATP to another molecule
membrane potential
the voltage difference across a membrane -40 to -80 mV can rise to 35mV during depolarization
degenerate code
there are more codons (64) than there are amino acids to be coded, so most amino acids are coded by more than one code.
globular proteins
these are compact, generally rounded, and soluble in water.
small nuclear ribonucleoproteins (snRNPs)
these enzymes cut out introns and splice together exons in the pre-RNA to create a functional mRNA
pyruvate dehydrogenase complex cofactors and coenzymes
thiamine pyrophosphate, CoA, FAD, NAD+, lipoic acid
wobble position
third position of the codon two bases are usually the same - the third base in the codon is usually variable this is an evolutionary development used to protect against mutations in the coding regions of DNA mutations in this position tend to be *silent or degenerate*
tripeptide
three amino acids bonded together
Transferases
transfer functional groups from one substrate to another
Shuttle Mechanism
transfers the high-energy electrons of NADH to a carrier that can cross the inner mitochondrial membrane
cell adhesion molecules
transmembrane proteins that bind to each other and to extracellular materials cadherins, integrins, selectins
Galactokinase
traps galactose inside the cell by phosphorylating it galactose --> galactose 1 phosphate
pancreactic proteases
trypsin, chymotrypsin, and carboxypeptidases A and B secretes as zymogens when protein catabolism occurs
trp operon
tryptophan binds to the repressor protein and enables it to repress gene transcription.
Supercoiling
twisting in the opposite direction to the turns of the double helix during the first stage of mitosis.
Ribosomal RNA (rRNA)
type of RNA that combines with proteins to form ribosomes
dideoxynucleotide
type of nucleotide used during DNA sequencing to terminate synthesis
fatty acid oxidation (beta oxidation) of unsaturated
unsaturated fatty acids- isomerase to move double bond, then produce NADH to create ketone, break off acetyl-CoA, repeat in mitochondrial matrix needs *2 ATP* to initially activate fatty acid need 1 FAD, 1 NAD+ for each 2 C removed produces *1 FADH2, 1 NADH*
Bicinchoninic Acid (BCA) Assay
used for quantitation of total protein in a sample. The principle of this method is that proteins can reduce Cu+2 to Cu+1 in an alkaline solution (the biuret reaction) and result in a purple color formation by bicinchoninic acid
omega numbering system
used for unsaturated fatty acids omega described the position of the last double bond relative to the end of the chain identifies the major precursor fatty acid
dihydroxyacetone phosphate
used in hepatic and adipose tissue for triacylglycerol synthesis can be ismoerized to glycerol 3 phosphate to be converted to glycerol
Brain metabolism
uses glucose except in prolonged starvation, when it can use ketolysis
F1 portion of ATP synthase
uses the energy released by the gradient to phosphorylate ADP into ATP
Michaelis-Menten equation
v = (vmax [S])/(Km + [S]) when rxn rate= half of Vmax, Km =[S] substrate concentration increases, enzyme increase rxn rate until Vmax is reached
migration velocity
v = Ez/f -directly proportional to the electric field strength (E) and to the net charge on the molecule (z) -inversely proportional to a frictional coefficient (f)
Michaelis-Menten equation and Kcat
v= Kcat [E][S]/Km + [S]
Km >> [S] (low substrate concentration)
v=(Kcat/Km)[E][S]
Vmax and Kcat
vmax = kcat[E] -kcat = measures the # of substrate molecules converted to product per enzyme molecule per second
postprandial state
well fed/absorptive state --> insulin secretion is high and anabolic metabolism prevails
Hypertonic
when comparing two solutions, the solution with the greater concentration of solutes
ketolysis in the brain
when the body has been in ketosis for longer than a week - 2/3 of of the energy comes from ketone bodies when ketones are broken down into acetyl CoA, pyruvate dehydrogenase will be INHIBITED glycolysis and glucose uptake by the brain will be inhibited
isotonic
when the concentration of two solutions is the same
negatively charged under basic conditions
~ At basic pH carboxyl group = deprotonated (COO-) ~ Amino group = deprotonated
positively charged under acidic conditions
~ pH 1 (many protons) Amino group = fully protonated and + charged. Carboxyl group = fully protonated and neutral ~ Sums to + charge
Lecithin-cholesterol acyltransferase (LCAT)
• made in the liver • activated by apo-a1 • constituent of HDL • job is to esterify cholesterol and make it really hydrophobic
Glycosphingolipids
• sphingolipids w/ head groups composed of sugars bonded by glycosidic linkages -not phospholipids b/c they have no phosphodiester linkage - found on the outer surface of the plasma membrane