MCAT Biochemistry Combined
What is the structure of glycogen? what type of glycosidic links exist in a glycogen granule?
-Glycogen is made up of a core protein of glycogenin with linear chains of glucose enamating out from the center, connected by alpha-1,4-glycosidic links. -Some of these chains are branched, which requires alpha-1,6 glycosidic links
snRNPS
(small nuclear ribonucleoproteins) composed of RNA and protein molecules, recognize the splice sites, join with additional proteins to form a spliceseome
ketoses
* Carbohydrates with a ketone group *Keto group: C=O in b/w 2 carbons (typically in the middle of the chain)
sesquiterpenes
* sesqui means ½ *contain 3 isoprene units
dehydrogenases
***subtype of oxidoreductases -transfer a hydride ion (H+) to electron acceptor, usually NAD+ or FAD.
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
Succinate Formation
- catalyzed by succinyl CoA synthetase - ATP formed from GTP by nucleosidediphosphate kinase
Succinyl-CoA and CO2 formation
- catalyzed by α-Ketoglutarate dehydrogenase complex
apoproteins
- form the protein component of lipoproteins - receptor molecules - involved in signaling
globosides
- glycosphingolipids - have two or more sugars attached to sphingosine
Postabsorptive (fasting) state
- insulin secretion decreases - glucogon and catecholamine secretion increases - observed in short-term fasting (overnight) - transition to catabolic metabolism
GLUT 4
- is in adipose tissue and muscle and reponds to glucose concentration in peripheral blood - insulin stimulates the additional movement of GLUT 4 to the membranes of these tissues Km is close to normal glucose levels in the blood (~5mM) -so when transporter is saturated when blood glucose levels are just a bit higher than normal. -When person has high blood sugar concentration these transporters will still only plermit a constant rate of glucose b/c they will be saturated (zero-order kinetics) -therefore the only way GLUT 4 transports to increase their intake of glucose is to increase the number of transporters
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 - as liver glycogen stores are depleted, gluconeogenesis activity continues to play an important role in maintaining blood glucose levels during prolonged fasting - after 24 hours, gluconeogenesis is the predominant source of glucose for the body - lipolysis is rapid resulting in excess acetyl-CoA that is used in the synthesis of ketone bodies - once levels of fatty acids & ketones are high enough in the blood, muscle tissue will utilize fatty acids as the major fuel & the brain will adapt to using ketones for energy - after several weeks of fasting, the brain derives approx. 2/3 energy of ketones & 1/3 from glucose - the shift from glucose to ketones as the major fuel reduces the amount of essential amino acids that must be degraded to support gluconeogenesis, which spares proteins that are vital for other functions - cells that have few, if any mitochondria, like RBCs, continue to be dependent on glucose for their energy
Triacylglycerols (triglycerides)
- storage lipids involved in human metabolic processes - contain three fatty acid chains esterified to a glycerol molecule
Triacylglycerols (triglycerides)
- storage lipids involved in human metabolic processes - contain three fatty acid chains esterified to a glycerol molecule
calorimeters
- can measure basal metabolic rate (BMR) based on the heat exchange w/ the environment - human calorimetry makes use of large insulated chambers w/ specialized heat sinks to determine energy expenditure
Cardiac muscle metabolism
- uses fatty acid oxidation in both the well-fed and fasting states
unsaturated fatty acids
-"healthier" fats b/c have 1+ double bonds -exist in liquid at room temp -in plasma membrane, these characteristics impart fluidity to the membrane -humans can only synthesize a few of the unsaturated fatty acids; rest come from the essential fatty acids in the diet that are transported as triacylglycerols from the intestine inside chylomicrons.
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
Gluconeogenesis Pathway
-2 molecules of pyruvate into glucose
promoter regions
-75 CAAT box (eukaryotes) -25 Hogness/TATA box (pro/eukaryotes) -10 Pribnow/TATAAT box
Lowry reagent assay
-A 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.
operator site
-A component of the operon in prokaryotes -a nontranscribable region of DNA that is capable of binding a repressor protein
Disaccharide
-A double sugar, consisting of two monosaccharides joined by dehydration synthesis. -glycosidic bonds formed between hydroxyl groups of two monosaccharides result in the formation of a disaccharide.
Why must pyruvate undergo fermentation for glycolysis to continue?
-Fermentation must occur to regenerate NAD+, which is in limited supply in cells. -Fermentation generates no ATP or energy carriers; it merely regenerates the coenzymes needed in glycolysis
secondary active transport
-Form of active transport which does not use ATP as an energy source; rather, transport is coupled to ion diffusion down a concentration gradient established by primary active transport.
What is the primary method of transporting free fatty acids in the blood?
-Free fatty acids remain in the blood, bonded to ALBUMIN and other carrier proteins -A much smaller amount will remain unbonded.
Step 7 of Citric Acid Cycle
-Fumarase catalyzes the hydrolysis of the alkene bond in fumarate, giving rise to malate. -Only L-malate is formed in this reaction.
Orexin
-Further increases appetite, also involved in alertness and sleep-wake cycle -hypoglycemia is also a trigger for orexin release -SECRETED BY THE HYPOTHALAMUS
How does insulin promote glucose entry into cells?
-GLUT 4 is saturated when glucose levels are only slightly above 5mM, so glucose entry can only be increased by increasing the number of transporters. -Insulin promotes fusion of vesicles containing preformed GLUT4 with the cell membrane
What are the important enzymes to know for Galactose Metabolism?
-Galactokinase -Galactose-1-phosphate uridyltransferase
Under what physiological conditions should the body carry out gluconeogenesis?
-Gluconeogenesis occurs when an individual has been fasting for >12 hours. -To carry out gluconeogenesis, hepatic (and renal) cells must have enough energy to drive the process of glucose creation, which requires sufficient fat stores to undergo beta-oxidation.
What is the preferred fuel for most cells in the well fed state? What is the EXCEPTION and its preferred fuel?
-Glucose -Cardiac muscle is the exception, as it ulitizes fatty acids instead. -Lack of glycogen storage mechanisms is why.
Resting skeletal muscle metabolism
-Glucose and Fatty acids are major fuel source -after meal, insulin promotes glucose uptake, replenishing glycogen and AAs for protein synthesis -fasting, uses fatty acid derivatives from free fatty acids circulating. -can also use ketone bodies
Brain metabolism
-Glucose is primary fuel -In hypoglycemic conditions (<70mg/dL) hypothalamic centers trigger release of glucagon and epinephrine -Fatty-acids can't cross blood-brain barrier, so they are not used at all -Only during prolonged starvation can ketone bodies be used by the brain
Glycine
-Gly, G -the only amino acid that is not optically active, because the alpha-carbon is not chiral, therefore will not reflect light
Ketogenesis
-Metabolic process that produces ketone bodies via beta-oxidation of fatty acids and ketogenic Amino Acids. -occurs in the mitochondria of liver cells when excess acetyl-CoA accumulates in the fasting state -Enzyme HMG-CoA synthase forms HMG-CoA, and and enzyme HMG-CoA lyase breaks down HMG-CoA into acetoacetate, which can be subsequently reduced to 3-hydroxybutyrate -Acetone is a minor side product, but not used as energy for tissues
motif
-a repetitive organization of secondary structural elements together. -this regularity gives many structural proteins a fibrous nature
response element
-a sequence of DNA that binds only to specific transcription factors
corepressor
-a small molecule that binds to a bacterial repressor protein and changes the protein's shape, allowing it to bind to the operator and switch an operon off
chromosomes
-a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes. -46 chromosomes in humans -found in the nucleus of the cell
catabolite activator protein (CAP)
-a transcriptional activator used by E. coli when glucose levels are low to signal that alternative carbon sources should be used -falling levels of glucose causes increases in cAMP, which bind to CAP, causes a conformational change that allows it to bind to promoter region of lac operon, increasing transcription of the lactase gene -positive control mechanism.
Citrate Isomerized to isocitrate
-aconitase removes water and then adds water back changing stereochemistry making isocitrate - aconitase is a metalloprotein and requires Fe 2+
Gq protein
-activates phospholipase C, which cleaves a phospholipid from the membrane to form PIP2. PIP2 is then cleaved into DAG and IP3: -IP3 can then open calcium channels in the endoplasmic reticulum, increasing calcium levels in the cell.
DNA methylases
-add methyl groups to A and C nucleotides -methylation of genes is often linked with the silencing of gene expression. -during development, methylation places an important role in silencing genes that no longer need to be activated. -heterochromatin regions of the DNA are more heavily methylated, hindering access of the transciptional machinery to the DNA
polyadenosyl (poly-A) tail
-added to the 3' tail of mRNA -protects against rapid degradation -many adenine bases -as soon as mRNA leaves nucleus, it starts to get degraded from 3' end --> the longer the tail, the safer it is -assists with export of the mature mRNA from the nucleus.
subunits
-aggregate of smaller globular peptides and represents the functional form of the protein.
gap junctions
-allow for cell-cell communication and are often found in small bunches together
Activation Domain
-allows for the binding of several transcription factors and other important regulatory proteins. -Such as RNA polyermase and histone acetylases, which function in the remodeling of the chromatin structure.
chemiosmotic coupling
-allows the chemical energy of the gradient to be harnessed as a means of phosphorylating ADP to ATP. -ETC generates high concentration of protons in the intermembrane space; protons then flow through the Fo ion channel of ATP synthase back into the matrix. As this is occurring, F1 portion of ATP synthase utilizes the energy released from this electrochemical gradient to phosphorylate ADP to ATP -Describes a direct relationship between the proton gradient and ATP synthesis.
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
salinity on enzymes
-altering [salt] can change enzyme activity in vitro. Increasing levels of salt can disrupt hydrogen and ionic bonds, causing a partial change in the conformation of the enzyme, and in some cases can cause denaturation.
glucogenic amino acids
-amino acids that can be used to form glucose through gluconeogenesis -All AA's except for leucine and lysine
trypsin
-an enzyme from the pancreas that digests proteins in the small intestine -cleaves at the carboxyl end of arginine and lysine
arachidonic acid
-an omega-6 polyunsaturated fatty acid with 20 carbons and four double bonds; present in small amounts in meat and other animal products and synthesized in the body from linoleic acid. -act as paracrine or autocrine signaling molecules
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. -can be overcome by addition more substrate to increase substrate/inhibitor ratio. -adding competitive inhibitor doesn't affect Vmax, but increases Km.
Leucine
Leu, L nonpolar aliphatic
Based on NEEDS, which of the two shuttle mechanisms is cardiac muscle most likely to utilize? why?
Malate-Aspartate shuttle. -This mechanism is more efficient for ATP generation, making sense for a highly aerobic organ such as the heart to utilize it in order to maximize its ATP yield.
sodium dodecyl sulfate (SDS)
Negatively-charged detergent used to denature and confer a negative charge to proteins before separation by electrophoresis
epinephrine
Neurotransmitter secreted by the adrenal medulla in response to stress. Also known as adrenaline.
small nuclear RNA (snRNA)
Noncoding RNA found in eukaryotes and involved in splicing, polyadenylation, and other processes in the nucleus.
introns
Noncoding segments of nucleic acid that lie between coding sequences.
What is the difference between a nucleoside and a nucleotide?
Nucleosides: -contain a five-carbon sugar (pentose) and a nitrogenous base Nucleotides: -Contain a five-carbon sugar (pentose) a nitrogenous base, AND 1-3 phosphate groups
Nucleosome structure
Nucleosomes are composed of DNA wrapped around histone proteins
What is the key structural difference in the types of lesions corrected by nucleotide excision repair vs. those corrected by base excision repair?
Nucleotide Excision Repair: -Corrects lesions that are large enough to distort the double helix structure Base Excision Repair: -Corrects lesions that are small enough not to distort the helix.
What are the key regulators of oxidative phosphorylation?
O2 and ADP -If O2 is limited, the rate of oxidative phosphorylation decreases, and the concentrations of NADH and FADH2 increase. This increase of NADH inhibits the citric acid cycle. -ADP and ATP are reciprocally related, high of one means a depleted storage of another. -ADP allosterically activates isocitrate dehydrogenase, increasing the rate of the citric acid cycle and the production of NADH and FADH2. These coenzymes then in turn increase rate of ETC and ATP synthesis.
passive transport
Requires NO energy, Movement of molecules from high to low concentration, Moves with the concentration gradient
lacteals
Specialized lymphatic capillaries in the intestines that take up lipids as well as lymph.
Name the three types of sphingolipids, classify them as phospholipids or glycolipids, and their functional group(s):
Sphingomyelin -Phospholipid -Phosphatidylethanolamine/phosphatidylcholine Glycosphingolipid -glycolipid -Sugars (mono- or polysaccharide) Ganglioside -Glycolipid -Oligosaccharides and N-acetylneuraminic acid (NANA)
Starch Structure
Starches are polymers of 1,4-linked alpha-D-glucose
The Genetic Code
Start: -AUG (methionine) Stop: -UAA, UAG, UGA
Fumarate Formation
Step 6: takes place in the mitochondrial inner membrane Only step of the cycle that does not occur in the matrix Succinate + FAD -> FADH2 + Fumarate
What are the five steps in the addition of acetyl-CoA to a growing fatty acid chain?
Steps for attachment of acetyl-CoA to a fatty acid chain: -Attachment to acyl carrier protein -bond formation between molecules -reduction of a carbonyl group -dehydration -reduction of a double bond Figure11.6 in biochem book
template strand
The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript.
Exergonic reaction diagram
The activation energy required for a catalyzed reaction is lower than that of an uncatalyze reaction while the free energy and enthalpy remains the same.
membrane potential
The voltage across a cell's plasma membrane. -resting membrane potential is between -40 and -80 mV -can rise as high as +35 during repolarization
Liver metabolism
Two main roles in fuel metabolism: -maintain constant level of blood glucose under a wide range of conditions -synthesize ketones when excess fatty acids are being oxidized. -After meal, glucose concentration increases, liver extracts and uses it to replenish glycogen, w/ remaining glucose being converted to acetyl-CoA for fatty acid synthesis. -In well fed state, liver gets most energy from oxidation of excess amino acids -between meals and during fasting, liver releases glucose into the blood.
Describe the structure and function of triacylglycerols:
Triacylglycerols, also called triglycerides, composed of a glycerol backbone esterified to three fatty acids. They are used for energy storage.
Tryptophan
Trp, W
ketohexose
a six-carbon monosaccharide that is a ketone
aldohexose
a six-carob monosaccharide with an aldehyde group on one end.
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).
Hydrolases
catalyze the breaking of a compound into two molecules using twater. -many hydrolases are named for their substrate. Ex: -common one is phosphatase, which cleaves a phosphate group from another molecules -Other ones include peptidases, nucleases, and lipases, which break down proteins, nucleic acids, and lipids.
d-galactose
aldohexose
d-glucose
aldohexose
d-mannose
aldohexose
d-ribose and d-arabinose are c-2 epimers
aldotetroses
glucogenic amino acids
all except leucine and lysine; can be converted into intermediates that feed into gluconeogenesis
True/False: Fatty acids are synthesized in the cytoplasm and modified by enzymes in the smooth ER
True, Fatty acids are synthesized in the cytoplasm
True/False: It is easier to GAIN weight than LOSE weight
True: -The threshold is lower for uncompensated weight gain than it is for uncompensated weight loss. Therefore, easier to pass the threshold and gain weight than to lose weight.
expression libraries
cDNA library where it only includes genes that are expressed in the tissue from which the mRNA was taken from
Monoterpenes (C10H16)
contain 2 isoprene units
Michaelis-Menten plot of enzyme kinetics
as the amount of substrate increases, the enzyme is able to increase its reaction until it reaches a maximum enzymatic reaction rate (Vmax); once Vmax is reached, adding more substrate will not increase the rate of reaction only way to increase Vmax - increasing enzyme concentration
negatively charged amino acids
aspartate, glutamate
allosteric activators
assist the enzyme by building the enzyme on a site other than the active site to boost the activity.
Look at table on pg. 278 for membrane transport processes:
bet
Study configurations of eight aldohexoses
bet
Which secondary structure is proline found in?
beta-turns, and the residue at the start of an alpha helix
protein folding MCAT
beyond scope of MCAT know that: 1. secondary structures probably form first 2: hydrophobic interactions and hydrogen bonds cause the protein to "collapse" into proper 3d structure
Binding proteins
bind a specific substrate, either to sequester it in the body or hold its concentration at steady state Ex: -hemoglobin, calcium-binding proteins, DNA-binding proteins, etc.
noncompetitive inhibitors
bind to another part of an enzyme (allosteric site), causing the enzyme to change shape and making the active site less effective. -decreases Vmax, doesn't affect Km
Selectins
bind to carbohydrate molecules that project from other cells -expressed in white blood cells & endothelial cells that line blood vessels -role in host defense (inflammation & white blood cell migration)
allosteric effects
binding of a ligand at one site on a protein can lead to conformational changes that affect the binding of another ligand molecule at a different site
allosteric inhibitors
binds to allosteric enzymes causing a conformational change binding of this will result in a shift that makes the active site LESS AVAILABLE for binding to the substrate
Thiamine pyrophosphate (TPP)
bound to E1, decarboxylates pyruvate, yielding a hydroxyethyl-TPP carbanion -coenzyme used along with CoA-SH to convert pyruvate to Acetyl-CoA.
What organ consumes the greatest amount of glucose relative to its percentage of body mass?
brain
pyruvate dehydrogenase
converts pyruvate to acetyl-CoA. -Pyruvate is oxidized, while remaining 2-carbon molecules binds covaently to thiamine phyrophosphate (vitamin B1, TPP). - stimulated by insulin - inhibited by acetyl-CoA
Pyruvate Dehydrogenase
converts pyruvate to acetyl-CoA. - stimulated by insulin - inhibited by acetyl-CoA
phosphorylation of glucose
creates a phosphate ester this process is very important reaction in which a phosphate group from ATP is transferred to glucose (and ending with ADP) *hexokinase* *glucoinase* - in liver and pancreatic beta islet cells both enzymes does this reaction
homogenization
crushing, grinding, or blending the tissue of interest into an evenly mixed solution
alpha subunit of G protein
-anchored to the plasma membrane by lipid tails -may contain a GDP/GTP bound depending on its activation state -GDP-bound inactive, GTP active -posses a intrinsic GTPase activity (GTP to GDP) -in its inactive form, the alpha subunit binds GDP and is in a complex with the beta and gamma subunits.
beta subunit of G-protein
-anchored to the plasma membrane by lipids - is associated with the gamma subunit to form a beta-gamma complex
reducing sugar
-any monosaccharide w/ a hemiacetal ring (since they can be oxidized, they are considered reducing agents)
ApoC-II
-apolipoprotein -actiavtes lipoprotein lipase
ApoB-100
-apolipoprotein -permits uptake of LDL by the liver
ApoE
-apolipoprotein -permits uptake of chylomicron remnants and VLDL by the liver
Elongation Factors (EF)
-assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used
embedded proteins
-associated with only the interior or exterior surface of the cell membrane
Affinity chromatography
-beads are coated w/ a receptor that binds the protein of interest (high affinity) - protein is retained in column - can be eluted by washing the column w/ a free receptor that competes w/ the bead bound receptor & frees protein -eluted also by changing pH or salinity levels to disrupt bond b/w ligand & protein
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
steroid hormones
derived from cholesterol
primary structure
-linear arrangement of amino acids coded in an organism's DNA. -listed from N-terminus to C-terminus -stabilized by peptide bonds between adjacent amino acids -encodes all the information needed for folding at higher level structure
Ketone bodies
-liver converts excess Actyl- Coa from Beta oxidation of fatty acids to these two different ones: -acetoacetate -3-hydroxybutyrate -these can be used for energy for other tissues -cardiac, skeletal and renal cortex can use these to go back into acetyl CoA - will use them as soon as they are metabolized in the blood stream to prevent a build up in the blood -in starvation state they are high enough of concentration in the blood that the brain can metabolize them
apurinic/apyrimidinic (AP) site
-location in DNA (also in RNA but much less likely) that has neither a purine nor a pyrimidine base - created during base excision repair
polysaccharides
-long chains of monosaccharides linked together by glycosidic bonds
Transcription factors (gene expression eukaryotes)
-transcription-activating proteins that search the DNA looking for specific DNA-binding motifs -Usually have two recognizable domains: DNA-binding domain and activation domain
What are the names and functions of the four fat-soluble vitamins?
A (carotene): -As retinal: vision; as retinoic acid; epithelial development. D (cholecalciferol): -As calcitriol: calcium and phosphate regulation. E (tocopherols): -Antioxidants, using aromatic ring. K (phylloquinone and menaquinones): -Posttranslational modification of prothombrin, addition of calcium-binding sites on many proteins.
missense mutation
A base-pair substitution that results in a codon that codes for a different amino acid.
hemiketals
A carbon atom bonded to two alkyl groups, an -OR group, and an -OH group From ketoses Formed from intermolecular reactions from electro- and nucleophiles
The Citric Acid Cycle
A chemical cycle involving eight steps that completes the metabolic breakdown of glucose molecules to carbon dioxide; occurs within the mitochondrion; the second major stage in cellular respiration.
Bradford protein assay
A colorimetric method of determining the concentration of protein in an isolate against a protein standard; relies on a transition of absorption between bound and unbound Coomassie Brilliant Blue dye
Of the four types of reversible inhibitors, which could potentially increase Km?
A competitive inhibitor increases Km b/c substrate concentration has to be higher to reach Vmax in presence of inhibitor. Mixed inhibitor will only increase Km only if the inhibitor preferentially binds to the enzyme over the enzyme-substrate complex
sphingosine
A complex alcohol backbone for membrane lipids
Glycolysis
A cytoplasmic pathway that converts a molecule of glucose into two molecules of pyruvate, releasing a model amount of energy captured in two substrate-level phosphorylations and one oxidation reaction.
mixed inhibition
A decrease in enzyme activity that results from the interaction of an inhibitor with an allosteric site; mixed inhibitors bind to the free enzyme and to the substrate-bound enzyme with different affinities. They cannot be overcome by addition of substrate and impact both Km and vmax
Trehalose
A disaccharide of two glucose molecules, but with a linkage different from maltose. Used as a food additive and sweetener. -disaccharide with an alpha,alpha-1,1 linkage between the alpha-anomeric carbons of two glucose molecules.
deoxyribonucleic acid (DNA)
A double-stranded, helical nucleic acid molecule capable of replicating and determining the inherited structure of a cell's proteins. -bulk of eukarotic DNA is found in chromosomes in the nucleus of cells, althought some is also present in mitochondria and chloroplasts.
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. -have greater van der Waals forces, and a most stable overall structure
Types of Sphingolipids
1) Ceramide - H as head group 2) Sphingomyelins - major component of plasma membrane of oligodendrocytes and Schwann cells. 3) Cerebrosides - single sugar 4) Globosides - two or more sugars 5) Gangliosides - "gangly" sphingolipids, the most complex structure. Contain NANA negatively charged head group.
Types of sphingolipids
1) Ceramide - H as head group 2) Sphingomyelins - major component of plasma membrane of oligodendrocytes and Schwann cells. 3) Cerebrosides - single sugar 4) Globosides - two or more sugars 5) Gangliosides - "gangly" sphingolipids, the most complex structure. Contain NANA negatively charged head group.
Plasma Membrane Proteins
1) Transmembrane proteins 2) Embedded proteins 3) Membrane-associated proteins
What are the three major posttranscriptional modifications that turn hnRNA into mature mRNA
1- Splicing: -removal of introns, joining of exons; uses snRNA and snRNPs in the spliceosome to create a lariat, which is then degraded; exons are ligated together 2- 5'cap: -Addition of a 7-methylguanylate triphosphate cap to the 5' end of the transcript 3- Poly-A tail: -addition of adenosine bases to the 3' end to protect against degration.
unsaturated fatty acids
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. -have kinds in their chains, which makes it difficult for them to stack and solidify. -tend to be liquid at room temp.
furanose
A five-membered ring sugar One of two stable cyclic molecules
transgene
A gene that has been extracted from the DNA of one organism and transferred into the DNA of an organism of another species.
What are the three important intermediate of glycolysis?
1: -Dihydroxyacetone phosphate (DHAP) 2: -1,3-biphosphoglycerate 3: -phosphoenolpyruvate (PEP)
What are the two major metabolic products of the pentose phosphate pathway (PPP)?
1: -NADPH 2: -Ribose 5-phosphate
What are the three outcomes of an antigen binding to an antibody?
1: -Neutralize the antigen, making the pathogen or toxin unable to exert its effect on the body 2: -Marking the pathogen for destruction by other white blood cells immediately;this marking functioning is also called opsonization 3: -Clumping together (agglutinating) the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages
What are the three irreversible enzymes in glycolysis?
1: -glucokinase or hexokinase 2: -PFK-1 3: -Pyruvate Kinase
What are the three primary functions of NADPH?
1: -lipid biosynthesis 2: -bactericidal bleach formation in certain white blood cells (antibacterial) 3: -maintains of glutathione stores to protect against reactive oxygen species. (antioxidant)
What are the three major structural differences between DNA and RNA?
1: DNA contains deoxyribose, while RNA contains ribose 2: DNA contains thymine, while RNA contains Uracil 3: DNA is usually double-stranded, while RNA is single stranded
What four groups are attached to the central (alpha) carbon of a proteinogenic amino acid?
1: hydrogen 2: amine (-NH2) 3: Carboxylic Acid (-COOH) 4: R-Group
How do enzymes function as biological catalysts?
1: reduce the activation energy of a reaction, thus speeding up the reaction, and they are not used in the actual reaction 2: Improve the environment in which particular reactions take place, which lowers the activation energy.
How to figure out the number of stereoisomers in a compound
2^n where n = number of chiral carbons.
trioses
3 carbon sugars
carotenoids
An accessory pigment, either yellow or orange, in the chloroplasts of plants. By absorbing wavelengths of light that chlorophyll cannot, carotenoids broaden the spectrum of colors that can drive photosynthesis.
allosteric sites
An allosteric site is a region of the enzyme other than the active site to which a substance can bind, and can regulate enzymatic activity.
peptidyl transferase
An enzyme in the ribosome responsible for peptide bond formation during translation.
What strands of RNA do prokaryotic ribosomes have?
5S: -in 50S 16S: -in 30S 23S: -50S
What strands of RNA do eukaryotic ribosomes have?
5S: -in 60S 5.8S: -in 60S 18S: -in 40S 28S: -in 60S
esterification of glucose
Because carbohydrates have hydroxyl groups they are able to participate in reactions with carboxylic acids and carboxylic derivatives to form esters. Similar to phosphorylation of Glucose
Structure of tRNA
75-90 nucleotides, 2ary structure, cloverleaf form, anticodon end is opposite. 3' aminoacyl end. All tRNAs, both eukaryotic and prokaryotic, have CCA at 3' end along w/a high percentage of chemically modified bases. The amino acid is covalently bound to the 3' end of the tRNA
During DNA sequencing, why does the DNA polymer stop growing once a dideoxyribonucleotide is added?
Dideoxyribonucleotides lack the 3' -OH group that is required for DNA strand elongation. This causes no more nucleotides to be added b/c dideoxyribonucleotides have no 3' -OH group with which to from a bond.
Cancer cells
Do not have a properly functioning cell-cycle system; instead, they divide excessively and can invade other tissues of the body
In which way are proteins read?
Drawn and read from: N-terminus on the left, and C-Terminus on the right so read from N-terminus to C-terminus
aldoses
carbohydrates containing an aldehyde group *Aldehyde group: H—C =O *CHO at the end of the chain on the first carbon
glycosidic bonds
carbons on adjacent sugar units are bonded to the same oxygen atom like links in a chain
Fatty acids
carboxylic acids that contain a hydrocarbon chain and terminal carboxyl group
What could permit a binding protein involved in sequestration to have a low affinity for its substrate and still have a high percentage of substrate bound?
If the binding protein is present in sufficiently high quantities relative to the substrate, nearly all substrate will be bound despite a low affinity.
isoleucine
Ile, I nonpolar aliphatic
parent strand
In DNA replication, refers to the pre-existing single strand of DNA that is copied into a new strand of DNA via complementary base pairing.
DNA polymerase III
In charge of synthesizing nucleotides onto the leading end in the classic 5' to 3' direction. -PROKARYOTES
dyneins
In cilia and flagella, a large motor protein extending from one microtubule doublet to the adjacent doublet. ATP hydrolysis drives changes in dynein shape that lead to bending of cilia and flagella. -bring vesicles of waste or recycle neurotransmitter back toward the negative end of the microtubule (toward the soma)
denaturation
In proteins, a process in which a protein unravels and loses its native conformation, thereby becoming biologically inactive. In DNA, the separation of the two strands of the double helix.
Impact of insulin on fat metabolism
Increases: -Glucose and triacylglycerol uptake by fat cells. -Lipoprotein lipase activity, which clears VLDL and chylomicrons from the blood. -Triacylglycerol synthesis (lipogenesis) in adipose tissue and the liver from acetyl-CoA/ Decreases: -Triacylglycerol breakdown (lipolysis) in adipose tissue. -Formation of ketone bodies by the liver.
cristae
Infoldings of the inner membrane of a mitochondrion that houses the electon transport chain and the enzyme catalyzing the synthesis of ATP. -foldings increase the surface area for the integal proteins associated with the membrane.
Lineweaver-burk plot of competitive inhibition
increases Km
phagocytosis
ingestion of large solids such as a bacteria
What are the stages of digestion?
ingestion, digestion, absorption, elimination
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
vesicle-coating proteins
initiates invagination during endocytosis, most notably clathrin
What are the three processes of translation?
initiation, elongation, termination
What are the three types of membrane proteins?
integral, peripheral, embedded
molten globules
intermediate state in between the secondary structure and the tertiary structure
Fo portion of ATP synthase
ion channel, allowing protons to flow down the gradient from the intermembrane space to the matrix
Hemoglobin
iron-containing protein in red blood cells that carries oxygen for delivery to cells -4 subunits, each of which can bind one molecule of oxygen, which are called hemes.
amphoteric species
is one that can act either as an acid or a base, depending on its chemical environment
isoelectric point (pI)
is the pH at which a particular molecule carries no net electrical charge in the statistical mean
enantiomers
isomers that are mirror images of each other
anomers
isomers that differ at a new asymmetric carbon atom formed on ring closure
polyterpene
isoprene chains between 1000-500 units long ex. rubber
d-fructose
ketohexose
G protein-coupled receptors (GPCRs)
large family of integral membrane proteins involved in signal transduction -characterized by their 7 membrane-spanning alpha-helices -utilize heterotrimeric G protein to transmit signals to effector cells
omega-6 family
linoleic acid and arachidonic acid are the precursors for the omega-6 family
active site
location within the enzyme where the substrate is held during the chemical reaction -assumes a defined spatial arrangement in the enzyme-substrate complex, which dictates the specificity of that enzyme for a molecule or group of molecules.
polypeptides
long chains of amino acids
sphingolipids
long fatty acid chain polar head group backbone=amino alcohol (not glycerol)
fibrous proteins
long, insoluble, structural proteins. Ex: -collagen
surfactant
lowers the surface tension at the surface of a liquid, serving as a detergent or emulsifier
positively charged amino acids
lysine, arginine, histidine
What are the three main types of RNA found in cells
mRNA tRNA rRNA
zwitterions
molecules with both a positive and negative charge that cancel each other out
Kinesins
motor protein associated with microtubules two heads - one must stay attached to tubulin at all times step like walking aligns chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis important in vesicle transport *bring vesicles toward the positive end of the microtubule (periphery)* bring vesicles of neurotransmitter to the positive end of the axonal microtubule - toward the synaptic terminal
simple diffusion
movement of a solute from an area of high concentration to an area of low concentration
aldonic acids
oxidation of aldolases during open-chain aldehyde form
Enzyme-linked receptors
participate in cell signaling through extracellular ligand binding and initiation of second messenger cascades
Ribose and Deoxyribose
pentose sugars found in nucleic acids. deoxyribose is found in DNA, ribose in RNA -ribose with the 2' -OH group is replaced by -H, then it is DNA
Nonpolar aromatic amino acids
phenylalanine, tyrosine, tryptophan
Nucleotides
phosphate backbone , pentose (sugar) , nitrogenous base (A T/U GC) - hydrogen bonds hold the two nitrogenous bases together (weak bonds/break easily) -Phosphate + sugar + base -ATP and ADP are high energy b/c of energy associated with the repulsion between closely associated negative charges on the phosphate groups. -building blocks of DNA
Amino Acid Structure at Acidic pH
pka>pH (acidic/ LOW pH/ lots of H) COOH pka>pH (acidic/ LOW pH/ lots of H) NH3+ POSITIVE
expressed mutations
point mutations that can effect the first or second nucleotide in the codon - changing the primary amino acid sequence of the protein can be a missense or nonsense mutation
proteins
polypeptides that range from just a few amino acids in length up to thousands -functioning as enzymes, hormones, membrane pores and receptors, and elements of cell structure. -have four levels of structure
Replication forks
portions of DNA where the double helix separates during DNA replication
osmotic pressure
pressure that must be applied to prevent osmotic movement across a selectively permeable membrane
palmitic acid (palmitate)
primary end product of fatty acid synthesis
fibroin
primary protein component of silk fibers and composed of B-sheets
four levels of protein structure
primary structure, secondary structure, tertiary structure, quaternary structure
Biosignaling
process in which cells receive and act on signals Proteins participate in biosignaling in different capacities including acting as extracellular ligands, transporters for facilitated diffusion, receptor proteins and second messengers
facilitated diffusion
process of diffusion in which molecules pass across the membrane through cell membrane channels -diffusion of molecules occurs down a concentration gradient through a membrane pore created by the transmembrane protein. -allows for integral membrane proteins to serve as channels for these substrates to avoid the hydrophobic fatty acid tails of the phospholipid bilayer.
centrifugation
process of separating out particles of different sizes and densities by spinning them at high speed in a centrifuge.
hexose monophosphate shunt
production of 5-carbon monosaccharides and NADPH -activated by NADP+ -inhibited by NADPH
What amino acid is rarely found in alpha-helices and beta sheets
proline
catalytic domain
protein domain in enzyme-linked receptors, activated by a conformational change induced by the ligand-binding domain, causes the initiation of a second messenger cascade.
membrane-spanning domain
protein domain in enzyme-linked receptors, anchors the receptor in the cell membrane
nucleoproteins
proteins with nucleic acid prosthetic groups
nucleoproteins
proteins with nucleic acid prosthetic groups proteins that associate with DNA ex. histones other than histones (basic) they tend to be acidic and stimulate process such as transcription
Overall Reaction of Pyruvate Dehydrogenase Complex
pyruvate + CoA-SH + NAD⁺ → acetyl-CoA + CO₂ + NADH + H⁺ -inhibited by accumulated acetyl-CoA and NADH.
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
metabolism of the liver
receives amino acids and glucose after digestion, synthesis, storage and mobilisation of glycogen, fat synthesis and export via VLDL, synthesis of plasma proteins, gluconeogenesis, synthesis of ketone bodies, conversion of toxic excess ammonia to urea.
thoracic duct
receives lymph from the left side of the head, neck, chest, abdomen, left arm, and lower extremities
d and l isomers
refers to the chiral carbon furthest away from ketone or aldehyde -D sugars mostly used in humans -all D-sugars have the hydroxide of their highest-numbered chiral center on the right, and all L- sugars have that hydroxide on the left.
What is enzyme specificity?
refers to the idea that a given enzyme will only catalyze a given reaction or type of reaction
what is feedback inhibition?
refers to the product of an enzymatic pathway turning off enzymes further back in that same pathway; this helps maintain homeostasis: as product levels rise, the pathway creating that product is appropriately downregulated
What is irreversible inhibition?
refers to the prolonged or permanent inactivation of an enzyme, such that it cannot be easily renatured to gain function
dephosphorylation
removal of a phosphate group from a molecule
Telomere
repeating nucleotide at the ends of DNA molecules that do not form genes and help prevent the loss of genes
DNA polymerase gamma
replicates mitochondrial DNA
What are the two types of operons?
repressible (can be turned off) and inducible (can be turned on)
alpha-helix
rodlike structure in chick peptine chain coils clockwise around a central axis -stabilized by intramolecular hydrogen bonds between carbonyl oxygen atom and an amide hydrogen atom 4 resides down the chain -side chains point away from helix core
cell lysis
rupturing membranes of foreign cells
partitioning
separation of components within the stationary phase
Polar, uncharged amino acids
serine, threonine, asparagine, glutamine, cysteine
imidazole
side chain of histidine aromatic ring with two nitrogens pka of side chain is 6 - so at a physiological pH the side chain is neutral amide then will be protonated at a higher pH
What are the three types of point mutations?
silent, missense, nonsense
dihydroxyacetone
simplest ketose (ketotriose)
zymogens
digestive enzymes secreted as inactive proteins, converted to active enzymes by removing some of their amino acids Ex: -trypsionogen (nonactive) -> trypsin (active) -most zymogens have the suffix -ogen.
What is the primary thermodynamic factor responsible for passive transport?
entropy
Na+/K+ ATPase
enzyme that pumps three sodium ions out of the cell and two potassium ions into the cell using a single molecule of ATP
epimerases
enzymes that catalyze the conversion of one sugar epimer to another
holoenzymes
enzymes with their cofactors
apoenzymes
enzymes without their cofactors
Glucose vs Galactose
epimers at C4
exons
expressed sequence of DNA; codes for a protein
Describe role of flippases and lipid rafts in biological membranes:
flippases: -responsible for movement of phospholipids between the layers of the plasma membrane b/c it is otherwise energetically unfavorable Lipid Rafts: -Aggregates of specific lipids in the membrane that function as attachment points for other biomolecules and play roles in signaling.
Monosaccharides
glucose, fructose, galactose, ribose -simple sugars
Triacylglycerol Structure
glycerol and 3 fatty acids
lecithins
glycerophospholipids containing choline as the amino alcohol
Nonpolar, aliphatic amino acids
glycine, alanine, proline, valine, leucine, isoleucine, methionine
What is the rate limiting enzyme of glycogenolysis?
glycogen phosphorylase
allosteric enzymes
have both an active site for substrate binding and an allosteric site for binding of an allosteric effector (activator, inhibitor)
cerebrosides
have one sugar connected to sphingosine
Hexokinase vs Glucokinase
hexokinase is ↑ affinity (↓ Km) but ↓ capacity (↓ Vmax) in almost all tissues (tortoise) glucokinase is ↓ affinity but ↑ capacity in liver & pancreatic β-cells (hare)
connexons
hold tissues/membranes together; hollow cylinders composed of proteins that span the entire width of the abutting membranes
what is the difference between apoenzymes and holoenzymes?
holoenzymes are bound with their specific cofactors/coenzymes, while apoenzymes don't have their specific cofacter/coenymes bound
Ghrelin
hormone secreted by empty stomach; sends "I'm hungry" signals to the brain -sight, sound, taste, and especially smell all act as signals for its release -SECRETED BY THE STOMACH
what stabilizes the active site of an enzyme?
hydrogen bonding, ionic interactions, and transient covalent bonds.
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*
Chylomicrons
the class of lipoproteins that transport lipids from the intestinal cells to the rest of the body
Enzymes specificity
the degree to which enzymes bind to specific binding sites on their substrates. Ex: -urease only catalyzes the breakdown or urea -chymotrypsin, on other hand, can cleave peptide bonds around the amino acids Phe, Trp, and Tyr in a variety of polypeptides.
N-terminus
the end of a polypeptide or protein that has a free amino group
RNase H (eukaryotes)
the enzyme that helps to remove the RNA primer during DNA replication
Saponification
the ester hydrolysis of triacylglycerols using a strong base.
intermembrane space
the fluid filled space between the inner and outer mitochondrial membranes
globular proteins
these are compact, generally rounded, and soluble in water. ex: -myoglobin, hemoglobin
B vitamins
these water soluble vitamins interact with other water-soluble vitamins and act as coenzymes (catalysts) by facilitating enzymatic reactions. B Vitamins include: niacin, riboflavin, thiamine, pyridoxine, folacin, biotin, cobalamine, and pantothenic acid.
Cell Membrane
thin, flexible barrier around a cell; regulates what enters and leaves the cell
which amino acids have chiral carbons in their side chains?
threonine and isoleucine
prosthetic groups
tightly bound cofactors or coenzymes that are necessary for enzyme function
micelles
tiny spherical complexes of emulsified fat that arise during digestion; most contain bile salts and the products of lipid digestion, including fatty acids, monoglycerides, and cholesterol -also important in the body for the absorption of fat-soluble vitamins (A, D, E, and K).
Galactokinase
traps galactose inside the cell by phosphorylating it galactose --> galactose 1 phosphate
What type of operons are the trp and lac operon?
trp: -negative repressible system lac: -negative inducible system
Kcat
turnover number (molecules catalyzed per second in optimal conditions) Vmax / [E]
What are the major posttranslation modifications that occur in proteins?
includes: -proper folding by chaperones -formation of quaternary structure -cleavage of proteins or signal sequences -addition of other biomolecules (through phosphorylation, carboxylation, glycosylation, prenylation)
ungated channels
type of ion channel have no gates and are unregulated all cells possess ungated potassium channels - there will be a net efflux of potassium through these channels unless potassium is at equilibrium
fatty acids
unbranched carbon chains that make up most lipids
What type of ion channel is active at all times?
ungated channels are always open
What are the three types of ion channels?
ungated, voltage-gated, and ligand-gated
Vitamin A (carotene)
unsaturated hydrocarbon that is important in vision, growth and development, and immune function
R group
used to represent one of 20 possible side chains found in amino acids of living systems Ex: Lysine
pKa value for amine groups on amino acids
usually between ph 9-10
Michaelis-Menten equation
v = (vmax [S])/(Km + [S]) -when reaction rate is equal to half of vmax, Km= [S]
Migration Velocity Equation
v=Ez/f Velocity of migration during electrophoresis where v is velocity, z is charge, f is friction coefficient (resistance). E is the electric field strength. Its more important to know that velocity=E=z=1/f
migration velocity
velocity at which the protein will move to the anode (+) or move to the cathode (-) directly proportional to the electric fields strength (E) and the net charge of the molecule (z) and inversely proportional to the frictional coefficient (f)
exocytosis
when secretory vesicles fuse with the membrane, releasing material from inside of the cell to the extracellular environment -important in the nervous system and intercellular signaling.
Supercoiling
wrapping of DNA on itself as its helical structure is pushed ever further toward the telomeres during replication. Ex: -Old-fashioned telophone cord that's become tangled on itself
Titration curve for glycine
~ Glycine normally exists as fully protonated and positive ~ Titrate with NaOH (carboxyl group with deprotonate 1st) ~ At 0.5 equivalents of base fully protonated and zwitterion are = ~ When pKa and pH are similar (acts as buffer --> flat) ~ Add more base (C group = fully deprotonated and AA stops acting like buffer) ~ @ 1 equivalent glycine is in zwitterion form) ~ 2nd buffering phase when amino group deprotonates
modified standard state equation
ΔG = ΔG° + RTlnQ -R= gas constant -T= Temperature -Q=reaction quotient
Gibbs Free Energy equation
ΔG = ΔH - TΔS
chaperones
Proteins that assist in protein folding during posttranslational processing
Respirometry
- allows accurate measurement of the respiratory quotient, which differs depending on the fuels being used by the organism
Thyroid hormones (T3 and T4)
-Increase the basal metabolic rate, increasing O2 consumption and Heat production when they're secreted.
Origins of Replication
Replication forks form on both sides of the origin, increasing the efficiency of replication.
homopolysaccharide
-a polysaccharide that contains only one kind of monosaccharide Ex: -long chain of polymerized glucose monomerized
LDL
-cholesterol carrying particle, along with HDL -Delivers cholesterol to tissues for biosynthesis
sphingomyelins
(Sphingophospholipids) sphingolipids that contain a phosphocholine or phosphoethanolamine head group. -major components in the plasma membranes of cells producing myelin (oligodendrocytes and Schwann cells), the insulating sheath for axons.
Transcription
(genetics) the organic process whereby the DNA sequence in a gene is copied into mRNA
Translation
(genetics) the process whereby genetic information coded in messenger RNA directs the formation of a specific protein at a ribosome in the cytoplasm -requires mRNA, tRNA, ribosomes, amino acids, energy from GTP
gamma subunit of G-protein
- associated to the gamma subunit to form a beta-gamma complex - is not anchored to the plasma membrane
single stranded DNA binding proteins
- bind to the unraveled strand preventing the re-association of the DNA strands & degradation of DNA by nucleases -Unpaired strands of DNA are very "sticky" so proteins are required to hold the 2 strands apart
heteropolysaccharide
- a polymer made up of more than 1 type of monosaccharide
Acetyl-CoA Shuttling
- acetyl CoA accumulates in the matrix after a large meal (produced by pyruvate dehydrogenase complex). - it couples with oxaloacetate to form citrate that diffuses across the mitochondrial membrane - citrate is split into acetyl CoA and oxaloacetate by citrate lyase, after which oxaloacetate can then return to the mitochondrion to contrinue moving acetyl-CoA.
sequencing proteins
*Why: sequence >> function (folding) *x-ray could be used for sequencing *some proteins don't form crystals *there are regions of disorder(N.C terminus) *a single site mutation (SNP) can cause disease.
Disulfide bond formation
- 2 *cysteine* become *oxidized* to form *cystine* - Loss of 2 protons & 2 e-'s
What is the ratio of free fatty acids to glycerol produced through lipid mobilization?
- 3:1 -A triacylglycerol molecule is composed of glycerol and THREE fatty acids.
Step 1 of citric acid cycle
- Acetyl-CoA + Oxaloacetate undergoe condensation reaction to form citryl-CoA, an intermediate -Hydrolysis of citryl-CoA yields citrate and CoA-SH. -Reaction is catalyzed by citrate synthase (which form new covalent bonds w/o needing significant energy)
Keratins
- Intermediate filament proteins in epithelial cells - Contribute to mechanical integrity of cell and as regulatory proteins. -primary protein that makes up hair and nails.
Mitochondrial Structure
- Outer membrane - Inner membrane (with ATP synthase proteins) - Cristae - Matrix
2,3-bisphosphoglycerate (BPG)
- Precursor is an intermediate in glycolysis - Levels of 2,3-BPG increase when glucose concentrations become abundant - Stimulates release of O2 from Hb and stabilizes T formation -shifts curve to the right, raise P50, lowering affinity
Resonance in the Peptide Bond
- This double bond character between the nitrogen atom and the carbonyl carbon adds to the rigidity and stability of the backbone of proteins. - The single bonds on either side of the peptide bond permit free rotation.
Chromatography
- Uses chemical and physical properties to separate and identify compounds from a complex mixture based on how strongly they adhere to the solid. - Sample onto a solid medium called the stationary phase; then run the mobile phase , usually a liquid or a gas through the stationary phase. - Ex) Thin Layer (TLC), Column Chromatography (Ion exchange, size-exclusion, affinity), Gas, and High performance liquid chromatography
conformational coupling
-A less-accepted mechanism of ATP synthase activity in which the protons cause a conformational change that releases ATP from ATP synthase. -suggest that the relationship between the proton gradient and ATP synthesis is indirect. -In this mechanism, the F1 portion of ATP synthase is reminiscent of a turbine, spinning with a stationary compartment to facilitate the harnessing of gradient energy for chemical bonding.
Cholesterol
-A lipid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids. -Plays major role in synthesis of cell membranes, steroid hormones, bile acids, and vitamin D.
Cholesterol
-A lipid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids. -regulates membrane fluidity -cholesterol stabilizes adjactent phospholipids, while occupying space between them. This prevents the formation of crystal structures in the membrane, increasing fluidity at lower temperatures -At high temps, cholesterol has the opposite effect; instead it limits movement of phospholipids within the bilayer, decreasing fluidity and helps hold the membrane intact.
coenzyme A (CoA)
-A molecule that is required for many cellular reactions and that is often transiently linked to other molecules, such as acetyl groups.
What are the base-pairing rules according to the Watson-Crick Model?
-A pairs with T (DNA) or U (RNA) using 2 H-bonds -C pairs with G using 3 H-bonds
repressor
-A protein that binds to an operator and physically blocks RNA polymerase from binding to a promoter site
Motor proteins
-A protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell. -display enzymatic activity acting as ATPases that power the conformational change necessary for motor function. -have transient interactions w/ either actin or microtubules.
hypertonic
-A solution that is more concentrated than the cell in it -Solutes inside cell move OUT
repressible system
-A system that is normally "turned on" but can be inactivated by the addition of a repressor or corepressor. -Allows for constant production of a protein product. -the repressor made by the regulator gene is inactive until it binds to a corepressor. -respressible systems tend to serve as negative feedback, b/c often the final structural product can serve as a corepressor. -Thus, as its levels increase, it can bind the repressor and the complex will attach to the operator region to prevent further transcription of the same gene Ex: -trp operon
polymerase chain reaction (PCR)
-A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules, and nucleotides. -requires primers that are complementary to the DNA that flanks the region of interest, nucleotides (dATP, dTTP, dCTP, and dGTP) and DNA polymerase -reaction also needs heat to cause the DNA double helix to melt apart (denature). -since DNA polymerase in humans denatures at high temps, the DNA polymerase from Thermus aquaticus, a bacteria that thrives in the hot springs of Yellowstone at 70*C, is used instead. -During PCR, the DNA of interest is denatured, replicated, and then cooled to allow reannealing of the daughter strands with the parents strands. -Process is repeated, doubling the amount of DNA with each cycle, until enough copies of the DNA sequence are available for further testing.
steroids
-A type of lipid characterized by a carbon skeleton consisting of four rings with various functional groups attached. -cholesterol derivatives
Citrase Synthase (Checkpoint):
-ATP and NADH function as allosteric inhibitors of citrate synthase, which makes sense b/c both are products (indirect and direct, respectively). -Citrate also allosterically inhibits citrate synthase directly, as does succinyl-CoA.
Acetyl-CoA Carboxylase
-Acetyl CoA is activated in cytoplasm for incorporation into fatty acids by acetyl-CoA carboxylase, which is the rate limiting enzyme of fatty acid biosynthesis. -Requires both biotin and ATP to function -Adds CO2 to acetyl-CoA to form malonyl-CoA. (CO2 is never actually incorporated into the fatty acid because it is removed by fatty acid synthase during addition of the activated acetyl group to the fatty acid). -ACTIVATED by INSULIN and CITRATE
How does acetyl-CoA shift the metabolism of pyruvate?
-Acetyl-CoA inhibits pyruvate dehydrogenase complex while activating pyruvate carboxylase -The net effect is to shift from burning pyruvate in the citric acid cycle to creating new glucose molecules for the rest of the body. -The acetyl-CoA for this regulation comes from beta-oxidation of fatty acids (liver), not glycolysis.
How does acetyl-CoA affect PDH complex activity? Why?
-Acetyl-CoA inhibits the PDH complex. As a product of the enzyme complex, a buildup of acetyl-CoA from either the citric acid cycle or fatty acid oxidation signals that the cell is energetically satisfied and that the production of acetyl-CoA should be slowed or stopper. -Pyruvate can then be used to form other products, such as oxaloacetate for use in gluconeogenesis.
Step 2 of Citric Acid Cycle:
-Achiral Citrate is isomerized to one of four possible isomers of isocitrate -First, citrate binds at three points to aconitase. -Water is lost from citrate, yielding cis-aconitate -afterwards, water is added back to form isocitrate -Aconitase is a metalloprotein that requires Fe2+ -OVERALL REACTION IS A SWITCHING OF A HYDROGEN AND A HYDROXYL GROUP, THAT IS NECESSARY TO FACILIATE THE SUBSEQUENT OXIDATION DECARBOXYLATION
primary active transport
-Active transport in which ATP is hydrolyzed, yielding the energy required to transport an ion or molecule against its concentration gradient. -generally involve use of a transmembrane ATPase
Purines
-Adenine and Guanine -contain two rings in their structure -both are found in DNA and RNA
What condition does deltaG' adjust for that are not considered with deltaG?
-Adjusts only for the pH of the environment by fixing it at 7. -Temperature and other concentrations of all other reagents are still fixed at their values from standard conditions and must be adjusted for if they are not 1M.
Adipose Tissue Metabolism
-After meal, insulin levels stimulate glucose uptake by adipose tissues, also triggering fatty acid release from VLDL and chylomicrons -insulin also induces lipoprotein lipase -fatty acids that rae released from lipoproteins are taken up by adipose tissue and re-esterified to triacyl-glycerols for storage. -During fasting, decreased insulin and increased epinephine activate hormone-sensitive lipase, allowing fatty acids to be released into circulation.
Recombinant DNA
-Allows a DNA fragment from any source to be multiplied by either gene cloning or polymerase chain reaction (PCR). -This provides a means of analyzing and altering genes and proteins -also providews the reagents necessary for genetic testing, such as carrier detection (like testing heterozygote status for a particular disease), and prenatal diagnosis of genetic diseases. -also can provide a source of a specific protein, such as recombinant human insulin, in unlimited quantities.
Which of the two forms of starch is more soluble in the solution? Why?
-Amylopectin is more soluble in solution than amylose b/c of its branched structure. The highly branched structure of amylopectin decreases intermolecular bonding between polysaccharide polymers and increases interaction with the surrounding solution.
retinoic acid
-An active, acid form of vitamin A that plays an important role in cell growth and immune function -regulates gene expression during epithelial development
ApoA-I
-An apoprotein -activates LCAT, an enzyme that catalyzes cholesterol esterification
Are motor proteins enzymes?
-An enzyme is a protein or RNA molecule with catalytic activity, which motor proteins do have. Motor function is generally considered nonenzymatic, but the ATPase functionality of motor proteins indicates that these molecules do have catalytic activity.
primase
-An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template. -produces short primer (~10 nucleotides) in 5' to 3' direction to start replication on each side -these short strands are constantly being added to the lagging strand b/c each Okazaki fragment must start with a new primer. In contrast, the leading strand only requires one (theoretically)
Glycogen
-An extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch. -stored in the cytoplasm as granules, each with a central protein core with polyglucose chains radiating outward to form a sphere.
A diabetic patient begins insulin injections for blood glucose management, what is the expected impact on the patient's weight?
-An increase in insulin levels will increase lipid storage and decrease lipid mobilization from adipocytes, leading to weight gain in diabetic patients who begin insulin injections.
Cholesteryl esters
-Are converted to free cholesterol by lysosomal acid lipase.
How does the aromaticity of purines and pyrimidines underscore their genetic function?
-Aromaticity of nucleic acids make these compounds very stable and unreactive. -This stability is important to allow for storing genetic information and avoiding spontaneous information.
What is the relationship between osmotic pressure and the direction of osmosis through a semipermeable membrane?
-As osmotic pressure increase, more water will tend to flow into the compartment to decrease solute concentration. -Osmotic pressure is often considered a "sucking" pressure because water will move toward the compartment with the highest osmotic pressure.
lac operon
-Bacteria can digest lactose, but more energetically expensive than using glucose. -therefore, only use when lactose is high and glucose is low, so presence of lactose induces the lac operon. -assisted by binding of the catabolite activator protein (CAP) -falling levels of glucose cause an increase in the signaling cyclic AMP (cAMP), which binds to CAP, inducing a conformational change that allows it to bind the promoter region of the operon, increasing transcription of the lactase gene. -lac operon is a positive control mechanism b/c the binding of CAP increases transcription of the gene.
Chargaff's Rule
-Because of specific base-pairing, the amount of A equals the amount of T, and the amount of G equals the amount of C. -[A]=[T] and [G]=[C], they pair up across from one another forming two strands also called base pairing.
Urea Cycle
-Body's primary way of removing excess nitrogen from the body. -Occurs in the liver -Amino groups removed by transamination or deamination constitute a potential toxin to the body in the form of ammonia, which need to be excreted safely. -Basic AA side chains feed into the urea cycle, while other side chains act like the carbon skeleton and produce energy through gluconeogenesis or ketone production.
What purposes do Tollen's and Benedict's reagent serve? How do they differ from one another?
-Both tollen's and benedict's reagent are used to detect the presence of reducing sugars (oxidizable). -Tollen's reagent is reduced to produce a silvery mirror when aldehydes are present whereas Benedict's reagent is indicated by a reddish precipitate of Cu2O
Ketolysis
-Breakdown of ketone bodies to acetyl-CoA for energy -Occurs in: Muscle Renal Cortex Brain in prolonged Fast Acetoacetate is picked up from the blood is activated in the mitochondria by succinyl-Coa acetoacetyl-CoA transpherase (thiophorase), which is an enzyme that is present only in tissues outside of the liver. -During reaction, 3-hydroxybutyrate is oxidized to acetoacetate. -The liver lacks this enzyme, so it cannot catabolize the ketone bodies that it produces.
Formation of Oxaloacetate
-By pyruvate carboxylase (pyruvate + CO2) From malate, only + delta G step in the CAC, but is followed by a highly favorable one.
The Gibbs free energy of NADH reducing oxygen directly is significantly greater than any individual step along the ETC. If this is the case, why does transferring electrons along the ETC generate more ATP than direct reduction of oxygen by NADH?
-By splitting up electron transfer into several complexes, enough energy is released to facilitate the creation of a proton gradient at many locations, rather than just one. The greater the proton gradient is, the greater the ATP generation will be. -Direct reduction of oxygen by NADH would releases a significant amount of energy to the environment, resulting in inefficient eletron transport.
Gene duplication
-Cells can increase expression of a gene product by duplicating a relevant gene -Can be duplicated in series on the same chromosome, making many copies of the same genetic info in a row -Can also be duplicated in parallel - opening up the gene and allowing DNA replication
What tissue is least able to change its fuel source in periods of prolonged starvation?
-Cells that rely solely on anaerobic respiration are the least adaptable to different energy sources -Therefore, red blood cells are the least flexible during period of prolonged starvation and stay reliant on glucose
Why can heat be used as a measure of internal energy in living systems?
-Cellular environment has a relatively fixed volume and pressure, thus eliminating work (W) from calculations of internal energy; If DeltaU=Q-W, and W=O, then DeltaU=Q
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). -MORE SCIENTIFICALLY THEORY -change in the shape of enzymes active site is ENDERGONIC b/c it requires energy, while the release of the product is EXERGONIC.
catalysts
-Chemical agents that selectively speed up chemical reactions without being consumed by the reaction. -Don't effect the thermodynamics of a biological reaction.
Primary function of cortisol
-Increases lipolysis and amino acid mobilization, while decreasing glucose uptake in certain tissues and enhancing the activity of the other counterregulatory hormones
What are the control points in the Citric Acid Cycle?
-Citrate Synthase -Isocitrate Dehydrogenase -alpha-Ketoglutarate Dehydrogenase Complex
Cloning Recombinant DNA
-Cloning allows production of recombinant proteins, or identification and characterization of DNA by increasing its volume and purity.
lipid rafts
-Collections of similar lipids with or without associated proteins that serve as attachment points for other biomolecules. -rafts often serve roles in signaling -both lipid rafts and proteins also travel within the plane of the membrane, but more slowly.
What is the purpose of all the reactions that collectively make up the citric acid cycle?
-Complete oxidation of carbons in intermediates to CO2 so that reduction reactions can be coupled with CO2 formation, thus forming energy carriers such as NADH and FADH2 for the electron transport chain.
Complex III (CoQH2-cytochrome c oxidoreductase) also called cytochrome reductase
-Complex III faciliates the transfer of electrons from coenzyme Q to cytochrome C in a few steps. Overall Reaction: CoQH2 + 2 chtochrom c [with Fe3+] -> CoQ + 2 cytochrome c [With Fe2+] + 2H+ -In the transfer of electrons from iron, only one electron is transferred per reaction, but because coenzyme Q has two electrons to transfer, two cytochrome c molecules will be needed -contributes to proton-motive force via Q cycle
How do cytoskeletal proteins differ from motor proteins?
-Cytoskeletal proteins tend to be fibrous with repeating domains, while motor proteins tend to have ATPase activity and binding heads. Both types of protein function in cellular motility.
Glycerol-3-phosphate shuttle
-Cytosol contains one isoform of glycerol-3-phosphate dehydrogenase, which oxidizes cytosolic NADH to NAD+ while forming glycerol 3-phosphate from dihydroxyacetone phosphate (DHAP). -On out face of inner mitochondrial membrane, there is another isoform of glycerol-3-phosphate dehydrogenase that is FAD-dependendt. This mitochondrial FAD is the oxidizing agent, and ends up being reduced to FADH2. -Once reduced, FADH2 proceeds to transfer electrons to ETC via Complex II, generating 1.5 ATP for every molecule of cystolic NADH that participates in this pathway.
Replicating the ends of the chromosomes
-DNA polymerase does a excellent job of synthesizing DNA but it unfortunately cannot complete synthesis of the 5' end of the strand. -therefore, each time DNA synthesis is carried out, the chromosome becomes a little shorter, and to lengthen the tinme that cells can replicate and synthesize DNA before neccessary genes are damaged, chromosomes contain telomeres. -this repetition of sequences with high GC content allows for telomeres to be slightly degraded between replication cycles without loss of function.
Nucleotide Excision Repair (NER)
-DNA repair system in which several nucleotides in the damaged strand are removed from the DNA and the undamaged strand is used as a template to resynthesize a normal strand. -How thymine dimers are eliminated from DNA -First, specific proteins scan DNA molecule and recognize the lesion b/c of a bulge in the strand. -Exicision endonuclease then makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligoncleotides. -DNA polymerase can then fill in the gap by synthesizing DNA in the 5' to 3' direction, using the undamaged strand as a template. -Finally, nick in the strand is sealed by DNA ligase
Reannealed DNA
-Denatured, single-stranded DNA can be brought back togehter if the denaturing condition is slowly removed. -If a solution of heat-denatured DNA is slowly cooled, then the two complementary strands can become paired again.
Digestion
-Dietary fats consist mainly of triacylglycerols with the remainder comprised of cholesterol, cholesteryl esters, phospholipids, and free fatty acids. -Lipid digestion is minimal in the mouth and stomach; lipids are transported to the small intestine essentially intact. -Upon entering the duodenum, emulsification occurs (mixing of fat and water). -This increases SA of the lipid, allowing for greater enzyme interaction and processing.
What is the difference between a sphingolipid that is a phospholipid and one that is NOT?
-Difference is the bond between the sphingosine backbone and the head group. When this is a phosphodiester bond, it's a phospholipid (note the phospho- prefixed). Nonphospholipid sphingolipids include glycolipids, which contain a glycosidic linkage to a sugar
osmosis
-Diffusion of water through a selectively permeable membrane -move from a region of low solute concentration to a high solute concentration. -thus moves from region of high water concentration down its gradient to a low water concentration
peptide hormones
-Drugs that cause the production of other hormones Ex: -Insulin
elongation (translation)
-During elongation, the ribosome moves in the 5' to 3' direction along the mRNA, synthesizing the protein from its amino (N-) to carboxyl (C-) terminus -3 Important binding sites: A, P, and E
During which metabolic state is there the greatest decrease in the circulating concentration of insulin?
-During the postabsorptive state, there is the greatest decrease in insulin levels. -The concentrations of the conterregulatory hormones (have oppostive effect of insulin) begin to rise, being glucagon, cortisol, epinephrine, norepinephrine, and growth hormone
What role does ETC play in ATP generation?
-ETC generates the proton-motive force, which is an electrochemical gradient across the inner mitochondrial membrane, which provides the energy for ATP synthase to function.
What is the difference between the ETC and oxidative phosphorylation? what links the two?
-ETC is made up of the physical set of intermembrane proteins located on the inner mitochondrial matrix, and they undergo oxidation-reduction reactions as they transfer electrons to oxygen, the final electron acceptor. -As electrons are transferred, a proton-motive force is generated in the intermembrane space. -Oxidative phosphorylation is the process by which ATP is generated via harnessing the proton gradient, and it utilizes ATP synthase to do so.
Activation of Amino Acid for Protein Synthesis
-Each type of amino acid is activated by a different aminoacyl-tRNA synthetase (amino acid ads into 3' end using deprotonated oxygen from carboxylic acid) -each requires two high-energy bonds from ATP, which implies the attachment of the AA is an energy-rich bond. -transfers activated AA to the 3' end of the tRNA sequence. -each tRNA has a CCA nucleotide sequence where the amino acids binds. -high energy aminoacyl-tRNA bond will then be used to supply the energy needed to create a peptide bond during translation.
Succinyl-CoA acetoacetyl-CoA transferase (thiophorase)
-Enzyme present during ketolysis that oxidized 3-hydroxybutyrate to acetoacetate in: muscle, renal cortex or brain in prolonged fast
DNA polymerase
-Enzyme responsible for reading the DNA template (parent strand) and synthesizing the new daugher strand -DNA polymerase READS the template strand in the 3'->5' direction (opposite of nearly every other process). -DNA polymerase SYNTHESIZES the complementary strand in the 5'->3' direction. -this results in a new double helix of DNA that has the required antiparallel orientaion
Temperature on enzymes
-Enzyme-catalyzed reacitons tend to double in velocity for every 10*C increase until the optimum temperature is reached (human body, this is 37*c, 98.6*F or 310K), which afterwards, activity falls off quickly.
Which if the aldohexoses are epimers and enantiomers of d-glucose?
-Epimers: D-mannose(C-2) d-allose (C-3) d-galactose (C-4) -enantiomers: none of the d-stereoisomers are enantiomers for glucose; l-glucose is the enantiomer of d-glucose
What bonds are broken during saponification?
-Ester bonds of triacylglycerols are broken to form a glycerol molecule and salts of fatty acids (soap).
Difference in beta-oxidation between even and odd numbered fatty acid chains?
-Even number of fatty acid molecules yield TWO acetyl-CoA molecules (from the four-carbon remaining fragment) -Odd number of fatty acid molecules yield ONE acetyl-CoA and ONE propionyl-CoA
Why are fatty acids used to create ketone bodies instead of creating glucose?
-Fatty acid degradation results in large amounts of acetyl-CoA, which cannot enter the gluconeogenic pathway to produce glucose. -Only ODD NUMBERED fatty acids can act as a source of carbon for gluconeogenesis;even then, only the final malonyl-CoA molecules can be used -Instead, energy is packed into ketone bodies for consumption by the brain and muscles.
When physicians order a lipid panel to evaluate a patient, which value do they prefer to see over a minimum threshold rather than below a maximum?
-HDL values are checked for being over a minimum (HDL is "good" cholesterol because it picks up excess cholesterol from blood vessels for excretion, which is why they want it to be over a minimum value)
When/under what condition is HMG-CoA reductase most active? In what cellular region does it exist?
-HMG-CoA Reductase is most active in the ABSENCE of cholesterol or when STIMULATED by INSULIN. -Cholesterol reduces the activity of HMG-CoA reductase, which is located in the SMOOTH ER (lipid synthesis).
What is the advantage of analyzing the half-reactions in biological oxidation and reduction reactions?
-Half-reactions can help determine the number of electrons being transferred. -This analysis also facilitates balancing equations and the determination of electrochemical potential if reduction potentials are provided.
What property of telomeres and centromeres allows them to stay tightly raveled, even when the rest of the DNA is uncondensed?
-High GC-content increases H-bonding, making the association between DNA strands very strong at telomeres and centromeres
Checkpoints and Regulation of the Citric Acid Cycle
-High levels of ATP and NADH inhibit citric acid cycle -High levels of ADP and NAD+ promote it.
By what histone and DNA modifications can genes be silenced in eukaryotic cells? Would these processes increase the proportion of heterochromatin or euchromatin?
-Histone deacetylation and DNA methylation will both downregulate the transcription of a gene. These processes allow the relevant DNA to be clumped more tightly, increasing the proportion of heterochromatin.
P site
-Holds the tRNA that carries the growing polypeptide chain. Also where the first amino acid (methionine) binds because it is starting the polypeptide chain. -Peptide bond is formed when polypeptide is passed from the tRNA in the P site to the tRNA in the A site, which requires peptidyl transferase, an enzyme that is part of the large subunit, which uses GTP for bond formation energy.
How does the human body store spare energy? Why doesn't the human body store most energy as sugar?
-Human body stores energy as glycogen and triacylglycerols. Triacylglycerols are preferred because their carbons are more reduced, resulting in a larger amount of energy yield per unit weight. In addition, due to their hydrophobic nature, triacylglycerols do not need to carry extra weight from hydration.
How does coupling with ATP hydrolysis alter the energetics of a reaction?
-Hydrolysis of ATP yields ~30KJ/mol of energy, which can be used to drive other reactions forwards, which can allow for previously non-spontaneous reactions to become spontaneous.
Step 5 of Citric Acid Cycle
-Hydrolysis of thioester bond on succinyl-CoA yields succinate and CoA-SH, coupled to the phosphorylation of GDP to GTP. -reaction is catalyzed by succinyl-CoA synthetase. -phosphorylation of GDP to GTP is driven by the energy released by thioester hydrolysis . -once GTP is formed, nucleosidediphosphate kinase catalyzes phosphate transfer from GTP to ADP. THIS IS ONLY TIME IN THE ENTIRE CITRIC ACID CYCLE THAT.
Thyroid storm is a potentially lethal state of hyperthyroidism in which T3 and T4 are significantly above normal limits. What vital sign abnormalities might be expected in a patient with thyroid storm?
-Hyperthermia (high temp) -Tachycardia (high heart rate) -Hypertension (high blood pressure) -Tachypnea (high respiratory rate)
Which organs are the primary synthesizers of lipoproteins?
-INTESTINE and LIVER are the primary synthesizers of lipoproteins
Trimeric G Protein Cycle
-Inactive: alpha subunit binds GDP w/ beta and gamma subunits -When ligand binds to GPCR, it becomes activated and engages G protein -When GDP becomes GTP, it dissocaites from beta and gamma -Activated alpha alters adenylate cyclase: alpha s means enzyme is activated, alpha i means enzyme is inhibited -Once GTP is dephosphorylated, then it will bind to beta and gamma again
Primary function of glucagon
-Increase blood glucose levels -Does this by promoting glycogenolysis, gluconeogenesis, lipolysis, and ketgenesis
Effects of glucagon through secondary messengers
-Increases liver glycogenolysis. Glucagon activates glycogen phosphorylase and inactivates glycogen synthase -Increased liver gluconeogenesis. Glucagon promotes the conversion of pyruvate to phosphoenolpyruvate by pyruvate carboxylase and phosphoenolpyruvate carboxykinase (PEPCK) Glucagon increases the conversion of fruction-1,6-bisphosphate to fructose 6-phosphate by fructose-1,6-bisphosphatase -Increased liver ketogenesis and decreased lipogenesis -Increased lipolysis in the liver. Glucagon activates hormone-sensitive lipase in the liver. B/c the action is on the liver and not the adipocyte, glucagon is not considered a major fat-stabilizing hormone
Chromatin Remodeling by Acetylation
-Increases the space between histones, allowing for better access to DNA for transcription factors.
Impact of insulin on carbohydrates
-Increases the uptake of glucose and increases carbohydrate metabolism in muscle and fat. -Also increases glycogen synthesis in the liver by increasing the activity of glucokinase and glycogen synthase, while decreasing the activity of glycogen phosphorylase and glucose-6-phosphate
cristae
-Infoldings of the inner membrane of a mitochondrion that houses the electon transport chain and the enzyme catalyzing the synthesis of ATP. -maximizes surface area.
What distinguishes the inner mitochrondrial membrane from other biological membranes? what is the pH gradient between the cytoplasm and the intermembrane space?
-Inner mitochondrial membrane lacks cholesterol, which differentiates it from most other biological membranes. -There is no pH gradient between the cytoplasm and the intermembrane space because the outer mitochondrial membrane has such high permeability to biomolecules (the proton-motive force of the mitochondria is across the inner mitochondrial membrane, not the out mitochondrial memebrane
Step 3 of Citric Acid Cycle
-Isocitrate is oxidized by Oxalosuccinate by isocitrate dehydrogenase. -oxalosuccinate is then decarboxylated to produce alpha-ketoglutarate and CO2 -ISOCITRATE DEHYDROGENASE IS THE RATE-LIMITING ENZYME OF CITRIC ACID CYCLE. -first of the two carbons from the cycle is lost here. -also first NADH produced from intermediates in the cycle.
Fructose Metabolism
-It is "trapped" in the cell by fructokinase and then cleaved by aldolase B to form glyceraldehyde and DHAP. -These products are downstream from the rate-limiting enzyme in glycolysis (PFK-1) , a high-fructose drink supplies a quick source of energy in both aerobic and anaerobic cells
What would happen if an amphipathic were placed in a nonpolar solvent rather than an aqeous solution?
-It would be opposite of what happens in a polar solvent -The hydrophobic, polar part of the molecules would be sequestered inside, while the nonpolar, hydrophobic part of the molecules would be found on the exterior and exposed to the solvent.
What is the stereochemistry of all Chiral amino acids that appear in eukaryotic proteins?
-L configuration -(S) in prelog system -one exception is cysteine, b/c cysteine is the only amino acid where an R group has higher priority than a carboxylic acid
What proteins are specific to the formation and transmission of cholesteryl esters, and what are their functions.
-LCAT (Lecithin-cholesterol acyltransferase) catalyzes the esterification of cholesterol to form cholesteryl esters. -CETP (cholesteryl ester transfer protein) promotes the transfer of cholesteryl esters from HDL to IDL, forming LDL.
Given that the glycogen storage disorder von Gierke's affects the last enzyme of gluconeogenesis, predict the associated metabolic derangement that occurs:
-Last enzyme of gluconeogenesis is glucose-6-phosphatase so patients with von Gierke's disease are unable to perform glucogenesis in addition to glycogenolysis. -This means patients will be unable to produce glucose during periods of fasting (results in hypoglycemia). -Furthermore, given a blocker in the gluconeogenic pathway, a buildup of intermediates (including lactate resulting in lactic acidosis) would also be expected.
Isocitrate dehydrogenase (checkpoint)
-Likely to be inhibited by ATP and NADH -ADP and NAD+ function as allosteric activators and enhance its affinity for substrates.
Absorption
-Micelles diffuse to the brush border of the intestinal mucosal cells, where they're absorbed. -Digested lipids pass through brush border, where they are absorbed into the mucose and re-esterified to form triacylglycerols and cholesteryl esters and packaged, along with certain apoproteins and fat-soluble vitamins and other lipids, into chylomicrons.
pyruvate carboxylase
-Mitochondrial enzyme that is activated by acetyl-CoA (from beta-oxidation) -converts pyruvate to oxaloacetate (OAA), which is a citric acid cycle intermediate and cannot leave the mitochondrion. -It is reduced to malate, which can leave the mitochondrion via the malate-aspartate shuttle, where once in cytoplasm, is oxidized back to OAA. -Acetyl-CoA inhibits pyruvate dehydrogenase b/c high levels of ACoA means high energy, so no more CAA. -Source of Acetly-CoA is not from glycolysis and pyruvate dehydrogenase, but from fatty acids.
pH on enzymes
-Most enzymes depend on pH in order to function properly, b/c changes in pH can lead to denaturation of the enzyme -enzymes that circulate in blood, optimum pH is 7.4 Where/what is the exception to this rule? -pepsin, which works in the stomach, has a pH optimum of 2, wherease pancreatic enzymes in the small intestine work best around pH of 8.5
Example of disequilibrium that is maintained at the expense of cellular energy?
-Muscle tissue and neurons -Cell volume and membrane transport are regulation by action of Na+/K+ pump, which can maintain a stable disequilibrium state in most tissues
High-energy electron carriers
-NADH, NADPH, FADH2, ubiquinone, cytochromes, glutathione -some are used by mitochondrial ETC, leading to oxidative phosphorylation of ADP->ATP. -Besides soluble electron carriers, there are also membrane-bound electron carriers in the inner mitochondrial membrane for example flavin mononucleotide (FMN), which is bonded to complex I of ETC, and can also act as a soluble electron carrier.
What are the tissues in which the uptake of glucose is NOT affected by insulin?
-Nervous tissues -Kidney Tubules -Intestinal mucosa -Red Blood Cells -B-cells of the pancreas (b/c they secrete insulin)
Step 6 of Citric Acid Cycle
-OCCURS ON INNER MEMBRANE -succinate undergoes oxidation to yield fumarate -catalyzed by succinate dehydrogenase, a flavoprotein that is an integral protein on the inner mitochondrial membrane -as succinate is oxidized to fumarase, FAD is reduced to FADH2, which passes the electrons it carries to ETC, leads to production of 1.5ATP
Fatty Acid biosynthesis
-Occurs in liver and the products are transported to adipose tissue for storage Major enzymes: acetyl-CoA carboxylase and fatty acid synthase (stimulated by insulin) Primary end product: palmitic acid (palmitate), which is trnasported to adipose tissues for storage.
IDL (VLDL remnants) (Intermediate density lipoproteins)
-Once triacylglycerol is removed from VLDL, resulting particle is referred to as a VLDL remnant or IDL -Some IDL is reabsorbed by the liver by apolipoproteins on its exterior, and some is further processed in the bloodstream. -IDL exists as a transition particle between triacylglycerol transport (w/ chylomicrons and VLDL) and cholesterol transport (w/ LDL and HDL)
chymotrypsin
-One of the main pancreatic proteases; it is activated (from chymotrypsinogen) by trypsin. -cleaves the carboxyl end of phenylalanince, tryptophan, and tyrosine.
dihydrolipoyl transacetylase
-One of three enzymes that make up the pyruvate dehydrogenase multienzyme complex. -Responsible for catalyzing the addition of a CoA molecule to the acetyl-lipoamide structure. -
Phosphoenolpyruvate carboxykinase (PEPCK or PEP carboxykinase)
-Oxaloacetate -> phosphoenolpyruvate -requires GTP. -combination of pyruvate carboxylase and PEPCK are used to circumvent the action of pyruvate kinase by converting pyruvate back into PEP. -induced by glucagon and cortisol, which act to raise blood sugar levels (which is why gluconeogenesis is occuring in the first place)
Glucagon
-Peptide hormone secreted by the alpha-cells of the pancreatic islets of Langerhans -Primary target for glucagon is the hepatocyte
Insulin
-Peptide hormone secreted by the beta-cells of the prancreatic islets of langerhans. -Key player in uptake and storage of glucose
1,3-biphosphoglycerate (1,3-BPG)
-a high-energy intermediate used to generate ATP by substrate-level phosphorylation -used by 3-phosphoglycerate kinase -Important intermediate of glycolysis -ONLY ATP GAINED IN ANAEROBIC RESPIRATION
Pyruvate dehydrogenase complex regulation
-Phosphorylation of PDH, facilitated by enzyme pyruvate dehydrogenase kinase. -When ATP levels rise, phosphorylating PDH inhibits acetyl-CoA production. -PDH complex is reactivated by pyruvate dehydrogenase phosphotase in response to high ADP levels (able to reactivate acetyl-CoA production).
When lipids leave the stomach, what stages of digestion have been accomplished? What enzymes are added to accomplish the next phase?
-Physical digestion is accomplished in the mouth and the stomach, reducing the particle size. -Beginning in the small intestine, pancreatic lipase, colipase, cholesterol esterase, and bile assist in the chemical digestion of lipids. -In the more distal portion of the small intestine, absorption occurs.
alpha-ketoglutarate dehydrogenase complex (checkpoint)
-Products of succinyl-CoA and NADH function as inhibitors of this enzyme complex. -ATP is also inhibitory and slows the rate of the cycle when the cell has high levels of ATP. -The complex is stimulated by ADP and calcium ions.
Primary Function of Insulin
-Promotes glucose uptake by adipose tissue and muscle, glucose utilization in muscle cells, and macromolecule storage (glycogenesis, lipogenesis)
NSAIDs block prostaglandin production in order to reduce pain and inflammation. What do prostaglandins do to bring about these symptoms?
-Prostaglandins regulate the synthesis of cAMP, which is involved in many pathways, including those that drive pain and inflammation.
apolipoproteins
-Protein molecules responsible for the interaction of lipoproteins with cells and the transfer of lipid molecules between lipoproteins; also called apoproteins
carrier proteins
-Proteins that bind solutes and transport them across the plasma membrane -brief period of bind between carrier and solute is called an occluded state, in which carrier is not open to either side of phospholipid bilayer
fructose-1,6-bisphosphatase
-RATE-LIMITING ENZYME IN GLUCONEOGENESIS - catalyzes fructose 1,6-bisphosphate to fructose 6-phosphate -reverse the action of PFK-1, which is the rate-limiting step of glycolysis, by removing the phosphate from fructose-1,6-bisphosphate to fructose-6-phosphate. -phosphatases opposes kinases -activated by ATP -inhibited by AMP and fructose-2,6-bisphosphate.
Messenger RNA (mRNA)
-RNA molecule that carries the information specificying the amino acid sequence of the protein to the ribosome. -mRNA is transcribed from template (parent) strands by RNA Polymerase enzymes -occurs in the nucleus of the cell. -may undergo posttranscriptional modifications prior to being released from the nucleus.
Transfer RNA (tRNA)
-RNA molecule that is responsible for converting the language of nucleic acids to the language of amino acids and peptides. -each tRNA contains a folded strand of RNA that includes a 3-nucleotide anticodon. -this anticodon recognizes a pairs with the appropriate codon on an mRNA molecules while in the ribosome. -20 AAs in eukaryotic proteins, each of which is represented by at least one codon -to become part of newly forming polypeptide, amino acids connected to a specific tRNA molecule, which makes said tRNA molecules CHARGED or ACTIVATED w/ an amino acid.
degenerate genetic code
-Refers to the fact that the genetic code contains more information than is needed to specify all 20 common amino acids.
phosphoenolpyruvate (PEP)
-a high-energy intermediate used to generate ATP by substrate-level phosphorylation -used by pyruvate kinase -Important intermediate of glycolysis -ONLY ATP GAINED IN ANAEROBIC RESPIRATION
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. -Helix in D-DNA makes a turn every 3.4nm and contains about 10 bases within that span. -Major and minor grooves can be identified between the interlocking strands and are often the site of protein binding.
beta-oxidation of unsaturated fatty acids
-Same as beta-oxidation of saturated fatty acids, except two additional enzymes are necessary b/c double bonds disturb the terochemistry needed for oxidative enzymes to act on the fatty acid. -Enoyl-CoA isomerase rearranges cis double bonds at 3,4 position to trans double bonds at 2,3 position once enough acetyl-CoA has been liberated to isolate the double bond within the first three carbons. -In polyunsaturated fatty acids, a further reduction is required using 2,4-dienoyl-CoA reductase to convert two conjugated double bonds to just one double bond at the 3,4 position, where it undergoes the same rearrangement as monounsaturated fatty acids
Fatty Acid Entry into Mitochondria
-Short fatty acid chains (2-4 carbons) and medium fatty acid chains (6-12) diffuse FREELY into mitochondria, where they are oxidized. -Long fatty acid chains (14-20) are also oxidized in the mitochondria, but require transport via a carnitine shuttle. -Carnitine acyltransferase I is the rate-limiting enzyme of fatty acid oxidation. -Very long fatty acid chains (20+) are oxidized elsewhere in the cell.
Origin of Replication
-Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.
Initiation of translation
-Small rbosomal subunit binds to the mRNA -In prokaryotes, small subunit binds to the Shine-Dalgarno sequence in the 5' untranslated region of the mRNA. -In Eukaroytes, the small subunit binds to the 5' cap structure -Charged initiator tRNA bind to the AUG start codon through base pairing w/ its anticodon within the P site of the ribosome. Starting Amino Acids: -in prokaryotes, its N-formylmethionine (fMet) -in eukaryotes, its methionine -Large subunit then binds to the small subunit, forming the completed initiation complex. This is assisted via Initiation Factors (IF) that are not permanently associated with the ribosome.
Why does soap appear to dissolve in water, and how is this fact important in cleaning?
-Soaps appears to dissolve in water because amphipathic free fatty acid salts form micelles, with hydrophobic fatty acid tails toward the center and carboxylate groups facing outward toward the water. -Fat-soluble particles can then dissolve inside micelles in the soap-water solution and wash away. Water-soluble compounds can freely dissolve in the water.
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
Respiratory complexes on the inner mitochondrial membrane
-Steps and 2 of complex III are drawn as separate steps here for clarity; however, the same CoQH2-Cytochrome c oxidoreductase complex is used for both steps.
Cortisol
-Steroid hormone that promotes the mobilization of energy stores through the degradation and increases delivery of amino acids and increased lipolysis. -Also elevates blood glucose levels, increasing glucose availability for nervous tissue through two different mechanisms. -Inhibits glucose uptake in muscle, lymphoid and fat tissues, increasing hepatic output of glucose via gluconeogenesis, particularly from AA's -enhances the activity of Glucagon, epinephrine, and other catecholamines.
phosphoylation
-The addition of a phosphate group to a molecule, often from ATP - which generally increases the molecules energy. -added by protein kinases to activated or deactive proteins.
DNA methylation
-The addition of methyl groups to bases of DNA after DNA synthesis; may serve as a long-term control of gene expression.
Why is it necessary that fetal hemoglobin does not bind 2,3-BPD?
-The binding of 2,3-BPG decreases hemoglobin's affinity for oxygen (raises P50). Fetal hemoglobin must be able to "steal" oxygen from maternal hemoglobin at the placental interface; therefore, it would be disadvantageous to lower its affinity for oxygen.
rickets
-a lack of vitamin D, a condition seen in children and characterized by underdeveloped, curved long bones as well as impeded growth.
phospholipids
-a lipid consisting of a glycerol bound to two fatty acids and a phosphate group.
mismatch repair
-The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides. -G2 phase of the cell cycles -Enzymes are encod3ed by genes MSH2 and MLH1, which detect and removed errors introduced in replication that were missed during the S phase of the cell cycle. -Enzymes are homologues of MutS and MutL in prokaryotes, which serve similar function.
chylomicrons
-The class of lipoproteins that transport lipids from the intestinal cells to the rest of the body -Leave the intestinal tract via lacteals, the vessels of the lymphatic system, and re-enter the bloodstream via the thoracic duct, a long lymphatic vessel that empties into the let subclavian vein at the base of the neck.
substrate-level phosphorylation
-The enzyme-catalyzed formation of ATP by direct transfer of a phosphate group to ADP from an intermediate substrate in catabolism.
Why is ATP and inefficient molecules for long-term energy storage?
-The high energy bonds in ATP and the presence of a significant negative charge makes it inefficient molecule to pack into a small space. -Long term storage molecules are characterized by energy density and stable/nonrepulsive bonds, which are primarily seen in lipids, which is why they are the ideal storage molecules for energy
Between the leading and lagging strands, which is more prone to mutations? Why?
-The lagging strand, because it must constantly start and stop the process of DNA replication. -Additionally, it contains more RNA primers, all of which must be removed and filled in with DNA
euchromatin
-The less condensed form of eukaryotic chromatin that is available for transcription. -appears light under light microscopy -contains genetically active DNA
Describe major metabolic functions of the liver
-The liver is responsible for maintaining a steady-state concentration of glucose in the blood through glucose uptake and storage, glycogenolysis, and gluconeogenesis. -The liver also participates in cholesterol and fat metabolism, the urea cycle, bile synthesis, and detoxification of foreign substances.
How is the resting membrane potential maintained?
-The membrane potential, which results from a difference in the number of positive and negative charges on either side of the membrane, is maintained primarily by the SODIUM-POTASSIUM PUMP which moves three sodium ions out of the cell for every two potassium ions pumped in, and to a minor extent by leak channels that allow the passive transport of ions
How does DNA polymerase recognize which strand is the template strand once the daughter strand is synthesized?
-The parent (template) strand is more heavily methylated, whereas the daughter strand is barely methylated at all. This allows DNA polymerase to distinguish between the two strands during proofreading.
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.
How is the respiratory quotient expected to change when a person transitions from resting to brief exercise
-The proportion of energy derived from glucose increases. -This transitions to almost exclusively carbohydrate metabolism, and will cause the respiratory quotient to approach 1.
HMG-CoA synthase
-The rate-limiting enzyme of ketogenesis. -Transforms acetyl-CoA into HMG-CoA in the liver
Q cycle
-The shuttling of electrons between ubiquinol and ubiquinone in the inner mitochondrial membrane as a part of Complex III's function -Two electrons are shuttled from a molecule of ubiquinol (CoQH2) near the intermembrane space to a molecule of ubiquinone (CoQ) near the mitochonria matrix. -Another two electrons attached to heme moieties, reducing two molecules of cytochrome c. Carrier w/ iron and sulfur assists this process. -In shuttling these electrons, four protons are also displaced to the intermembrane space;therefore, the Q cycle continues to increase the gradient of the proton-motive force across the inner mitochondrial membrane.
Coding strand
-The strand of DNA that is not used as a template during transcription; also called the sense strand. -B/c coding strand is complementary to template, it is identical to the mRNA transcript except that all the thymines are replaced with uracils.
connexin
-The type of protein found in gap juntions
Lock and Key theory
-Theory of enzyme catalysis stating that the active site's structure is complementary to the structure of the substrate.
How does beta-oxidation of unsaturated fatty acids differ from that of saturated fatty acids?
-There is an additional isomerase and an additional reducase for the beta-oxidation of unsaturated fatty acids b/c of the steric hindrances of the double bonds. These steps provide the stereochemistry necessary for further oxidation.
If a strand of RNA contained 15% cytosine, 15% adenine, 35% guanine, and 35% uracil, would this violate Chargaff's rules? Why or why not?
-This would not violate Chargaff's rules. -RNA is single-stranded, and thus the complementary seen in DNA doesn't hold true. -For a ss-RNA, %C does not necessarily equal %G -And %A does not necessarily equal %U.
Tertiary structure
-Three dimension shape of a protein -mostly determined by hydrophilic and hydrophobic interactions between R groups of AA's. -presence of disulfide bonds, that form when two cysteine molecules are oxidized to form cystine. These create loops in protein chains. -disulfide bonds determine how wavy or curly human hair is, the more disulfide bonds, the more curly.
transamination and deamination
-Transfer/removal of amino group from the amino acids.
membrane receptors
-Transmembrane protein molecules that act enzymatically or as ion channels to participate in signal transduction -transporters can be activated or deactivated by these. Ex: -ligand-gated ion channels are membrane receptors that open a channel in response to the binding of a specific ligand.
Triacylglycerol (triglyceride) synthesis
-Triacylglycerols are formed by attaching three fatty acids (as fatty acyl-CoA) to glycerol. -Triacyl glycerol formation from fatty acids and glycerol 3-phosphate occurs primarily in the liver and somewhat in adipose tissue, w/ small contributions from the diet. -In liver, triacylglycerols are packed and sent to adipose tissues as VLDL (very-low density lipoproteins), leaving only a small amount of stored triacylglycerols.
antioncogenes
-Tumor supressor genes -p53 or Rb (retinoblastoma) -Normally function to stop tumor progression -mutations of these allels result in the loss of tumor suppression activity, and therefore promote cancer. -inactivation of both alleles is necessary for the loss of function b/c in most cases, even one copy of the normal protein can function to inhibit tumor formation, so multiple mutations (hits) are required.
Alpha-linolenic acid (ALA) (18:3 all-cis-9,12,15)
-Unsaturated omega-3 fatty acid, see linolenic acid -important for maintaining cell fluidity
Proofreading by DNA polymerase
-Verifies accuracy -Can back up, excise nucleotide -Incorporate correct nucleotide -Very efficient but not flawless
Alcohol (Acetyl-CoA)
-When alcohol is consumed in moderate amount, the enzymes alcohol dehydrogenase and acetaldehyde dehydrogenase convert it to acetyl-CoA. -However, this reaction is accompanied by NADH buildup, which inhibits the Krebs cycle. -Therefore, the acetyl-CoA formed through this process is used primarily to synthesize fatty acids.
Ketolysis in the brain
-When body has been in ketosis (prolonged fast) for longer than a week, the brain begins to derive up to 2/3 of its energy from ketone bodies. -Ketones are metabolized to acetyl-CoA, and pyruvate dehydrogenase is inhibited -Glycolysis and glucose uptake in the brain decrease -This switch spares essential protein in the body, which otherwise would be catabolized to form glucose via gluconeogenesis in the liver, and allows the brain to indirectly metabolize fatty acids as ketone bodies.
beta-oxidation Activation
-When fatty acids are metabolized, they first become activated by attachment to CoA, which is catalyzed by fatty-acyl CoA synthetase. -Product is referred to as a fatty acyl-CoA or acyl-CoA Ex: -Acetyl-CoA w/ a 2-carbon acyl group or -palmitoyl-CoA w/ 16-carbon acyl group.
E site
-Where the now inactivated (uncharged) tRNA pauses transiently before exiting the ribosome. As the now-uncharged tRNA enters the site, it quickly unbinds from the mRNA and is ready to be recharged.
DNA polymerases alpha, delta, and epsilon:
-Work together to synthesize both the leading and lagging strands; DNA polymerase delta also fills in the gaps left behind when RNA primers are removed.
Glucose-6-phosphate dehydrogenase deficiency
-X-linked -low NADPH oxidase leads to increased free radical damage. Hemolytic episodes are induced by infections, medications (like sulfa drugs) and other oxidants (fava beans). -Heinz bodies and bite cells on blood smear
Bile
-a bitter greenish-brown alkaline fluid that aids digestion and is secreted by the liver and stored in the gallbladder. -contains bile salts, pigments, and cholesterol.
Operon
-a cluster of genes transcribed as a single mRNA. -incredibly common in prokaryotic cells Ex: -lac or trp operon
peptide bond formation
-a condensation or dehydration reaction (releases one molecule of water) -the nucleophilic amino group of one amino acid attacks the electrophilic carbonyl group of another amino acid, and the hydroxyl group of the carboxylic acid is kicked off
lactone
-a cyclic ester w/ a carbonyl group persisting on the anomeric carbon
How many carbons in a diterpene?
-a diterpene has 20 carbon molecules in its backbone. One terpene unit is made from two isoprene units, each of which has five carbons.
keratin
-a fibrous protein found in human hair -mostly composed of alpha-helices
structural gene
-a gene that codes for a product, such as an enzyme, protein, or RNA, rather than serving as a regulator -in an operon
electrochemical gradient
-a gradient produced by the combined forces of the electrical gradient and the chemical gradient. -b/c its based on protons, the electrochemical gradient across the inner mitochondrial membrane is often referred to as the proton-motive force. -any electrochemical gradient stores energy, and it will be the responsibility of ATP synthase to harness this energy to form ATP from ADP and an inorganic phosphate.
The propionic acid pathway
-beta-oxidation of a Fatty acid w/ odd number of carbons yield ONE acetyl-CoA and ONE propionyl CoA -Propionyl-CoA is convereted to methylmalonyl-CoA by enzyme propionyl-CoA carboxylase -Propionyl-CoA carboxylase requires biotin (Vitamin B7). -Methylmalonyl-CoA is then converted into succinyl-CoA by methylmalonyl-CoA mutase, REQUIRES COBALAMIN (vitamin B12) *exception to the rule that fatty acids cannot be converted to glucose in humans!
positive control mechanisms
-binding of a molecule increases transcription of a gene
negative control mechanism
-binding of a protein reduces transcriptional activity Ex: -in inducible systems when the repressor is bonded to the operator, so RNA polymerase cannon get to the structural gene.
DNA-binding domain
-binds to a specific nucleotide sequence in the promoter region or to a DNA response element to help in the recruitment of transcriptional machinery -one of transcription factors recognizable domains.
What starting transcription, where does RNA polymerase bind?
-binds to the TATA box, which is located within the promoter region of the relevent gene, at about -25.
calcitriol
-biologically active form of vitamin D -increases calcium and phosphate uptake in the, which promotes bone production
Vitamin K
-blood clotting -vital to the post-translational modifications required to form prothrombin, an important clotting factor in blood. -required to introduce calcium-binding sites on several calcium-depending proteins.
difference between oncogenes and mutated tumor suppressor genes
-both result in cancer, but the cause is different -Oncogenes promote the cell cycle while mutated tumor suppressors can no longer slow the cell cycle. -Oncogenes are like stepping on the gas pedal; -Mutated suppressors are like cutting the break lines.
HMG-CoA Lyase
-breaks down HMG CoA into acetoacetate in the liver -this acetoacetate can be broken down into 3 hydroxybutarate
Glycogen phosphorylase
-breaks the alpha-1,4-glycosidic bonds, releasing glucose-1-phosphate from the periphery of the granule. -cannot break alpha-1,6 bonds, therefore stops when it nears the outermost branch points.
amino acids
-building blocks of proteins contain two functional groups: -an amino group (-NH2) -a carboxyl group (-COOH) -all the amino acids that will be tested will be alpha-amino acids, in which both functional groups are attached to the same carbon.
Vitamin D (cholecalciferol)
-can be consumed or formed in a UV light-driven reaction in the skin.
glycogen
-carbohydrate storage unit in animals -similar to starch, except it has more alpha-1,6 glycosidic bonds, which makes it a highly branched compound. -this branching optimized the energy efficiency of glycogen and makes it more soluble in solution, thereby allowing more glucose to be stored in the body.
citrate shuttle
-carries mitochondrial acetyl-CoA into the cytoplasm, where synthesis occurs -NADPH from the pentose phosphate pathwya supplies reducing equivalents.
ribozymes
-catalytic RNA molecules that function as enzymes and can splice RNA -enzymes made of RNA molecules instead of peptides (proteins).
ligases
-catalyze addition or synthesis reactions, generally between large similar molecules, and often require ATP -most likely to be encourntered in nucleic acid synthesis and repair on test day.
lyases
-catalyze cleavage of a single molecule into 2 products don't require water as substrate -some enzymes can catalyze the reverse of their specific reactions, which can be catalyzed by a lyase, and when they do this, their referred to as synthases.
Oxidoreductases
-catalyze oxidation-reduction reactions that involve the transfer of electrons -often have a cofactor that acts as an electron carrier, such as NAD+ or NADH -electron donor is known as reductant, and electron acceptor is known as the oxidant. -enzymes with dehydrogenase or reductase in their names
Transketolase and transaldolase
-catalyze the interconversion between fructose 6-P/glyceraldehyde 3-P and the pentose sugars -allows for the formation of pentose sugars without going through the glucose 6-P dehydrogenase reaction
Transferases
-catalyze the movement of a functional group from one molecule to another -Ex: aminotranferase can convert aspartate to alpha-ketoglutarate, as a pair, to glutamate and oxoaloacetate by moving the amino group from aspartate to a-ketoglutarate. -kinases are a member of this class, which catalyze the transfer of a phosphate group from ATP to another molecule
isomerases
-catalyze the rearrangement of bonds within a molecule -some isomerases can be classified as oxidoreductases, tranferases, or lyases, depending on the enzyme mechanism.
Glyceraldehyde-3-phosphate dehydrogenase
-catalyzes the oxidation and addition of inorganic phosphate (Pi) to its substrate; glyceraldehyde 3-phosphate. -this results in the production of a high-energy intermediate 1,3-biphosphoglycerate and the reduction of NAD+ to NADH. -if glycolysis is aerobic, NADH can be oxidized by mitochondrial ETC, providing energy for ATP synthesis via oxidative phosphorylation.
cholesteryl ester transfer protein (CETP)
-catalyzes the transition of IDL to LDL by transferring cholesteryl esters from HDL.
Amino Acid catabolism
-certain amino acids can be used to form acetyl-CoA. -AAs must lose their amino group via transamination; Their carbon skeletons can then form ketone bodies. -These amino acids are termed KETOGENIC for that reason.
Lipids
-characterized by insolubility in water and solubility in nonpolar organic solves. -hydrocarbon chains. -major component of the phospholipid bilayer, components are amphipathic molecules
Waxes
-class of lipids that are extremely hydrophobic and rarely found in the cell membrane of animals -sometimes found in the cell memebranes of plants -composed of a long chain fatty acid and a long chain alcohol, which contributes to the high melting point of these substances. -can provide both stability and rigidity within the nonpolar tail region only -serve as an extracellular function in protection or waterproofing.
isoforms
-closely related proteins whose function is similar but whose affinity for ligands differs.
Regulator gene
-codes for the production of the repressor protein
What do cofactors and coenzymes do? How do they differ?
-cofactors and coenzymes both act as activators of enzymes. Cofactors tend to be inorganic (mineral) while coenzymes tend to be small organic compounds (vitamins). In both cases, these regulators induce a conformational change in the enzyme that promotes its activity. Tightly bound cofactors or coenzymes that are necessary for enzyme function are termed prosthetic groups.
ribosome
-composed of proteins and rRNA -has two subunits that only bind during protein synthesis -structure dictates its function, which is to bring the mRNA message together with the charged aminoacyl-tRNA complex to generate the protein. -3 binding sites: A site (aminoacyl), P site (peptidyl) E site (exit).
Adenosine Triphosphate (ATP)
-compound used by cells to store and release energy -formed by substrate-level phosphorylation, as well as oxidative phosphorylation -Provide ~30kJ/mol of energy under physiological conditions
Optical Isomers (stereoisomers)
-compounds that have the same chemical formula but have different spatial arrangement of atoms
cDNA (complementary DNA) library
-constructed by reverse-transcribing processed mRNA. -Lack noncoding regions, such as introns, and only includes the genes that are expressed in the tissue from which the mRNA was isolated. -Also called expression libraries -Only cDNA libraries can be used to reliably sequence specific genes and identify disease-causing mutations, produce recombinant proteins (like insulin, clotting factors, vaccines, etc.) or produce transgenic animals
Genomic Libraries
-contain large fragments of DNA - include both coding (exon) and non-coding (intron) regions of DNA
phosphofructokinase-2 (PFK-2)
-converts fructose-6-phosphate to fructose 2,6-biphosphate (F2,6BP) -then F2,6BP then activates PFK-1. - activated by insulin - inhibited by glucagon -By activating PFK-1, it allows these cells to overridew the inhibition causes by ATP so that glycolysis can continue, even when the cell is energetically satisfied. The metabolites of glycolysis can thus be fed into the production of glycogen, fatty acids, and other storage molecules rather than just being burned to produce ATP.
glycoprotein coat
-created by carbohydrates associated with the plasma membrane -the carbohydrates are attached to protein molecules on the extracellular surface because the carbohydrates are hydrophilic they are interact with glycoproteins and water creating the coat
Malate-Aspartate shuttle
-cystolic oxaloacetate, which cannot pass through the inner mitochondrial membrane, is reduced to malate, which can pass through the membrane. -accomplished by cystolic malate dehydrogenase. -oxidation of NADH to NAD+ also occurs here. -Once malate crosses the matrix, mitochondrial malate dehydrogenase reverses the reaction to form mitochondrial NADH -Now NADH is in the matrix, and can pass along electrons to ETC via complex I and generate 2.5 ATP per molecule NADH. -recycling the malate requires oxidation to oxaloacetate, and can be reconverted to oxaloacetate to restart the cycle.
Pyrimidines
-cytosine, thymine, uracil -contain only one ring in their structure -Cytosine is found in both RNA and DNA -Thymine is only in DNA -Uracil is found only in RNA
terpenoids
-derivatives of terpenes -have undergone oxygenation & rearrangement of the carbon skeleton -contribute to steroid biosynthesis -similar characteristics w/ terpenes
Base Excision repair
-detection system for small non-helix-distorting mutations. -First, affected base is recognized and removed by a glycosylase enzyme, leaving behind an apurinic/apyrimidinic (AP) site, also called an abasic site. -AP site is recognized by an AP endonuclease that removes the damaged sequence from the DNA. -DNA polymerase and DNA ligase can then fill in the gap and seal the strand.
Tollen's reagent
-detects presence of reducing sugar -uses Ag(NH3)2+ as oxidizing agent *in a + test, aldehydes reduce Ag+ to metallic silver
Benedict's reagent
-detects presence of reducing sugar using Cu(OH)2 -aldehyde group of an aldose is readily oxidized indicated by a red precipitate of Cu2O
absolute configuration
-determined by the 3D arrangement of the groups attached to the chiral carbon -Organic chemists use (R) and (S) naming, biochemists use D- and L-
Lineweaver-Burk Plot
-double reciprocal of michaelis menten -x int: is -1/Km -y int: 1/vmax
A site
-holds the incoming aminoacyl-tRNA complex. This is the next amino acid that is being added to the growing chain, and is determined by the mRNA codon within the A site
Proofreading
-during DNA-synthesis, ds-DNA molecules will pas through a part of the DNA polermerase enzymes. When the complementary strands have incorrectly paired bases, the H-bonds can be unstable, and this lack of stability is detected as the DNA passes through this part of the polymerase. -Incorrect base in excised and can be replaced with the correct one. -Enzyme discriminates between template and incorrectly pair daughter strand by the level of methylation. -Since template strand has existed in the cell longer, it therefore has been more heavily methylated. -This system is very efficient, corecting most of the errors put into the sequence during replication -DNA ligase LACKS proofreading ability, so likelihood of mutations in the lagging strand is considerably higher than the leading strand.
Glycogen phosphorylase
-enzyme that cleaves glucose from the non-reducing end of a glycogen branch by phosphorylating it -glycogen is more branched (branches occur more frequently) --> more points where enzymes can come in & break down glycogen *permits rapid release of glucose from glycogen stores *animals require rapid mobilization of glucose (more than plants)
RNA polymerase
-enzyme that links together the growing chain of RNA nucleotides during transcription using a DNA strand as a template -travels along the template strand in the 3' to 5' direction, which allows for the construction of the transcribed mRNA in the 5' to 3' direction -doesn't proofread like DNA polymerase
Vitamin
-essential nutrient that cannot be adequately synthesized by the body & must be consumed by the diet -Lipid soluble vitamins (A, D, E, and K) can accumulate in stored fat & excess water-soluble vitamins are excreted through the urine
waxes
-esters of long-chain fatty acids w/ long chain alcohols - form pliable solids at room temp. - function as protection for plants and animals
DNA polymerases alpha, delta, and epsilon
-eukaryotic DNA polymerase -synthesizes the daughter strands of DNA (5' to 3') -uses 5' deoxyribonucleotide TRIphosphates -PPi (pyrophosphate) is released when new phosphodiester bonds are made
Complex IV (cytochrome c oxidase)
-facilitates the transfer of electrons from cytochrome c to oxygen, the final electron acceptor. -Includes subunits of cytochrome a, cytochrome a3, and Cu2+ ions. -cytochrome a and a3 make up cytochrome oxidase. -through redox reactions, cytochrome oxidase gets oxidized as oxygen, becomes reduced, and forms water. -Final location on transport chain where proton pumping occurs, as two protons are pumped across the membrane. Overall Reaction: 4 cytochrome c [w/ Fe2+] + 4H+ + O2 -> 4 cytochrome c [w/ Fe3+] + 2H2O
alditol
-forms when the aldehyde group of an aldose is reduced to an alcohol
Glucose-6-phosphatase
-found only in the lumen of ER in liver cells -G6Phosphate is transported to ER, and free glucose is transported back to cytoplasm. -used to circumvent gluco/hexokinase.
voltage-gated channels
-gate is regulated by the membrane potential near the channel Ex: -excitable cells like neurons possess voltage-gated sodium channels. Channels close undering resting conditions, but membrane depolarization causes a protein conformation change that alows them to quickly open and clock as the voltage increases.
Gene amplification
-gene expression can be increased/amplified in response to specific signals. -can in response to things such as hormones, growth factors, and other intracellular conditons. -eukaryotic cells accomplish this through enhancers and cell duplication
knockout mice
-gene is intentionally deleted (knocked out) - used to study human diseases
fermentation
-glycolysis in the absence of oxygen -key enzyme is lactate dehydrogenase, oxidized NADH to NAD+, replenishing the oxidized coenzyme for glyceraldehyde-3-phosphate dehydrogenase. -without mitochondria and oxygen, pyruvate is reduced to lactate, and oxidizing NADH to NAD+. -in yeast cells, fermentation is the conversion of pyruvate (3-carbons) to ethanol (two-carbons) and carbon dioxide (one carbon) -end products are different, while the end result of mammalian and yeast fermentation is the same; replenishing NAD+
Cadherins
-group of glycoproteins -mediate calcium-dependent cell adhesion -often hold similar cell types together
Integrins
-group of proteins that all have two membrane-spanning chains called alpha and beta. -chains are important in binding to and communicating with the extracellular matrix. -play important role in cell signaling, and can greatly impact cellular function by promoting cell division, apoptosis, and other processes.
antigen-binding region
-has specific polypeptide sequences that bind only one specific antigenic sequence -at the tips of the "Y"
triterpenes
-have 6 isoprene units -can be converted to cholesterol & various steroids
unsaturated fatty acids
-have one or more double bonds -liquid at room temp -humans can only synthesize a few unsaturated fats, the rest come from essential fatty acids in diet that are transported in chylomicrons as triacylglycerols from the intestine.
saturated fatty acids
-have the maximum number of hydrogen atoms possible -NO DOUBLE BONDS
outer mitochondrial membrane
-highly permeable due to many large pores that allow for the passage of ions and small proteins
promoter site
-provides a place for RNA polymerase to bind
catecholamines
-hormones secreted by the adrenal medulla that affect the sympathetic nervous system in stress response -dopamine, norepinephrine, epinephrine -increase activity of liver and muscle glycogen phosphorylase promoting GLYCOGENOLYSIS, increasing glucose output. -also act on adipose tissue to increase lipolysis by increasing the activity of hormone-sensitive lipase.
Absorption of Amino Acids and Peptides in the intestine
-illustrates major transport mechanisms involved in moving amino acids across the luminal and basal membranes of intestinal cells.
Elastin
-important component of the extracellular matrix of connective tissue. -primary role to stretch and then recoil like a spring, which restores the original shape of the tissue.
sphingolipids
-important constituents of cell membranes -do not contain glycerol -contain hydrophilic region and two fatty acid-derived hydrophobic tails -include ceramide, sphingomyelins, cerebrosides, and gangliosides
Fatty Acid Oxidation (beta-oxidation)
-in cytosol, activation causes a thioester bond to form between carboxyl groups of fatty acids and CoA-SH. -This activated fatty acyl-CoA cannot cross inner mitochondrial membrane, so the fatty acyl group is transferred to carnitine via a transesterification reaction. -Cartinite can cross the inner membrane, so once it crosses, it transfers the fatty acyl group to a mitochondrial CoA-SH via another transesterification reaction. -Once acyl-CoA is formed in the matrix, beta-oxidation can occur, which removes two-carbon fragments from the carboxyl end.
Primary function of catecholamines
-increase glycogenolysis in muscle and liver and lipolysis in adipose tissue
cholesterol regulation
-increased levels of cholesterol inhibit further syntesis of cholesterol (feedback inhibition) -insulin promotes cholesterol synthesis
primary function of thyroid hormones
-increases basic metabolic rate and potentiate the activity of other hormones
Gi protein
-inhibits adenylate cyclase, which decreases levels of cAMP in the cell
DNA topoisomerases
-introduce negative supercoils to alleviate torsional strain produced by the + supercoiling created when helicase unwinds DNA and to reduce risk of strand breakage -Create nicks on the strands to allow relaxation of torsional pressure and then reseal the cut strands
replisome (replication complex)
-is a set of specialized proteins that assist the DNA polymerases.
hybridization
-joining of complementary base pair sequences -can be DNA-DNA recognition or DNA-RNA recognition. -This technique uses two single-stranded sequences and is a vital part of polymerase chain reaction and Southern blotting.
DNA libraries
-large collection of known DNA sequences -In sum, these sequences could equate to the genome of an organism. -to make, DNA fragments, often digested randomly, are cloned into vectors and can be utilized for further strudy. -Can consist of either genomic DNA or cDNA
Fatty Acid synthase (palmitate synthase)
-large multienzyme complex found in the CYTOSOL that is rapidly induced in the liver following a meal high in CARBOHYDRATES b/c of elevated insulin levels. -enzyme complex contains an acyl carrier protein (ACP) that requires pantothenic acid (Vitamin B5). -NADPH is also required to reduce the acetyl groups added to the fatty acid. -Eight acetyl-CoA groups are required to produce palmitate (16:0). 1: attachment to an acyl carrier protein 2: bond formation between activated malonyl Coa (malonyl-ACP) and the growing chain 3: reduction of a carbonyl group 4: dehydration 5: reduction NOTE: many of these reactions are reversed in beta-oxidation
pyruvate kinase
-last enzyme in aerobic glycolysis -catalyzes substrate-level phosphorylation of ADP using high-energy substrate phosphoenolpyruvate (PEP) -pyruvate kinase is activated by fructose-1,6-biphosphate from the PFK-1 reaction -example of feed-forward activation since earlier production of PFK-1 causes pyruvate kinase to be activated
Z-DNA
-left handed double helix that has a turn every 4.6nm and contains 12 bases within each turn. -Characterized by a high GC-content or a high salt concentration may contribe to the formation of this form of DNA -zigzag appearance -No biological activity has been attributed to Z-DNA partly because it is unstable and difficult to research
ketogenic amino acids
-leucine and lysine -can be convered into ketone bodies, which can be used as an alternative fuel, particularly during periods of prolonged starvation
Ketogenic amino acids
-leucine, lysine, isoleucine, phenylalanine, threonine, tryptophan, and tyrosine. -These can be converted into acetyl-CoA and then into ketone bodies via ketogenesis.
Complex II (Succinate-CoQ oxidoreductase)
-like complex I, complex II transfers electrons to coenzyme Q. -While complex I recevied electrons from NADH, complex I receives electrons from succinate. -Refresher that succinate is a citric acid cycle intermeditae, and that it is oxidized to fumarate upon interacting with FAD -FAD is covalently bonded to complex II, and once succinate has been oxidized, its converted to FADH2. -FADH2 then gets reoxidized to FAD as it reduces an iron-sulfur protein. -Final step reoxidizes the iron-sulfur protein as coenzyme Q is reduced. -B/c succinate dehydrogenase was responsible for oxidizing succinate to fumarate in the citric acid cycle, it makes sense that succinate dehydrogenase is also a part of complex II. -NO HYDROGEN PUMPING OCCURS HERE TO CONTRIBUTE TO THE PROTON GRADIENT. Net effect is passing energy from succinate to CoQ succinate + CoQ + 2H+ -> fumarate + CoQH2
GLUT 2
-low affinity glucose transporter found on *hepatocytes and pancreatic cells* -liver cells and in the Betal Islet Cells captures the excess glucose primarily for storage when glucose concentration drops below the Km for this transporter (has a high KM - low affinity for glucose - takes a lot of glucose to bind to this transporter) - it will go past the liver and straight into the periphery - (first-order kinetics) the liver will only pick up EXCESS glucose and store it - preferably right after a meal when glucose concentration exceeds the KM this transporter and glucokinase serves as the glucose sensor for insulin RELEASE in the Beta Islet cells of the pancreas.
Key Features of Enzymes
-lower the activation energy -increase the rate of the reaction -do no alter equilibrium constant -are not changed or consumed in the reaction -are pH and temperature sensitive -do not affect the overall Δ G of the reaction -are specific for a particular reaction or class of reactions
saturated fats
-main components of animal fat -exist as solids at room temp -found in processed food and considered less healthy -when in phospholipid membranes, they decrease the overall fluidity of the membrane
RNA polymerase II
-main player in transcribing mRNA -binding site in the promoter region is the TATA box named b/c it has high thymine and adenine bases.
cellulose
-main structural component of plants. -homopolysaccharide, which is a chain of beta-D-glucose molecules linked by a beta-1,4 glycosidic bonds, with hydrogen bonds holding the actual polymer chaings together for support. -humans can't digest b/c don't have cellulase enzyme.
From a metabolic standpoint, does it make sense for carbohydrates to get oxidized or reduced? What is the purpose of this process?
-makes sense for oxidation while reducing other character. This is the case because aerobic metabolism requires reduced form of electron carriers to allow/facilitate for processes such as oxidative phosphorylation, because carbohydrates are a primary energy source, they are oxidized.
Step 8 of the Citric Acid Cycle
-malate is oxidized by malate dehydrogenase to oxaloacetate -third and final molecule of NAD+ is reduced to NADH -Oxaloacetate is then ready to part in another turn of the citric acid cycle.
membrane-associated (peripheral) proteins
-may be bound through electrostatic interactions iwth the lipid bilayer, especially at lipid rafts, or to other transmembrane or embedded proteins, like the G proteins found in G protein-coupled receptors -may act as recognition molecules or enzymes
Terpenes
-metabolic precursors to steroids and other lipid signaling molecules -odiferous chemicals -class of lipids built from isoprene - carbons are grouped in multiples of 5 -grouped according to the # of isoprene units present -a single terpene consists of 2 isoprene units
Jacob-Monod model
-model used to describe the structure and function of operons. in this model, operons contain: -structural genes -an operator site -a promoter site -a regulator gene
cartinine
-molecule that can cross the inner membrane with a fatty acyl group attached. -merely to carry the acyl group from a cystolic CoA-SH to a mitochondrial CoA-SH.
hemiacetal formation
-monosaccharides are generally found in their cyclic form -when cyclization occurs, an alcohol group reacts with the aldehyde or ketone
frameshift mutation
-mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide. -usually more serious than point mutations.
Nucleoside
-nitrogenous base + sugar -composed of a five-carbon sugar (pentose) bonded to a nitrogenous base and formed by covalently linking the base to C-1' of the sugar.
Proto-oncogenes
-normal cellular genes that are important regulators of normal cellular processes, they promote growth. -alterations in the expression of these cells result in oncogenes
flavoproteins
-nucleic acid derivatves, generally either flavin adenine dinucleotide (FAD) or flavin mononucleotide (FMN) -contain a modified vitamin B2, riboflavin -act as electron carriers, modification of B vitamins to active forms, and function as cofactors for enzymes
de novo synthesis of cholesterol
-occurs in the liver -driven by acetyl-CoA and ATP -citrate shuttle* carries mitochondria acetyl-CoA into the cytoplasm in the cytoplasm is where acetyl CoA is converted to cholesterol, and NADPH from PPP supplies the reducing equivalents -synthesis of *mevalonic acid* in the SER is the rate limiting step which is catalyzed by *3 hydroxyl 3 methylglutaryl (HMG) CoA reductase* -dependent on regulation of HMG-CoA reductase gene expression in the cell.
beta oxidation of fatty acids
-occurs in the mitochondrial matrix. -INSULIN directly inhibits beta-oxidation -GLUCAGON stimulates beta-oxidation
endocytosis
-occurs when the membrane invaginates and engulfs material to bring it into the cell
Gene therapy
-offers potential cures for individuals with inherited diseases. -intended for diseases in which a given gene is mutated or inactive, giving rise to pathology. -by transferring a normal copy of the gene into affected tissues, pathology should by fixed, essential curing the individual. -needs effecient gene delivery vectors to be used to transfer cloned DNA into the target cells' DNA. -viruses are mostly used b/c they insert DNA into the host they occupy.
chimera
-offspring that has patches of cells, including germ cells, derived from each of the two lineages. -will have patchy coats of two colors, allowing them to be easily identified. -These chimeras can then be bread to produce mice that are heterozygous for the transgene and mice that are homozygous for the transgene.
Biological Systems
-often considered open systems b/c they exchange energy and matter w/ environment -energy is exchanged via work or heat. -matter exchanged via food consumption, elimination, and respiration. -Subcellular level is a closed system b/c no matter exchange
gluconeogenesis
-one of the ways that the liver maintains glucose levels in blood during fasting. -pathway is promoted by glucagon and epinephrine, which act to raise blood sugar levels -inhibited by insulin, which acts to lower blood sugar levels. Important substrates are: -glycerol-3-phosphate (from stored fats, triacylglycerols, in adipose tissues) -Lactate (from anaerobic glycolysis) -Glucogenic Amino Acids (from muscle proteins)
trp operon
-operates in the way as a negative repressible system -when trp is high in environment, it acts as a corepressor. -the binding of trp to repressor causes the repressor to bind to the operator site. -this causes the cell to turn off its machinery to synthesize its own trp, which is an energetically expensive process b/c of its easy availability in the environment.
lactate dehydrogenase
-oxidized NADH to NAD+ -replenishes the oxidized coenzyme for glyceraldehyde-3-phosphate dehydrogenase. -happens when oxygen is not present.
Fructose
-part of the disaccharide sucrose, linked to a glucose molecule.
transmembrane proteins
-pass completely through the lipid bilayer
cell (plasma) membrane
-phospholipid bilayer that protects and encloses the cell; controls transport; maintains homeostasis -permits fat-soluble compounds to easily cross, while large and water-soluble compounds must seek alternative entry,
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 -occurs in the duodenum. -aided by bile, which contains bile salts, pigments, and cholesterol.
Homeostasis
-physiological tendency toward a relatively stable state that is maintained and adjusted, often w/ the expenditure of energy.
Starches
-polysaccharides - chain of α-D glucose monomers - digestible by humans -2 types: amylopectin and amylose
bisphosphoglycerate mutase
-present in red blood cells -produces 2,3-bisphosphoglycerate from 1,3-BPG in glycolysis -2,3-BPG binds allosterically to the beta-chain of hemoglobin A, decreasing it's affinity for oxygen
NADPH
-primarily acts as an electron donor in a number of biochemical reactions -reducing agent Functions include: -biosynthesis, mainly of fatty acids and cholesterol -assisting in cellular bleach production in certain white blood cells, thereby contributing to bactericidal activity -maintenance of a supply of reduced glutathione to protect against reactive oxygen species (acts as body's natural antioxidant)
Active skeletal muscle metabolism
-primary fuel depends on magnitude and duration of exercise -short lived (2-7) comes from creatine phosphate -high intensity exercise also supported by anaerobic glycolysis -moderately high-intensity, continuous exercise, oxidation of glucose and fatty acids are both important, but after 1-3 hours, muscle glycogen stores become depleted.
Myosin
-primary motor protein that interacts with actin. -in addition to role as thick filament in a myofibril, myosin can be involved in cellular transport. -each myosin subunit has a single head and neck
VLDL (Very-Low-Density Lipoprotein)
-produced and assembled in liver cells -Transport of triacylglycerols to other tissues (like chylomicrons) -Also contain fatty acids that are synthesized from excess glucose or retrieved from chylomicron remnants.
Actin
-protein that makes up microfilaments and the thin filaments in myofibrils. -most abundant protein in eukaryotic cells. -have a positive and negative side, which allows motor protein to travel unidirectional along actin filaments.
Tubulin
-protein that makes up microtubules -microtubules provide structure, chromosome separation in mitosis and meiosis, and intracellular transport w/ kinesin and dynein. -also has polarity w/ negative and positive end. -negative end is located adjacent to nucleus, positive is in the periphery of the cell.
Cell adhesion molecules (CAMs)
-proteins found on surface of most cells -aid in binding the cell to the extracellular matrix or to other cells
cell adhesion molecules (CAMs)
-proteins found on surface of most cells -aid in binding the cell to the extracellular matrix or to other cells -all integral membrane proteins
Antibodies (immunoglobulins, Ig)
-proteins produced by B-cells that function to neutralize targets in the body, such as toxins and bacteria, and then recruit other cells to help eliminate the threat. -Y-shaped proteins that are made up of two identical heavy chains and two identical light chains -disulfide linkages and noncovalent interactions hold the light and heavy chains together -each antibody has an antigen-binding region at the tip of the Y, which has specific polypeptide sequences that will bind one, and only one, specific antigenic sequence.
isoelectric focusing
-proteins separated based on isoelectric point (pI) -electric charge is applied to the sample - protein migrates and stops when it reaches its isoelectric point(stops b/c charges cancel out)
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 -acetylation of the histone proteins decreases the positive charge on the lysine residues and weakens the interaction between DNA and the histone proteins - the chromatin starts to open and allows for easier access of the transcription machinery to the DNA -it increases the space between the histones, allowing for better access to DNA for other transcription factors
What is an apolipoprotein?
-proteins that bind lipids (oil-soluble substances such as fat and cholesterol) to form lipoproteins. They transport the lipids through the lymphatic and circulatory systems
Ion channels
-proteins that create specific pathways for charged molecules -all three groups of ion channels allow for facilitated diffusion
histone deacetylases
-proteins that function to remove the acetyl groups from histones -make the chromatin in a more closed conformation -overall decreases the gene expression levels of the cell
Phosphofructokinase-1 (PFK-1)
-rate limiting enzyme and main control point in glycolysis. -fructose-6-phosphate is phosphorylated to fructose-1,6-biphosphate. -PFK-1 is inhibited by ATP and Citrate -PFK-1 is activated by AMP -this makes sense as cell should turn off glycolysis when it has sufficient energy (high ATP) and turn on when it needs high energy (high AMP). -Citrate is an intermediate of the citric acid cycle, so high levels of citrate also imply that the cell is producing sufficient energy. -Insulin stimulates PFK-1 -Glucagon inhibits PFK-1
Tautomerization
-rearrangement of bonds in a compound -by moving a Hydrogen and forming a double bond -Ketose sugars are also reducing sugars and give positive tollen's or benedict's reagents to form a carboxylic acid. In this case, ketone group picks up a hydrogen while the double bond is moved between adjacent carbons, resulting in an enol, where it has a double bond and an alcohol.
glutathione
-reducing agent that can help reverse radical formation before damage is done to the cell
centromeres
-region of DNA found in the center of chromosomes - composed of heterochromatin (made of tandem repeat sequences w/ high GC content) -during cell division, two sister chromatids can therefore remain connected at the centromere until microtubules separate the chromatids during anaphase
constant region
-remaining part of antibody molecule -involved in recruitment & binding of other cells of the immune system (like macrophages)
Inducible System
-repressor is bonded tighly to the operator system, acting as a roadblock against RNA polymerase, -since its roadblocked, RNA polymerase cannot get from the promoter to the structural gene. -to reduce the blockage, an inducer must bind to the repressor protein so that RNA polymerase can move down the gene -Analogous to competitive inhibition for enzymes; as the concentration of the inducer increases, it will pull more copies of the repressor of the operator region, which frees up those genes for transcription. -allows for gene products to be produced only when they are needed. Ex: -lac operon
Enhancer region
-response elements group together to form an enhancer, which allows for the control of one gene's expression by multiple signals
Branching enzyme (glycogenesis)
-responsible for introducing alpha-1,6-linked branches into the granule as it grows. 1: Glycogen synthase makes a linear alpha-1,4-linked polyglucose chain 2: Branching enzyme hydrolyzes an alpha-1,4-bond 3: Brancing enzyme transfers the oligoglucose unti and attached it with an alpha-1,6 bond to create a branch 4: glycogen synthase extends both branches.
beta-oxidation in mitochondria
-reverse the process of fatty acid synthesis by oxidizing and releasing (rather than reducing and linking) molecules of Acetyl-CoA. -Four Steps, with each cycle releasing one acetyl-CoA and reducing NAD+ and FAD, which produces NADH and FADH2. -FADH2 and NADH are oxidized in the ETC, producing ATP. -in muscle and adipose tisue, acetyl-CoA enters the citric acid cycle -In liver. acetyl-CoA cannot be converted to glucose, stimulates gluconeogenesis by activating pyruvate carboxylase. -In fasting state, Liver produces more acetyl-CoA from beta-oxidation than is used in the citric acid cycle. -Much of acetyl-CoA is used to synthesize ketone bodies (essentially two acetyl-CoA molecules that are linked) that are released into the bloodstream and transported to other tissues.
covalent modification of enzymes
-reversible on and off switch -addition or removal of a chemical group (phosphate, methyl, adenyl)
Pancreas in lipid metabolism
-secretes bile -also secretes pancreatic lipase, colipase, and cholesterol esterase into the small intestine, which hydrolyze the lipid components into 2-monoacylglycerol, free fatty acids and cholesterol.
hydrogen bonding and spatial configuration of an alpha-helix
-side chains point away from helix core
facilitated diffusion
-simple diffusion for molecules that impermeable to the membrane -energy barrier too high to cross freely, requires integral membrane proteins. -happens via carrier or channel protein
fischer projection
-simple, 2D drawing of stereoisomers -Horizontal lines: wedges (out of the page) -Vertical lines: dashes (into the page)
micelles vs liposomes
-small monolayer vesicles -bilayered vesicles
Formation of Acetyl CoA
-sources: pyruvate, amino acids, carbohydrates, ketones, alcohol -pyruvate-->acetyl CoA occurs in the mitochondrial matrix using the PDH complex -the PDH complex is inhibited by PDH kinase (phosphorylated) when ATP is high. -when ATP is low, PDH phosphatase reverses this to turn it on
adipocytes
-specialized fat cells whose cytoplasm contains nothing but triglycerides -store large amounts of fat and are found primarily under the skin, around mammary glands, and in the abdominal cavity.
flippases
-specific membrane proteins that maintain the bidirectional transport of lipids between the layers of the phospholipid bilayer in cells.
Mutarotation
-spontaneous change of configuration about C1 (occurs more rapidly if rxn is catalyzed w/ acid or base) -Exposing hemiacetal rings to water causes them to spontaneously cycle b/w open & closed forms -b/c the substituents on the single bond b/w C1 and C2 can rotate freely, either the α or β anomer can be formed
polyacrylamide gel
-standard medium for protein electrophoresis. -gel is slightly porous, allows smaller particles to move through more easily. -molecules separate based on size
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
cholesterol
-steroid of primary importance. -major component of phospholipid bilayer, reponsible for mediating membrane fluidity. -amphipathic molecules containing both hydrophilic and hydrophobic components. -at low temperatures, it keeps the cell membrane from solidifying -at high temperatures, it holds the membrane intact and prevents it from becoming too permeable.
Gs protein
-stimulate adenylate cyclase, which increases levels of cAMP in the cell -works opposite of Gi
lagging strand
-strand that is copied in a direction opposite the direction of the replication fork -on this side of the replication fork, the parental strand has 5' to 3' polarity. -DNA polyermase cannot simply read and synthesize on this strand, so uses a trick. Since DNA polymerase can only synthesize in the 5' to 3' direction from a 3' to 5' template, small strands called okazaki fragments are produced. -Each time DNA polymerase completes an okazaki fragment, it turns around to find another gap that needs to be filled
nuclear pores
-structures in the nuclear envelope that allow passage of certain materials between the cell nucleus and the cytoplasm. -how mRNA leaves the nucleus to be later translated
electrophoresis
-subjects compounds to an electric field which moves them according to their charge & size -negatively charged particles will move towards the anode, and positively charged will move towards cathode.
internal energy
-sum of all the difference interactions between and within atoms in a system -via vibration, rotation, linear motion, and stored chemical energies all contribute.
Glycogenesis
-synthesis of glycogen granules from glucose
HDL
-synthesized in the liver and intestines and released as dense, protein-rich particles into the blood. -Contains apolipoproteins used for cholesterol recovery, that cleans up excess cholesterol from blood vessels for excretion. -Delivers some cholesterol to steroidogenic tissues and transfers necessary apolipoproteins to some of the other lipoproteins
Ribosomal RNA (rRNA)
-synthesized in the nucleous -functions as an integral part of the ribosomal machinery used during protein assembly in the cytoplasm. -help catalyze the formation of peptide bonds and also important for splicing out its own introns within the nucleus.
DNA cloning
-technique that can produce large amounts of a desired sequence -Often presented in a small quantity and is part of a heterogeneous mixture containing other DNA sequences. -Goal is to produce a large quantity of homogeneous DNA for other applications. -requires that the investigator ligate the DNA of interest into a piece of nucleic acid referred to as a vector
What is alternative splicing and what does it accomplish?
-the ability of some genes to use various combinations of exons to create multiple proteins from one hnRNA transcript. This increases protein diversity and allows a species to maximize the number of proteins it can create from a limited number of genes.
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
Ligand-gated channels
-the binding of a specific substance or ligand to the channel causes it to open or close Ex: -neurotransmitters act at ligand-gated channels at the postsynaptic membrane; GABA binds to a chloride channel and opens it. -Km and Vmax parameters can apply to transporters such as ion channels. Km would refer to the solute concentration at which the transporter is functioning at half of its maximum activity.
Proteolysis
-the breakdown of proteins or peptides into amino acids by the action of enzymes. -Beigins in STOMACH w/ pepsin -Continues in the pancrease with the proteases trypsin, chymotrypsin, and carboxypeptidases A and B, which are secreted as ZYMOGENS. -Protein digestion is completed by the small intestinal brush-border enzymes dipeptidase and aminopeptidase. -Main products: -amino acids, dipeptides, and tripeptides. -absorption of amino acids and small peptides through the luminal membrame is accomplished y secondary active transport linked to sodium.
Chylomicrons
-the class of lipoproteins that transport dietary triacylglycerols, cholesterol, and cholesteryl ester from intestine to tissues. -highly souluble in both lymphatic fluid and blood. -assemblies of chilomicrons occur in intestinal lining and results in a nascent chylomicron that contains lipids and apolipoproteins.
Micelle Formation
-the free fatty acids, 2 monoacyclglycerol, cholesterol with bile salts all form into micelles. -clusters of amphipathic lipids that are soluble in the aqueous environment of the intestinal lumen. -Micelles are water-soluble spheres with a lipid-soluble interior. -Micelles are vital in digestion, transport, and absorption of lipid-soluble subtances starting from the duodenum all the way to the end of the ileum -After the ileum, bile salts are actively reabsorbed and recycled:
activation energy
-the minimum amount of energy required to start a chemical reaction -enzymes make it easier for the substrate to reach the transition state.
parental strands
-the original strand in DNA replication
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
Glycogenolysis
-the process of breaking down glycogen
Glycogen synthase
-the rate-limiting enzyme of glycogenesis (glycogen synthesis) -forms the alpha-1,4-glycosidic bond found in the linear glucose chains of the granule -stimulated by glucose-6-phosphate and insulin -inhibited by epinephrine and glucagon through a protein kinase cascade the phosphorylates and inactivates the enzyme.
glyceraldehyde
-the simplest (3-carbon) aldose -carbonyl carbon is most oxidized, always lowest number -aldehyde carbon can participate in glycosidic linkages
Cell-Cell Junctions
-they form a cohesive layer via intercellular junctions -they provide direct pathways for communication between neighboring cells or between cells and the extracellular matrix -generally composed of cell adhesion molecules (CAM) 1) Gap junctions 2) Tight junctions 3) Desmosomes and hemidesmosomes
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* , means no effect on expression of AA, so no effect to polypeptide
Complex I (NADH-CoQ oxidoreductase)
-transfer of electrons from NADH to coenzyme Q (CoQ) is catalyzed in this comlex. -complex has over 20 subunits, but the two highlighted here include a protein that has an iron-sulfur cluster and a flavoprotein that oxidized NADH. -Flavoprotein has a coenzyme called flavin mononucleotide (FMN) covalently bonded to it. FMN is quite similar in structure to FAD< flavin adenine dinucleotide. -First step is NADH transferring electrons to FMN, oxidized to NAD+ , FMN is reduced to FMNH2. -Reduced iron-sulfur subunt donates the electrons from FMNH2 to coenzyme Q. -Coenzyme Q becomes CoQH2. -ONE OF THE THREE SITES WHERE PROTON PUMPING OCCURS, AS FOUR PROTONS ARE MOVED TO THE INTERMEMBRANE SPACE. Net Effect: NADH + H(+) + CoQ -> NAD+ + CoQH2
shuttle mechanisms
-transfers the high-energy electrons of NADH to a carrier that can cross the inner mitochondrial membrane -depending on the mechanism NADH participates in, either 1.5 or 2.5 ATP will end up being produced 2 main mechanisms: -Glycerol-3-phosphate shuttle -Malate-Aspartate shuttle
3-Phosphoglycerate Kinase
-transfers the high-energy phosphate from 1,3-biphosphoglycerate to ADP -This forms ATP and 3-phosphoglycerate -this is an example of substrate-level phosphorylation
Collagen
-trihelical fiber, consisting of left-handed helices woven together to form a secondary right-handed helix. -makes up most of extracellular matrix of connective tissue -providing strength and flexibility
Double Helix
-two linear polynucleotide chains of DNA are wound together in a spiral orientation along a common axis.
Debranching Enzyme
-two-enzyme complex that deconstructs the branches in glycogen that have been exposed by glycogen phosphorylase 1: Glycogen phosphorylase releases Glucose-1-phosphate from the periphery of the granule until it encounters the first branch point 2: Debranching enzyme hydrolyzes the alpha-1,4-bond nearest the branch point 3: Debranching enzyme transfers the oligoglucose unit to the end of another chains, then: 4: Hydrolyzes the alpha-1,6-bond, releasing the single glucose from the former branch.
gene
-unit of DNA on a chromosome that is encoded with the instructions for a single protein or RNA molecule. -Gene is expressed through transcription and translation
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 (DHAP)
-used in hepatic and adipose tissue for triacylglycerol synthesis -DHAP is formed when fructose 1,6-biphosphate. It can be isomerized to glycerol 3-phosphate, which can then be converted to glycerol, the backbone of triacylglycerols.
Edman degradation
-used to analyze small proteins - selectively & sequentially removes the N terminal AA of the protein which is analyzed by mass spectroscopy
bioenergetics
-used to describe energy states in biological systems. -ATP plays a crucial role in transferring energy from energy-releasing catabolic processes to energy-requiring anabolic processes.
Southern blot
-used to detect presence and quantity of various DNA strands in a sample -After electrophoresis, the sample is transferred to a membrane that can be probed w/ single stranded DNA molecules to look for a sequence of interest -probe binds to its complementary sequence & forms double stranded DNA. -probes are labeled with radioisotopes or indicator proteins, which indicate the presence of a desired sequence.
Ketones (Acetyl-CoA)
-usually acetyl-CoA --> ketones when pyruvate dehydrogenase complex is inhibited, but reverse can happen too.
Channels
-viable transporters for facilitated diffusion -may be in the open or closed conformation -open conformation - channels are exposed to both sides of the cell membrane and act like a tunnel
Termination (translation)
-when any of the three stop codons moves into the A site, a protein called release factor (RF) binds to the termination codon, causing a water molecule to be added to the polypeptide chain -Addition of water allows peptidyl transferase and termination factors to hydrolyze the completed polypeptide chain from the final tRNA. -Polypeptide is then released from the tRNA in the P site, and the two ribosomal subunits will dissociate.
hypotonic
-when the concentration of solutes inside the cell is higher than the surrounding solution -SOLUTES MOVE INTO CELL
denatured DNA
-when the hydrogen bonds connecting the strands are disrupted and the two strands separate; can happen when heated, immersed in a high concentration salt solution, high pH -temperature required to separate strands is the melting temperature (Tm); DNA with more C-G pairs has a greater Tm because C-G have 3 H-bonds, and more H-bonds = harder to melt. -heating to about 95 degrees C is enough to denature any DNA sequence; denatured DNA is less viscous, denser, and more able to absorb UV light -none of the covalent links between the nucleotides in the backbone of the DNA break during the process. -Heat, Alkaline pH, and chemicals like formaldehyde and urea are commonly used to denature DNA
Alternative splicing
-when the primary transcript of hnRNA may be spliced togehter in different ways to produce multiple variants of proteins encoded by the same gene. -allows organism to make many more different proteins from a limited number of genes.
Isotonic
-when the solutions inside and outside are eqimolar -prevents the NET movement of particles
Step 4 of Citric Acid Cycle
-α-ketoglutarate --> succinyl-CoA -Uses α-ketoglutarate dehydrogenase complex -CoA + NAD+ --> NADH + CO2
Processing eukaryotic hnRNA to form mRNA
1. 5'-cap and 3' poly A tail addition 2. splicing of introns by spliceosome (snRNA and snRNPs in the nucleus) 3. excised intron degraded in the nucleus 4. mRNA is made with only 5'cap, exons, 3'poly A tail 5. mRNA is transported to cytoplasm for translation
What are the six classes of enzymes?
1. Oxidoreductases 2. Transferases 3. Hydrolases 4. Lyases 5. Isomerases 6. Ligases
What are the four steps of beta-oxidation?
1. dehydrogenation -Oxidation of the fatty acid to form a double bond -FAD -> FADH2 2. hydration -From a double bond to a hydroxyl group (adds H20). -Adds H2O 3. oxidation -Oxidation of hydroxyl to a carbonyl (beta-ketoacid) -NAD+ -> NADH 4. thiolysis -splitting of the B-ketoacid into a shorter acyl-CoA and Acetyl-CoA -CoA-SH splits the molecules into two molecules, at the beta-position from the carboxylic acid Cycle keeps going until the chain has been shortened to two carbons, creating a final acetyl-CoA
Prostaglandins
A group of bioactive, hormone-like chemicals derived from fatty acids that have a wide variety of biological effects including roles in inflammation, platelet aggregation, vascular smooth muscle dilation and constriction, cell growth, protection of from acid in the stomach, and many more. -regulates the synthesis of cyclic adenosine monophosphate (cAMP), which is a ubiquitous intracellular messenger. -includes downstream effects on smooth muscle function, influence over the sleep-wake cycle, and the elevation of body temperature -NSAIDs like aspirin inhibit the enzyme cyclooxygenase (COX) which aids in the production of prostaglandins.
pyruvate dehydrogenase complex
A group of three enzymes that decarboxylates pyruvate, creating an acetyl group and carbon dioxide. The acetyl group is then attached to coenzyme A to produce acetyl-CoA, a substrate in the Krebs cycle. In the process, NAD+ is reduced to NADH. The pyruvate dehydrogenase complex is the second stage of cellular respiration.
cooperativity
A kind of allosteric regulation whereby a shape change in one subunit of a protein caused by substrate binding is transmitted to all the other subunits, facilitating binding of additional substrate molecules to those subunits.
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.
amylose
A linear glucose polymer linked by alpha-1,4 glycosidic bonds Type of starch - stored by plants Degraded by alpha-amylase and beta-amylase
DNA ligase
A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain.
cholesterol
A lipid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids.
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.
beta-oxidation
A metabolic sequence that breaks fatty acids down to two-carbon fragments that enter the citric acid cycle as acetyl CoA.
nonsense mutation
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.
Norepinephrine
A neurotransmitter involved in arousal, as well as in learning and mood regulation
endergonic reaction
A non-spontaneous chemical reaction in which free energy is absorbed from the surroundings. -REQUIRES THE INPUT OF ENERGY TO PROCEDE
enzyme saturation
A point of substrate concentration at which all enzymes are engaged, and adding more substrate will not increase reaction rate.
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.
colligative property
A property that depends only upon the number of solute particles, and not upon their identity
Release Factor (rf)
A protein that binds to the A site of the ribosome when a stop codon is in the mRNA.
glycoproteins
A protein with one or more covalently attached carbohydrates.
Hill's coefficient
A quantitative measure of cooperative binding effects in enzymes Hills Coefficient is: -x>1, positively cooperative binding is occuring, such that after one ligand is bound, the affinity of the enzyme for further ligand(s) increases. - x<1, negatively cooperative binding is occurring, such that after one ligand is bound the affinity of the enzyme for further ligands decreases - x=1, the enzyme does not exhibit cooperative binding.
cell wall
A rigid structure that surrounds the cell membrane and provides support to the cell.
pyranose
A six-membered ring sugar One of two stable cyclic molecules
stationary phase
A solid medium onto which a sample is placed for chromatography; also called the adsorbent.
initiator tRNA
A special type of transfer ribonucleic acid (RNA) that initiates protein synthesis by binding to the amino acid methionine (or fMet) and delivering it to the small ribosomal subunit.
exergonic reaction
A spontaneous chemical reaction in which there is a net release of free energy. -DOESN'T require the input of energy to proceed.
epimers
A subtype of diastereomers that differ in absolute configuration at exactly one chiral carbon Ex: -D-ribose and D-arabinose, which differ at C-2 carbon.
X-ray crystallography
A technique that depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule to study the three-dimensional structure of the molecule.
enzyme-substrate complex
A temporary complex formed when an enzyme binds to its substrate molecule(s).
glycerol
A three-carbon alcohol to which fatty acids are covalently bonded to make fats and oils.
codons
A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.
sodium-potassium pump
A transport protein in the plasma membrane of animal cells that actively transports sodium out of the cell and potassium into the cell.
steroids
A type of lipid characterized by a carbon skeleton consisting of four rings with various functional groups attached. -three cyclohexane and one cyclopentane
ribonucleic acid (RNA)
A type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U); usually single-stranded; functions in protein synthesis and as the genome of some viruses.
beta-pleated sheet
A type of protein secondary structure; results from hydrogen bonding between polypeptide regions running antiparallel to each other. -can be parallel or antiparallel, w/ antiparallel being more b/c the hydrogen bond between sheets is more linear, whereas in parallel the bond is at an angle. -R groups point above or below the plane of the beta-pleated sheet
Major apolipoproteins
A-I B-48 B-100 C-II E
ATP Synthase Reaction
ADP + Pi + energy --> ATP + H2O -generates by allowing high-energy protons to move down the concentration gradient created by the ETC. Free energy change is -220 kJ/mol, highly exergonic.
ATP hydrolysis
ATP is converted to ADP & phosphate energized myosin heads (removal of phosphate) need energy
start codon for translation
AUG (methionine)
glycosides
Acetals of carbohydrates
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.
What is the Pyruvate Dehydrogenase complex affected by?
Acetyl-CoA
Citrate Formation
Acetyl-CoA + OAA → Citryl-CoA → Citrate + CoA (via citrate synthetase)
DNA polyermase delta
Adds DNA nucleotides where the RNA primer has been
Base-Pairing in DNA
Adenine, Thymine, Guanine, Cytosine
What does Km represent? What would an increase in Km signify?
Affinity of an enzyme for its substrate, and is defined as the substrate concentration at which an enzyme is functioning at half of its maximal velocity. As Km increases, an enzymes affinity for its substrates decreases.
alanine
Ala, A nonpolar aliphatic
Positive test for an aldose using benedict's reagent
Aldose will react, forming copper (1) oxide; ketones may react more slowly.
zwitterion
Amphoteric (reacts as acid or base) compound with no net electric charge.
telomerase
An enzyme that catalyzes the lengthening of telomeres. The enzyme includes a molecule of RNA that serves as a template for new telomere segments. -more expressed in rapidly dividing cells -progressive shortening of telomeres contribute to aging. -Also their high GC content creates exceptionally strong strand attractions at the end of chromosomes to prevent unraveling; Think of telomeres as "knotting off" the end of the chromosome
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.
helicase
An enzyme that untwists the double helix at the replication forks, separating the two parental strands and making them available as template strands.
opsonization
An immune response in which the binding of antibodies to the surface of a microbe facilitates phagocytosis of the the microbe by a macrophage
coenzymes
An organic molecule that is a necessary participant in some enzymatic reactions; helps catalysis by donating or accepting electrons or functional groups; e.g., a vitamin, ATP, NAD+.
cofactors
Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis -most cofactors are generally inorganic molecules or metal ions, often ingested as dietary minerals.
Aromatic
Any stable ring system that adheres to four rules: -1: The compound is cyclic -2: compound is planar -3: compound is conjugated, meaning has alternating single and multiple bonds, or lone pairs, creating at least on unhybridized p-orbital for each atom in the rule -4: compound has 4n+2 (n=any integer) pi electrons, called Huckel's rule
Arginine
Arg, R positively charged (basic)
Asparagine
Asn, N, polar uncharged
aspartate
Asp, D negatively charged
What are the three major families of Cell Adhesion Molecules (CAMs)? What type of adhesion does each class form?
Cadherins: -Two cells of the same or similar type using calcium Integrins: -One cell to proteins in the extracellular matrix Selectins: -One cell to carbohydrates, usually on the surface of other cells
During protein processing, what is the eventual fate of each of the following components: Carbon skeleton Amino Group Side Chains
Carbon Skeleton: -Transported to the liver for processing into glucose or ketone bodies Amino Group: -Will feed into the urea cycle for excretion Side Chains: -Will be processed like amino groups, while other functional groups will be treated like the carbon skeleton.
Enzymes
Catalysts for chemical reactions in living things
If you were designing a study to assess metabolism, which measurement would you choose and why?
Chemical analysis: -Objective and can quantify specific metabolic substrates, products and enzymes; Calorimetry: -Most accurate for determing the basal metabolic rate, but also most expensive. Respirometry: -provides basic information about fuel sources; Caloric analysis @ constant weight -Uses food logs, which is the least invasive
Classes of lipoproteins:
Chylomicrons: -Transport dietary triacylglycerols, cholesterol, cholesteryl esters from intestine to tissues. VLDL: -Tranports triacylglycerols and fatty acids from liver to tissues IDL (VLDL remnants): -Picks up cholesteryl esters from HDL and become LDL -Picked up by the liver LDL: -Delivers cholesterol into cells HDL: -Picks up cholesterol accumulating in blood vessels -Delivers cholesterol to liver and steroidogenic tissues -Transfers apolipoproteins to other lipoproteins
What are the three main sites of regulation within the citric acid cycle? What molecules inhibit and activate the three main checkpoints?
Citrate Synthase: -Inhibited by ATP, NADH, succinyl-CoA, citrate -No Activators Isocitrate Dehydrogenase: -Inhibited by ATP and NADH -Activated by ADP and NAD+ alpha-Ketoglutarate Complex: -Inhibited by ATP, NADH, succinyl-CoA -Activated by ADP and Ca(2+)
beta-amylase
Cleaves amylose at the reducing end of the polymer (end with anomeric carbon) to yield maltose
Transcription factors (TFs)
Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.
Thryoxine (T4) and Triiodothyronine (T3)
Collectively known as thyroid hormone Increases metabolic rate and body heat production Regulates tissue growth
Galactose Metabolism
Comes from lactose (lactose -> galactose and glucose) in milk. 1) Trapped in cell by glactokinase. 2) Converted to glucose 1-phosphate via lactose-1-phosphate uridylransferase and an epimerase.
What factors would cause an activity assay to display lower activity than expected after concentration determination?
Contamination of the sample with detergent or SDS could yield an artificially increased protein level, leading to lower activity than expected (because the protein concentration was calculated as higher than its actual value). Alternatively, the enzyme could have been denatured during the isolation analysis
What does the liver do when it has excess acetyl-CoA from beta-oxidation of fatty acids?
Convert acetyl-CoA into the ketone bodies which can be used for energy in various tissues: -Acetoacetate -3-hydroxybutyrate (beta-hydroxybutyrate)
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. -reduces a 4,5-C double bond to become a monounsaturated fatty acid.
What is enzyme cooperativity?
Cooperativity refers to the interactions between subunits in a multisubunit enzyme or protein. The binding of substrate to one subunit induces a change in the other subunits from the T (tense) state to the R (relaxed) state, which encourages binding of substrate to the other subunits. In the reverse direction, the unbinding of substrate from one subunit induces a change from R to T in the remaining subunits, promoting unbinding of substrate from the remaining subunits.
cysteine
Cys, C polar uncharged
D- and L- amino acids
D- and L- refer to where the AMINO group is drawn in the fischer projection. -this translates to an (S) absolute configuration if you were using the Cahn-ingold prelog system. -exception is cysteine, b/c while still an l- amino acid, has an (R) configuration because the -CH2SH group has priority over the COOH
Central Dogma of Molecular Biology
DNA -> RNA -> Protein (Replication-> Transcription-> Translation)
For each of the repair mechanisms below, in which phase of the cell cycle does the repair mechanism function? What are the key enzymes or genes specifically associated with each mechanism? DNA Polymerase (proofreading) Mismatch Repair Nucleotide Excision Repair Base Excision Repair
DNA Polymerase (proofreading): -S phase -DNA Polymerase Mismatch Repair: -G2 phase -MSH2, MLH1 in eukaryotes, MutS and MutL in prokaryotes Nucleotide Excision Repair: -G1 + G2 -Excision Endonuclease Base Excision Repair: -G1 + G2 -Glycosylase, AP endonuclease
DNA Strand Polarity
DNA strands run antiparallel to one another; -enzymes that replicate and transcribe DNA only work in the 5'->3' direction.
complementary base pairing
DNA: -T pairs with A (2 H-bonds) -G pairs with C (3-H-bonds) RNA: -U pairs with A -G pairs with C
What is the relationship between the carbonyl carbon, anomeric carbon, and the alpha and beta forms of a sugar molecule?
During hemiacetal or hemiketal formation, the carbonyl carbon becomes chiral and is termed the anomeric carbon. The orientation of the -OH substituent on this carbon determines if the sugar molecules is the alpha or beta anomer
What are the enzymes in pyruvate dehydrogenase complex?
E1= Pyruvate dehydrogenase (PDH) E2= Dihydrolipoyl transacetylase E3= Dihydrolipoyl dehydrogenase
tetraterpenes
Eight isoprene units Contain carotenoids group (i.e. beta-carotene and lutein)
active transport
Energy-requiring process that moves material across a cell membrane against a concentration difference
what are the three types of stereoisomers?
Entiomers, diastereomers epimers
Huckel's rule
If a compound has planar, monocyclic rings with 4n+2 pi electrons (n being any integer, including 0), it is by definition an aromatic compound.
topoisomerase
Enzyme that functions in DNA replication, helping to relieve strain in the double helix ahead of the replication fork.
Contrast enzyme-linked receptors with G-protein coupled receptors
Enzymes Linked Receptors: -autoactivity -enzymatic activity G-protein coupled receptors: -two-protein complex -dissociation upon activation -trimer Both -extracellular domain -transmembrane domain -ligand binding
In what ways do enzymes affect the thermodynamics vs. the kinetics of a reaction?
Enzymes have no effect on the thermodynamics of the G or H of the reaction, although they do lower the energy of the transition state, thus lowering the activation energy Enzymes have a profound affect on the kinetics of a reaction, which allows equilibrium to be achieved faster, although the EQUILIBRIUM POSITION ISN'T CHANGED.
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) -isolated from bacteria, which can then be used to cut through the backbones of the double helix, allowing researchers to process DNA in very specific ways.
what is the difference between esterification and glycoside formation?
Esterification: -A hydroxyl group reacts w/ either a carboxylic acid or a carboxylic acid derivative to form an ester. Glycoside formation: -refers to the reaction between an alcohol and a hemiacetal (or hemiketal) group on a sugar to yield an alkoxy group
heterochromatin
Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed. -appear dark under light microscopy and is transcriptionally silent. -often consists of DNA with highly repetitive sequences
heterochromatin
Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed. -dark under a microscope -inacitve (silent)
What are the subunits of eukaryotic and prokaryotic ribosomes?
Eukaryotic: -total is 80s -big subunit is 60s -small subunit is 40s Prokaryotic: -total is 70s -big subunit is 50S -small subunit is 30S
Do all lipids enter the circulation through the lymphatic system?
False, small free fatty acids enter the circulation directly
True/False: Body mass can be predicted by the leptin receptor phenotype and caloric intake alone
False: -Energy expenditure, genetics, socioeconomic status, geography, and other hormones also play a role in body mass regulation.
True or False: Bodily proteins will commonly be broken down to provide acetyl-CoA for lipid synthesis.
False: Proteins are more valuable to the cell than lipids, thus they will not commonly be broken down for lipid synthesis
histidine
His, H positively charged (basic) -aromatic ring w/ two nitrogen atoms, which is caled an imidazole
Sliding clamp
Holds DNA polymerase in place during strand extension
What other molecules can be used to make acetyl-CoA, and how does the body perform this conversion for each?
Fatty Acids: -Shuttle acyl group from cytosolic CoA-SH to mitochondrial CoA-SH via carnitine; then undergo beta-oxidation Ketogenic Amino Acids: -Transaminate to lose nitrogen; convert carbon skeleton into ketone body, which can be converted into acetyl-CoA Ketones: -Reverse of Ketone body formation Alcohol: -Alcohol dehydrogenase and acetaldehyde dehydrogenase convert alcohol into acetyl-CoA.
C-terminus
Free carboxyl end of a polypeptide On right side of drawings Read from N-terminus -> C-terminus
Malate Formation:
Fumarase = Fumarate → L-Malate
what is the function and key regulators of PHOSPHOFRUCTOKINASE-1? reversible?
Function: -PFK-1 catalyzes the rate-limiting step of glycolysis, phosphorylating fructose-6-phosphate to fructose-1,6-biphosphate using ATP Inhibited: -Inhibited by ATP, citrate and glucagon. Reversible: -NOT REVERSIBLE
what is the function and key regulators of PYRUVATE KINASE? reversible?
Function: -Performs another substrate-level phosphorylation, transferring a phosphate from phosphoenolpyruvate (PEP) to ADP, forming ATP and pyruvate. Inhibited: -Activated by fructose-1,6-bisphosphate (F1,6BP) Reversible: -NOT REVERSIBLE
what is the function and key regulators of GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE? reversible?
Function: -generates NADH while phosphorylating glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate. Inhibited: -N/A Reversible: -Reversible Yes
what is the function and key regulators of 3-PHOSPHOGLYCERATE KINASE? reversible?
Function: -performs a substrate-level phosphorylation, transferring a phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate Inhibited: -N/A Reversible: -Reversible Yes
what is the function and key regulators of glucokinase? reversible?
Function: -phosphorylates and "traps" glucose in liver cells, and works with GLUT 2 as part of the glucose sensor in beta-islet cells. Inhibited: -in liver cells, it is induced by insulin Reversible: -NOT REVERSIBLE
what is the function and key regulators of HEXOKINASE? reversible?
Function: -phosphorylates glucose to form glucose-6-phosphate Inhibited: -by glucose-6-phosphate Reversible: -NOT REVERSIBLE
Compare and contrast GLUT 2 and GLUT 4 in following regards: important tissues Km saturated at normal blood glucose levels responsive to insulin
GLUT 2: -Liver, pancrease -High (~15 mM) -No, cannot be saturated under normal physiological conditions -no (but serves as glucose sensor to cause release of insulin in pancreatic B-cells) GLUT 4: -Adipose Tissue (fat), muscle -Low (~5 mM) -Yes, saturated when glucose levels are only slightly above 5 mM -Yes
When creating a DNA library, what are some of the advantages of genomic libraries? What about cDNA libraries?
Genomic: -include all of the DNA in an organism's genome, including noncoding regions. This may be useful for studying DNA in introns, centromeres, or telomeres. cDNA: -only include expressed genes from a given tissue, but can be used to express recombinant proteins or to perform gene therapy.
Glutamine
Gln, Q polar uncharged
Histones
Globular protein that assist in DNA packaging in eukaryotes. Histones form octamers around which DNA is wound to form a nucleosome. -5 histone protones found in eukaryotic cell H2A, H2B, H3, H4, and H1
glutamate
Glu, E, acidic
Cyclic sugar formation via intramolecular nuclophilic addition
Glucose forms a six membered ring w/ two anomeric forms: alpha (left) and beta (right).
Glycerophospholipids (phosphoglycerides)
Glycerol backbone bound by ester linkages to two fatty acids and phosphodiester link to polar head
Glycerophospholipids (phosphoglycerides)
Glycerol backbone bound by ester linkages to two fatty acids and phosphodiester link to polar head -assemble in micelles and liposomes due to hydrophobic interactions
What are the two main enzymes of glycogenolysis, and what does each accomplish?
Glycogen Phosphorylase: -Removes a glucose molecule from glycogen using a phosphate, breaking the alpha-1,4 link and creating glucose 1-phosphate. Debranching enzyme: -Moves all of the glucose from a branch to a longer glycogen chain by breaking an alpha-1,4 link and forming a new alpha-1,4 link to the longer chain. The branchpoint is left behind; this is removed by breaking the alpha-1,6 link to form a free molecule of glucose.
What are the two main enzymes of glycogenesis, and what does each accomplish?
Glycogen Synthase: -Attached the glucose molecule from UDP-glucose to the growing glycogen chain, forming an alpha-1,4 link in the process. Branching enzyme: -creates a branch by breaking an alpha-1,4 link in the growing chain and moving a block of oligoglucose to another location in the glycogen granule. The oligoglucose is then attached with an alpha-1,6 link.
Regarding glycogen and amylopectin, which of these two polymers should experience a higher rate of enzyme activity from enzymes that cleave side branches? Why?
Glycogen, because it has a higher rate of enzymatic branch cleavage because it contains significantly more branching than amylopectin.
gangliosides
Glycolipids with a head group composed of oligosaccharides with a terminal sialic acid (NANA) molecule. -also considered glycolipids b/c they have a glycositic linkage and no phosphate group.
What are the rate-limiting enzymes for the following processes? Glycolysis Fermentation Glycogenesis Glycogenolysis Gluconeogenesis Pentose Phosphate Pathway
Glycolysis: -phosphofructokinase-1 (PFK-1) Fermentation: -lactace dehydrogenase Glycogenesis: -Glycogen Synthase Glycogenolysis: -Glycogen phosphorylase Gluconeogenesis: -fructose-1,6-biphosphatase Pentose Phosphate Pathway: -Glucose-6-phosphate dehydrogenase
Mmenomic for functions of heterotrimeric G proteins
Gs Stimulates Gi Inhibits "mind your P's and Q": Gq activates phospholipase C
What are the three main types of G proteins?
Gs, Gi, Gq
What are the five histone proteins in eukaryotic cells? which one is not part of the histone core around which DNA wraps to form chromatin?
H1, H2A, H2B, H3, H4, H1 wraps around the outside to secure the outside, so it is not in the histone core
Order the lipoproteins from greatest percentage of protein to least percentage of protein. Circle the molecules that are primarily involved in triacylglycerol transport.
HDL > LDL > IDL > VLDL > Chylomicrons -VLDL and chylomicrons are the primary triacylglycerol transporters. HDL and LDL are mostly involved in cholesterol transport.
How does heat denature proteins?
Heat = increased kinetic energy of atoms. They move more and this kinetic energy overcomes the weak, non-covalent bonds within the protein. The protein often precipitates out due to hydrophobic group aggregation.
Enzymes of DNA replication
Helicase, binding proteins, primase, DNA polymerase, ligase
For each of the enzymes, list the function and if it is found in eukar/prokar or both: Helicase SS- DNA binding protein Primase DNA polymerase III DNA polymerase alpha DNA polymerase I RNase H DNA ligase DNA topoisomerases
Helicase: -Both -Unwinds DNA double Helix SS-DNA binding protein -Both -prevents annealing of DNA double helix during replication Primase: -Both -places ~10 nucleotide RNA primer to begin DNA synthesis DNA polymerase III: -Prokaryotes -Adds nucleotides to growing daughter strand DNA polymerase alpha: -Eukaryotes -Adds nucleotides to growing daughter strand DNA Polymerase I: -Prokaryotes -Fills in gaps left behind after RNA primer excision RNase H: -Eukaryotes -Excises RNA primer DNA Ligase: -Both -Joins DNA strands (especially between Okazaki fragments) DNA topoisomerases: -Both -Reduces torsional strain from positive supercoils by introducing nicks in the DNA strand
Glycosidic linkage formation
Hemiacetal (or hemiketal) sugars react with alcohols under acidic conditions to form acetals (or ketals).
Compare and contrast heterochromatin and euchromatin based on the following characteristics: Density of chromatin packing Appearance under light microscope Transcriptional activity
Heterochromatin -Highly Dense -Dark -Silent (inactive) Euchromatin -Uncoiled -Light -Active
What are the enzymes of glycolysis that are likely to be tested on?
Hexokinase Glucokinase Phosphofructokinases (PFK-1 and PFK-2) Glyceraldehyde-3-phosphate dehydrogenase 3-phosphoglycerate kinase pyruvate kinase
Leptin
Hormone secreted by adipose tissue that decreae appetide by suppressing orexin production.
amino-acid derivative hormones
Hormones that are synthesized by modifying amino acids. Most amino acid-derivative hormones act via secondary messengers, while some act in a fashion similar to steroid hormones
Mnemonic for remembering the irreversible enzymes in Glycolysis:
How Glyolysis Push Forward the Process: Kinases -Hexokinase -Glucokinase -PFK-1 -Pyruvate Kinase
Where do hydrophobic and hydrophilic amino acids tend to reside within a protein?
Hydrophobic: -Tend to reside in the interior of the protein, b/c it is away from water Hydrophilic: -tend to remain on the surface of the protein, in contact with water.
osmotic pressure equation
II=iMRT i: # of particles in solution M: molarity R: gas constant T: tempt in Kelvins -osmotic pressure is directly proportional to the molarity of the solution -thus it depends on the presence and number of particles in solution, not their actual identity.
sister chromatids
Identical copies of a chromosome; full sets of these are created during the S subphase of interphase.
integral proteins
Integral proteins that span the membrane.
What enzyme catalyzes the rate-limiting step of the citric acid cycle?
Isocitrate dehydrogenase
What separation methods can be used to isolate a protein on the basis of isoelectric point?
Isoelectric focusing and ion-exchange chromatography both separate proteins based on charge; the charge of a protein in any given environment is determined by its isoelectric point (pI)
Turnover number equation
Kcat = Vmax/[Et] or Vmax=[E]*Kcat
catalytic efficiency
Kcat/Km, large Kcat (high turnover) and small Km (high affinity) will result in higher catalytic efficiency, which indicates a more efficient enzyme.
Which conditions and tissues favor ketogenesis and ketolysis?
Ketogenesis: -Favored by a prolonged fast -occurs in the LIVERT -Stimulated by increasing concentrations of acetyl-CoA Ketolysis: -Also favored during prolonged fast, but stimulated by a low-energy state in MUSCLE and BRAIN TISSUES, not in the liver.
Ketogenesis and Ketolysis
Ketogenesis: favored by a prolonged fast and occurs in the liver, stimulated by increasing concentrations of acetyl-CoA Ketolysis: favored during prolonged fasting, but is stimulated by low-energy state in muscle and brain tissue and does not occur in the liver
Stepwise Activity of Kinesins
Kinesins move along microtubules in a stepping motion such that one or both heads remain attached at all times.
Mnemonic for major enzyme classifications
LIL HOT ligase isomerase lyase hydrolase oxidoreductase transferase
conjugated proteins
Proteins requiring a covalently bonded prosthetic group to function properly. Hemoglobin is an example.
What are the names and functions of the six different classes of enzymes?
Ligase -addition or synthesis reactions, generally between large molecules; often require ATP isomerase -rearrangement of bonds within a compound lyase -cleavage of a single molecule into two products, or synthesis of small organic molecules (synthases) hydrolase -cleavage of compound into two molecules w/ addition of water oxidoreductase -oxidation-reduction reactions (transferring electrons) transferases -movement of a functional group from one molecule to another
List the following membrane components from most to least plentiful: Carbohydrates Lipids Proteins Nucleic Acids
Lipids: -including phospholipids, cholesterol and others are most plentiful Proteins: -including transmembrane proteins (channels and receptors), membrane associated proteins, and embedded proteins are next most plentiful Carbohydrates: -including the glycoprotein coat and signaling molecules are next Nucleic Acids: -essentially absent.
How do the lock and key theory and induced fit model differ?
Lock and Key: -Active site of enzyme fits exactly around substrate -no alterations to tertiary or quaternary structure of enzyme -less accurate model Induced Fit -Active site of enzyme molds itself around substrate only when substrate is present -Tertiary and Quaternary Structure modified for enzyme to function
Fatty acids
Long chain carboxylic acids that make up most lipids
lysine
Lys, K positively charged
Which components of membrane lipids contribute to their structural role in membranes? Which components contribute to function?
Membrane lipids are amphipathic -they have hydrophilic heads and hydrophobic tails, allowing for the formation of bilayers in aqueous solution. The fatty acid tails form the bulk of the phospholipid bilayer, and play a predominantly structural role. -On the other hand, the functional differences between membrane lipids are determined by the polar head group, due to its constant exposure to the exterior environment of the phospholipid bilayer (can be inside or outside the cell). The degree of unsaturation of fatty acid tails can also play a small role in function.
methionine
Met, M nonpolar aliphatic
Semiconservative replication
Method of DNA replication in which parental strands separate, act as templates, and produce molecules of DNA with one parental DNA strand and one new DNA strand.
Describe the structure of a micelle:
Micelles are collections of lipids with their hydrophobic ends oriented toward the center and their charged ends oriented toward the aqueous environment. Micelles collect lipids within their hydrophobic centers.
Cross-Section of a Micelle
Micelles organize in aqueous solution by forcing hydrophobic tails to the interior, allowing the hydrophilic heads to interact with water in the environment.
km
Michaelis constant, equal to the substrate concentration at Vmax/2 Low Km = high affinity for substrate -measure of affinity of the enzyme for its substrate. -When comparing enzymes, one with higher Km has lower affinity for substrate, b/c it requires higher [S] to be half-saturated.
amphipathic
Molecules are said to be this when it has regions that are both hydrophilic and hydrophobic.
What is the primary motivation for hydrophobic residues in a polypeptide to move to the interior of a protein?
Moving hydrophobic residues to interior increase entroy be allowing water molecules on the surface of the protein to have more possible positions and configurations. This positive S makes G<0, stabilizing the protein
Name Five SOLUBLE electron carriers and their relevant metabolic pathways.
NADH: -glycolysis, fermentation, citric acid cycle, ETC NADPH: pentose phosphate pathway, lipid biosynthesis, bleach formation, oxidative stress, photosynthesis Ubiquinone (CoQ): -ETC Cytochromes: -ETC Glutathione: -Oxidative stress
NADPH vs NADH
NADPH - e- donor/reducing agent - NADP+ --> NADPH (NADP+ reduced to NADPH) NADH - used for the ETC to indirectly make ATP - NAD+ --> NADH (NAD+ REDUCED to NADH) - NAD+ is a high E e- acceptor/oxidizing agent NADPH and NADH both used as e- carriers
reading frame
On an mRNA, the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis.
What is the difference between an oncogene and a tumor suppressor gene?
Oncogenes (proto-oncogenes) code for cell cycle-promoting proteins; when mutated, a proto-oncogene becomes an oncogene, promoting rapid cell cycling. Tumor suppressor genes code for repair or cell cycle-inhibiting proteins; when mutated, the cell cycle is allowed to proceed unchecked -Oncogenes are like stepping on gas pedal, mutated tumor suppressor genes are like cutting the brakes.
Preferred Fuels in the Well-Fed and Fasting States
Organ : Well-fed : Fasting Liver : glucose, AA : FA Resting Skeletal Muscle: glucose : FA, ketones Cardiac muscle : FA : FA, ketones Adipose tissue : glucose : FA Brain : glucose : glucose (Ketones in prolonged fast) RBC : glucose : glucose
What are the relative benefits of PAGE compared to SDS-PAGE
PAGE: -allows a complete protein to be recovered after analysis; also more accurately determines the relative globular size of proteins SDS-PAGE: -can be used to eliminate conflation from mass-to-charge ratios.
DNA polymerases delta and e are assisted by....
PCNA protein, which assembles into a trimer to form the sliding clamp, which strengthens the interaction between these DNA polymerases and the template strand.
What does PCR accomplish for a researcher? Southern blotting?
PCR: -increases the number of copies of a given DNA sequence and can be used for a sample containing very few copies of the DNA sequence Southern Blotting: -Useful for searching for a particular DNA sequence because it separates DNA fragments by length and then probes for a sequence usually by usually a radioisotope or indicator proteins
phenylalanine
Phe - F aromatic / hydrophobic
isoelectric point (pI)
Point at which a compound is electrically neutral. -acidic side chains have relatively low isoelectric points -basic side chains have relatively high ones
Cellulose Structure
Polymer of Beta 1,4 glycocidic linkages in a straight line.
What is a positive control system? what is a negative control system?
Positive control: -require the binding of a protein to the operator site to INCREASE transcription Negative control: -require the binding of a protein to the operator site to DECREASE transcription
Triacylglycerols (triglycerides)
Preferred method of storing energy for long term use. Contain: 1) One glycerol attached to three fatty acids via ester bonds. The FA usually vary within the three tails 2) Can have saturated or unsaturated FA tails. -deposits can be observed in cells as oily droplets in the cytosol. -travel bidirectionally in the bloodstream between the liver and adipose tissue.
What are the definitions of primary and secondary structure, how do they differ in subtypes and the bonds that stabilize them
Primary -Linear sequence of AA's in a sequence -no subtypes -stabilized by peptide bonds (covalent) Secondary -Local structure determined by nearby AA's -alpha-helices and beta-sheets -stabilized by H-bonds
Compare the two types of active transport. What is the difference between symport and antiport?
Primary active transport: -uses ATP as an energy source for the movement of molecules AGAINST concentration gradient Secondary Active Transport: -uses an electrochemical gradient to power the transport. Symport: -Moves both particles in secondary active transport across the membrane in the same direction -both move either IN or OUT at the same time Antiport: -moves particles across the cell membrane in opposite directions -one goes OUT while one comes IN
proline
Pro, P nonpolar aliphatic cyclic amino acid
gel electrophoresis
Procedure used to separate and analyze DNA fragments by placing a mixture of DNA fragments at one end of a porous gel and applying an electrical voltage to the gel
At which side does the Edman degradation proceed from?
Proceeds from the Amino (N-) terminus.
glycosylation
Process of covalently attaching a carbohydrate to a protein or lipid
DNA replication in Prokaryotes and Eukaryotes
Prokaryotes -One origin of replication -faster Eukaryotes -Multiple origins of replication -slower b/c more bases compared to prokaryotes
What role does proline serve in secondary structure?
Proline's rigid structure causes it to introduce kinks in alpha-helices or creates turns in beta-pleated sheets
Why are proteins analyzed after isolation?
Protein isolation is generally only the first step in an analysis. The protein identity must be confirmed by amino acid analysis or activity. With unknown proteins, classification of their features is generally desired.
lipoproteins
Protein-and-lipid substances in the blood that carry fats and cholesterol; classified according to size, density, and chemical composition conjugated protein where the prosthetic group is a lipid
protoeinogenic amino acids
Proteinogenic amino acids are amino acids that are incorporated biosynthetically into proteins during translation. The word "proteinogenic" means "protein creating". Throughout known life, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard genetic code and an additional 2 that can be incorporated by special translation mechanisms
What complex(es) are associated with the following? Pumping a proton into the intermembrane space Acquiring electrons from NADH Acquiring electrons from FADH2 Having the highest reduction potential
Pumping protons: -Complex I, III, and IV. NADH: -Complex I FADH2: -Complex II Having the highest reduction potential: -Complex IV (reduction potentials increase along the ETC).
What is the overall reaction of the pyruvate dehydrogenase comlex?
Pyruvate + CoA-SH + NAD+ -> acetyl-CoA + CO2 + NADH + H+
What are the four enzymes unique to gluconeogenesis? What irreversible glycolytic enyzmes do they replace?
Pyruvate carboxylase: -replaces pyruvate kinase phosphoenolpyruvate carboxykinase (PEPCK or PEP carboxykinase): -pyruvate kinase Fructose-1,6-bisphosphatase: -Phosphofructokinase-1 Glucose-6-phosphatase: -Glucokinase
Hydrogen bonding and spatial configuration of a beta-pleated sheet
R groups point above of below the place
What are the three types of RNA polymerase? what are their functions? which one is involved in transcription of mRNA?
RNA polymerase I: -located in the nucleolus -synthesized rRNA RNA Polymerase II: -located in the nucleus -synthesizes hnRNA (pre-processed mRNA) and some small nuclear RNA (snRNA) RNA Polymerase III: -Located in the nucleus -Synthesizes tRNA and some rRNA
Respiratory Quotient (RQ)
RQ = VCO2/VO2 Normal: 0.8 Range: 0.67-1.3
What are the reactants and products of the pyruvate dehydrogenase complex?
Reactants: -Pyruvate, NAD+ and CoA Produts: -Acetyl-CoA, NADH and CO2
Action of Fatty Acid Synthase
Reactions include: -activation of the growing chain (a) and malonyl-CoA (b) with ACP. -bond formation between these activated molecules (c). -Reduction of a carbonyl to a hydroxyl group (d). -Dehydration (e). -Reduction to a saturated fatty acid (f).
palindromic
Reading the same in both directions; describes sequence identity along the paired strands of a duplex DNA molecule; a symmetry typical of restriction sites.
centromere
Region of a chromosome where the two sister chromatids attach
From 5' to 3' what are the components of the operon and what are their roles?
Regulator gene: -transcribed to form repressor protein Promoter site: -site of RNA polyermase binding (similr to promoters in eukaryotes Operator site: -Binding site for repressor protein Structural gene: -Gene of interest; its transcription is dependent on the repressor being absent from the operator site.
DNA polymerase I (prokaryotes)
Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides
Galactose-1-phosphate uridyltransferase
Responsible for converting Galactose-1-phosphate to Glucose-1-P Absence in this enzyme leads to *Classic Glactosemia* Much more severe than galactokinase deficiency - Failure to thrive, Jaundice, Hepatomegaly, *Infantile Cataracts*, Treatment: exclude galactose and *Lactose* (galactose+glucose) from diet. Phosphate deficiency occurs similar to fructose intolerance (aldolase B deficiency)
Retroviral Gene Therapy
Retrovirus picture was used here, but other viruses may also be used for gene therapy.
Triiodothyronine (T3)
Secreted by the thyroid gland; T3 increases metabolism in cells, more rapid than Thryoxine (T4)
Thyroxine (T4)
Secreted by the thyroid gland; also called tetraiodothyronine. T4 increases metabolism in cells, Less rapid but more long lasting than triiodothyronine (T3)
Serine
Ser, s Polar uncharged
side chain
Side chain is another name for an R group, and is a group of atoms attached to the main part of a molecule and having a ring or chain structure.
In an enhancer, what are the differences between signal molecules, transcription factors, and response elements?
Signal molecules include steroid hormones and second messengers, which bind to their receptors in the nucleus. These receptors are transcription factors that use their DNA-binding domain to attach to a particular sequence in DNA called a response element. Once bonded to the response element, these transcription factors can then promote increases expression of the relevant gene.
For each of the mutations listed, what changes in DNA sequence are observed? What effect do they have on the encoded peptide? Silent (degenerate) Missense Nonsense Frameshift
Silent (degenerate): -Substitution of bases in the wobble position or noncoding DNA -no change observed Missense: -substitution of one base, creating an mRNA codon that matches a different amino acid -One amino acid is changed in the protein; variable effect on function depending on the specific change Nonsense: -Substitution of stop codon for a base -early truncation of protein; variable effects on function, but usually more severe but usually more severe than missense mutations. Frameshift: -insertion or deletion of bases, creating a shit in the reading frame of the mRNA -change in most amino acids after the site of insertion and deletion; usually the most severe of the types listed here
How are the Michaelis-Menten and Lineweaver-Burk plots similar? How are they different?
Similarities: -Both MM and Lineweaver burk relationships account for the values of Km and Vmax under various conditions. They both provide simple graphical interpretations of these two variables and are derived from the michaelis-menten equation. Differences: -Axes of the graps and visual representation of information is different. -Michaelis-Menten plot is V vs. [S], which creates a hyperbolic curve for monomeric enzymes. -Lineweaver-burk plot is 1/V vs 1/[S[, which creates a straight line
Know the concentration gradient, if a membrane protein required, if energy is required, and examples of molecules transported for the following: Simple diffusion osmosis Facilitated diffusion Active Transport
Simple Diffusion -High to Low -No -No: passive process -small, nonpolar (O2, CO2) Osmosis: -Low to high (solute) -No -No: passive process -H2O Faciliated diffusion: -High to Low -Yes -No: passive process -Polar molecules (glucose) or ions (Na/Cl) Active Transport: -Low to High -Yes -Yes: Active process requiring energy -Polar molecules or ions (Na, Cl, K)
Okazaki fragments
Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.
What is the difference between a steroid and a steroid hormone?
Steroid: -defined by its structure; includes three cyclohexane rings and a cyclopentane ring. Steroid Hormone: -A molecule within this class that also functions as a hormone, meaning that it travels in the bloodstream, is active at low concentrations, has high-affinity receptors, and affects gene expression and metabolism.
disulfide bond
Strong chemical side bond that joins the sulfur atoms of two neighboring cysteine amino acids to create one cystine, which joins together two polypeptide strands like rungs on a ladder. -forming a disulfide bond requires the loss of two protons and two electrons, therefore an oxidation
Fluid Mosaic Model
Structural model of the plasma membrane where molecules are free to move sideways within a lipid bilayer.
Chromatin
Substance found in eukaryotic chromosomes that consists of DNA tightly coiled around histones
synthase vs synthetase
Synthetases: use ATP in the reaction Synthases: do not use ATP
Lipid Transport in Lipoproteins
TGL= triacylglycerol CE= cholesteryl esters chol= cholesterol
What is the function of a telomere?
Telomeres are the ends of eukaryotic chromosomes and contain repetitive sequences of noncoding DNA. These protect the chromosome from losing important genes from the incomplete replication of the 5' end of the DNA strand.
What it the ideal temperature for enzymes? (C, K, and F) ideal pH for enzymes? (blood, gastric, and pancreatic)
Temp: -98.6*F, 37*C, 310K pH: -blood = 7.4 -Gastric = 2 -Pancreatic = 8.5
What are the effects of temperature, pH, and salinity on the function of enzymes?
Temp: -Enzyme activity increases until you go above average body temperature, after which it decrease, pH: -enzymes have maximal small pH range, outside of range activity drops quickly as ionization of the active site changes, and protein denatures Salinity: -disrupts bonds within an enzymes, causing disruption of tertiary and Quaternary structure, leading to loss of enzyme function.
What are the definitions of tertiary and Quaternary structure, and how do they differ in subtypes and the bonds that stabilize them?
Tertiary Structure: -three-dimension shape of protein Subtypes: -hydrophobic interactions -acid-base/salt bridges -disulfide links Stabilizing bonds -van der Waals forces -hydrogen bonds -ionic bonds -covalent bonds Quaternary structure -interaction between separate subunits of a multisubunit protein -No subtypes Stabilizing bonds (same as tertiary) -van der Waals forces -hydrogen bonds -ionic bonds -covalent bonds
Disaccharide Formation
Th two monosaccharides in a disaccharide are connected by a glycosidic bond, the bond may be α or β as in cyclic monosaccharides, the structures include glycosidic bond that create a 1,4 link between C1 of one monosaccharide and C4 of the second monosaccharide The naturally occurring disaccharides are maltose, lactose, and sucrose
sugar-phosphate backbone
The backbone of DNA and RNA; composed of alternating molecules of phosphate and ribose or deoxyribose sugar. -always read from 5'->3'. -formed as nucleotides are join by 3'-5' phosphodiester bonds. Phosphate group links the 3' carbon of one sugar to the 5' phosphate group of the next incoming sugar in the chain. -have an overall negative charge b/c of phosphates. -5' end of DNA will have an -OH or phosphate group bonded to C-5' of the sugar -3' end has a free -OH on C-3' of the sugar -DNA sequences must be written 5'-ATG-3' -Written backwards: 3'-GTA-5'
peptide bonds
The bonds connecting amino acids together to form polypeptide chains. -lose of water, connects the -COO group of one amino acid to the NH3+ group of another.
Where does the bulk of protein digestion occur?
The bulk of protein digestion occurs in the small intestine
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.
mitochondrial matrix
The compartment of the mitochondrion enclosed by the inner membrane and containing enzymes and substrates for the Krebs cycle.
Carnitine acyltransferase I
The enzyme that is the rate-limiting enzyme of fatty acid oxidation
isoprene
The five carbon units that are joined together to form Vitamin A1.
substrate-level phosphorylation
The formation of ATP by directly transferring a phosphate group to ADP from an intermediate substrate in catabolism. -contrasts oxidative phosphorylation in mitochondria, which doesn't depend on oxygen.
quaternary structure
The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits. Ex: -Hemoglobin has a quaternary structure, myoglobin doesn't b/c only one subunit.
inner mitochondrial membrane
The inner mitochondrial membrane is the 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. -more resstricted permeability compared to the outer mitochondrial membrane
euchromatin
The less condensed form of eukaryotic chromatin that is available for transcription. -light under a microscope -actively transcribed
germ line
The lineage of reproductive cells that contributes to the formation of a new generation of organisms, as distinct from somatic cells, which form the body and leave no descendants in the next generation.
nontemplate synthesis (lipid and carbohydrate synthesis)
The method of de novo synthesis of lipids and carbohydrates that relies on gene expression and enzyme specificity rather than the genetic template of DNA or RNA
leading strand
The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.
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.
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.
What are the two potential drawbacks of affinity chromatography?
The protein of interest may not elute from the column b/c its affinity is too high, or it may be permanently be bound to the free receptor in the eluent.
Esterification
The reaction of an alcohol with a carboxylic acid to produce an ester and water.
secondary structure
The second level of protein structure; the regular local patterns of coils or folds of a polypeptide chain. -alpha helix or b-pleated sheet
ceramide
The simplest sphingolipid, with a single hydrogen as its head group.
Honeycomb stucture made from beeswax
The solid and plastic nature of waves, which contain esters with long alkyl chains, permits their use for structure building.
metastasis
The spread of cancer cells to locations distant from their original site, usually by blood stream or lymphatic system
feed-forward activation
The stimulation of an enzyme by an intermediate that precedes the enzyme in a metabolic pathway Ex: -in glycolysis, the activation of pyruvate kinase is activated by PFK-1, which is generated earlier in the process of glycolysis.
phosphorylation
The transfer of a phosphate group, usually from ATP, to a molecule. Nearly all cellular work depends on ATP energizing other molecules by phosphorylation.
How do solutes denature proteins?
They can disrupt tertiary and quaternary structures by breaking disulfide bridges, reducing cystine back to two cysteine residuces. They can even overcome H-bonds and other side chain interactions -detergents such as SDS can solubilize proteins, disrupting noncolvanet bonds and promoting denaturation
Are amino acids found eukaryotes D- or L- isomers?
They're L-isomers
vitamin b1, b2, b3, b5, b6, b7, b9, b12
Thiamine Riboflavin Niacin Pantothenic Acid pyridoxal phosphate biotin folic acid cyanocobalamin
Threonine
Thr, T Polar uncharged
Vitamin E
Tocopherol, serves as an antioxidant to the body
What is the difference between a transgenic and knockout mouse?
Transgenic: -Have a gene introduced into their germ line or embryonic stem cells to look at the effects of the gene on the mouse. Therefore they are the best suited for studying the effect of dominant alleles Knockout: -Have a gene of interest removed, rather than added.
What are some examples of transient and covalent enzyme modifications?
Transient: -allosteric activation or inhibition Covalent -phosphorylation, dephosphorylation, glycosylation
How do transport kinetics differ from enzyme kinetics?
Transport kinetics display both Km and Vmax values. They also can be cooperative, like some binding proteins. However, transporters do not have analogous Keq values for reactions b/c there is no catalysis
Which enzyme is responsible for trapping fructose in the cell? What enzyme in fructose metabolism results in a product that can feed directly into glycolysis, linking the two pathways? "trapping" enzyme: "linking" enzyme:
Trapping: -Fructose is phosphorylated by fructokinase, trapping it in the cell (small contribution from hexokinase) Linking: -Aldolase B produces dihydroxyacetone phosphate (DHAP) and glyceraldehyde (which can be phosphorylated for form glyceraldehyde 3-phosphate) whcih are glycolytic intermediates, thus linking the pathways.
Which enzyme is responsible for trapping galactose in the cell? What enzyme in galactose metabolism results in a product that can feed directly into glycolysis, linking the two pathways? "trapping" enzyme: "linking" enzyme:
Trapping: -Galactose is phosphorylated by galactokinase, "trapping" it Linking: -Galactose-1-phosphate uridyltransferase produces glucose-1-phosphate, a glycolytic intermediate, thus linking the pathwyas
Tyrosine
Tyr, Y aromatic R groups
Stop codons for translation
UAA, UAG, UGA -signals the end of the coded message
Mnemonic for remember the stop codons:
UAA- U Are Annoying UGA- U Go Away UAG- U Are Gone
pKa value for carboxyl amino acids
Usually around ph of 2
valine
Val, V, nonpolar aliphatic
Structure of an Antibody molecule
Variable region (top): 1. Forms the antigen binding sites. 2. Complementary to a particular antigen. Hinge region: 1. Allows flexibility when the antibody binds to the antigen. Constant region (bottom): 1. Has the same sequence of amino acids in all antibodies. 2. Disulphide bridges hold the polypeptide chains of the proteins together.
What is wobble, and what role does it serve?
Wobble refers to the fact that the third base in a codon often plays no role in determining which amino acid is translated from that codon. Ex: -any codon starting with CC codes for proline regardless of which base is in the third "wobble" position, so this is protective b/c mutations in the wobble position will not have any effect on the protein translated from that gene.
Structure of a Glycerophospholipid
X denotes the head group connect to the glycerol backbone by a phosphodiester linkage
What do the x and y intercepts in a Lineweaver-Burk plot represent?
X-intercept: -represents -1/Km y-intercept -1/Vmax
Why are some enzymes released as enzymes?
Zymogens are precursors of active enzymes. It is critical under certain enzymes (like the digestive enzymes of the pancreas) remain inactive until arriving at their target site, where they will then become active.
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
What is the effects of increasing [S] on enzyme kinetics? what about increasing [E]?
[S]: -when [S] is low, an increase in [S] causes a proportional increase in enzyme activity. At high [S], when the enzyme is saturated, increasing [S] has no effect on activity b/c Vmax has already been attained. [E] -increasing [E] will always increase Vmax, regardless of the starting concentration of enzyme.
alpha-anomer
[carbohydrate structure and function] -OH on anomeric carbon trans to functional group -trans to the -CH2OH substrate
UV spectroscopy
[spectroscopy] involves passing uv light through a chemical sample and plotting absorbance v wavelength.
Bicinchoninic Acid (BCA) Assay
a biochemical assay for determining the total concentration of protein in a solution (0.5 μg/mL to 1.5 mg/mL), similar to Lowry protein assay, Bradford protein assay or biuret reagent. The total protein concentration is exhibited by a color change of the sample solution from green to purple in proportion to protein concentration, which can then be measured using colorimetric techniques.
retinal
a chemical synthesized from vitamin A; joins with an opsin to form a photopigment -component of the light-sensing molecular system in the human eye.
column chromatography
a column is filled with silica of alumina beads as an absorbent, and gravity moves the solvent and compounds down the column. -as solution flows through, both size and polarity have a role in determining how quickly a compound moves through the polar silica or alumina beads: -less polar compound, the faster it can elute.
splicesome
a complex of specialized RNA and protein subunits that removes introns from a transcribed pre-mRNA segment.
phosphate ester
a compound formed by reaction of an alcohol with phosphoric acid
glycosidic linkage
a covalent bond formed between 2 monosaccharides by a dehydration reaction
phospholipids
a lipid consisting of a glycerol bound to two fatty acids and a phosphate group.
phospholipids
a lipid consisting of a glycerol bound to two fatty acids and a phosphate group. Polar head: -phosphate and an alcohol hydrophobic tail: -joiny bed to a hydrophobic fatty acid tail by phospodiester bonds. One or more fatty acids are attached to a backbone to form the hydrophobic tail region.
glycolipid
a lipid with one or more covalently attached carbohydrates
Liposome
a minute spherical sac of phospholipid molecules enclosing a water droplet, especially as formed artificially to carry drugs or other substances into the tissues.
colloid
a mixture consisting of tiny particles that are intermediate in size between those in solutions and those in suspensions and that are suspended in a liquid, solid, or gas.
deoxy sugar
a monosaccharide produced by replacement of an OH group by H Ex: -d-2-deoxyribose, carbohydrate found in DNA
second messenger cascade
a multistep process that couples activation of a neurotransmitter receptor to activation of intracellular enzymes
termination factors
a protein that triggers the release of a polypeptide from a ribosome
EcoRI
a restriction enzyme that specifically cuts DNA with sequence GAATTC and creates sticky ends
lariat structure
a ring of intron segments that has been spliced out of a messenger ribonucleic acid molecule by enzymes
Recombinant vector
a vector that contains an inserted fragment of DNA, such as a gene from a chromosome. -vectors are usually bacterial or viral plasmids that can be transferred to a host bacterium after instertion of the DNA of interest -Usually grown in colonies, colony containg recombinant vector is isolated from colony by exposing the colony to an antibiotic since recombinant usually has a gene for the specific antibiotic resistance. -Bacteria can then be made to express the gene of interest or lyses to reisolate the replicated recombinant vectors.
postprandial state
absorptive state well fed state occurs shortly after eating marked by greater *anabolism* - synthesis of molecules usually lasts three to five hours after a meal blood glucose releases insulin insulin targets the liver, adipose tissue and muscle insulin promotes glycogen synthesis in the liver and muscle once glycogen stores are filled, the liver converts the excess glucose to fatty acids and triglycerides insulin promotes triglyceride synthesis in adipose tissue and protein synthesis in muscle also allows glucose to enter both tissues liver energy needs are met by oxidation of excess amino acids nervous tissue and RBC are insensitive to insulin nervous tissue gets it energy from oxidizing glucose to CO2 and water RBC use glucose anaerobically for all their energy needs
Irreversible inhibition
active site is made unavailable for prolonged period of time or enzyme is permanently altered -this type of inhibition is not easily overcomed or reversed.
carboxylation
addition of carboxylic acid groups, usually to serve as calcium-binding sites
prenylation
addition of lipid groups to certain membrane-bound enzymes
glycosylation
addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination
Pentose Phosphate Pathway (PPP)
aka "hexose monophosphate shunt (HMP)", occurs in the cytoplasm of most cells, generates NADPH and sugars for biosynthesis (derived from ribulose-5-phosphate) Two major functions: 1: production of NADPH 2: Source of ribose 5-phosphate for nucleotide synthesis
Describe key structural features of the alpha-helix and beta-pleated sheets
alpha helix: -rodlike structure in which the peptide chain coils clockwise around a central axis. H-bonding every 4th residue from carbonyl oxygen and amide hydrogen every 4th amino acid beta pleated sheet: -peptide chains lie alongside another, forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogens in an adjacent chain.
Starch
alpha-linked chains of glucose
omega-3 family
alpha-linolenic acid is the primary precursor of the omega-3 family.
Peptide Residues
amino acid subunites
retention time
amount of time a compound spends in stationary phase
What are the two forms of starch?
amylose (linear) and amylopectin (branched)
Retinol
an active, alcohol form of vitamin A that plays an important role in healthy vision and immune function.
Micelle
an aggregate of molecules in a colloidal solution, such as those formed by detergents.
Kinase
an enzyme that catalyzes the transfer of a phosphate group from ATP to a specified molecule. Ex: -Hexokinase, adds a phosphate to glucose in the first step glycolysis
Nernst equation
an equation predicting the voltage needed to just counterbalance the diffusion force pushing an ion across a semipermeable membrane from the side with a high concentration to the side with a low concentration
linoleic acid (18:2 all-cis-9,12,15)
an essential polyunsaturated fatty acid of the omega-6 family
Enzyme activity, velocity, enzyme rate
are all synonymous terms on MCAT
DNA polymerases beta and epsilon
are important to the process of DNA repair
oligopeptides
chains of fewer than 20 amino acids
point mutations
changes in a single nucleotide pair of a gene
leak channels
channels that are always open and allow ions to move along their gradient
bile salts
cholesterol derivatives that function in fat emulsification and absorption
alpha-amylase
cleaves randomly along the chain to yield shorter polysaccharide chains, maltose, and glucose
agglutinating
clumping together the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages
what are the four types of reversible inhibition
competitive, noncompetitive, mixed, uncompetitive
feedforward regulation
effectors prepare the body for an anticipated challenge to homeostasis before the challenge is even felt
How many d- stereoisomers are there of glucose?
eight total 2^3= 8 b/c 3 chiral carbons.
Pinocytosis
endocytosis of a fluids and dissolved particles
acetals
formed when hemiacetals react with alcohol the anomeric hydroxyl group is transformed into a alkoky 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)
What is the rate-limiting enzyme of gluconeogenesis?
fructose-1,6-biphosphatase
oncogenes
genes that cause cancer by blocking the normal controls on cell reproduction
counterregulatory hormones
glucagon cortisol epinephrine norepinephrine growth hormone have the opposite effects of insulin
sucrose
glucose + fructose -(glucose-alpha-1,2-fructose)
Lactose
glucose + galactose - (galactose-beta-1,4-glucose)
maltose
glucose + glucose - (glucose-alpha-1,4-glucose)
What are the roles of the three main types of RNA?
mRNA: -carries information from DNA by traveling from the nucleus (where it was transcribed) to the cytoplasm (where it is translated) tRNA: -Translate nucleic acids to amino acids by pairing its anticodon w/ mRNA codons -it is charged with an AA, which can be added to the growing peptide chain. rRNA: -forms much of the structural and catalytic component of the ribosome, and acts as a ribozyme to create peptide bonds between amino acids.
Structure of amylopectin
made of many 1,4 linked a-glucose molecules, but the chains are shorter than in amylose, and branch out to the sides. The branches are formed by 1,6 linkages.
excision endonuclease
makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligonucleotide.
Magnetic resonance spectroscopy
maps the distribution of elements other than hydrogen to reveal more about how disease changes body chemistry.
vmax
maximum initial velocity or rate of an enzyme-catalyzed reaction. -only way to increase vmax is to increase the enzyme concentration. In cell, this can be accomplished by inducing the expression of the gene encoding the enzyme.
ApoB-48
mediates chylomicron secretion
tocopherols
members of the vitamin E family having the chemical structure of a complex ring structure with a long saturated side chain
tocotrienols
members of the vitamin E family having the chemical structure of a complex ring structure with a long unsaturated side chain
Polyacrylamide gel electrophoresis (PAGE)
method for analyzing proteins in their native states; compare molecular size or charge of proteins
What are the three most biologically important polysaccharides?
starch, cellulose, and glycogen.
occluded state
state in which the carrier is not open to either side of the phospholipid bilayer
Diastereomers
stereoisomers that are not mirror images of each other
ligand-binding domain
stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain
Structure of glycogen
straight chain of alpha-glucose (1,4-glycosidic bond) with side branches (1,6-glycosidic bond)
solvation layer
the layer of solvent particles that interacts directly with the surface of a dissolved species
Goldman-Hodgkin-Katz equation
the membrane potential that results from the contribution of all ions that can cross the membrane
substrate
the molecule being acted upon by an enzyme
immunoglobulin G
the most abundant class of antibodies; found in blood serum and lymph; active against bacteria, fungi, viruses, and foreign particles.
anomeric carbon
the new chiral center formed in ring closure; it was the carbon containing the carbonyl in the straight-chain form
daughter strands
the newly made strand in DNA replication
feedback regulation
the output or product of a process regulates that very process
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 ?G°'= -30kj/mol
DNA sequencing
the process of determining the precise order of nucleotides within a DNA molecule -uses dideoxyribonucleotide -contains a hydrogen at C-3' rather than hydroxyl, so polymerase cannot add to the chain, so sample will contain many fragments, each of which terminates with one of the modified bases, which are then exposed to gel electrophoresis, last base for each fragment can be read, and because gel electrophoresis separates the strands by size, the bases can easily be read in order.
basal metabolic rate (BMR)
the rate at which the body burns energy when the organism is resting
Glucose-6-phosphate dehydrogenase
the rate-limiting enzyme in the pentose phosphate pathway, the major source of NADPH, which is necessary to reduce glutathione but also the biosynthesis of cholesterol, fatty acids, and steroids. -activated by NADP+ and insulin -inhibited by NADPH
elute
the sample running through the stationary phase
antisense strand (template)
the strand of DNA that runs 3' to 5' and is complementary to the sense strand. It acts as a template strand during transcription.
antigens
the targets of antibodies
ATP cleavage
the transfer of a high-energy phosphate group from ATP to another molecule, generally activating or inactivating the target molecule.
Hormone Sensitive Lipase (HSL)
• Enzyme in the adipose cell that is responsible for the hydrolysis of triglyceride into free fatty acids (FFAs) and glycerol, which then leave the adipose cell and enter circulation. -glycerol from fat may be transported to the liver for glycolysis or gluceneogenesis -activated by epinephrine and cortisol • Inhibited by the hormone insulin
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 -adds a fatty acid to choplesterol, producing soluble cholesteryl esters such as those in HDL, which can then be distrubited to other lipoproteins like IDL, which becomes LDL by acquiring these cholesteryl esters. -The above process is faciliated by Cholesteryl ester transfer protein (CEPT)
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 -further classified into cerebrosides and globosides