Biochemistry Flashcards
Amphoteric
a molecule can act as an acid or base because it can either accept or donate a proton
Zwitter ion
a overall neutral molecule, but has positive and negative groups . They are called dipolar ions
Isoelectric point (pI)
The pH at which the molecule is electrically neutral
pI = (pKa(amino) + pKa(carboxy)) / 2
pI (acidic AA) = (pKa(carboxyl)+pKa(side chain)) / 2
pI (basic AA) = (pKa(amino)+pKa(side chain)) / 2
Peptide
Composed of amino acid subunits (residues). There can be dipeptides, tripeptides, oligopeptides (up to 20), or polypeptides.
Peptide bonds
Links residues between the -COO of 1 AA and the N of another AA. It is hard to denature them with heat, unlike secondary, tertiary, and quaternary structure. Their formation is a condensation or dehydration reaction because its results in the removal of a water molecule
Chymotrypsin
Hydrolytic enzyme that cleaves peptide bonds next to large hydrophobic amino acids
Antiparallel
When strands are running in opposite directions. It is more stable
Common beta turns
Proline and Glycine, in position 2 and 3
Tertiary structure
Overall spatial arrangement of atoms in a polypeptide chain or in a protein, the arrangement of secondary structure. Makes up the active site! Ex/ disulfide bridges
Solvation layer
Formed when solvent molecules form around a solute when a solute dissolves in the solvent. If hydrophobic side chains are placed in aqueous solution, water molecules can not interact with the side chain and are forced to arrange themselves in organized fashion to maximize H bonds. This decreases entropy (non-spontaneous process)
Quarternary structure
Aggregate of subunits (smaller globular proteins). Ex/ hemoglobin and immunoglobulin
Conjugated proteins
Proteins with covalently attached prosthetic groups
Ex/ carbohydrate, nucleic acid, lipid, vitamins, metal ions
Lipoproteins
lipid prosthetic groups
Glycoproteins
carbohydrate prosthetic groups
Nucleoproteins
nucleic acid prosthetic groups
Association rule
Groups of similar polarity tend to group together. This interaction between side chains is what influences the tertiary structure of a protein
Competitive inhibition
Inhibitors that bind the active site and prevent substrate access. Increase Km (cause the [S] to be higher in order to reach Km) and do no effect Vmax. Can only be overcome with the addition of more [S]
Noncompetitive inhibition
Allosteric inhibitors that induce a conformation change in the enzyme when binding. Do not alter Km (any copies of the enzyme that are active maintain the same affinity) and decrease Vmax (less [E] available to react). Adding more [S] has no effect. Only adding more [E] overcomes the inhibitor
Mixed inhibition
Allosteric inhibitors that can either increase Km if bound to free enzyme or decrease Km if bound to the ES complex, depending on the affinity for each. They decrease Vmax. They cause less [E] to be available to react
Uncompetitive inhibition
Allosteric inhibitors that decrease the Km and decrease Vmax. They lock the ES complex and dont allow the formation of P
Irreversible inhibition
When the active site is made unavailable for a prolonged period of time, or the enzyme is permanently altered
Zymogens
Enzymes that are secreted in inactive forms
Binding proteins
They have the ability to transport substances that are otherwise insoluble. They can regulate gene transciption but do not have enzymatic activity @ active site
Enzyme
Lower activation energy, increase reaction rate, do not alter Keq, are not consumed in the reaction, are pH and temperature sensitive, and do not effect ΔG
Lyase
Enzymes that cleave a molecule into 2 products
Synthase
A lyase that can catalyze the synthesis of 2 molecules into a single molecule
Isomerase
Enzymes that catalyze the rearrangement of bonds within a molecule
Ligase
Enzymes that catalyze addition or synthesis reactions
Hydrolase
Enzymes that catalyze the breaking of a compound into 2 molecules using the addition of water.
Ex/ phosphatase, peptidase (protease), nuclease, lipase
Phosphatase
A type of hydrolase that cleaves a phosphate group
Oxidoreductase
Enzymes that catalyze redox reactions (transfer of e- between molecules)
Transferase
Enzymes that catalyze the movement of a functional group between molecules
Ex/ aminotransferase in protein metabolism
Kinase
a type of transferase that catalyze the transfer of phosphate groups
Mutase
a type of transferase that moves a functional group
Substrate
the molecule that the enzyme acts upon
Apoenzyme
enzymes without their cofactors
Holoenzyme
enzymes with their cofactors
Prosthetic groups
Cofactors or coenzymes that determine (permit) the function of proteins. They are tightly bound and can direct a protein to be delivered to a specific location. Ex/ heme, glycoproteins, lipoproteins, nucleoproteins
Cofactors
Inorganic molecules or ions that help an enzyme carry out its function (like carrying charge through ionization, protonation, or deprotonation) Ex/ ingested dietary minerals
Coenzymes
Organic molecules that help an enzyme carry out its function (like carrying charge through ionization, protonation, or deprotonation) Ex/ vitamin derivatives like NAD, FAD and CoA
Vmax
The maximum velocity of an enzyme when it reaches saturation. All active sites are filed. The only way to increase Vmax is to increase [E]
Michaelis-Menten equation
Describes how the rate of reaction (v) depends on [E] and [S] which forms the products [P]. It is a measure of enzyme-substrate affinity.
v = vmax[S] / Km + [S]
Michaelis constant, Km
the [S] when the enzymes active sites are 1/2 full. It is a measure of enzyme affinity for the substrate. High Km = low affinity
Turnover number, Kcat
the number of substrate molecules converted into product per enzyme molecule per second
Catalytic efficiency
This is how enzyme efficiency is measured
= kcat/Km
Lineweaver-Burk plots
Double reciprocal plot of the Michaelis-Menten equation that is used to better visualize the values of the MM equation because it plots them as a strait line
1/V = Km/Vmax( 1/[S] ) + 1/Vmax
X-intercept = Km
Y-intercept = 1/Vmax
Cooperativity (enzymes)
Binding of a substrate to an enzyme encourages the transition from the low affinity tense state (T state) to the high affinity relaxed state (R state).
Hill’s coefficient
The numerical value of cooperativity
HC > 1 = (+) cooperative binding
HC < 1 = (-) cooperative binding
Collagen
Structural protein that contains cross linked triple helices. Makes up most of the ECM
Elastin
Structural protein that stretches and recoils within the ECM
Keratin
Intermediate filament in epithelial cells. Ex/ hair
Actin
Structural protein that makes up microfilaments and thin filaments in myofibrils. They have a (+) and (-) pole which allows them to travel unidirectionally
Tubulin
Structural protein that makes up microtubules. Important when separating chromosomes and intracellular transport with kinesin and dynein
Myosin
Primary motor protein (power stroke in sarcomere contraction). Thick filament in myofibril
Kinesin
Motor protein that aligns chromosomes in metaphase. Transports vessels along microtubule via anterograde transport (away from cell body)
Dynein
Motor protein that is involved in sliding movement of cilia and flagella. Transports vessels along microtubules to via retrograde transport (toward the cell body)
Cadherins
Cell adhesion proteins that mediate Ca dependent cell adhesion. They hold similar cell types together
Integrins
Cell adhesion proteins with membrane spanning chains. Important for binding/communicating w/ the ECM and white blood cell migration
Selectins
Cell adhesion proteins that bind to carbohydrate molecules. They are expressed on WBC and endothelial cells of blood vessels. Important for inflammation (immune function) and WBC migration
Opsonization
marking an antigen for destruction
Agglutination
clumping of antigens into insoluble protein complexes to get eaten my macrophages
Facilitated diffusion
passive transport of molecules (charged particles) down a concentration gradient through a pore created by a transmembrane protein
Ungated channels
unregulated channels (always open). Free movement of particles until equilibrium is achieved. Ex/ K channels
Voltage gate channels
regulated by the membrane potential. Opened during depolarization or whenever the voltage changes. Ex/ Na/K channels in the SA node
Ligand gated channels
the binding of a ligand to a channel causes it to open or close. Ex/ GABA, glycine, serotonin
Homogenization
crushing, grinding, or blending a tissue of interest into an evenly mixed solution
Electrophoresis
Subjecting compounds to an electric field which will move them according to their charge (towards the anode or cathode) and size (larger molecules move slower)
SDS-PAGE
Method used to separate proteins based on charge to mass ratio while also linearizing the proteins. Used in gel electrophoresis of proteins (not nucleic acids) to denature proteins and coat them with a uniform charge, so the electrophoresis depends on size alone. Measured in daltons (1 Da = 1 g/mol)
Isoelectric focusing
Seperating proteins by their isoelectric point (pI) by placing them in a gel with a pH gradient. Proteins that are (+) charged will move towards the (-) cathode and (-) charged proteins move towards the (+) anode
Southern blot
used for identifying specific sequences of DNA
Northern blot
used to detect specific sequences of RNA using hybridization of complementary DNA
Western blot
Used to identify specific sequences of amino acids in proteins. A larger band indicates increased protein expression
Glycosidic bond
bond between the anomeric and hydroxyl carbon
D and L classifications
Stereochemistry of a carbohydrate is dictated by the chiral center farthest from the carbonyl carbon. All D-sugars have the hydroxide of their highest numbered chiral center on the right. All L sugars have it on the left. Only L amino acids exist in cells
Enantiomers
Stereoisomers that have the same chemical formula but are stereoisomers with non-superimposable mirror images. They have chiral centers with opposite S and R designations
Diastereomers
Stereoisomers that are not identical mirror images.
These are 2 molecules that differ at 1 or more chiral centers
Epimers
Differ in configuration at only one chiral center. Ex/ glucose and galactose
Anomer
An epimer at the hemiacetal/ketal carbon or the anomeric carbon
Anomeric carbon
formed from the carbonyl that is attacked by the nucleophilic alcohol intramolecularly
Hemiacetal
1 OR group, 1 OH group, 1 R group, and a H bound to it
Hemiketal
1 OR group, a OH group, and 2 R groups attached to it
Acetal
2 OR groups, a R group, and a H bound to it
Ketal
2 OR group and 2 R groups
Carbohydrate β configuration
when the OH- group on the anomeric carbon and the CH2OH group are both above or below the plane of the sugar (cis)
Carbohydrate α configuration
when the OH- and CH2OH group are on opposite sides of the plane (trans)
Mutorotation
Spontaneous change in configuration around C1. The OH- group on the anomeric carbon of the hemiacetal within a glycosidic bond can rotate from the α or B config
Aldonic acids
An oxidized aldose. Strait chain carboxylic acids formed from the aldehyde when there is a shift between α and β configurations
Tollen’s reagent
used to detect sugars
Benedict’s reagent
oxidizes the aldehyde of an aldose and produces a precipitate Cu₂O
Tautomerization
rearrangement of bonds in a compound, usually moving a H and forming a double bond
Alditol
when an aldose aldehyde is reduced to an alcohol
Deoxy sugar
when a H replaces a hydroxyl group on the sugar
Esterification
Formation of esters that occurs when hydroxyl groups of carbohydrates participate in reactions with carboxylic acids and their derivatives
Glycoside
formed from a glycosidic bond between two acetals
Furanosides
glycosides formed from furanose rings (5 membered ring)
Pyranosides
glycosides formed from pyranose rings (6 membered ring)
Homopolysaccaride
polysaccharide composed entirely of 1 monosaccharide
Heteropolysaccaride
polysaccharide composed of more than 1 monosaccharide
Glycerophospholipids
Contain a glycerol backbone bounded by ester linkages to one saturated fatty acid on the C1 and an unsaturated fatty acid on the C2, and a phosphodiester linkage on C3 to a polar head group. The head group is at the surface of membranes and is important for signaling, cell recognition, and binding. These are named by their head group
Amphipathic
A molecule that contains hydrophobic and hydrophilic regions
Sphingolipids
Contain a sphingosine backbone, long chain nonpolar fatty acid tails connected by amide linkages, and polar head groups. Ex/ cell surface antigens on RBC
Spingosine
Backbone of sphingolipids. It is an amino alcohol (secondary alcohol/*amide bond/ether attached to head group)
Glycospingolipids
Also called glycolipids, they are sphingolipids with sugar head groups bound by glycosidic linkages. Found mainly on the outer surface of the plasma membrane.
Gangliosides
Glycosphingolipids with polar head groups composed of oligosaccharides, *sialic acid (N-acetylneuraminic acid), and a negative charge. Play a role in cell interaction, recognition, and signal transduction
*Sialic acid distinguishes gangliosides from globosides
Wax
Esters of long chain saturated/unsaturated fatty acids with long chain alcohols
Cholesterol
Steroid that is an amphipathic molecule that maintains the constant fluidity of the membrane. At low temp, it prevents the membrane from solidifying. At high temp, it prevents the membrane from becoming to permeable
Prostaglandins
Regulate the synthesis of cAMP. Downstream effects include effects on smooth muscle function, influence on the sleep-wake cycle, and elevation of body temp. They act as vasodilators and inhibit platelet formation
Vitamins
Nutrients that can not be synthesized by the body. They are either water soluble (excreted in urine) or fat soluble (accumulate in fat)
Vitamin A
Carotene. Important for vision, growth, and immune function
Vitamin D
Consumed or formed in a UV light reaction in the skin. It is used for calcium regulation
Vitamin E
Antioxidants (lipids called tocopherols and tocotrienols, the aromatic ring interacts with free radicals and destroys them)
Vitamin K
Important for post-translational modification of prothrombin (blood clotting factor for coagulation)
*K is for Koagulation
Triacylglycerols
Composed of 3 fatty acids bonded by ester linkages to glycerol. Used to store energy as adipocytes
Free fatty acids
circulate in the blood bonded non-covalently to serum albumin
Saponification
Ester hydrolysis of triglycerides using a strong base (NaOH, lye). It results in the cleavage of the fatty acid -> glycerol and the salt of the fatty acid
Nucleotide
Base with a pentose and phosphate group
Nucleoside
Base with a pentose group
Histones
proteins that come together to form nucleosomes
Nucleosomes
bead-like, primary structure of chromatin
Heterochromatin
chromatin that remains compacted during interphase. It appears dark and is transcriptionally silent (genetically inactive DNA)
Euchromatin
appears light and contains genetically active DNA
Telomere
repeating unit at the end of DNA (TTAGGG). Their high GC content has strong attractions that prevent unraveling. They shorten after every round of replication
Centromere
located within the chromosome. Sometime centrally, sometimes not. Breaking point of chromosomes
Helicase
unwinds DNA
ssDNA binding proteins
bind to unraveled strand and prevents reassociation and degredation by nucleases
Topoisomerase
works ahead of helicase and introduces negative supercoils by relaxing the torsional pressure. Reseals the cut strands afterwards
Semiconservative
1 parental strand is retained in each of the resulting strands
DNA glycosylase
Used in base excision repair. Removes bases by cleaving the N-glycosl bond and forms an apurinic/apyrimidinic site (AP, abasic site)
Restriction enzymes
used prior to electrophoresis to cut DNA into pieces by cleaving specific sequences (recognize palindromic sequences)
Palindromic sequences
The 5’ to 3’ sequence of one strand is the same as the 5’ to 3’ sequence of the antiparallel strand (2 complementary strands that have the same sequence)
Genomic libraries
contain large fragments of DNA and include both coding (exon) and noncoding (intron) regions of the genome
Hybridization (DNA)
Joining of complementary base pair sequences. Can be DNA-DNA or DNA-RNA recognition
Polymerase chain reaction (PCR)
When you have a DNA region of interest, you use specific primers that are complementary to the DNA and flank the region on both sides in order to produce multiple copies of DNA. Used to amplify DNA sequences present in a sample
Restriction fragment length polymorphisms
Variations in the length of restriction fragments. They are the most reliable and accessible way to compare DNA using electrophoresis
Dideoxyribonucleotide
modified base that contains a H at C3 rather than a hydroxyl. When incorporated in strands, the fragments will terminate at those modified bases making it easier to read the bases in order after a gel electrophoresis
Gene therapy
if a gene is mutated or inactive (giving rise to pathology), it can be replaced with a normal copy of the gene
Prokaryote ribosome
30s and 50s (70s)
Eukaryote ribosome
40s and 60s (80s)
Ribozyme
Enzymes made of RNA molecules instead of peptides
Stop codons
UAA, UAG, UGA
Point mutation
Affecting 1 nucleotide in a codon. They are called expressed mutations because they effect the primary sequence of the AA
Missense mutation
Point mutation where 1 AA substitutes for another
Nonsense mutation
Point mutation where the codon encodes for a premature stop codon
Frameshift mutation
when a number of nucleotides are added or deleted from the mRNA sequence
Template strand
The antisense strand. One of the 2 unwound DNA strands used for transciption
Coding strand
The sense strand. Complementary to the template strand and identical to the mRNA transcript (except all T’s are U’s)
Introns
Non-coding sequence
Exons
Coding sequences
Alternative splicing
When the primary transcript of the hnRNA is spliced together in different ways to produce variants of proteins encoded by the same gene
Chaperones
Assist in the protein folding process which is necessary for the final product. They also inhibit the formation of nonprotein aggregates
Phosphorylation
addition of a phosphate group by kinases to activate or deactivate proteins
Glycosylation
addition of oligosaccharides as proteins pass through the ER and Golgi to determine their destination
Operon
A cluster of genes transcribed as a single mRNA. They contain structural genes, an operator site, a promotor site, and a regulatory gene
Structural gene
Site on the operon that codes for a protein of interest
Operator site
Site on the operon upstream of the structural gene. Capable of binding a repressor protein. It is non-transcribable
Promotor site
Site on the operon upstream of a operator site where RNA polymerase binds
Regulator gene
Site on the operon upstream of a promotor site. Codes for a repressor protein which can inhibit transciption
Inducible system
Type of operon where a repressor is bound to the operator site and RNA pol is not able to start transciption (negative control mechanism). This is overcome when an inducer binds the repressor. Genes are produced when needed
Lac operon
Inducible system that is used when lactose is high and glucose is low (because it is more energetically expensive to digest lactose). The structural gene codes for lactase
Repressible system
allow the constant production of a protein product. It is active until bond by a repressor at the operator site (negative feedback)
Enhancer
response elements outside the normal promotor region that allow for control of gene expression by binding to receptors on the DNA strand
Histone acetylation
acetylation of histone proteins decreases the (+) charge on Lys residues and weakens the interaction with DNA which allows the chromatin to open up and allow easy access for transciption
Flippase
enzyme that catalyze transverse diffusion of lipids from the outside to the inside of a membrane
Cell adhesion molecules
proteins that allow cells to recognize each other and contribute to proper cell differentiation
Gap junctions
Allow for direct communication. Also called connexons. Permit the movement of water and some solutes
Tight junctions
prevent solutes from leaking into the space between cells by a paracellular route. They form a continuous band around the cell
Desmosomes
bind adjacent cells by anchoring to their cytoskeleton. Interaction between transmembrane proteins and intermediate filaments
Hemidesmosomes
attach epithelial cells to underlying structures like the basement membrane
Hypotonic
when the concentration of solutes inside the cell is greater than outside
Hypertonic
when the concentration of solutes outside the cell is greater than inside
Resting potential of cell
between -40 and -80 mV
Hexokinase
converts glucose into glucose 6-phosphate. Phosphorylation prevents glucose from crossing the membrane
PFK-1
phosphorylates fructose 6 phosphate —> fructose 1,6 bisphosphate using ATP
PFK-2
converts fructose 6 phosphate —> fructose 2,6 bisphosphate. F2,6-BP activates PFK-1
G3P DHase
converts G3P —> 1,3 bisphosphoglycerate using NAD (oxidation rxn)
Phosphoglycerate kinase
converts 1,3 bisphosphoglycerate —> 3 phosphoglycerate using ADP
Pyruvate kinase
converts phosphoenolpyruvate —> pyruvate using ADP
Lactate dyhygrogenase
reduces pyruvate into lactate using NADH (oxidized to NAD)
Pyruvate DHase complex
Converts pyruvate into acetyl CoA if ATP is needed or for fatty acid synthesis if ATP is sufficient. Uses CoA-SH and NAD+. CO2 is lost
Glycogen
Branched polymer of glucose that is stored in the cytoplasm as granules in the liver and skeletal muscle
Isoforms
different versions of the same protein
NADPH
used for lipid and cholesterol (steroid hormone precursor) biosynthesis
The Cori cycle
Conversion of lactate into glucose for use in muscles
β-Oxidation
Breakdown of fatty acids and occurs in the mitochondria. Fatty acyl CoA can be converted to Acetyl CoA or ketone bodies (primary method). Each round generates 1 FADH2 and NADH
Hormone sensitive lipase
hydrolyzes triacylglycerols in adipose tissue and yields fatty acids and glycerol. It is released when insulin levels are low (like at night)
Lipoprotein lipase
Necessary for the metabolism of chylomicrons and VLDL. It can release triacylglycerols in lipoproteins
Very low density lipoproteins (VLDL)
Produced in liver cells. High triacylglycerol to protein ratio. Transports triacylglycerols and fatty acids to tissues.
Low density lipoproteins (LDL)
Delivers cholesterol into cells
High density lipoproteins (HDL)
“good cholesterol”. It picks up cholesterol accumulating in blood vessels. Synthesized in the liver and released into the blood
Apoproteins
The protein component of lipoproteins. They are receptor molecules and are involved in signaling
Fatty acid synthase
converts malonyl CoA into palmitate (16C)
Ketone bodies
Converted from acetyl CoA into acetoacetate or β-hydroxybutyrate+ acetone after fasting
Ketogenesis
Occurs in the mitochondria. HMG synthetase takes acetyl CoA and forms HMG CoA. This is used to form ketone bodies by HMG CoA lyase
Glucogenic amino acids
All but Leu and Lys. They can be converted to glucose by gluconeogenesis
Ketogenic amino acids
Leu, Lys, Ile, Phe, Thr, Trp, and Try. They can be converted to acetyl CoA and ketone bodies
Flavoproteins
Modified vitamin B₂ or riboflavin. They function as coenzymes for enzymes in the oxidation of fatty acids and the decarboxylation of pyruvate. Ex/ FAD, FMN
Counter regulatory hormones
Glucagon, cortisol, epinephrine, norepinephrine, and GH all oppose insulin
Glucocorticoids
Steroid hormones that regulate glucose levels
Catecholamines
They increase glucose output by the liver by increasing activity of glycogen phosphorylase in liver and muscle (glycogenolysis). Ex/ Epinephrine and norepinephrine
Respiratory quotient
A way to measure metabolic function
RQ = CO₂ produced / O₂ consumed
Transient enzyme modifications
Reversible modifications to enzymes. Ex/ allosteric activation and inhibition
Allosteric activators
binds and results in a conformational shift that makes the active site more available for binding of the substrate
Allosteric inhibitors
binds and results in a conformational shift that makes the active site less available for binding of the substrate
Covalent enzyme modifications
activation or deactivation of enzymes by glycosylation or phosphorylation
Silent mutation
Mutations in the wobble position that have no effect on expression of the amino acid and therefore no adverse effects on the polypeptide sequence
Monocistronic
1 molecule is translated into one protein product. Ex/ eukaryotic mRNA
Polycistronic
1 molecule is translated into multiple different proteins. Ex/ prokaryotic mRNA
Messenger RNA
Carries information specifying the amino acid sequence of the protein to the ribosome. Read in codons
Transfer RNA
Converts nucleic acids into amino acids and peptides. It contains an anticodon that recognizes and pairs with the appropriate codon on the mRNA molecule while in the ribosome.
Aminoacyl-tRNA synthase
Activates each type of amino acid and transfers it to the 3’ end of the correct tRNA. Requires 2 high energy bonds from ATP
Ribosomal RNA
Synthesized in the nucleolus. Many rRNA function as ribozymes and help catalyze the formation of peptide bonds.
Trp operon
The cluster of genes that code for tryptophan in E.Coli
Negative control mechanisms
Operon systems in which binding of a protein reduces transcriptional activity
Positive control mechanisms
Operon systems in which binding of a molecule increases transcription of a gene
Catabolite activator protein (CAP)
Transcriptional activator used by the lac operon. Decreasing levels of glucose cause an increase in cAMP which binds CAP -> CAP binds promotor -> increase lactase gene. Positive control mechanism
A site
Holds the incoming aminoacyl-tRNA complex (the next amino acid to be added to the growing chain determined by the mRNA codon within the A site)
P site
Holds the tRNA that carries the growing polypeptide chain
Peptidyl transferase
Ribozyme in the large subunit that catalyzes peptide bond formation during translation elongation (passing of the polypeptide from the tRNA in the P site to the tRNA in the A site). GTP is used for energy during peptide bond formation
E site
Where the inactivated (uncharged) tRNA pauses before exiting the ribosome. The tRNA unbinds from the mRNA as it enters the E site
RNA polymerase I
located in the nucleolus and synthesizes rRNA
RNA polymerase II
located in the nucleus and synthesizes pre-processed mRNA (hnRNA). It binds to the TATA box promotor region
RNA polymerase III
located in the nucleus and synthesizes tRNA
Translocation mutation
When a segment of DNA from one chromosome is swapped with another. This can lead to either partial trisomy in some chromosomes or monosomy in others
Saturated fatty acid
Only single bonds. More stable because they have greater Van der Waals forces. Solids at room temperature
Unsaturated fatty acid
Includes one or more double bonds. More difficult to stack so they are liquids at room temperature. Make up the more fluid areas of membranes
Phospholipids
Contain a phosphate and alcohol that make up the polar head group, joined to a hydrophobic fatty acid tail by phosphodiester linkages (distinguishing part of phospholipids)
Ceramide
Simplest sphingolipid. Has a single H as its head group
Sphingomyelins
Sphingophospholipids that are the component in the plasma membrane of cells producing myelin. Head group is either a phosphatidylcholine or phosphatidylethanolamine with no net charge.
Cerebrosides
Glycosphingolipids with a single sugar head group
Globosides
Glycosphingolipids with two or more sugar head groups
Steroids
4 cycloalkane rings (3 cyclohexane, 1 cyclopentane)
Glutathione
Reducing agent that helps reverse free radical formation before damage is done to the cell. Needs NADPH to be formed
Free radicals
When atoms lose one of their electrons. These radicals are dangerous because the look for electrons to rip away. They attack lipids (weaken cell membrane/lysis), RBC, and DNA. Ex/ H2O2 (byproduct in aerobic metabolism)
GLUT 2
Low affinity transporter in hepatocytes and pancreatic cells. Captures excess glucose mainly for storage. Activity is lowest when the blood and liver have low [glucose]
GLUT 4
Transporter in adipose tissue and muscle. Responds to glucose in peripheral blood
Glucokinase
Phosphorylates glucose only in liver cells and pancreatic B islet cells. High Km and induced by insulin
Rate limiting enzyme of glycolysis
PFK-1
Rate limiting enzyme of fermentation
lactate dehydrogenase
Rate limiting enzyme of glycogenesis
glycogen synthase
Rate limiting enzyme of glycogenolysis
glycogen phosphatase
Rate limiting enzyme of gluconeogenesis
fructose 1,6-bisphosphatase
Rate limiting enzyme of PPP
glucose-6-phosphate dehydrogenase
G protein coupled receptors (GPCR)
Heterotrimeric proteins that bind GDP and GTP. In the inactive form, the α subunit binds GDP in complex with the β and γ subunits. In the active form, GDP is replaced with GTP and the α subunit dissociates from the β and γ subunits. Ex ligands/ hormones
G𝑠
Stimulates adenylate cyclase -> increases cAMP levels
Gᵢ
Inhibits adenylate cyclase -> decreases cAMP levels
G𝑞
Activates phospholipase C -> opening of Ca channels in the endoplasmic reticulum -> increases intracellular Ca levels
Lactose
Glucose and galactose
Sucrose
Glucose and fructose
Goldman-Hodgkin-Katz equation
Used to determine the membrane potential taking into account the contribution of each major ion
V𝑚 = 61.5 log ( 𝔭Na+[Na+]out + 𝔭K+[K+]out + 𝔭Cl-[Cl-]in / 𝔭Na+[Na+]in + 𝔭K+[K+]in + 𝔭Cl-[Cl-]out )
Nerst equation
Used to determine the membrane potential of various ions
E = 61.5/z log ( [ion outside] / [ion inside] )
NADPH
Reducing agent that is involved in the biosynthesis of fatty acids and cholesterol, production of glutathione, and cellular bleach production of WBC (bactericidal activity)
Primer
Runs before DNA polymerase from the 3’ to 5’ end during replication. It must be complementary to the 3’ end of DNA
Glycogen phosphorylase
Breaks α-1,4-glycosidic bonds (glycogen) in order to release glucose 1 phosphate. Does not break 1,6 links. Activated by glucagon, AMP, epinephrine
Debranching enzyme
Hydrolyzes α-1,4 and α-1,6 glycosidic bonds. Hydrolyzing 1,6 releases glucose while hydrolyzing the 1,4 transfers the oligoglucose unit to the end of another chain
Insertion mutation
A segment of DNA is moved from one chromosome to another
Inversion mutation
When a single chromosome undergoes breakages and rearrangement within itself
Chylomicrons
Lipoprotein rich in triacylglycerol. Originate from ingested food and formed in the small intestines. Deliver fat to liver and tissues
Genomic DNA library
Represent the entire genome of an organism. Generated from clones DNA fragments that have been digested by restriction enzymes
cDNA (complementary DNA) library
Generated from reverse transcribed mRNA sequences and only contains coding regions of DNA
Lecithin-cholesterol acetyltransferase (LCAT)
Esterifies cholesterol and allows it to be soluble in HDL
Fluid mosaic model
Describes the phospholipid bilayer as fluid in motion. Ex/ consistency like vegetable oil
Oncogenes
Mutated genes that cause cancer. Primarily encode cell cycle related proteins
Proto-oncogenes
Oncogenes before mutations occur
Tumor suppressor genes
Encode proteins that inhibit the cell cycle or participate in the DNA repair process. Mutations of these cause cancer, but inactivation of both alleles is necessary for the loss of function. Ex/ p53, Rb (retinoblastoma)
Proofreading
Function of DNA polymerase during synthesis. It is the detection of incorrect base pairs due to the instability of H bonds. The mutations on the daughter (lagging) strand are identified due to less methylation than the template strand
2,3-bisphosphoglycerate (2,3-BPG)
Present in RBC and binds allosterically to B chains of hemoglobin to decrease affinity for oxygen. Allows for oxygen unloading in tissues.
*1,3-BPG -> 2,3-BPG by bisphosphoglycerate mutase
Lipase
Enzyme that hydrolyzes fatty acids
UDP glucose
Uridine diphosphate glucose. The glycosyl moity from UDP glucose is transferred to glycogen polymers. Contains uridine which is a nucleic acid in RNA (ribose)
3 irreversible enzymes of glycolysis
Hexokinase (glucokinase), PFK-1, and pyruvate kinase
ATP production in RBC
2 ATP per glucose
Chemiosmotic coupling
Allows the chemical energy of the electrochemical proton gradient of the mitochondria to phosphorylate ADP to ATP
Aminopeptidase
Released from the small intestine to digest proteins
α-amylase vs. β-amylase
Cutting polysaccharides randomly to yield shorter polysaccharides VS. cleaving polysaccharides at the acetal end to produce maltose
Malate-aspartate shuttle
Since cytosolic OAA can not cross the inner mitochondrial membrane by itself, it is reduced to malate (NADH is oxidized) which can pass. NADH is reformed when malate reforms OAA inside the mitochondria
Blunt vs. sticky ends of enzymes
No overhanging DNA sequences VS. overhanging DNA sequences. Separately they create bidirectional sequences but when used together they create palindromic sequences (restriction enzymes)
Rate limiting enzyme of TCA
isocitrate dehydrogenase
