MM1

Gene-Specific Regulatory Proteins Transcription factors are regulatory proteins that bind directly to ___ (aka activators, transactivators, inducers, repressors, or nuclear receptors). Contain a DNA binding domain and a domain for binding mediator proteins (___ and ___) Coactivators may contain ___ activity to ___ the rate of transcription Corepressors contain ___ activity and ___ transcription by inhibiting binding of ___ or coactivators

DNA coactivators corepressors HAT increase HDAC repress activators

product of replication #2

DNA, adds dNTPs

Solute-Free Water IV -Aka 1.5L of isotonic with 5% glucose: Glucose metabolized to carbon dioxide and water (same as infusing pure water) -Increases ECF volume initially -___ ECF osmolality by diluting pre-existing solutes +No 9% NaCl to maintain osmolality once infused -Water will then flow into the cell and increase ICF volume (SLIGHTLY) -Effective in diluting osmolality of body fluids -Water is the determinant of osmolality; by adding pure water you can dilute solute decreasing osmolality or by losing only water can increase solute concentration increasing osmolality

Decreases

The Peptide Bond Amino acids joined sequentially in proteins ___ reaction removes water molecule Carboxyl groups in ____ joins amino on second Backbone is amino N to ___-carbon to carboxyl ___ Synthesized from amino to ___ end

Dehydration first α C carboxyl

Clinical Case 1 ___ ___ - cells don't get the glucose they need for energy so the body begins to burn ___ for energy which produces ketones. -Ketones are acids that build up in the blood and appear in urine when the body doesn't have enough ___. -High level of ketones will result in DKA. Important message: glucose cant get into the cell because of the lack of insulin to facilitate transport via ___ ___transporter

Diabetic Ketoacidosis (DKA) fat insulin GLUT 4

___ - random molecular movement of substances molecule by molecule either through intermolecular spaces in the membrane or in combo with a carrier protein; ___ of normal kinetic motion of matter

Diffusion energy

___ Bonds Cysteine has a free ___ group Can be ___ and reduced Oxidation joins two side chains via ___ bond Can link two parts of one protein or different peptide chains

Disulfide sulfhydryl oxidized covalent

A chronic COPD patient would have which of the following transporters downregulated?

Downregulated means decreased expression of a transporter Chronic exposure to elevated pCO2 results in decreased intracellular pH: respiratory acidosis Increase expression of acid extruders Decrease expression of acid loaders Refer to slide 12 for answer A

pKa of Amino Acids Amino acids have both basic and acidic groups ___ and ___ acids are ionized in different ways in a solution The overall charge on a protein depends on contribution from ___ (positive charge) and ___ (negative) amino acids and varies with pH of solution! -These vary with ___ of aa functional groups and ___ of solution

Monoamino and monocarboxylic basic and acidic pKa - disassociation constant pH

___-___ Volume Change *In adrenal insufficiency, inadequate aldosterone production results in excess sodium excretion, decreasing ECF osmolality. -Osmotic gradient favors water moving into cells (ICF). -result: +ECF: volume down, osmolality down +ICF: volume up, osmolality down ultimately *When sweating without adequate water replacement, loss of water via sweat leads to a decreased ECF volume and increased osmolality. -Osmotic gradient favors fluid leaving cells. -result: +ECF: volume down; osmolality up +ICF: volume down; osmolality up *Volume expansion. In excess sodium and water intake (too many pretzels and lemonade?), ECF increases in volume and osmolality. -Osmotic gradient favors fluid leaving cells. -Final result: +ECF: volume up; osmolality up +ICF: volume down; osmolality up

Hypo-Osmotic ???? Like drinking salt water last slide.

Osmolality and Water Movement Water moves from a compartment of low osmolality to one of high osmolality to achieve equal osmolality. -the force to maintain equal osmolality is osmotic pressure. ___ solution cells swell because water is moving into the cell. ___ omolality is high amount of solutes.

Hypotonic Low

Overview of tRNA Synthesis and Processing tRNA ensures the genetic code is translated into the correct sequence of amino acids. Precursors are synthesized by RNA pol ___ ~___ nucleotides long Cloverleaf shaped pre-tRNA is cleaved at the 5' and 3' ends; ___ removed Bases are ___ Finally, a ___ sequence is added to the 3' end; exported.

III 100 introns modified CCA

Regulation at the Level of Translation and the Stability of mRNA (2)

Initiation of Translation microRNAs

Overview of Translation Translation occurs in 3 Steps: #3 1. Once a tRNA has donated its amino acid to the growing chain, it is released 2. A new ___ binds to the correct codon in the mRNA to donate it's amino acid to the growing polypeptide

Initiation, Elongation, and Termination aminoacyl-tRNA

Insulin Structure -Protein structure and function very dependent on specific amino acids in certain spots -___ in different species has many conserved residues -Required to make ___, bind ___, allow for ___-peptide removal to make mature ___

Insulin structure receptor C hormone

___ Agents Prevent DNA synthesis, inhibit ___, and induce mutations Anticancer drugs used in treatment of leukemia Ex: ___, Doxorubicin

Intercalating transcription Daunorubicin

Fluid Compartments in the Body 60% is ___: fluid inside cells 40% is ___ water includes: fluid in plasma and interstitial fluid (tissue spaces) as well as transcellular water

Intracellular extracellular

The Transcribed Region: Introns and Exons ___: do not code for proteins Left behind "IN" the nucleus ___: code for proteins "Exits" the nucleus for translation "Expressed"

Introns Exons

Notes: ___ solution=no change in cell shape=water moves freely across membrane ___ sol=cells shrink= water moves out of cell into hypertonic solution ___ (distilled water)=cell swells=water moving into the cell

Isotonic Hypertonic Hypotonic

Transposons: "___ ___" Transposons: segments of DNA that can move from their original position in the ___ to a new location -found in all organisms. -encode for enzyme ___ that cleaves the transposon from genome and moves it to another location

Jumping Genes genome transposase

Major component of Intracellular?

K+

Binding properties of proteins -Binding of ligands to proteins will have specific affinities that can be measured (called binding constant) -Wide range of values possible -___ is the affinity constant, ___ is the dissociation constant, reciprocals of each other -Ka high, Kd will be low -___ measured in molarity (a concentration), lower value means ___ concentration to give 50% saturation

Ka Kd Kd lower

Summary Amino acids in proteins are ___ forms Side chains are key to function and ___ Interactions may occur between side chains and/or backbone Related proteins share structural similarities and reflect ___ descent Proteins may contain modified amino acids Protein differences may be useful in ___

L-alpha pKa evolutionary diagnosis

Acid Loader versus Acid Extruder Acid Loader -___ intracellular pH (pHi) -Intracellular pH is the pH concentration in the ___ of a cell Acid ___ - typically achieved by the action of ___+-coupled transport proteins. These transporters take advantage of the inwardly directed Na+ gradient established by the Na+, K+ ATPase to either extrude ___ from the cell or to accumulate a ___ ___, such as ___− -a process that tends to raise ___

Lowers cytosol Extruder Na H+ weak base HCO3 pHi

Classification Sulfur containing aa: ___: nonpolar with bulky side chain, hydrophobic ___: can form covalent disulfide bond with another cysteine Resultant amino acid is called cystine (present in blood and tissues)

Methionine Cysteine

Regulation of Intracellular Ion Concentration -Sodium and potassium make up the MOST IMPORTANT gradients across the cell -Sodium - ___ -Potassium -___ -Sodium-Potassium Pump regulates the intracellular ion concentration

ECF (145 mM) ICF (120 mM)

SODIUM -___ - transepithelial transport -___ cells - entry of sodium back into the cell occurs through voltage-dependent sodium channels and functions in generation of action potentials -Drive secondary active transport of nutrient and ions

ENaC Excitable

Important Points for Cl- -Vm and ___ are extremely close in magnitude and charge, chloride ions are usually in equilibrium -No matter the membrane conductance to chloride, chloride will ___ diffuse at steady state

Ecl- not

___: process of ion permeation through the membrane. Both ___ and ___ gradients are responsible for ion ___.

Electrodiffusion electrical concentration permeation

Electrical Signals ___ - the study of the electrical activity of the body Electrical events serve to communicate information between 2 points Variations ___#4 The flow of ___ through specific channels is the basis of electrical signals.

Ellectrophysiology Variation in voltage Variations in current Variations in frequency Variations in phase or duration ions

Translation Occurs in Three Steps: Initiation, Elongation and Termination ___: Peptide bonds are formed between amino acids as they are added to form a growing polypeptide chain.

Elongation

___ is used to refer to changes in gene expression without altering the sequence of the DNA.

Epigenetics

Application of the Nernst Potential When the equilibrium potential for an ion equals the membrane potential: Ion is in equilibrium: No Net Flux If NOT equal, not in equilibrium +The difference between Equilibrium potential and Membrane Potential represents the net force on the ion +The ion will always diffuse in a direction that brings the Membrane potential toward its ___ potential

Equilibrium

Respiratory Alkalosis ___ elimination of CO2 from the body pCO2 ___ and the pH of the blood increases ___, ___ventilation, ___ Acute changes -___ breathing to allow pCO2 to rise and thus lower pH No real other chronic changes to account for respiratory alkalosis

Excess decreases Hypoxia hyper meningitis Decrease

Translational Regulation of Ferritin Synthesis ___-protein involved in the storage of ___ within cells and is synthesized when iron levels increase. The mRNA for ferritin has an ___ response element (IRE) which binds the regulatory protein called the ___ protein (IRE-BP). When the IRE-BP does not contain bound iron, it binds to IRE, ___ translation. When IRE-BP binds iron, it dissociates, and the mRNA in ___

Ferritin iron iron IRE-binding preventing translated

DIFFUSION Rate at which molecule diffuses from point A to point B is quantified by ___ Law J = -PA (Ci - Co) J = flux or ___ of diffusion across the membrane P = permeability coefficient (includes the diffusion coefficient and ___ ___) A = ___ Ci = concentration of the molecule inside the cell Co = concentration of the molecule outside the cell

Fick's rate membrane thickness Area

Mutations ___ Mutation: nucleotides inserted into or deleted from the DNA is not a multiple of three causing a shift in the reading frame.

Frameshift

Which of the following is an inhibitory neurotransmitter in the central nervous system (CNS)?

GABA

Targets for Gene Therapy ___ ___: Duchenne Muscular dystrophy, Cystic fibrosis, Hemoglobinopathies ___ ___: Cancer, Diabetes mellitus, HIV ___: transgenic pigs to produce human blood suitable for transfusion

Genetic disorders Acquired diseases Transgenesis

GWAS stands for

Genome Wide Association Studies

Classification ___: simplest, does not fit into any classification (simple side chain of H) ___: ring structure promotes "kinks" or bends in proteins ___ and branched amino acids: bulky, non-polar side chains +Hydrophobic, in proteins will cluster to form hydrophobic ___

Glycine Proline Alanine cores

The Story of HbA1c Proteins can be modified by chemical reactions over time Depends on both time and concentration Diabetics can have elevated blood glucose over extended periods ___ of proteins proceeds from this Hemoglobin reacts with glucose at the amino terminus to make several forms HbA1c with glucose on ___ is measured clinically, marker of long term elevation

Glycosylation valine

The Fate of RER Synthesize Proteins Secreted proteins are transferred in small vesicles to the ___ ___. Processes and sorts proteins so they are delivered to their appropriate destinations

Golgi complex

Acid Excretion: Volatile vs Nonvolatile Acidic pH affects protein structure and function, therefore excess ___ must be excreted to maintain normal blood pH.

H+

Clinical Correlation A 54-year-old female with Type 2 diabetes presents for a routine evaluation Fasting blood glucose is normal, but the physician suspects she is only compliant when an examination is due How can her past blood glucose levels be assessed?

HbA1c

Separation and Unwinding of the DNA Strands 1. ___ separates and unwinds the parental duplex. 2. Single stranded binding proteins (SSBPs) prevent the strands from ___ and protect them from degradation. 3. ___ relieves supercoils by cleaving and reforming the phosphodiester bonds of the DNA backbone.

Helicases re-annealing Topoisomerase

Eukaryotic Replication Complex 1. ___ unwind dsDNA at the replication fork; ___ relieves supercoiling 2. Single Stranded Binding Proteins (SSBPs) stabilize single stranded DNA and prevent ___ and ___. 3. Primase and Pol ___ synthesize one RNA primer on the leading strand; continuously synthesized by DNA pol ___ in the ___ direction. 4. ___ and Pol α synthesize multiple RNA primers on the lagging strand; Pol ___ and ___ generate Okazaki fragments via discontinuous DNA synthesis. 5. Pol ___ replaces the RNA primer and DNA ___ joins the Okazaki fragments.

Helicases topoisomerase re-annealing cleavage α ε 5'3' Primase α and δ α ligase

Regulation of eIF2α Activation ___ regulates translation of globin mRNA in ___ by controlling the phosphorylation of ___ (initiation factors) Why regulated globin at the translational level and not at transcription? ___ it inactivates the heme-regulated inhibitor ___ eIF2α is ___ and active, producing globin. When heme levels are low, the inhibitor kinase phosphorylates and ___ eIF2α Inhibits globin translation

Heme reticulocytes eIF2α Heme kinase unphosphorylated inactivates

Tertiary structure of transmembrane helices -Proteins that span membranes need specific structures -___ (7 transmembrane helices) is common -___-terminus outside, ___-terminus in cytoplasm -___ ___ (shown a squiggle), binding domains, regulatory sites (phosphorylation sites, shown in red)

Heptahelical N C Palmitoyl anchor

Clinical Case 2 Cont'd -___ ___ -Loss of membrane surface area relative to intracellular volume that leads to the spheroidal shape -Defects in proteins of the RBC membrane lead to loss of surface area and membrane fragility -___ shape is vulnerable to splenic sequestration and destruction

Hereditary Spherocytosis Spheroidal

Water and Thermal Regulation ___-a large drop in temperature is required to change states. ___, facilitating heat dissipation-high energy areas such as the brain can be cooled by the blood and total body pool. ___ and heat of vaporization-water evaporation results in a cooling effect.

High heat of fusion High thermal conductivity High heat capacity

Interactions Side chain structure allows for specific types of interactions in proteins -___ interactions between aliphatic or aromatic -___ bonds with polar side chains and/or backbone

Hydrophobic Hydrogen

OSMOSIS *TRANSPORT OF WATER DEPENDS ON: -___ pressure: pressure the fluid exerts -___ gradients: differences in osmolality across the membrane -___ osmotic pressure (___ pressure): osmotic pressure difference established by the plasma proteins in the intravascular compartment compared to the interstitial fluid -Water is equal across a capillary when ___ osmotic pressure equals ___ pressure

Hydrostatic Osmotic Colloid oncotic colloid hydrostatic

Osmolality *High blood osmolality Dehydration Diabetes Head trauma ___glycemia ___natremia (high sodium) ___ (accumulations of toxins in the blood Poisoning - ethanol *Low Blood osmolality ___ fluid intake (over hydration) Hyponatremia Inappropriate ADH secretion (SIADH)

Hyper Hyper Uremia Excess

An inhibitory postsynaptic potential

Hyperpolarizes the postsynaptic membrane by opening Cl- channels

Gene Amplification Certain regions of a chromosome undergo repeated cycles of DNA replication. -Newly synthesized DNA is excised and integrates into to other chromosomes throughout the genome, amplifying the gene in the process Not the usual physiological means of regulating gene expression in normal cells; occurs during errors of DNA replication -Cells containing amplified genes may have a growth advantage -Can also occur in response to certain stimuli. ___ resistance in non-Hodgkin lymphoma -Dihydrofolate reductase (DHR) is required for synthesis of thymine & purine nucleotides -Methotrexate inhibits DHR to limit cell ___ -Cancer cells amplify the DHR gene and normal doses of drug no longer work -Methotrexate is no longer used for non-Hodgkin lymphoma

Methotrexate proliferation

Urinary Hydrogen, Ammonium, and Phosphate Ions What is excreted in urine^^^ ___ metabolic acids cannot be exhaled as CO2 ___ acids are excreted in the urine (uric acid)

Nonvolatile Undissociate

___= Nitrogenous Base + Sugar ___= Nitrogenous Base + Sugar + Phosphate

Nucleoside Nucleotide

DNA Repair -___ ___ ___ (NER) -Base Excision Repair -___ Repair -___-coupled Repair

Nucleotide Excision Repair Mismatch Transcription

___ ___ ___ ___r (NRTI) The HIV virus mutates very rapidly (mostly because reverse transcriptase lacks 3'-to5' exonuclease activity (aka the proofreading activity) and frequently develops resistance to one or more of these drugs. Therefore, it is recommended that AIDS patients take several drugs, including two NRTIs.

Nucleotide Reverse Transcriptase Inhibito

___ Law -Voltage = current x resistance (V=IR) -Voltage = current/conductance (V=I/G) -The current carried by a particular ion varies with membrane voltage as described by the I-V relationship. -Any change in conductance or current will change the membrane potential.

Ohm's

___ governs water movement between Extra & Intra.

Omolality

Simultaneous Regulation of Related Genes ___: units of DNA where structural genes with related function are grouped (ex enzymes of a ___ pathway) Gene organization contributes to gene regulation Multiple genes are under the control of a single promoter A ___ mRNA is produced that codes for all proteins of the operon containing multiple start and stop codons. Operon promotor cistronic polycistronic.

Operons biosynthetic polycistronic

Chronic Changes in Cell Volume *___ - response to chronic ECF hyperosmolality (cell shrinkage) -Organic solute within the cell (synthesized within the cell or transported into the cell) -Transport osmolytes via sodium-coupled ___-___ +Sorbitol +Inositol +Betaine +Taurine -Osmolytes will ___ intracellular osmolality to restore cell volume

Osmolytes co-transporters increase

Osmolality and Water Movement ___ ___ - high levels of blood glucose and ketone bodies increase the osmolality of the ___ ___. As a result, much more water is being excreted in the urine.

Osmotic Diuresis glomerular filtrate

How to Measure Membrane Potential -___ Clamp -Developed in late ___'s -Allows study of ___ channels or whole cells -Technique that allows the study of the certain channels and their electrophysiology in excitable and non-excitable cells -Many diseases are related to malfunction of ion channels -Utilizing patch-clamp allows screening of therapeutic agents as well

Patch 1970 single

Identifying Individuals Sometimes the purpose is to identify an individual person or their descent -___ test, forensics, genealogy, anthropology Short repetitive sequences can be best for this Length varies with number of repeats, lots of alleles Generally unique

Paternity

2 rules of forces *___ -Favorable driving force -Open pathway through which the driving force can exert its effect *Driving Force Electrochemical potential energy difference

Permeable

Classification Aromatic: ring structures Polarities differ ___: non-polar, hydrophobic, rings can stack ___: hydroxyl group engages in hydrogen bonds, polar, hydrophilic ___: contains N, can form hydrogen bonds, slightly polar

Phenylalanine Tyrosine Tryptophan

Intracellular pH-Phosphate 6. ___ anions (H2PO4-) combine with H+ and thereby act as an ___ buffer. Intracellular pH-Proteins 7. ICF contains high level of proteins with amino acids that buffer through its capacity to can accept or release protons. Ex: ___ Intracellular pH 8. Metabolic ___ are transported out of the cell together with H+ to maintain intracellular pH. -H+ can be transported out in exchange for ___ and ___- can be transported out in exchange for ___.

Phosphate intracellular albumin anions Na+ and HCO3 Cl-

RNA Polymerase Forms ___ Bonds -RNA polymerases catalyze the formation of ___ bonds between nucleotides that base-pair with the complementary nucleotides on the DNA template +Adds new base at the ___' end, uses ___ as source +Need 3'___ to add another base +___ produced and degraded to drive reactive RNA and DNA nucleotides base-pair ___-A; C-G

Phosphodiester ester 3 NTPs OH Pyrophosphate U

SUMMARY -___ is the science that is concerned with the function of living organisms and its parts, including the physical and chemical processes involved - the state of disordered function leads to disease. The basis for clinical medicine. -___ is the maintenance of a constant internal environment. -Many pathways will disrupt homeostasis. The feedback loops (positive, negative, and feed-forward loops) will either bring the cell back to homeostasis or will result in disease. Describe examples of each of the feedback loops.

Physiology Homeostasis

Unsaturated Fatty Acids -___ fatty acids contain 1 double bond -___ fatty acids contain ≥2 double bonds -Low melting temperature (liquid at room temp) -Lipids with lower melting points contribute to ___ of our cellular membranes

Monounsaturated polyunsaturated fluidity

Na+ foes into cell = membrane potential inside becomes ___ positive.

More

DNA Damage by Mutagens ___-chemicals produced in cells, inhaled, or absorbed from the environment that cause mutations ___-mutagens that cause normal cells to become cancer cells Benzo[a]pyrene becomes carcinogenic once ___ in cells. Then it binds covalently to guanine residues, interrupting H-bonding in ___ base pairs and producing distortions of the helix

Mutagens Carcinogens oxidized G-C

Clinical Markers Markers of cardiac damage vary in specificity and time course in the blood -___ rises quickly, also found after damage to muscles, non-specific -___ are very specific, not seen until later -___ kinase MB (CK-2) is intermediate, not quite as specific, only primarily in heart Time of appearance and rate of decline different for each, can help determine ___ damage occurred

Myoglobin Troponins Creatine when

Quartenary structure and cooperative binding -Binding curves are useful in determining how proteins function -___ is a monomer, ___ a tetramer -Sigmoidal vs. saturable curves suggests ___ binding of oxygen to hemoglobin

Myoglobin hemoglobin cooperative

Chemical Bonds -Bases connect to sugar by ___ bonds +1' C of sugar to N1 of pyrimidine or N9 of purine -Phosphate attached to ___ carbon of sugar -New bases added at ___ carbon, need OH

N-glycosidic 5' 3'

Blood Plasma *___ - protein-rich fluid left behind after platelets, RBCs, and WBCs have been removed -Helps to regulate body's ___ ___ -___ compounds -Plays a role in the immune system and ___ mechanism -Imbalance can lead to disease

Plasma osmotic pressure Transports clotting

DNA Polymerase Binds at the Replication Fork Problem: Presence of RNA (primers) in new DNA strand Solution: DNA ___ removes RNA primers removed and fills the gaps with new DNA, and the ends are ligated by ___.

Pol I ligase

___ Bonds-covalent bonds where the electron cloud is more dense around one atom.

Polar

Polysomes and Protein Processing ___: complex of mRNA and multiple ribosomes, each of which is producing a polypeptide chain - allows for faster translation overall ___ Proteins: proteins that bind the ___ polypeptide and mediate the folding process.

Polysome Chaperone nascent

Difference between pore and channel.

Pore is always open. Channels can be activated: open or close.

During hyperpolarization, which ion has the highest conductance?

Potassium

CHEMICAL SYNAPSES -___ cell - cell that releases the neurotransmitter that will bind to the ___-synaptic cell -___ cleft - space between the two cells -___ is propagated in one direction: from the presynaptic cell to the postsynaptic cell

Presynaptic post Synaptic Current

TRANSPORT ACROSS CELL MEMBRANES -Passive transport - simple diffusion -Facilitated diffusion -Active diffusion +___ active +___ active >Co-transport >Counter-transport -Water transport

Primary Secondary

ACTIVE TRANSPORT THROUGH MEMBRANES -___ Active Transport - energy is derived directly from breakdown of ATP or of some other high-energy phosphate compound -___ Active Transport - ATP is not used directly. Transporter protein couples the movement of an ion down its concentration gradient to the uphill movement of another molecule against its concentration gradient. +___-transporter (exchanger)- move 2 or more molecules in opposite directions i.e. Na/H exchanger +___-transporter - move 2 or more molecules in the same direction i.e. Na/glucose transporter

Primary Secondary Counter Co

___ ACTIVE TRANSPORT NA/K pump. Because it is going against it's gradient. NA wants to move ___ naturally. K wants to go ___. *___ Active Transport -Against electrochemical gradient Carrier mediated -Utilizes direct input of metabolic energy

Primary in out Primary

DNA Polymerase Binds at the Replication Fork Problem: DNA Pol cannot initiate synthesis of new DNA strands as it requires a free 3'OH group. Solution: ___ creates RNA primers providing a free 3'-OH that is extended by DNA Pol. Problem: As the replication fork moves, the same problem presents on the lagging strand as that DNA strand is synthesized away from the direction of the fork. Solution: Primase creates another RNA ___. Okazaki fragments are created.

Primase primer

Resting Membrane Potential -___ of the distribution of charged ions -___ is directly proportional to charge that is separated

Product Voltage

Prokaryote vs Eukaryotic Promoter Structure ___ promoters simpler -Short region, a few specific sequences ___ more complex -More elements, vary with type of gene

Prokaryotic Eukaryotic

Eukaryotic Transcription is More Complex -Untranscribed Region (___ and ___ Region) -mRNA Processing

Promoter Enhancer

Recombinant ___ ___ Discover a useful protein like ___ Determine best way to produce it while retaining function -Hormones vs. enzymes vs. ___ antibodies, very different Some use recombinant DNA like insulin, can be made in ___ ___ and mammalian cell culture are better for some things Scale up, test, approve, manufacture and distribute

Protein Therapeutics insulin monoclonal bacteria Yeast

Targeting of Proteins to Subcellular and Extracellular Locations -The SRP docks the ribosome on the ___ membrane -Once docked to the ribosome, protein synthesis resumes through ___ into the ribosome. The signal peptides is cleaved by signal ___. The completed protein is released into the RER ___. -The signal peptides is cleaved by signal peptidase. The completed protein is released into the RER lumen.

RER pores peptidase lumen

Important Points for Na+ -THE ___ MEMBRANE POTENTIAL IS NOT SENSITIVE TO CHANGES IN EXTRACELLULAR SODIUM -At rest, there is not a significant number of sodium channels open -Conductance of sodium is close to zero at rest -Because sodium channels are closed under resting conditions, changes in extracellular sodium will not affect the resting membrane potential -An increase in membrane conductance to sodium will produce an influx of sodium ions and depolarization -At resting potential Na+ does not flow in or out.

RESTING

Control Polymerase, Control Transcription Repressors-regulatory proteins that prevent the binding of ___ ___ to the promoter (___ control). Repressor protein binds a site within the ___ called the operator. Block the ability of RNA polymerase to initiate ___. Block binding of RNA polymerase to the ___ Repressors are controlled through ___#2

RNA pol negative promoter transcription promoter Induction Repression

RNA Polymerase bind Promoters, Upstream of the Transcription Start Site Promoters: Sequences of DNA upstream of the start site that bind ___ ___ and determine the ___ of transcription

RNA polymerase frequency

Termination of Prokaryotic Transcription Prokaryotic Transcription Ends when: -___ ___ encounters a transcription termination signal 1. Formation of a hair pin loop in the transcript 2. ___ ___ binding causes release of the RNA transcript from the template in an energy-requiring mechanism

RNA polymerase rho factor

product of transcription #2

RNA, adds NTPs

___ of Transcription Factors Availability of coactivators or other mediator proteins Amount of transcription factor synthesized Presence of other transcription factors (RXR) Phosphorylation Binding of stimulator or inhibitor ligands

Regulation

Accomplishments of Gene Therapy ___ - 13 patients were treated by DNA carrying genes for angiogenesis Breast, prostate, lung, brain and ovarian cancers treated using this method Activation of ___ _ gene in patients with ___ and sickle cell disease Trials to enhance genes of intelligence, height and athleticism Trials to treats individuals with genetic predisposition to psychiatric disorders such as Schizophrenia and manic depression

Restenosis Hb F Thalassemia

Ion concentration and Membrane Potential -___ potential - cell is at rest +Sodium/potassium pump +Leak channels -Depolarized - membrane is ___ negative +___ the potential difference across the membrane -___ - membrane is more negative +___ the polarization across the membrane

Resting less Decreasing Hyperpolarized Increasing

Other Systems for Other Proteins Hepatitis B vaccine in yeast Protein does not need to be active, just provides antigenic stimulation Yeast can do some post-translational modifications Factor VIII from cultured mammalian cells Allows for proper folding and post-translational modifications Important for normal activity of protein! The system used depends on the use of the product - does it just have to have the right amino acid sequence, or does it need to be processed and folded to have normal function.

Retroviral Transduction

Current-Voltage Relationship -___ Potential - voltage in which the current reverses (i.e. the net current is o) -Inward current - ___ charge flowing into the cell or ___ ions out of the cell -___ Current - positive charge flowing out of the cell or negative ions into the cell -Vm values more negative than Vrev, the net driving force for CATION is ___ the cell -Vm values more positive than Vrev, the net driving force for a CATION is ___ of the cell

Reversal positive negative Outward into out

Retroviruses Reverse Flow -Retroviruses have RNA genomes, not DNA -Use the enzyme ___ ___ to make DNA copy to insert into nucleus -Use the DNA to make RNA ___ for new virions

Reverse Transcriptase genomes

Unusual Amino Acid Exception to the rule ___ is added to a few proteins during translation -Enzyme converts ___ (selenium rather than sulfur), then linked to special tRNA - Cysteine ___ into protein as it is made -Considered "___ amino acid"

Selenocysteine - so not a post-translational modification. Cysteine incorporated 21st

Action Potential ___ of an action potential reflects the specialized function of the cell. Therefore, the threshold, amplitude, time course, and duration of the action potential depend on the following: -The opening and closing of specific ion channels and the permeability properties of these channels -Concentration gradients of the ions that pass through the channels: #3 -#3 of the cell membrane (how easily can the ions permeate the cell membrane)

Shape sodium, potassium, chloride Capacitance, resistance, and geometry

DIFFUSION 1. ___ Diffusion - kinetic movement of molecules or ions occurs through a membrane opening or through intermolecular spaces without any interaction with carrier proteins in the membrane. 2. ___ Diffusion - interaction with carrier protein Carrier proteins different from transport proteins. Difference based on rate.

Simple Facilitated

How do you do that? SNP = ___ Occur all over ___, large number known Most have no effect on the ___ Come in groups called ___ Find one, you have figured out surrounding changes as well

Single Nucleotide Polymorphism genome phenotype haplotypes

Major component of Extracellular?

Na+

Principles of Cell Volume Homeostasis -Adding or removing ___ will affect ECF volume -Adding or removing ___-___ ___ will affect the osmolality of body fluids

Na+ solute-free water

Cell Volume -The cell maintains volume by excluding ___ -Exclusion of NaCl is maintained by sodium-potassium pump -This mechanism maintains the ___ osmotic pressure difference with the ___ pressure difference

NaCl colloid hydrostatic

FEEDBACK LOOPS ___ Feedback Thermoregulation Blood glucose Small bleed - barorecptors Respiratory feedback ___ Feedback Child Birth Severe hemorrhage Clotting __ Pavlov's dogs Potassium Excretion

Negative Positive Feed-Forward

HOMEOSTASIS CONTROL SYSTEMS *___ Feedback -Feedback compares current conditions to set ranges -Negative feedback ___ the change -Mechanism to restore conditions to their original state -Most feedback loops in the body are negative *___ Feedback -Increases change *___-___ -Anticipates change *___ - Maintenance of a constant internal environment

Negative stops Positive Feed-forward Homeostasis

The Double Helix -Double-stranded DNA forms a helical structure naturally -Bases are stacked, ring structures make them essentially flat +___ charges phosphate backbone is on the outside -Offset nature of backbone creates major and minor grooves +Bases more exposed in ___ groove +Some drugs target the major groove

Negatively major

Edema ___ Edema -___ syndrome -___ heart failure -___ -Pregnancy

Nephrotic Congestive Cirrhosis

What Ions are Most Critical in Maintaining the Membrane Potential? ___#3

Sodium Potassium Chloride

Mutations in Proteins Required in Eukaryotic Transcription Apparatus Mutations in Proteins Required in Eukaryotic Transcription Apparatus Two forms of xeroderma pigmentosum (XPB and XPD) are caused by mutation in ___ -___ recessive -inability to repair ___ damage no cure; preventative measures

TFIIH autosomal UV

What is responsible for the refractory periods? -#2!!! -In excitable cells, voltage-gated channels sodium and potassium channels are activated -During the depolarization phase, voltage-gated sodium channels are activated and will allow sodium to flow ___ its electrochemical gradient (into the cell) ___ the Vm to more positive (___) -During the repolarization phase, voltage-gated potassium channels allow potassium to flow down its electrochemical gradient (___ ___ ___ ___) ___ the Vm to more negative -Conductance of sodium and potassium result in either depolarization or repolarization of an action potential

Sodium and potassium down increasing depolarization out of the cell decreasing

___ composition among the different compartments is NOT the same ___ is the SAME among the compartments

Solute Osmolality

pH of intracellular organelles is important -Low pH inside organelles allow: ___ proteins Dissociating ___ from receptors ___ accumulation into vesicles -Cellular organelles that utilize transporters to maintain pH: #4

Sorting ligands Neurotransmitter Lysosomes Endosomes Secretory vesicles Golgi apparatus

Action Potential Stimulus: Successive Action Potentials ___- Duration Curve -Represents the combination of the minimum stimulus and duration required to reach threshold -If a stimulus is short in duration, then the ___ has to be very strong (high intensity) to reach threshold and generate an action potential (top picture) -If a stimulus is not strong in intensity but lasts for an extended duration, then an action potential can occur because the longer the stimulus duration the ___ will eventually reach threshold (bottom left picture

Strength stimulus

Drugs that Target this Process in Prokaryotes ___ binds 16S rRNA of the 30S subunit and inhibits translation initiation ___ binds 30S ribosomal subunit and blocks binding of the aminoacyl-tRNA to the A site of the ribosome ___ interferes with the peptidyl-transferase activity of the 50S ribosomal subunit of bacteria ___ binds 50S ribosomal subunit and prevents translocation

Streptomycin Tetracycline Chloramphenicol Azithromycin

___ ___ ___ (SLE) -Patients develop autoantibodies directed against ___ and various other cellular proteins -Inflammation results from antibodies and a "___ ___" is a common SLE presentation. -Pharmacological therapy is directed at ___ (ex. corticosteroids)

Systemic Lupus Erythematosus snurps butterfly rash immunosuppression

Transcription of Eukaryotic Genes -Different from Prokaryotes: processing of the RNA transcript -___ RNA polymerases vs 1 in prokaryotes -mRNA codes for only ___ polypeptide chain -mRNA transcribed in nucleus and migrates to cytoplasm for ___. Regulated by different promoters

Three one translation

How Do Channels Effect Membrane Potential? -___ Channels: have no gates, they are always open. Leak channels are an example. -___ channels: gates open or close in response to a membrane voltage change. (Na+ Ca+) -___ channels: channel includes a receptor that binds a specific ligand. The binding of this ligand regulates the opening and closing of the channel.

Un-gated Voltage-gated Ligand-gated

Action Potential Picture demonstrates how action potentials can vary ___ - action potential is short in duration (top left panel) ___ - action potential is longer in duration (top right panel) The type of cell also dictates the action potential. A skeletal muscle (bottom left) versus D) heart action potential are different because they perform different functions in the body (bottom right) Bottom line: action potentials can vary

Unmyelinated Myelinated

pH of intracellular organelles is important The pH is maintained by ___ Hydrogen pump

V-type

Membrane Potential -Expressed as ___ = voltage difference between intracellular and extracellular fluids -The resting Vm is usually ___ inside relative to outside -Range of resting Vm from -___ mV to -___ mV depending on the cell type -Any electrical signals involves deviating from the resting value

Vm negative 20 200

RATE OF DIFFUSION Facilitated Diffusion reaches ___ -Fixed # of carriers -Concentration maxes the carrier protein

Vmax

During hyperpolarization, which of the channels remains open until the resting membrane potential is achieved?

Voltage-gated potassium channels

What is Physiology Teleological vs Mechanistic Teleological "___" Mechanistic "___" EXAMPLE: Shivering What is the teleological purpose? What is the mechanistic process?

WHY HOW

THERMOREGULATION -___ detect an increase in body temperature -___ compares body temperature with set-point -___ signals sweat glands to initiate sweating -___ of sweat off skin causes cooling

Thermoreceptors Hypothalamus Hypothalamus Evaporation

pH<pKa acid will be in its ___ form (___) pH>pKa acid will be in its ___ form (___)

acidic protonated basic unprotonated

Ion Pair Bonding Allows interaction of ___ and ___ amino acids Attraction of ___ charges Stabilize protein structures and interactions

acidic and basic opposite

Acid Extruders Sensitive to pHi changes Channels activated by ___ Channels inhibited by ___ Function to get H+ out of the cell or bring in HCO3- The V(___-type) H+ pump is found on intracellular organelles as ___, ___, and ___ Primary active transport Extrudes H+ from the ___ Independent of an ion 2. Na-H exchanger Exchange 1 sodium ion for 1 H+ across the cell membrane Sodium follows its electrochemical gradient allowing H+ to move against its gradient out of the cell What type of transport is this? _____ 3. Na-driven Chloride/HCO3 exchanger Secondary active counter-transport Sodium travels down its electrochemical gradient driving the ___ entry of ___ into the cell Cl- keeps the electrical charges ___ when transporting bicarbonate into the cell

acidification alkalinization vacuolar lysosomes, endosomes, golgi cytosol Secondary active counter transporter uphill bicarbonate equal

Diabetic Ketoacidosis and Kussmaul Breathing Kussmaul Breathing: the abnormal breathing pattern observed in patients suffering from metabolic ___, diabetic ketoacidosis or some other medical condition which causes hyperventilation (a breathing pattern which involves ___ of carbon dioxide in blood due to increased rate or ___ of breathing).

acidosis reduction depth

Formation of Aminoacyl-tRNA: Get Charged! Charging Occurs in Two Steps STEP 1: The amino acid is ___ -amino acid carboxyl group reacts with ___ to form an ___/aminoacyl-AMP complex +___ of high energy bond in ATP provides energy +enzyme: ___ ___ ___ STEP 2: Amino acid is transferred to tRNA -transferred to the 2- or 3'-___ group of the ribose connected to the 3'-terminal ___ residue of the tRNA and ___ is released.

activated ATP enzyme cleavage Aminoacyl tRNA Synthetase OH A AMP

Binding of tRNA to a Codon on mRNA tRNA are "___"-links the mRNA codon with the amino acid it encodes for. Binds amino acid at the ___' that is determined by the tRNA anticodon: set of 3 ___ that interacts with a complementary codon in the mRNA.

adaptors 3 nucleotides

Viral Gene Therapy -Several types have been used - #3 -All have advantages and disadvantages -Many studies have been done, various stages -Some unexpected problems have been found along with ones that were expected -Long way to go before we get what would be best, gene replacement therapy

adenovirus, retrovirus, adeno-associated virus

Similarities and Differences Some families are very large May have very different, but related functions Example: catalytic regions of various ___ ___ types are very similar, other regions very different, different regulation, still make ___

adenylyl cyclase cAMP

Fatty Acids Fatty acids are straight ___ chains with a ___ group at one end (called the ω-carbon) and a carboxyl group at the other end. Most fatty acids in the human have an ___ number of carbon atoms, usually between 16 and 20.

aliphatic methyl even

Amino Acids and tRNAs -Amino acid is attached to specific tRNA by unique ___ ___ -Recognition site on tRNA varies for each -One aminoacyl-tRNA synthetase for each ___

aminoacyl-tRNA synthetase tRNA

Base Excision Repair (BER) The Damage: Lesions caused by damage to a single base. The Key Players in the Repair: -DNA glycosylase-cleaves the N-glycosidic bond to deoxyribose forming an ___ (lacking a base) site. -AP endonuclease-recognizes the AP site and cleaves the ___-phosphate strand. -DNA Polymerase-adds new dNTPs to the ___-end using intact complementary DNA as template. -DNA ___-joins the newly synthesized segment to the ___- end of the original strand.

apurinic sugar 3' ligase 5'

Classification Acidic: #2 --negative charge at physiological pH) Basic: #3; contain nitrogen that is protonated and positively charged (able to form ionic bonds with negatively charged groups)

aspartate (aspartic acid), glutamate (glutamic acid) histidine, lysine, arginine

Summary-Carbohydrates -A carbon atom containing 4 different chemical groups forms an ___ (or chiral) center -designated D- or L-sugars -___=same chemical formula but differ in the position of the OH group on one or more of the asymmetric carbons -___- stereoisomers that differ in the position of the OH group at only one of their asymmetric carbons -___ exist in solution as a ring structures where the original carbonyl carbon contains a OH group and becomes the anomeric carbon atom --OH group below the ring (α position), above the ring (β position) -Sugars frequently contain phosphate groups, amino groups, sulfate groups, or N-acetyl groups -Sugars can be oxidized or reduced -___ linkages are O- or N- glycosidic bonds

asymmetrical stereoisomers epimers Monosaccharides Monosaccharides

Translocations Damage: breaks in chromosomes Caused by: x-rays or chemical carcinogens Translocations The free ends of the DNA at the break point reseal with the free ends of a different broken chromosome, a translocation is produced. Result: These exchanges of large portions of chromosomes can have deleterious effects and are frequently observed in ___ cells.

cancer

Biological Compounds -Organic molecules of the body consist principally of #6 -The element, ___, forms 4 covalent bonds with other atoms.

carbon, hydrogen, oxygen, nitrogen, sulfur and phosphorus. carbon

Biological Compounds The number of ___ in a molecule contributes to its name.

carbons

Metabolic Alkalosis Increase ___ in the blood. This increase may be due to either a primary increase in bicarbonate reabsorption or be secondary to decreased production or ___ loss of H+. Increase in blood ___. vomiting, diuretics, or increased urinary excretion of Cl−. Acute The increased blood pH reduces the respiratory stimulus for breathing and hypoventilation occur to retain ___ and via carbonic anhydrase buffering system H+ is produced which ___ blood pH. Chronic A more chronic compensation occurs when the renal system decreases ___+ secretion. Decrease ___ ___ exchanger in the kidney Increased intracellular pH so to counter act this want to decrease the expression of the acid extruder to keep H+ inside the cell Decrease expression or activation of the acid extruder

bicarbonate increased pH CO2 lowers H sodium hydrogen

Electrolytes: Solutes within the Body Extracellular fluid (ECF) and intracellular fluid (ICF) contain electrolytes-a general term applied to ___ and ___ ___ are unevenly distributed between ECF and ICF. Electrolyte concentrations contribute to the ___ distribution between the ECF and ICF.

bicarbonate inorganic cations and anions. Electrolytes water

Summary-Lipids Fatty acids=contain an ω-carbon at one end, and a ___ group ___ fatty acids have single bonds, high melting temps ___ fatty acids have ≥1 double bonds, liquid at RT Double bonds can be in the cis or trans configuration Naming of fatty acids includes determining the number of carbons, number of double bonds, and position of the double bonds ___ =glycerol+ ≥1 fatty acids ___ =glycerol + fatty acids+ phosphate ___ =sphingosine instead of glycerol; derived from serine and palmitate ___ =sphingosine + fatty acids (attached to the amino group) ___ and ___ = sugars attached to OH group of ceramide ___ = ceramide + phosphorylcholine ___ are synthesized from cholesterol and contain a four-ring structure

carboxyl Saturated Acylglycerol Phosphoacylglycerol Sphingolipids Ceramide Cerebrosides & gangliosides Sphingomyelin Steroids

SIMPLE DIFFUSION Simple Diffusion -Not ___ mediated -Occurs ___ electrochemical gradient -Does NOT require ___ energy

carrier down metabolic

Have to have ___ in order for Na+/Cl- to move and flow.

channels

Amino acids -Unique ___ of a protein are dictated by its primary structure -Primary structure = ___ sequence of amino acids -Primary structure synthesized from 20 amino acids arranged in a linear sequence determined by the genetic code

characteristics linear

Protein modifications Proteins can be modified by ___ reactions over time

chemical

Action Potential Stimulus An action potential only occurs if it is stimulated A stimulus can range from #3 +Basically anything that results in depolarization of the membrane

chemical stimuli, sensory stimuli, mechanical stimuli

Unsaturated Fatty Acids: Double Bond Configuration -double bonds in naturally occurring fatty acids are in the ___ configuration --___ are on the same side of double bond and acyl chains are on the other side In trans-fatty acids the ___ chains are on opposite sides of the double bond -___ and the fat used in preparing french-fries are likely the major sources of trans-fatty acids found in humans -Trans-fatty acids are produced by the chemical hydrogenation of ___ fatty acids in vegetable oils; not a natural food product

cis hydrogens acyl Margarine polyunsaturated

Sodium channels are usually ___ during resting membrane.

closed

Voltage-Gated Sodium Channel -At resting Vm the voltage-gated sodium channel is ___ -A stimulus opens the voltage-gated channel and sodium flows through channel causing Vm to increase -Once sodium entry through the opened voltage-gated sodium channels reach threshold, more voltage-gated sodium channels are activated -Once this channel is activated, it will transition to the inactive state. It is the inactivation of the voltage-gated sodium channel that is responsible for the ___ ___ ___. The sodium channels cannot be opened again during this time and therefore an action potential cannot be generated until enough sodium channels have recovered from the ___ state.

closed absolute refractory period inactivation

The Genetic Code Degenerate -amino acids are specified by more than 1 ___ (an amino acid may have more than one codon) Unambiguous -codons only code for 1 amino acid

codon

Reading Frames of mRNA Reading frame-the order in which the sequence of bases in the mRNA is sorted into ___ The start codon (AUG) ___ the reading frame The order of codons in the mRNA determines the amino acid sequence in the protein.

codons sets

Comparing Expression Levels -Can use with RNA too! -Two samples can be compared for relative amounts -Label with different fluorescent dyes, use ___ hybridization -Equal amount appear ___, unequal show as ___ or ___ depending on relative amounts present

competitive yellow green red

Base Pairing and Replication -Hydrogen bonding allows strands to separate -Free nucleotides can pair with partner in single stranded regions -These nucleotides will be joined into new ___ strands -Same sequence as original DNA strands

complementary

Translation Occurs in Three Steps: Initiation, Elongation and Termination 3. Translocation -The ribosome undergoes a ___ change that moves the mRNA and base paired tRNAs -___ ___ provides energy for conformational change -the uncharged tRNA moves from the ___ site to the ___ site -the tRNA in the E site is released when the ___ site binds another charged tRNA

conformation GTP hydrolysis P E A

Induction of the lac Operon by Lactose Enzymes that metabolize glucose are ___ expressed. If lactose is available, cells adapt and begin to produce ___ additional enzymes (encoded by the lac operon) required for lactose metabolism A metabolite of lactose (___) serves as an ___, binding to the repressor and inactivating the ___. Polymerase is free to transcribe the ___ operon.

constitutively 3 allolactose inducer repressor lac

Controlling Repressors through Repression Repression-the repressor is inactive until a ___ (a nutrient or metabolite) binds to the repressor and activating it. The corepressor-repressor complex binds the operator, preventing RNA ___ binding Ex: trp operon - encodes ___ enzymes required for the synthesis of the amino acid ___. -tryptophan acts as a ___; binds the inactive repressor causing it to change shape and bind the ___ -Tryptophan inhibits ___ of the operon Repression model: repressor is inactive without a corepressor (___ operon) Induction model: repressor is active unless an inducer is present (lac operon)

corepressor polymerase 5 tryptophan corepressor operator transcription trp

The Glucocorticoid Receptor binds the steroid hormone ___ and dissociates from ___, exposing a nuclear localization signal forms ___ that translocates to the nucleus, and binds ___ response elements in the gene control region ___ domains on the dimer bind mediator proteins, activating transcription of specific

cortisol HSPs homodimer glucocorticoid transactivation

More Than One Helix Left-handed helix will turn ___ Right-handed helix will turn ___ Three helical forms are known -B-DNA is most ___; ___-handed helix -A-type helix known in DNA-RNA ___; ___-handed helix, most ___ -Z-DNA seen in ___-rich regions; ___-handed helix

counterclockwise clockwise common right hybrids right compact GC left

Base Pairing -Bases pair specifically, one purine to one pyrimidine -Always pair A to T, G to C -Hydrogen bonding holds pairs together -Not ___, not chemically linked -___ bonds, can be broken when needed

covalent Weak

DNA Damage by Ultraviolet Light Ultraviolet (UV) rays excite adjacent pyrimidine bases on DNA strands, causing them to form ___ ___

covalent dimers

Classification of Relationships Proteins with similar structures and functions are classified in ___ Similar proteins are homologs, or described as homologous Other terms refer to specific relationships -___ proteins are proteins in different species with the same function -___ proteins diverged after ___ duplication, may be in the same or different species

families Orthologous gene Paralogous

Light Chain Domains -Variable regions have ___ ___ ___ -Antigen binds tightly between variable regions of heavy and light chains, not in ___! -Binding affinities can be very high, with a very low ___ -Constant domain is called the ___ ___

flattened beta barrel barrel Kd immunoglobulin fold

Steroids and Cholesterol -Steroids contain a ___-ring structure call the Steroid Nucleus (green box). -Steroids are synthesized from cholesterol by modifications to the ring or the ___-___ side chain. -Cholesterol is synthesized from an ___ unit.

four C-20 isoprenyl

Recycling eEF1A in Eukaryotes -Once released, the free eEF1A-GDP binds with the ___, which accelerates the replacement of bound GDP with ___. -Thus, eEF1A-GTP is ready to bind another ___-tRNA molecule and continue elongation

eEFB1α GTP aminoacyl

Translation Occurs in Three Steps: Initiation, Elongation and Termination Elongation: Facilitated by eukaryotic elongation factors (___) 1. Aminoacyl-tRNA binds the ___-site -aminoacyl-tRNA binds GTP bound ___ -requires energy from GTP ___ 2. Formation of a peptide bond -amino acid on the tRNA in the A site forms a ___ bond with the amino acid on the tRNA in the ___ site. ___ ___-rRNA (not protein) of the large ribosomal subunit catalyzes the formation of peptide bonds.

eEFs A eEF1A hydrolysis peptide P peptidyl transferase

Basics of Translation Assembly of major components -mRNA, Ribosomes, tRNAs with amino acids Provision of energy -ATP and GTP Additional protein factors -Initiation and ___ factors Recognition of reading frame

elongation

Bicarbonate Buffer System The acid-base balance involves the lungs, the ___, and the kidneys. ___ - Control plasma bicarbonate synthesis and the excretion of hydrogen ions

erythrocytes Kidneys

Acylglycerols An acylglycerol-glycerol with one or more fatty acids (the acyl group) attached through ___ linkages

ester

DNA Polymerases Catalyze DNA Synthesis -An ___ bond is formed between the first (or α) 5'-___ of the incoming nucleotide and the free 3'-___ group at the end of the growing chain. -Pyrophosphate is cleaved and released providing the required energy

ester phosphate OH

Lipids: Phosphoacylglycerols Glycerol + fatty acids ___ to positions 1 and 2 and a phosphate attached to carbon 3. ___ acid- "only" a phosphate group attached to carbon 3. -precursor for the synthesis of other ___ ___-phosphatidic acid + amine group -___ (contains large polar and nonpolar regions) -one of the major phosphoglycerols found in the membrane

esterified Phosphatidic phosphoacyglycerols Phosphatidylcholine amphipathic

Translation Occurs in Three Steps: Initiation, Elongation and Termination Initiation of Translation: a complex forms containing Met-tRNAiMet, mRNA, and a ribosome. -facilitated by ___ ___ ___ (eIFs) The ribosome is complete it has three binding sites for tRNA : -Ejection (E) site, Peptidyl (P) site, and Aminoacyl (A) site

eukaryotic initiation factors

Whole genome sequencing is not common practice as is it very expensive Alternative to this is sequencing a subset or region of DNA that encodes proteins specifically the ___ Article- proves that exome sequencing could be used to identify a novel gene responsible for a rare ___ diseases demonstrates that exome sequencing has the potential to locate causative genes in complex diseases, which previously has not been possible due to limitations in traditional methods and cost Exome sequencing uses a targeted capture and massively parallel sequencing technique Cost-effective, reproducible and robust strategy with high sensitivity and specificity to detect variants causing protein-coding changes in individual human genomes

exons Mendelian

What is the Exome? -Human genes are interrupted, have ___ with coding sequence and ___ that intervene between them -Splicing removes ___ from initial RNA transcript to make functional messenger RNA (mRNA) -Introns and other ___ DNA makes up the vast majority of our genome -The exome is the exons, the coding part of the genome

exons intron introns non-coding

DNA Polymerases Proof-Read Synthesized DNA DNA Polymerases have ___ activity Exonuclease - enzyme that catalyzes the ___ of single nucleotides (via cleaving phosphodiester bonds) from the end (exo) of a DNA or RNA chain. If the nucleotide at the end of the growing chain is incorrectly base-paired with the template strand, ___ removes this nucleotide before continuing to lengthen the growing chain. This proofreading activity eliminates most base-pairing errors as they occur.

exonuclease hydrolysis pol III

Iso-Osmotic Volume Change -Only ___ fluid can enter or leave the body. -In diarrhea, the ___ fluid loses volume, but its osmolality does not change. -Result: ECF: volume down, osmolality unchanged. ICF: volume unchanged, osmolality unchanged

extracellular extracellular

Cell with 2 acid-base transporters Na-H exchanger represent the acid ___ transporters Cl-HCO3 exchanger represents an acid ___ Under normal conditions the acid extruders balance the acid loaders producing a steady state and maintain pHi Inject ___ cause a ___ in pHi: represents metabolic acidosis The acid extruders will be activated and the acid loaders will be inhibited Compensation for the metabolic acid load

extruder loader HCl decrease

Extracellular pH Extracellular acidosis inhibits acid ___ and stimulates acid ___ Intracellular acidosis will develop over a few minutes A shift in pHo shifts ___ As the pHo rises it relieves the ___ of acid extruder and cancels the stimulation of the acid loader

extrusion loading pHi inhibition

Action Potential Stimulus: Distance of Response Hyperpolarizing Stimulus: Does not result in an action potential but does cause a change in Vm The response ___ with distance from the stimulus site

decays

Article came out in the NEJM discussing the use of diagnostic clinic genome and exome sequencing in medicine Talks about patients visiting their doctors, and doctors sequencing your genome as a diagnostic tool Quite expensive but it is available Many physicians are ordering these tests with the goal of establishing ___ for care, or to help them with unrecognizable or puzzling disorders that they suspect have a genetic origin

diagnosies

SIMPLE DIFFUSION THROUGH CHANNELS OR PORES -Selectively permeable - ___ of a pore and its ___ charges provide selectivity -Can be open or closed states regulated by electrical signals (voltage-sensitive channels) or chemicals that bind (___ channels)

diameter electrical chemosensitive

Eukaryotic tRNA Loops The D loop- contains ___ (D) The Anticodon Loop-binds a specific sequence of three nucleotides in mRNA The TΨC loop- contains ___ (T) and ___ (Ψ)

dihydrouridine ribothymidine pseudouridine

Hydrogen Bonds in Water and Polar Molecules water is ___- having two poles (electrical charges). hydrogen bonds are ___ ___ interactions between the hydrogen of one water molecule and the oxygen of another. hydrogen bonds form between water and ___ molecules (___).

dipolar weak noncovalent polar solutes

Unsaturated Fatty Acids: Naming Fatty acids are also classified by the ___ of the double bond closest to the ω end (the methyl group at the end farthest from the carbonyl group)

distance

Immunoglobulin Structure All immunoglobulins have similar structure: +Four polypeptide chains; two heavy chains and two light chains Held together by ___ bonds Have ___ and ___ regions Variable regions make up antigen binding domains

disulfide constant and variable

Summary 1 -Nucleic acids are composed of bases and sugar-phosphate backbone -DNA is ___ stranded and carries information in cell and between generations -Double helix structure is important -Denaturation of DNA disrupts hydrogen bonding, produces single strands -Histones are important to ___ structure

double chromatin

Replication is Bidirectional E. coli contains ___-stranded DNA organized into a ___ circular chromosome Synthesis begins at the origin of replication where replication forks (at each end of the ___) forms Synthesis occurs at ___ replication forks that move away from the origin in both directions at the same time (___). A 2nd round of synthesis can begin at the origin before the first round is finished allowing bacterial multiplication to occur quickly Replication ends on the other side of the chromosome at a ___ point.

double single bubble 2 bidirectional termination

Heme Structure -Also interacts with specific amino acids in ___ chains -Heme is considered a prosthetic group; ___ part of protein +A protein with prosthetic group: ___ +A protein without: ___

globin intrinstic holoprotein apoprotein

The -OH on the anomeric carbon of a monosaccharide can react with an -OH or an -NH group of another compound to form a ___ bond

glycosidic

This group of drugs inhibits bacterial DNA ___, a topoisomerase that unwinds the closed circular bacterial DNA helix ahead of the replication fork and thus inhibits bacterial DNA synthesis. Because eukaryotic cells have linear DNA and do not contain DNA gyrase, they are not affected by quinolones.

gyrase

Domain Structure Multiple ___ and ___ can form a domain May be repeated in related proteins, share functions ___ domain shows common features found in many ___ proteins +Group of beta sheets, twisting to the right +Connected by helices and turns +Specific site for ___ binding -LDH - Lactate dehydrogenase

helices and sheets LDH globular NAD

Fidelity is ___ in replication

high

Resistance low = conductance ___

high

Acid loaders Acid loaders are activated when intracellular pH is ___ Function in ___ pHi By getting rid of HCO3- can ___ pHi Cl-HCO3 exchanger Secondary active transport Inwardly directed ___ gradient drives ___ out of the cell Cl- can bind to H+ forming HCL inside the cell and ___ pHi

high Lowering lower chloride bicarb lowering

Binding Changes Conformation -Proximal ___ binds iron in heme -When oxygen binds to iron, iron moves into plane of ___ -Histidine still bound, alters conformation of protein

histidine heme

Removal of Introns Splice Junctions in ___ consensus sequences at the intron/exon boundaries of the pre-mRNA are ___ (___ in the DNA)

hnRNA AGGU AGGT

Other RNA Forms and Functions -Several more types of RNA exist -___, heterogeneous nuclear RNA is precursor to other forms, found in nucleus only -___, small nuclear RNA used in splicing -___, micro RNA, very short molecules involved in gene ___ -___, catalytic molecules that act like enzymes. Not a true enzyme.

hnRNA snRNA miRNA regulation Ribozymes

Generating Lots of Data -Sequencing genomes would take a LONG time -Using other methods speed things up - multiplexing rules! -Analyze much of genome in one experiment is best -DNA ___ is useful, each strand only binds perfect complement ___ -Use lots of ___ at once

hybridization strongly probes

Nucleic Acid Hybridization -Single strands with complementary sequences can ___ -Any combination of DNA and RNA strands will hybridize -Useful in molecular biology research -Reaneal=hybridize

hybridize

Levels of Protein Structure Primary - sequence of amino acids Secondary - local regions stabilized by repeating patterns of ___ bonds (___ helix, ___ pleated sheet, etc.) Tertiary - ___ folding of polypeptide chain Quaternary - overall structure of ___ polypeptides

hydrogen alpha beta 3-dimensional multiple

Body Buffer Systems Blood and tissues contain buffer systems that minimize changes in ___ ion concentration. -Buffers consist of a ___ acid and its ___ base. -Buffers cause a solution to resist changes in pH when hydrogen ions or ___ ions are added. -compensates for an influx/removal of hydrogen ions within ~1 pH unit of the pKa.

hydrogen weak conjugative hydroxide

Myoglobin and hemoglobin Myoglobin: Heme tightly bound in ___ O2-binding pocket with ___ at its center +Heme is a ___ ring structure +Holds ___ that binds oxygen in heme

hydrophobic iron porphyrin iron

Conserved Structure Proteins are similar in structure to related proteins (homologous) May contain runs of identical amino acids Differences may be conservative substitutions -Very similar amino acids; same charge or ___ Allows for classification into families (and to infer evolution)

hydrophobicity

The "Wobble" Hypothesis Variation in the third base of the codon -3' base in the codon and the 5' base in the anticodon does not follow strict base-pairing rules. Base pairs can "wobble". -G can pair with U, A, or C OR -G can pair with -___ (I) found in tRNA

hypoxanthine

pH and Cancer Tumor microenvironment may play a key role in tumor malignancy. It is hypothesized that ___ and acidity may contribute to the progression from benign to malignant growth. The acid microenvironment is modulated through the over-expression of H+ transporters that are also involved in tumor progression, invasiveness, distant spread and chemo-resistance.

hypoxia

Water Imbalance -Dehydration is a condition that occurs when the loss of body fluids, mostly water, exceeds the amount that is taken in. With dehydration, more water is moving out of our cells and bodies more than what we take in through drinking. This movement of water results in an ___ in blood osmolality.

increase

Respiratory Acidosis Caused by an ___ in pCO2 Compensated by an ___ in renal bicarbonate generation Associated with diseases and obstruction of the airway

increase increase

Respiratory Alkalosis Excess elimination of CO2 from the body PCO2 decreases pH ___ Acute: ___ breathing to allow pCO2 to rise and lower pH Chronic: no real other changes to account for respiratory alkalosis

increases decrease

allolactose (___) needed to inactivate the repressor causing it to dissociate from the operator Binding of cAMP-CRP activating complex stimulates RNA ___ to bind the promoter and initiate transcription.

inducer Pol

Acute Changes in Cell Volume -ECF decreases its osmolality -Water then moves ___ the cell to higher osmolality -Cell swells until osmolality equilibrates -Cell swelling activates regulatory volume decrease (RVD) -RVD activates chloride and potassium ___ channels to lower intracellular solute concentration (K/Cl co-transporter) and cause water to flow ___ of the cell

inside efflux out

Eukaryotic Cell Cycle 4 phases of cell cycle: Interphase includes G1,S, and G2 phases- Most cell spend the majority of their time in ___ carrying out normal metabolic activities. -G1 - length varies; cells prepare to duplicate their chromosomes (ex. producing nucleotide precursors) -S - DNA replicates and ___ proteins are produced at a higher rate -G2 - cells prepare to divide and synthesize ___ for microtubule construction Mitosis-Brief phase of cell division -cells then enter back into G1 or G0 (extended G1) depending on cell type.

interphase histone tubulin

Sodium-Potassium Pump and Cell Volume -Non -Functioning Sodium-Potassium Pump +Sodium moves into the cell +Potassium moves out of the cell +Increase in membrane potential +Chloride can now enter the cell +Increase in osmotically active particles (sodium and chloride) +Increase osmotic gradient inside the cell +Water moves ___ the cell increasing the cell volume

into

WATER Water location: 60% ___ 40% ___

intracellular extracellular

SECONDARY ACTIVE CO-TRANSPORT (same direction) and Counter-Transport (oppo direction) *Secondary Active -Against electrochemical gradient -Carrier mediated -Utilizes the electrochemical gradient of another ___ for energy Na naturally flowing uses it's energy to move glucose against its gradient. (co-transport move together)

ion

Background -Cellular communication in the nervous system is based on electrical and chemical signaling events that are mediated by ___ channels -A change in the membrane potential can generate an action potential -___ of the action potential allows information from sensory organs to be transmitted to the brain and back again -All action potentials are ___ created equal +Threshold, amplitude, time course, duration of action potentials can all be different

ion Conduction NOT

Feedback Loops -Feedback loops don't operate in ___ -Synergistically -Antagonistically -Redundant Feedback loops compensate when other things don't work (knockout gene)

isolation

Osmolality and Water Movement water lost from one compartment is replaced with water from another. Water flow through the ___ (example)

kidneys

Congestive Heart Failure -Increased ___ ___ pressure, increased venous pressure, increased capillary pressure, ultimately increases capillary hydrostatic pressure resulting in edema formation

left atrial

Depolarization for K+ means going ___ negative (less/more)

less

Gene Expression in Prokaryotes Prokaryotes require ___ regulatory mechanisms than eukaryotes. Cell organization influences gene regulation no ___ membrane no ___ mRNAs lack ___ transcription & translation occur ___. mRNA has a short ___ life and must be constantly generated to maintain protein synthesis regulation of ___ is sufficient to regulate the level of proteins within the cell.

less nuclear histones introns simultaneously half transcription

Summary: Prokaryotes 1. regulation of transcription regulates protein ___ within the cell. 2. The principle means of regulation is through ___. 3. Repressors bind the operator thereby blocking ___ binding site Repressors are controlled through ___ or repression Induction model: repressor is active unless an ___ is present (lac operon; induced by ___) Repression model: repressor is inactive without a corepressor (trp operon; where tryptophan is the ___)

levels repressors Pol induction inducer allolactose corepressor

Conserved Structure Primary structure of a protein is its ___ sequence of amino acids Amino acid sequence can vary somewhat among individuals Variations (in primary structure) are tolerated: -If not in critical regions of the protein (protein binding areas or areas needed for protein ___) -If they are conservative substitutions (amino acid with similar structure or properties) -If they confer an advantage

linear folding

Replication at the Ends of Chromosomes Eukaryotic chromosomes are ___, and the ends of the chromosomes are called ___ RNA ___ are removed from the end of the lagging strand resulting in a short ___ end, and there is a ___ overhang in the DNA strand being replicated. Without replacing the end of the chromosomes, there would be progressive ___ of the genetic information.

linear telomeres primers 5′ 3′ loss

Fidelity is ___ in transcription

low

OSMOSIS -Osmosis: movement of water driven by osmotic gradients -Water will move from ___ osmolality to ___ osmolality

low high

Extracellular pH will effect the rate of pHi recovery A ___ pHo slows the rate of pHi recovery from acute acid loads and ___ the final steady-state pHi (red curve) High pHo effects is a shift of the pHi dependence of acid ___ Basically the pHo shifts the pHi dependence of acid extrusion and acid loading. We will examine this concept further in the next slide

low reduces extrusion

The Fate of RER Synthesize Proteins Protein vesicles leave the Golgi as ___ or ___ vesicles. -secreted proteins are found in vesicles that fuse with the membrane and proteins are ___. -membrane proteins are found in vesicles with ___ residues that become embedded in the cell membrane

lysosomes secretory exocytosed hydrophobic

RNA Editing Bases can be altered or nucleotides added or deleted after the transcript is synthesized so the mature ___ differs in the different tissues ___ of C to U in the RNA generates a stop codon in intestinal mRNA resulting in a ___ protein

mRNA Deamination shorter

mRNA Capping-Eukaryotic mRNA Protects the 5' end of the RNA; uniquely identifies the RNA as ___ ___ (SAM) donates the ___ groups to position ___ of the ___ ring. SAM regeneration requires the vitamins ___ and ___. Thus, formation of mRNA is affected by ___ vitamin deficiency.

mRNA S-adenosylmethionine methyl 7 guanine folate B12 B

Homologous Recombination The exchange of segments between DNA molecules -beneficial or devastating consequences -exchanged DNA may be homologous or unrelated -4-10K nucleotide segments (large segments) -can include many genes or portions of genes "crossing over" -one type of genetic rearrangement between homologous chromosomes during ___

meiosis

SIMPLE DIFFUSION -Utilize ___ proteins -Lipid-insoluble molecules -Large or charged

membrane

Eukaryotic Replication (S Phase) Eukaryotes have ___ points of origin at which replication begins (in contrast to bacterial chromosomes). "___" appear at these points where replication forks form at the ends of each bubble. As the bubbles enlarge they eventually merge and ___ is completed.

multiple Bubbles replication

Relationship Between DNA Strands, mRNA, and Protein RNA polymerase uses the template strand to make an exact RNA nucleotide copy of the ___ strand including the ___ of the sequence. gene sequences refer to the ___ strand, which is identical to the base sequence and direction of the ___ transcript. gene sequences are written in the ___ direction

non-template directionality coding RNA 5'-3'

Nucleosome Packing -Nucleosomes are ___ (8 proteins) +2 each of H2A, H2B, H3 and H4 -About ___ base pairs of DNA wrap around each nucleosome core -H1 is binds to DNA between nucleosomes "on the ___" -Basis of higher-order packing in chromosomes

octamers 140 strings

Regulation of RNA Polymerase Binding by Sigma Factors E. Coli has only ___ RNA polymerase Sigma factors bind RNA polymerase stimulating its binding to certain sets of promoters ___- the standard sigma factor ___- helps RNA polymerase recognize promoters for the different operons that encode the ___-shock proteins, which prevent protein ___ at high temperatures

one σ70 σ32 heat denaturation

Heat Shock Proteins Folding is determined by primary structure of peptide Huge number of possible final structures, only ___ found Other proteins help folding, chaperones and heat shock proteins among them +Final state is ___ energy, many other possible states also are +Intermediate ___ energy states are folding barriers +ATP ___ overcomes barrier

one high hydrolysis

Induction of the lac Operon by Lactose -In the absence of inducer repressor protein binds the ___ -RNA Polymerase is ___ No transcription of the operon In the presence of inducer -Allolactose binds ___; prevents it from binding operator -RNA Polymerase binds ___ -lac operon is transcribed producing a ___ mRNA that encodes for three additional proteins.

operator inhibited repressor promoter polycistronic

lac operon is an example of a

operon

Bacterial Operon ___-a genetic unit where several ___-___ genes are linked together and controlled by a single ___ (ex. lac operon) ___-encodes a single polypeptide chain Regulatory Protein Binding -___-bind within the -___ and ___ region to stimulate polymerase binding -___-inhibit transcription

operon protein-producing promoter cistron Activators 35 upstream Repressors

NERNST POTENTIAL -The diffusion potential level across a membrane that exactly ___ the net diffusion of a particular ion (___). -___ potential of the ion : what the membrane potential must be for the ion to be at equilibrium -The main function of the Nernst equation is to calculate the ion's equilibrium potential at a given concentration gradient -The equilibrium potential is the ___ electrical potential that would be equal in ___ but opposite in ___ to the concentration force Nernst potential is the equal force to balance Net Diffusion

opposes Vx Equilibrium intracellular magnitude direction

Isotoniac IV -Increases ECF volume -No change on ECF or ICF ___ -No change in water movement -Effective in expanding ECF volume with no affect on ICF

osmolality

Osmolality and Water Movement Water distributes between the different compartments according to the ___ of each compartment. Water moves through channels in the cell membrane that separates intracellular from extracellular compartments. ___ - Refers to the concentration of solutes (mOsm per kg water)

osmolality osmolality

Changes in Cell Volume Acute (seconds to minutes) -Regulatory volume increase (RVI) -Regulatory volume decrease (RVD) Chronic (hours to days) -___

osmolytes

Sodium-Potassium Pump -Functioning Sodium-Potassium Pump +Maintains ___ equilibrium +Maintains a ___ membrane potential and thus prevents ___ from entering the cell +Maintains the ___ pressure by excluding sodium chloride (equal osmolality)

osmotic negative chloride hydrostatic

Acute Changes in Cell Volume -ECF increases in osmolality -Osmotic force drives water ___ of the cell (ICF to ECF) -Cell ___ until osmolality equilibrates -Cell ___ activates the cell's ___ ___ ___ (RVI) mechanism -RVI increases sodium and chloride uptake by the cell to ___ intracellular osmolality and draw water back into the cell

out shrinkage Shrinkage regulatory volume increase increase

Around the Helix -Side chains positioned around the ___ of the alpha helix -Allows for them to interact with other parts of protein or external environment

outside

Strong and Weak Acids -Metabolic acids are produced from fatty aid ___ -As the acid dissociates, hydrogen ions and ___ are released into the blood -As a result, the patient's blood pH is ___

oxidation ketones acidic

The Alpha Helix -One common secondary structure -Backbone amino and carboxyl groups can interact with each other -Each ___ of a carbonyl group of a peptide bond forms a hydrogen bond with the hydrogen atom attached to a ___ atom in a peptide bond ___ amino acids down the chain +Point in ___ directions along helix +Positioned to hydrogen bond with amino acid at ___ position further along the chain -Stabilizes the helical structure (makes it rigid) -___, with its odd structure, cannot be in the helix, can end it!

oxygen nitrogen four opposite 4th Proline

pKa of Amino Acids Charge on amino acids depends on ___ Charge on aa at physiological pH is a function of pKa for dissociation of protons from: -alpha-carboxylic acid groups -alpha-amino groups -side chains Changes association of groups with hydrogen ions The pKa is the pH at which ___% of protons have dissociated (two forms are equal) The ___ is the isoelectric point for the molecule; the pH at which there is ___ net charge

pH 50 pI no

Classification by Side Chain Side chains differ significantly Multiple ways to classify +Structure, ___, charge, polar or not, ___, etc. Some fall into two or more categories These groups are significant ones

pKa hydrophobicity

Henderson-Hasselbalch Equation The Henderson-Hasselbalch equation defines the relationship between the pH of a solution the ___ (extent of acid dissociation). When a pKa for a weak acid is known, the equation can be used to calculate the ratio of the ___-___ form. When the ratio of protonated to unprotonated form is 1:1, the ___ ___- the pH at which 50% dissociation occurs (equivalence point)

pKa protonated:unprotonated pH=pKa pKa

Mismatch Repair The Damage: Incorrect, but structurally normal, base is incorporated in the growing chain. If there is nothing structurally wrong with the base, then how does the repair machinery know which base is the parental and which one is the mismatch? Repair mechanisms can identify the ___ strand and therefore can identify which base to replace. -parental strands are ___ in bacteria. -mechanism in ___ is undetermined.

parental methylated eukaryotes

Replication is Semiconservative Semiconservative: ___ strands are conserved, but no longer ___. Each daughter chromosome contains one of the parental DNA strands and a newly synthesized ___ strand.

parental together complementary

Chloramphenicol interferes with the ___ activity of the ___ ribosomal subunit of bacteria

peptidyl-transferase 50S

GOLDMAN-HODGKIN-KATZ EQUATION Em = 60 x log (Concentration ion1 inside x Permeability of ion1 inside) + (Concentration ion2 inside x Permeability of ion2 inside)/ (Concentration ion1 outside x Permeability of ion1 outside) + (Concentration ion2 outside x Permeability of ion2 outside) -Membrane Potential: all the ionic currents across the cell membrane -Membrane Potential determined by the relative ___ of the cell membrane to various ions

permeability

Backbone of Nucleic Acids -Adjacent bases joined by sugar-phosphate backbone -5' phosphate attached to 3' carbon of previous nucleotide -This produces ___ bonds

phosphodiester

The Function of DNA Ligase Problem: Gaps left after removal of RNA primers. Pol I filled gaps but cannot join two strands together. Solution: DNA Ligase forms a ___ bond between the free 3'OH and free 5' phosphate.

phosphodiester

Not Always the Same -Carbon and nitrogen of peptide bond forms a series of rigid ___ -___ can occur around bonds attached to alpha-carbon -Side chains ___ above and below peptide chain -Peptide bond is a ___ between two ___ structures +Results in partial ___ charge on carbonyl oxygen, partial ___ charge on nitrogen, and characteristic of partial double-bond on peptide bond itself -Resists rotation around bonds of backbone, remains planar

planes Rotation alternate hybrid resonance negative positive

Therapeutic Protein from Bacteria Clone coding sequence into ___ ___ Transform and select Determine if ___ is made Purify and test function (combine more than one if needed) Test in cells, animals and humans as needed -Properly controlled clinical ___ only!

plasmid vector protein trials

Functional Groups -a group of atoms within a molecule that is responsible for characteristic chemical reactions of that molecule -Unlike C-C, these groups involve bonds between C-O, C-N, C-S or C-P groups -These bonds are ___ and ___ accounting for the types of reactions of the molecule

polar reactive

Classification Often grouped by ___ of side chain Charged, nonpolar hydrophobic, or uncharged polar Or by structural features Aliphatic or aromatic

polarity

Telomerase Preserves Chromosomal Ends Telomerase: an enzyme containing proteins and RNA that acts as an RNA-dependent DNA ___ 1. Chromosomal ends contain repeating sequences recognized by telomerase. 2. Telomerase contains an ___ template that binds repeating telomeric sequences. 3. Telomerase uses the 3'-OH of the overhang as a primer. The rest of its RNA sequence serves as a template for new DNA synthesis. 4. When the 3′-overhang is sufficiently long, ___ binds and synthesis of the complementary strand is completed.

polymerase RNA primase

Quaternary Structure Many proteins have multiple ___ chains Must bind to each other properly Form a specific final structure that can function Place functional groups in position to act

polypeptide

Beta-pleated Sheets -Two forms, parallel and anti-parallel +Refers to direction of ___ chains +Parallel: polypeptide chains run in same direction (as defined by their ___-terminals) +Antiparallel: run in opposite directions ++___ are often same polypeptide folded back on itself

polypeptide N- and C Antiparallel

Stimulation of RNA Polymerase Binding Activating proteins bind to the cleared promoter and stimulate the binding of RNA polymerase (___ control). -Transcription of the lac operon is induced by ___ in the absence of glucose, but not in the presence of ___ -The presence or absence of glucose is communicated to the promoter by the regulatory protein ___ ___ ___ (cAMP) receptor protein (CRP). -Decreased glucose cause an increase of ___ that binds CRP forming a cAMP-CRP complex -cAMP-CRP complex binds to a ___ region of the operon, stimulating binding of RNA polymerase to the promoter and transcription

positive allolactose glucose cyclic adenosine monophosphate cAMP regulatory

ELECTRONEUTRALITY -# of ___ charges must be the same as the # of ___ charges -___ anion gap

positive negative Serum

Action Potential Upon a stimulus in an electrically excitable cell, Depolarize phase- the Vm will become more ___ until it reaches its peak Threshold - minimum change in membrane potential required for an action potential to develop 2. Repolarize phase- the Vm will begin to become more ___ toward the resting Vm 3. Hyperpolarize phase- try and reach resting Vm following repolarization. After-hyperpolarization is when the repolarization phase leads to a more ___ Vm than the resting Vm We will go into more specifics about each of the phases and why they occur throughout this lecture. If the membrane potential (Vm) does not depolarize enough to reach the threshold, then an action potential does ___ occur.

positive negative negative not

Resting Membrane Potential -Sodium/potassium pump creates electrochemical gradient -Ion leak channels +Allow sodium and potassium to leak down their concentration (controls resting potential) +Membrane is more permeable to ___ than ___ -Combined sodium/potassium pump and leak channels creates a stable resting membrane potential that is negative inside the cell; ___ to -90 mV -Resting membrane potential will be close to the ion to which the membrane has the highest ___ ___ is the key player for controlling the resting membrane. -Why does K+ have the highest conductance? Because of the ___ channels.

potassium sodium -60mV conductance K+ Efflux

CRITERIA OF NEUROTRANSMITTERS 1. substance must be present on the ___ terminal 2. cell must synthesize the substance 3. released on depolarization of the terminal 4. specific receptors for it on the postsynaptic membrane

presynaptic

RNA Polymerase and the Central Dogma -Transcription: the synthesis of RNA (mRNA) from a DNA template. -Does not require ___ -___ Polymerase: the enzyme responsible for transcription -___ DNA template in 3'-5' direction -___ in a 5'-3' direction -lacks 3'-to-5' ___ activity

primers RNA Reads Synthesizes exonuclease

Prokaryotes Have Three DNA Polymerases that Synthesize DNA Under Specific Circumstances Pol III - the major replicative enzyme in ___. ___ - (fill gaps) synthesizes DNA as it fills in the gap left by the RNA primer (discussed next) ___ - (Repair)synthesizes DNA when damaged DNA is removed and new DNA is need to fill the gap (discussed next).

prokaryotes Pol I Pol II

Eukaryotic Transcription Apparatus -General Transcription factors-bind ___ elements and facilitate RNA ___ binding. +Six basal transcription factors (___) +TFIID composed of ___ ___ ___(TBP) and co-activator proteins +RNA Pol II is recruited followed by other TFIIs and transcription is ___

promoter Polymerase II TFIIs TATA binding protein initiated

More Than Just DNA -Human DNA is found in chromatin, not free -Chromatin is DNA plus various ___ -Has been seen as "___ ___ ___ ___" -Specific proteins cause packing of ___ into chromatin -That string of beads is chromatin

proteins beads on a string DNA

Post-translational Modifications -Amino acids can be chemically modified in ___ -May alter ___ and function of protein -Done to proteins, not ___ amino acids -May be retained or reversible for regulation of function -Phosphoralation is important for function of proteins can be reversible.

proteins location free

Many Types of RNA -RNA has many functions, different forms for each function -Generally single-stranded -Three major functional forms +___, structural and functional components of ribosomes, majority of RNA in most cells +___, carries protein coding sequence +___, matches amino acid with codon

rRNA mRNA tRNA

FACILITATED DIFFUSION -More ___ than simple diffusion -___ mediated and exhibits stereospecificity, saturation, and competition

rapid Carrier

Bicarbonate Buffer System 1: CO2 produced in tissue diffuses into interstitial fluid and blood plasma and then to ___ 2: Carbonic ___ within rbc converts CO2 to ___ acid (H2CO3) 3: Carbonic acid dissociates to H+ and ___- (bicarbonate) 4: H+ is buffered and combines with ___ via histidine 5: Bicarbonate is transported out the cell & in to the blood in exchange for ___- to buffer H+

rbc anhydrase carbonic HCO3 Hb Cl

Important Points for K+ -The cell membrane is VERY sensitive to potassium to changes in the extracellular potassium ion concentration -Potassium leak channels , there is a net flux of potassium across the membrane -Increased extracellular potassium ions will ___ the efflux of potassium causing ___ -Decreased extracellular potassium ions will ___ the efflux causing hyperpolarization

reduce depolarization accelerate

Genes and Chromosomes -Each genes is located at a ___ site on a specific chromosome (known as genetic ___) -Order of genes generally does not vary -Genes and the proteins they produce can vary -Homologues may differ, but function should not

specific locus

Lipids: Sphingolipids Lack glycerol and instead are formed from ___.

sphingosine

Removal of Introns: Splicing "snurps"-Small nuclear ribonucleoproteins (snRNPs) form the ___ Complex that ensure accurate ___ splicing -___ binds within the intron forming a loop -cleavage occurs between the 3'___ of intron and 5'___ of the exon -exons are joined together; introns are degraded to ___

spliceosome exon splicesome AG GU nucleotides

For now, we can ignore the Na+/HCO3- transporter The ___ of this transporter will determine whether it functions as an acid/extruder or acid loader

stoichiometry

Acid Dissociation Classified as "weak" or "strong" by the degree of dissociation to H+ ion and base. -___ acids (sulfuric acid, hydrochloric acid) dissociate completely in solution -___ acids containing carboxylic acid groups dissociate into hydrogen ions and an anionic component (conjugate base). Weak acids only partially dissociate.

strong weak

Action potentials can be generated different ways. Short duration but a ___ stimulus Long duration but a ___ stimulus This is important because different stimuli will result in different changes in Vm. Stimuli will be of different strength and different duration. The summation of these different stimuli can come together to generate an action potential in different ways.

strong weak

Sickle Cell Anemia -First disease known to be due to ___ variation -Patients have pain crises due to ___, block blood flow to tissues -Red cells in capillaries may have altered shapes, block flow under ___ oxygen tension -No oxygen, no waste removal, tissues ___ locally

structural infarctions low damaged

What Data Can We Use? -Lots of types available -Data on protein ___ differences -Data on gene sequence changes -Much of DNA is not protein coding genes, but ___ DNA, some of it ___ -Some differences are not in sequence but ___ levels

structure repetitive polymorphic expression

Tertiary Structure Combination of secondary structures to form structural patterns called domains and ___-domains Tertiary structure is the folding pattern of those secondary structural elements into a ___-dimensional structure designed to serve the protein's function +Creates sites for ___ binding, sites for protein trafficking (and location), and cell ___ +___ and dynamic! +Vander walls

sub three ligand signaling Flexible

DNA Polymerases Catalyze DNA Synthesis -Deoxyribonucleoside triphosphates (dATP, dGTP, dCTP, and dTTP) serve as ___ for the addition of ___ to the growing chain. -Incoming nucleotides form base pairs with their complementary nucleotide on the ___ strand.

substrates nucleotides template

Gene Deletions Gene Deletions can occur through errors in DNA replication and cell division and are usually noticed only if a disease results. -not a normal means of controlling transcription -various types of cancers result from loss of a good copy of a tumor ___ gene leaving the cell with a mutant copy.

suppressor

The Beta Turn Characterized by an abrupt change of direction Often found on the protein ___ β-turns: short regions of ___ amino acid residues +Connect strands of ___-parallel sheets Ω-loop: found in large ___ proteins

surface 4 anti globular

Ribose and Deoxyribose -Ribose in RNA -Deoxyribose in DNA -Carbons are numbered for identification -When linked to a base, add a ___ to indicate carbon is in sugar -Thus, 5 become 5' (5 prime) -Symbol means carbon is in the sugar (5')

symbol

NEUROTRANSMITTERS Electrical signals must pass from cell-cell at a ___ Communication between cells at a synapse can be either electrical or chemical Electrical synapse provide direct electrical continuity by means of a ___ junction Chemical synapse release a chemical neurotransmitter to relay electrical signals Neurotransmitters are Substances that mediate chemical signaling between neurons Neurotransmitters relay, amplify, and modulate signals between a neuron and another cell

synapse gap

Ribosomes -Ribosomes are site of protein ___ -Contain many proteins and a few ___ molecules -Prokaryotes differ from eukaryotes in ___ -___ RNA species derived from one large precursor, ___ is separate transcript -Pro. contains ___ RNA whereas Eu. contains ___

synthesis RNA size Larger 5S 3 4

R And T States in Binding Without oxygen, globin chains are in T (___) state Binding sites are hindered, binding is difficult When oxygen binds to one, conformation of all four changes somewhat Conversion to R (___) state relieves hindrance, binding is easier As binding to one globin can change all subunits, binding follows a ___ model

tense relaxed concerted

In contrast to a hyperpolarizing stimulus or a depolarizing stimulus that DOES NOT reach threshold (no action potential generated), a depolarizing stimulus that reaches threshold will not decay over distance away from the stimulus. (Think of it as the action potential needs to communicate. Therefore, the action potential needs to travel and NOT decay in order to communicate). However, even though the action potential does not decay, there is a delay between each successive action potential as it travels away from the stimulus. This delay in the subsequent action potential is due to the ___ ___ that will be discussed in the next couple of slides. Bottom line, action potential remains constant in magnitude and shape as it travels away from the stimulus. However, the delay between subsequent action potentials as it travels increases with distance due to the refractory period of the action potential.

refractory period

Action Potential Stimulus: Successive Action Potentials Refractory Periods Absolute Refractory - time after initiation of an action potential to time after the peak when ___ is almost complete Action potential ___ be initiated Relative Refractory - time at the end of the ___ and part of the ___ phase Action potential can be generated during this period but the stimulus must be stronger or longer than the stimulus for the ___ action potential

repolarization CANNOT repolarization hyperpolarization first

Alternative Splicing & Polyadenylation Sites Causes different proteins to be produced from the ___ gene Ex) genes that code for ___ are regulated by alterations in the splicing and polyadenylation sites

same antibodies

What is Physiology? *Homeostasis -(homeo = ___, stasis = to ___) -Maintenance of a constant internal environment -Maintenance of a condition of steady state or stability within its internal environment when dealing with external changes -The body's attempt to maintain "normal" levels within your body -Physiology is largely a study of processes related to homeostasis " All the vital mechanisms, varied as they are, have only one object, that of preserving constant the conditions of life in the internal environment." - Claude Bernard

same stay

Summary 2 -RNA replaces Thymine with Uracil and deoxyribose with ribose -Different RNA forms have different functions -Prokaryotic and eukaryotic ribosomes differ -RNA can have extensive ___ structure -Retroviruses can copy ___ to ___ with Reverse Transcriptase

secondary RNA DNA

Genes Gene - a ___ of DNA that functions as a ___ to generate an ___ product and a subsequent protein ___ The Gene Unit includes: ___ region contains the template for synthesis of an RNA, which begins at the start point Regulatory regions that regulate production of the ___ product, such as a ___ region

segment unit RNA product Transcribed encoded promoter

Osmosis versus Osmolality -Osmosis - diffusion of a solvent (water) through a ___ membrane from an area of ___ solute concentration to an area of ___ solute concentration -___ - the number of milliosmoles/liter (mOsm/L) of solution. It is the concentration of an osmotic solution -___ - the number of milliosmoles/ kg (mOsm/kg ) of solvent. It is the concentration of the particles that are free in a solution. Example: Serum osmolality: 282 - 295 mOsm/kg water

semi-permeable low higher Osmolarity Osmolality

-Prokaryotic DNA is not ___ from the rest of the cell -DNA is not ___ by protein -Eukaryotic DNA is located in the nucleus and ___ separated from the rest of the cell by the nuclear membrane -DNA i___ bound by proteins

separated bound is s

Osmolal Gap -Both ionic and nonionic substances contribute to ___ osmolality -Under normal conditions, serum ions and anions, glucose and ___ ___ ___ (BUN) contribute to the serum osmolality -Normal serum osmolality between 280 and 300 mOsm Calculated serum osmolality = 2[Na+] + ([Glucose]/18) + ([BUN]/18) -Use the calculated osmolality and compare to actual measured ___ osmolality (should not be much of a difference) -Elevated osmolal gap can be due to ethanol, methanol, ethylene glycol, isopropanol, excess serum lipids, excess serum proteins........

serum blood urea nitrogen serum

Undissociated vs Dissociated -Metabolism produces ___ acids -As dissociation occurs, there is increased [___] in the blood or other body fluids -undissociated acid "___ acid"; dissociated anionic compound "___"

several H+ -ic -ate

Gene Therapy is no longer a fantasy... In 1990, a 4-year-old girl names Ashi DeSilva was the first patient to receive gene therapy for ___ ___ ___ (SCID) She is now a healthy adult with an immune system that was able to fight off most infections

severe combined immunodeficiency

Water as a Solvent-NaCl Hydrogen bonds form hydration ___ that are strong enough to dissolve polar molecules. chloride (Cl-) and bicarbonate (HCO3-) are surrounded the δ+ hydrogens. inorganic cations such as Na+ and K+ are surrounded by the δ− oxygen. ___ bonds are weak enough to allow movement of water and solutes. Water is attracted to the negative of chloride with its hydrogen positive charge.

shells Hydrogen

Mutations Point Mutation: A single DNA base is altered producing a change in a ___ base of mRNA codon. ___: A change that specifies the same amino acid ___: A change that specifies a different amino acid -Sickle cell anemia (E6V) ___: A change that produces a stop codon - β-thalassemia

single Silent Missense Nonsense

Saturated Fatty Acids have ___ bonds between the carbons in the chain ___ acid (C16) and ___ acid (C18) are most common in cells ___ melting point (solid at room temperature)

single palmitic stearic High

Repetitive Sequences in Eukaryotic DNA Prokaryotes have ___ gene copies while eukaryotes have ___ sequences Highly repetitive sequences are ___ base pairs in length that are present in 100,000-1,000,000 copies clustered within a few locations in the genome.

single repetitive 6-100

Reverse Transcriptase Reverse Transcriptase: an enzyme that uses a ___ ___ ___ template and makes a DNA copy RNA source: Transcribed from DNA or from RNA virus (___) Produces a DNA copy of the RNA -___ (DNA that is complementary to the RNA copy) -RNA is degraded A ___-stranded cDNA is produced, which can become integrated into the human genome

single-stranded RNA retrovirus cDNA double

Action Potential Upon a stimulus in an electrically excitable cell, 0. Rest - sodium and potassium voltage-gated channels are closed 1. Depolarize - Sodium and potassium channels are opened. Potassium channels have a delayed opening so ___ conductance is solely responsible for this phase. -Some sodium channels are activated until threshold is met (first tiny bump of the depolarization phase) -More sodium channels are ___ once threshold is met (rise to peak) 2. Repolarize - Sodium channels are ___. Potassium channels are opened 3. Hyperpolarize - sodium channels ___. Potassium channels are open until ___ ___ is reached

sodium activated inactive closed resting Vm

Medicine makes Na+ go in cell then so will ___.

water

Dissociation of Weak Acids The tendency of acid (HA) to dissociate and donate a H+ to the solution is denoted by its Ka. -Ka= equilibrium constant for dissociation of a weak acid Large pKa=___ acid Low pKa=___ acid

weak strong

Two forms of ___ ___ (XPB and XPD) are caused by mutation in TFIIH

xeroderma pigmentosum

Summary -DNA synthesis replicates both strands at once -Antiparallel nature of strands means leading and lagging strands replicate differently -Several DNA polymerases exist with different capacities, some mainly for repair -Helicases, topoisomerases also necessary -Eukaryotes and prokaryotes differ in details -Telomerase necessary in eukaryotes -DNA damage can take many forms -Different types of damage require different initial repair steps -All repair involves gap creation, filling and ligation -Recombination may be normal or abnormal -Chain terminators important antivirals that act by preventing viral DNA replication

yeah

Why Map and Clone Genes? Locate causes of genetic disorders Determine identity of gene product Determine how mutations cause their effects Develop new diagnostic techniques Develop new therapies Increase human knowledge Human genome now almost completely mapped and sequenced

yeah

Acid-Base Disturbances Respiratory acidosis Respiratory alkalosis Metabolic acidosis Metabolic alkalosis

yeah bra

Chemical Transmission Step 1: Neurotransmitter molecules are packaged into synaptic vesicles Step 2: Action potential arrives at the pre-synaptic terminal Step 3: Depolarization opens voltage-gated calcium channels Step 4: The rise in intracellular calcium triggers fusion of synaptic vesicles with the presynaptic membrane Step 5: Neurotransmitter diffuses across synaptic cleft Step 6: Neurotransmitter binds to receptor on postsynaptic cell Step 7: Process is terminated

yeah bra

Summary Sequence of mRNA determines protein sequence Genetic code is almost universal, nonoverlapping, degenerate and unambiguous Mutations alter DNA and RNA sequence, may alter protein sequence Point mutations alter one base Aminoacyl-tRNA synthetases attach amino acids to tRNA Translation initiates with mRNA on small and Met-tRNA on large ribosomal subunit Initiation and elongation factors are necessary Polysomes may be in cytoplasm or on RER Modification alters protein function Targeting to organelles is important Some antibiotics act by inhibiting translation

yeah bra

The ALL-or-NONE Principle -If threshold is not reached, then no action potential is generated -If threshold is reached, then an action potential is always generated

yeah bra

A 42-year-old woman decides to lose weight on a diet prescribed by an anorexic friend. She loses about 30 pounds in 45 days, but her serum potassium level falls to 2.1 mmol/L (normal: 3.5 to 5.0 mmol/L). Which of the following changes is most likely to occur in this young woman?

yes

However... Gene therapy still in its early stages and is far from perfection -It can only be used in diseases caused by a single gene malfunction +Many diseases are caused by multiple genes -It can be hard to get a good gene to the specific place it needs to be +More damage can be caused by genes being put in the wrong place -Deaths can results due to infections and invasions of other viruses

yesh

The Zinc Finger Motif of Steroid Receptors -contains a bound ___ chelated at ___ positions with either ___ or ___ in a sequence of ~20 amino acids -Forms a relatively ___, autonomously folded domain (that look like fingers) -___ zinc-fingers that function independently +One zinc finger forms an ___-helix with nucleotide recognition signal (NRS) that that binds specific base sequences in the major groove of DNA

zinc four histidine, cysteine small 2-6 α

Amino Acid Structure Proteins are made from ___-amino acids Amino and ___ groups bound to α-carbon ___ and a side chain also bound to α-carbon Amino and carboxyl groups can be ionized, dependent on ___ Side chains may be ionized as well

α carboxyl Hydrogen pH

Prokaryote Transcription Binding of RNA polymerase with a ___ to the promoter region of DNA causes the two DNA strands to further ___ and separate As the polymerase transcribes the DNA, the untranscribed region of the helix continues to ___, whereas the transcribed region of the DNA template ___ its DNA partner

σ-factor unwind separate rejoins

5-Fluorouracil (5-FU) -5-FU is an inhibitor of ___ synthase, the enzyme required for synthesis of dTMP from dUMP (i.e. it makes thymidine) -prevents cells from making sufficient ___ for DNA replication -Suicide -Won't be able to base pair prevents DNA synthesis.

thymidylate dTTP

a protein that can potentially bind to a DNA sequence?

trans

No primer needed in ___

transcription

RNA polymerase

transcription

Attenuation (Interruption) of Transcription Some operons are regulated by a process that attenuates ___ after it has been initiated (trp operon). When tryptophan levels are low, levels of Trp-tRNATrp are low and ribosomes stall at codons for tryptophan; facilitated by a ___ ___. When tryptophan levels are high, high levels of Trp-tRNATrp and rapid translation of the transcript. However, rapid translation generates another hairpin loop that serves as a ___ signal for RNA polymerase.

transcription hair loop termination

Enhancer element: Region of DNA that binds to ___ ___ and Increases the transcription rate. Silencer element: Region of DNA that binds to ___ and lowers the transcription rate. Repressor: Proteins that binds to ___ ___ and lowers the transcription rate. Cis element vs. Trans factor: -___ element: a DNA sequence that can potentially bind to a protein factor -___ factor: a protein that can potentially bind to a DNA sequence

transcriptional activators REPRESSORS silencer elements cis trans

Stability of mRNA Degradation rate of mRNA is important ___ receptor mRNA has 3' IREs Low ___, bound IRE-BP protects 3' end More protein made, more iron can enter cell ___ iron, no binding, mRNA degraded faster

translated iron High

DIFFUSION -Not an efficient process -Cell 20 um in diameter with a PM composed of phospholipids dissipation of: +urea takes 8 minutes +glucose and amino acids take 14 hours +ion gradients would take years -Most important molecules cross via specific membrane transport (ion channels or solute carriers) What makes it more efficient? Uses ___ proteins.

transport

RATE OF DIFFUSION -The rate at which the molecule can be ___ can never be greater than the ___ at which the carrier protein molecule can undergo change back and forth between its two states.

transported rate

At Vm intracellular concentrations for K+ are 155mM and extracellular are 4.5mM. If we block the sodium-potassium pump, the intracellular potassium concentration will decrease?

true

Antibiotics that Target Transcription Rifampin -antibiotic used to treat infections, often ___ -inhibit bacterial RNA polymerase! (No ___) -eukaryotic nuclear RNA polymerase is not affected, but can inhibit synthesis of mitochondrial RNA (thus side effects) ___ D -binds to DNA and inhibits mRNA synthesis, with chain elongation more sensitive than initiation, termination, or release.

tuberculosis elongation Actinomycin

Familial Hypercholesterolemia In some cases, homologous recombination is believed to have occurred between ___ DNA repeats, resulting in a large deletion in the low-density lipoprotein (LDL) receptor gene. Patients who are homozygous for this mutation may die from cardiac disease as early as in their ___ or ___ decade of life. 40 yr old patient presents with ___ chest pain; and visible tuberous ___ familial ___ Total cholesterol: 550 mg/dL (<200) Triglycerides: 180 (<150) HDL: 34 (≥60) LDL: 480 (<100)

two 2nd 3rd exertional xanthomas hypercholesterolemia

Genome Wide Association Studies GWAS are common way to look at complex disorders that are not well ___ -Autism, schizophrenia, obesity, hypertension, etc. Many genes may contribute Need to study many ___, compare affected and not affected Need to study many gene ___ at once Locate those in common in ___ people

understood individuals loci affected

ANION GAP -Increase or decrease in anion gap requires looking into metabolic disorders or other pathological conditions -Increased anion gap indicates the number of ___ anions increased -Decreased anion gap indicates a reduction in the number of ___ anions

unmeasured unmeasured

RNA and Uracil -In RNA, ___ replaces thymine -Difference is one ___ group +Thymine might be called 5-___ -Same type of pairing occurs in hydrogen bonding -Also, ribose instead of deoxyribose in backbone

uracil methyl methyluracil

Gene Therapy Basics Idea is to replace function of mutated gene with normal product Have to get product made in the appropriate cells Identify gene needed, place in ___ that can enter cells and deliver gene -Viruses, liposomes, ___ material Determine if product is made in sufficient quantity to have effect Hope for no side effects!

vector polycationic

Ionic Currents -Movement of ion creates a current -The movement of ions across the cell membrane generates an electrical difference between ECF and ICF; membrane potential -Sum of ionic currents = total ionic current -Equation - ___ -Current carried by a particular ion varies with membrane voltage -The membrane ___ will dictate the direction of gradient for ions.

-Itotal= Ik+Ina+Ica+Icl voltage

Acid Loader versus Acid Extruder Acid Extruders: #3 Acid Loaders: #1

-Na-H exchanger -Na+-driven Cl-HCO3 exchanger -V-type H+ pumps -Cl-HCO3- exchanger

3 steps to initiation, elongation, and termination

1. Aminoacyl-tRNA binds the A-site 2. Formation of a peptide bond 3. Translocation

Transfer RNA -Small RNA, <___ bases -Typical ___ shape -Has site to attach specific amino acid -One loop has anticodon, complementary to coding sequence for one amino acid in mRNA -Important in flow of information, DNA>RNA>protein

100 cloverleaf

Eukaryotic DNA Polymerase In contrast to prokaryotes, eukaryotes have ___ identified polymerases! Replicative Enzymes: Pol δ (___) and ε (___) are the major replicative enzymes while Pol a (___) aids primase in primer formation. Repair Enzymes: Polymerases that lack ___ exonuclease activity are called bypass polymerases because they can "bypass" ___ DNA.

15 delta (lagging), epsilon(leading) major replication alpha (starting) 5' damaged

Streptomycin binds ___ rRNA of the ___ subunit and inhibits translation ___

16S 30S initiation

Calcium -Calcium ECF = ___ -Calcium ICF = ___ -Large inwardly directed electrochemical gradient for ___

1mM 100nM calcium

Human Genome Project -1990-2000 entire human genome was mapped -3 billion base pairs; ___ genes -Led to identification of a large number of single nucleotide ___ (SNPs) +Plentiful in genome occurring every ___ bp they are a useful tool for mapping diseases genes within the chromosome -Provided information that can be used to help replace genes that are defective or missing in people with genetic diseases

25,000-30,000 polymorphisms 100-300

NERNST POTENTIAL Nernst Potential for univalent ion: At room temp: RT/F = ___. Equation simplified to : Ex = - 61.5 mV/Z log10 [(concentration inside / concentration outside)] Ex= equilibrium potential for single ion Z = value of the charge (ignoring sign of charge)

25mV

Formation of Aminoacyl-tRNA: Get Charged! Aminoacyl-tRNA: tRNA that contains an amino acid attached covalently to its ___'-end, also known as "___ tRNA."

3 charged

Na+/K+ pump does what with Na+ and K+

3 Na+ out 2 K+ in

DNA Polymerases Catalyze DNA Synthesis DNA polymerase COPIES the parental template in a ___ direction

3'-5'

Structural Characteristics of RNA Similar to DNA -Composed of nucleotides -___ phosphodiester bonds -A, C, G -___ base pairing -5 carbon sugar attached to ___ Different from DNA -___ stranded -Ribose sugar, instead of deoxy -U instead of T binds A

3'-5' Complimentary base Single

DNA Synthesis Requires a Free ___ Group

3'OH

Tetracycline binds ___ ribosomal subunit and blocks binding of the ___ to the A site of the ribosome

30S aminoacyl-tRNA

Eukaryotic Transfer RNA (tRNA) Ensures the genetic code is translated into the correct sequence of amino acids. Structure= amino acid binding site + ___ loops Amino Acid Binding Site- binds the encoded amino acid Stems-___ pairing occurs in the stem regions contributing to 3D structure

4 base

D- and L- Variants The α-carbon is bound to ___ different groups 2 forms possible, not ___ (mirror images), the D- and L- forms Only the ___- form is used in proteins and for most metabolism Exception - ___, one form only

4 superimposable L glycine

Maturation of rRNA Transcribed as ___ S precursor Several cleavage steps 5.8 S RNA pairs with 28 S

45

Synthesis of Eukaryotic Ribosomal RNA (rRNA) -RNA Pol I synthesizes a large ___ transcript within the nucleolus -RNA Pol ___ synthesizes a ___ rRNA from outside the nucleolus -Processes rRNA combines with proteins to form the ___ and ___ ribosomal subunits

45S III 5S 60S 40S

pH and Ionization State pKa=___ What is the ratio of acidic:basic form at pH 5? Recall that a change in 1 pH unit=___ fold change in [H+]

5 10

Upstream is in the ___ direction

5'

Basics of mRNA Structure -Not all of mRNA codes for protein -___ end has leader sequence and protective cap structure -___ end has untranslated region and poly-A tail -Only ___ region is translated into protein

5' 3' coding

Strands are Antiparallel -Strands have a direction set by the backbone -Strands are synthesized from a ___ to ___ direction -Paired strands run in opposite directions -Necessary for hydrogen bonding to hold strands together

5' to 3'

DNA polymerase SYNTHESIZE the new strand in a ___direction

5'-3'

Methylation of DNA Cytosine residues in DNA can be methylated to produce ___ -near or within the ___ regions (located in ___ Islands) Methylated genes are ___ readily transcribed than those that are not methylated. -___ genes are more extensively methylated in cells that are not part of the red blood cell lineage

5-methylcytosine. promoter CpG less globin

Water - Key Concepts -Approximately ___% of our body weight is water. -Water is distributed between intracellular and extracellular (fluids, blood, lymph) compartments. -The dipolar nature of water allows it form hydrogen bonds with other polar molecules and acts as a solvent. -The concentration of electrolytes or solutes is referred to as ___: the concentration of a solution expressed as the total number of solute particles per kilogram water. -Osmolality drives water movement across ___ cellular membranes. -During osmotic diuresis, high levels of blood glucose and ketone bodies results in ___ osmolality of glomerular filtrate. As a result, ___ water is excreted in the urine.

50% osmolality semipermeable high more

Azithromycin binds ___ ribosomal subunit and prevents ___

50S translocation

Relationship Between DNA Strands, mRNA, and Protein mRNA codons are read ___ determine the amino acid sequence of the protein Thus, the base sequence of the ___ strand of the DNA can be used to determine the amino acid sequence of the protein.

5′ to 3′ coding

Blood Plasma *Plasma Protein -Make up ___% of total blood volume -#3 -Lab analysis used to determine health

7 -Albumin -Fibrinogen -Globulin

What is the body distribution of water? -60% of the adult body, (___% children) acts as a solvent, buffer important for molecule and heat transport participates in chemical reactions factors that affect body water include: Total fat percentage, gender Females less water than males

75

A patient with renal failure and increased extracellular H+ will have activation of which of the following transporters to correct extracellular pH?

A An increase in extracellular pH due to renal failure Want to bring bicarb into the extracellular compartment to increase pH Answer is A the chloride-bicarbonate exchanger (acid loader for intracellular pH) Activation of this transporter will cause acidosis inside the cell too until extracellular pH is corrected then intracellular pH will follow

Translation Occurs in Three Steps: Initiation, Elongation and Termination Termination: occurs when a stop codon moves into the ___ site on the ribosome. -There are no ___ that contain anticodons that can pair with stop codons -Instead, release factors bind the ribosome causing peptidyl transferase to ___ the bond between the peptide chain and tRNA and the peptide is released.

A tRNA hydrolyze

Activation of Sets of Genes by a Single Inducer The 1st regulatory protein stimulates the transcription of genes ___ and ___ which have a common regulatory sequence in their control regions The protein product of gene B is a transcriptional ___ that stimulates transcription of genes E, F, and G (contain common regulator sequence)

A and B activator

Gene Therapy Successes and Failures -Successes in many research and pre-clinical trials -Patients with Severe Combined Immune Deficiency (SCID) due to two different causes (___ and ___-linked) have had improvements Failures - hard to treat ___ types of cells Cannot treat all cells of body at once Some SCID patients had insertions activating ___ One died of leukemia, others required chemotherapy

ADA and X many oncogenes

pH -pH is one of the most important parameters for life. -Virtually every biological process is sensitive to changes in pH, and some are exquisitely sensitive. -A change in pH can affect membrane transporters, channels, and ____ pumps. Thus, dysregulation of pH is associated with a wide array of pathologies including cancer, hypertension, reperfusion injury and aging. -Thus transporters have evolved to regulate pH in organelles, the cytosol, and the extracellular fluid.

ATPase

Acid-Base Disorders-Key Concepts -___ is the accumulation of H+. -___ is the loss of H+. -The bicarbonate buffer system is in equilibrium between the metabolic component (___) and the respiratory component (___) -The respiratory and metabolic components compensate for changes in the other. -The four types of acid-base disorders are metabolic acidosis, metabolic alkalosis, respiratory acidosis, and respiratory alkalosis.

Acidosis Alkalosis H+ CO2

Acids and Bases-Key Concepts -___ donate hydrogen ions (H+) to solution. -___ (OH- for example) accept hydrogen ions. -___ refers to the concentration of hydrogen ions and is calculated as the -log [H+] . -___ acids are product of fatty acid metabolism; excess fatty acid metabolism (insufficient insulin) results in ___ and an increase in ___. -___ represents the dissociation of a weak acid and is used to calculate the ratio of unprotonated to the protonated form at any pH. (pH<pKa=___; pH>pKa=___) -1 pH unit change represent a 10 fold change in H+ ; inversely correlated (↑pH=↓[H+]).

Acids Bases pH Carboxylic ketoacidosis pH pKa protonated unprotonated

Domains and Sub-domains Domains may be comprised of several sub-domains Substructures may be defined and seen in other proteins For example, +___ fold shown with ATP bound in the ___ +Common to proteins that bind and use ___

Actin cleft ATP

Classification Side chains of nonpolar hydrophobic amino acids cluster together to exclude water: hydrophobic effect #6 Uncharged polar amino acids participate in hydrogen bonding #5

Alanine Valine Leucine Isoleucine Phenylalanine Methionine Serine Threonine Tyrosine Asparagine Glutamine

α-___ (Transcription Inhibitor) -Toxin produced by death cap mushroom and destroying angel mushroom -Inhibits eukaryotic RNA Pol II Prevents mRNA synthesis Symptoms: initial GI, then ___ failure Treatment: Liver transplant

Amanatin liver

Classification ___, ___: contain amide group, aliphatic, polar, uncharged ___, ___: contain hydroxyl group, aliphatic, polar, uncharged All four can form ___-bonds with water, each other, the peptide backbone, or other polar compounds

Asparagine, glutamine Serine, threonine H

If the concentration of sodium is 145mM outside the cell and 12mM inside the cell, what is the equilibrium potential for sodium? 42 slide turning point question =

B

Gene Rearrangement Movement of DNA segments from one location to another, associating with each other in various ways to produce different proteins Occurs in ___ cells that produce antibodies -2 light chains, 2 heavy chains -each chain contains a ___ region and ___ region. B cell precursors-hundreds of VH sequences, ___ DH sequences, and ___ JH sequences are located in clusters within a ___ region of the chromosomes. Recombination of these sequences results in a considerable immune response......

B variable constant 20 6 long

Steroids and Cholesterol ___ ___ is formed from cholesterol (line the surface of micelles in the lumen of the intestine and contains the ring structure. 17β-estradiol is a derivative of cholesterol and contains the ___ structure.

Bile salt ring

Nucleotide Excision Repair (NER) The Damage: Mismatched bases or bulky adducts cause DNA distortion (___). The Key Players in the Repair: Excision ___-remove the distorted region DNA ___-adds new dNTPs to the 3'-end using intact complementary DNA as template. DNA ___-joins the newly synthesized segment to the 5'- end of the original strand.

BAP endonucleases Polymerase ligase

Basic Nucleic Acid Structure Nucleic acids are polymers of repeating units (nucleotides) Nucleotides have 3 parts ___#3 4 different bases, order determines sequence ___#4

Base 5-carbon sugar Phosphate 2 sugars, DNA vs. RNA

Base Pairs and Denaturation -DNA can be denatured by heat +Strands separated after hydrogen bonds broken -___ composition determines denaturation temperature +___ pair denatures at lower temperature, only two bonds vs. 3 for ___ pair -Can be monitored by ___ absorption +Bases absorb at ___ nm, absorb more when more exposed in ___ strands

Base A-T GC UV 260 single

How can cell volume be manipulated? -Mannitol versus urea -Mannitol ___ cross the cell membrane -Urea ___ cross the cell membrane -How do these two affect osmolality and cell volume?

CANNOT CAN

The Bicarbonate Buffer System Functions in Delivery of Oxygen to Tissues As RBCs approach the lungs, the direction of the equilibrium reverses such that ___ is released from the RBC.

CO2

Respiratory Acidosis Results from the inability to eliminate ___ pH of the blood decreases as a result of CO2 retention ___, sleep apnea, obesity, alveolar ___ Acute changes occur that protect the cells against ___ acidosis -Respiratory chemoreceptors will sense this drop in pH and ___ respiratory drive Chronic exposure to elevated pCO2 -____ expression of acid extruders: Upregulate -___ expression of acid loaders: downregulate -Counter the ___ and maintain excitability of a cell

CO2 COPD hypoventilation ECF increase Increase Decrease acidosis

The Bicarbonate Buffer System: The Relationship Between CO2 and H+ Le Chatelier's Principle: A system at equilibrium Source of ___ : Cell metabolism (TCA cycle) Source of ___ : fatty acid oxidation

CO2 H+

Disorders of the Acid-Base Balance The respiratory and metabolic components: one tends to compensate for the untoward changes in the other. Bicarbonate reabsorption will adjust to respiratory induced changes is ___. Respiration rate will adjust for metabolic induced changes in ___ concentrations.

CO2 bicarbonate

Respiratory Acidosis Results from the inability to eliminate ___ CO2 retention ___ blood pH ACUTE: Respiratory chemoreceptors will sense the drop in pH and ___ respiratory drive to eliminate CO2 What happens if you have a disease like COPD and have chronic CO2 retention? See next slide for answers

CO2 decreases increase

The Bicarbonate Buffer System ___ acid is both the major acid produced by the body and its own ___.

Carbonic buffer

Regulation and Integration -Exists at all levels of organization -___: e.g. genes, operons, repressor proteins, transcription factors, membrane transport -___: e.g. autacoids, paracrines -___ ___: e.g. nervous and endocrine systems

Cells Tissues Organ systems

The Human Body - A Complex Society of Differentiated Cells -___: the basic structural and functional unit (~ 100 trillion) -___: (e.g. muscles, epithelial, nervous ) -___: (e.g. kidney, heart, liver, pancreas) -___ ___: (e.g. cardiovascular, urinary)

Cells Tissues Organs Organ systems

Change of K+ ....

Change in electroexcitability.

Change of in Na+ elicits .....

Change in movement of water.

The pCO2 Regulates Ventilation Rate via ___ The respiratory center within the hypothalamus controls the rate of breathing and is sensitive to pH. Rate of breathing contributes to the regulation of ___ through its affects on dissolved CO2 content of blood.

Chemoreceptors pH

___ -Liver disease results in decreased levels of proteins in the blood -Decreased proteins results in decreased ___ ___. -Water then moves out of the blood into spaces in the ___ or leg

Cirrhosis plasma osmolality abdomen

Clinical Correlation A 53-year-old male presents to the ED with substernal chest pain of 2 hours duration and diaphoresis. Pain is unrelieved by changing position or acetaminophen. Blood is drawn for analysis and a 12-lead EKG is attached. The EKG shows ST segment elevation consistent with a myocardial infarction. What about the blood tests?

Clinical Applications -Proteins are present in different tissues at different levels -May have different forms in different tissues -Levels of proteins in blood can change after damage to tissues -Blood tests can be useful in diagnosis or following disease progression -Myocardial infarctions release heart proteins after damage, found in blood -CK-MB (CK-2) is heart form, as are certain troponins, useful in identifying damage

Clinical Correlation A 7-year-old African-American male presents to the pediatrician with abdominal pain and swollen hands and feet Pain is in the lower left quadrant. History includes a painful episode three years earlier in the LRQ, with subsequent appendectomy. He remained hospitalized with persistent pain and anemia for a week after the operation Follow-up with a hematologist was not done as parents did not feel it was necessary

Clinical Correlation Blood is drawn for tests. CBC reveals low hematocrit, low hemoglobin, anisocytosis and poikilocytosis, normal white blood cells, normal platelets, and elevated reticulocytes Blood chemistry shows elevated bilirubin What is the diagnosis?

Clinical Correlation A 22-year-old male presents with intense pain in his left flank radiating to the pubic region and hematuria. He had a similar episode three years before. Imaging reveals calculi in both kidneys, with one on the left in the ureter. Urinalysis shows a moderate number of red cells. Acidification of the urine causes precipitation of hexagonal crystals.

Clinical Correlation Stones are primarily cystine Problem is defect in transport of basic amino acids Two amino groups on cystine means it is transported by the transporter that handles arginine, lysine and ornithine Least soluble of group, will precipitate first

Structure of tRNA ___ pattern due to base pairing Several bases altered after synthesis to bases not found in other RNA Includes ___ and ___ True 3-dimensional structure looks very different

Cloverleaf thymine pseudouracil

___ - increase hydrogen bonding with other molecules ___ - decreases bonding.

Cold Hot

Rate of Diffusion Depends on 3#

Concentration Electrical potential Pressure difference across the cell

Solute Transport *Permeable membrane *Driving Force -___ ___ of the solute -___ potential difference -___ difference

Concentration gradient Chemical Electrical

What Factors Control Ion Movement? Membrane ___ Proportional to the permeability of the membrane or the ease with which ions move through it Channel # Probability channel is open ___ of Open channel (resistance through plasma membrane)

Conduction - ability for stuff to move across membrane. Conductance

Promoters-Prokaryotes ___ sequences-most commonly found sequences in a region The E. coli RNA polymerase core enzyme has ___ subunits, (α2ββ'). Sigma factor (σ) directs ___ of RNA polymerase to promoter TATA Box- consensus sequence of TATAAT -serves as the ___. -centered at ___; recognized by σ___ ___-consensus sequence at ___ region -transcriptional activators bind.

Consensus 4 binding promoter -10 70 TTGACA -35

Gene-Specific Regulatory Control Region ___ expressed genes are regulated solely by the basal transcription Genes also contains gene specific regulatory sequences specific; increase transcription; binds to: -___ -Hormone ___ Elements Gene-specific transcription factors bind to these regulatory sequences and interact with ___ proteins such as ___.

Constitutively Enhancers Response mediator coactivators

Prion Diseases Neurological diseases such as ___ and Mad Cow disease due to prion misfolding Prion proteins fold into forms not ___ Abnormal form favors ___, ___ energy of activation for refolding of other molecules

Creutzfeldt-Jackob degraded aggregation lowers

Eukaryotic Gene Structure The first nucleotide incorporated into mRNA ("start point") is labeled ___ and belongs in the "transcribed region" -The mRNA strand grows in a 5' to 3' direction. The 5' flanking region of the gene is ___ -This region consists of the ___ and ___ sequences "upstream" of the start site.

+1 untranscribed promoter and enhancer

Acids and Bases Acids-donate hydrogen ions (H+) to a solution Bases- (OH- for example) accept hydrogen ions. H+ and OH- are at equilibrium at neutral pH (7) The concentration of hydrogen ions in a solution is usually denoted by the term, pH. pH = ___

- log[H+]

Sodium-Potassium Pump -Generates concentration gradients for sodium and potassium -Generates the membrane potential for the cell (___) +Net outward current of ___ charge from sodium. Thus a ___ membrane potential inside the cell is generated +Accumulation of potassium favors the ___ of potassium through channels. The movement of potassium leaves a ___ membrane potential inside the cell (contributes the most to the cell membrane potential)

-60mV positive negative exit negative

IV Fluids -Isotonic Solution: ___% NaCl in water ___ mOsm -Hypotonic: Solute-Free water: pure water or isotonic solution (5%) ___ -Hypertonic: Pure ___

0.9 290 glucose NaCL

Translation 4 characters in the nucleic acid "alphabet"-___#4 ___ characters required to code for 1 amino acid Codon-3 ___ combination that codes for 1 ___ ___ 43=___ possible combinations or "codons" 20 different amino acids

A,U,C,G 3 nucleotide amino acid 64

Blockage of the sodium-potassium pump, results in intracellular potassium concentrations decreasing to 10.0mM and extracellular concentrations increasing to 100mM. What's the new resting membrane potential for potassium at this stage?

A. +60mv

Why Regulate Gene Expression? Gene ___: The generation of a protein or RNA product from a particular gene Gene ___: The process of turning genes on (expressed) or off (not expressed); controlled by complex mechanisms "Gene Expression is Regulated for Adaptation and Differentiation" ___- Respond to changes in the environment +-cells conserve fuel by making proteins only when they are ___. ___- gene expression changes during development

Expression Regulation Adaptation needed Differentiation

Rate of Diffusion -Concentration -Electrical potential -Pressure difference across the cell -___ diffusion: rate of carrier molecule to undergo change (vmax)

Facilitated

Pure NaCL -___ ECF osmolality -Water moves out of ICF -ECF volume increase -ICF volume decrease -___ is the major determinant of ECF volume

Increase Sodium

Metabolic Alkalosis ___ in HCO3- in the blood either from ___ in bicarbonate reabsorption or secondary to ___ production of H+ ___ in pH Vomiting, ___ Acute: increased pH ___ respiratory stimulus for breathing to retain ___ Carbonic anhydrase buffering system then produces H+ which lowers blood pH Chronic? See next slide for answers

Increase increase secondary Increase diuretics reduces CO2

A 32-year-old female is suffering from severe vomiting from the stomach flu. Her intracellular pH has increased significantly. Which of the following transporters will be stimulated in this patient?

Increase in intracellular pH is an indication of metabolic alkalosis so want to activate the acid loaders The only acid loader transporter is A

Controlling Repressors through Induction ___-small molecules that bind repressor and change its ___ so it no longer binds to the operator The "default" is ___ In absence of an ___ transcription is blocked through binding of repressors In the presence of inducer, repressor falls off ___, RNA Pol can bind the ___ and transcribe the operon. Inducers are either a nutrient or a ___ of a nutrient.

Inducers shape repression inducer operator promoter metabolite

A lipid bilayer -___ the passage of water soluble substances through it

Inhibits

Gene Rearrangement and Antibodies In immature B cells, recombination events occur that joins one ___, one ___ and one ___ sequence into a single ___ which then encodes the variable region of the ___ chain. -given the large number of immature B cells, every recombination possibility occurs within this cell population. When the immune system encounters an antigen the one immature B cell that can bind to that antigen is stimulated to proliferation and produce antibodies to the antigen.

VH, DH, JH exon heavy

Action Potential Stimulus The stimulus preceding the action potential has 3 important function: 1. Determines the change in Vm (hyperpolarizing stimulus or depolarizing stimulus) The greater the strength of the stimulus the greater the change in ___ The change in Vm has to reach above threshold for an action potential to occur 2. Determines how far the action potential will travel i.e. the distance A hyperpolarizing stimulus ___ as a function of distance from stimulus (no action potential generated; only a change in Vm occurs due to the stimulus but no action potential because threshold is not reached) Depolarizing stimulus above threshold results in action potential that remains constant in magnitude and shape but the delay between stimulus and response increases with ___ 3. Determines how quickly a successive action potential will occur After an initial action potential, a refractory period occurs (absolute and relative refractory period) The ___ of the stimulus will determine if another action potential will develop in the relative refractory period

Vm decays distance strength-duration

Action Potential -Change in membrane potential (___) can trigger an action potential. -"Threshold - critical level the membrane potential must be ___ in order to initiate an action potential." -If the Vm becomes more ___ than the threshold voltage, then an action potential occurs. 1. The rise in the Vm is called ___ ___ 2. After the Vm has reached its maximum positive value, the Vm then slowly ___ (___- going) referred to as the repolarizing phase 3. After repolarizing, the Vm may lead directly back to the resting Vm or go beyond the resting Vm to a more ___ Vm. If Vm goes beyond the resting Vm, this stage is referred to as the ___ phase. -The figure on the next slide demonstrates each of the above concepts.

Vm depolarized positive depolarizing phase repolarizes negative negative hyperpolarizing

During a nerve action potential, a stimulus is delivered and an action potential is generated. A second stimulus is delivered while the sodium channels are open. In response to this second stimulus, a second action potential.......

Will not occur

___ ___ (XP) Mutations in Nucleotide Excision Repair -Caused by a dysfunctional Excision Endonuclease gene -Autosomal recessive -Very rare -Symptoms: +Extreme UV sensitivity +Excessive freckling +Multiple skin cancers +Corneal Ulcers -Families must live in the dark They can't repair

Xeroderma Pigmentosum

Key Concepts -Transcription is the synthesis of RNA from a DNA copy. -RNA polymerase transcribes genes into single-stranded RNA. -RNA produced is complementary to one of the strand of DNA, which is known as the template strand. The other DNA strand is the coding or sense strand. -Bacteria contain a single RNA polymerase; eukaryotic cells use three different RNA polymerases -The DNA template is copied in the 3'-5' direction and the RNA transcript is synthesized in the 5'-3' direction. -In contrast to DNA polymerases, RNA polymerases do not require a primer to initiate transcription, nor do they contain 3'-5' exonuclease activity -Promoter regions, specific sequences in DNA , determine where on the DNA template RNA polymerase binds to initiation transcription. -Transcription initiation requires several protein factors to allow for efficient RNA polymerase binding to the promoter. -Other DNA sequences, such as promoter proximal elements and enhancers, affect the rate of transcription initiation through the interactions of DNA binding proteins with RNA polymerase and other initiation factors. -Eukaryotic genes contain exons and introns. Exons specify the coding region of proteins, whereas introns have no coding function. -The primary transcript of eukaryotic genes is modified to remove the introns (splicing) before a final, mature mRNA is produced.

YOOU CAAN DO ITTT

Gluttonous Assistants admire Serious Threats (OH!) from polar bears forming Happy-bonds! [Glutamine Asparagine (amide groups) Serine Threonine (OH-groups) are polar and can form H-bonds]

Yeah

Human Chromosomes -Human DNA is found in 46 chromosomes -23 pairs, one of each pair from each parent -Can be identified by size and banding pattern -One pair is sex chromosomes, males XY, females XX

Yeah

Secondary Structure of RNA -Single stranded does not mean simple linear form -Complementary bases can pair -Complex 3-dimensional structures are formed -Especially true of rRNA -Allows parts to be removed

Yeah

pH = - log[H+] also equals

[H+] = 10 [-pH]

ELECTRONEUTRALITY -Difference in ionic composition between the ICF and ECF compartments are EXTREMELY important -Disruption of ___ o result in disturbances in heart rhythm -Disruption of ___o result in abnormal extracellular osmolality with water shifts into and out of brain cells; seizures, comas, or death

[K+] [Na+]

Nucleotides and Nucleosides -Nucleosides are ___ plus ___ -Nucleotides are ___ plus ___ -May be 1 to 3 phosphates -Deoxy- forms are prefaced with a "d", dATP vs. ATP

base, sugar nucleoside, phosphate

Denaturation of Nucleic Acids -Denaturation means separation of strands -Heat or highly ___ conditions -DNA strands only separate -RNA backbone is sensitive to base, can be ___

basic degraded

Histones -Histones are highly ___ proteins +High percentage of ___ and ___ +Interact with ___ on sugar-phosphate backbone -Five basic types are found in most chromatin +___#5 -All but ___ are found together in nucleosomes -H1 is found in the regions between the nucleosomes ("___")

basic lysine arginine charge H1, H2A, H2B, H3 and H4 H1 beads

Ketoacidosis blood and cellular pH ___ normal range, ketones in the blood

below

Polymerization of HbS -Sickle cell hemoglobin has single amino acid change in ___ chain; ___ ___ to valine -In T-form, ___ ___ can bind to hydrophobic region of beta chain on adjacent Hb (___ interactions) -Other interactions stabilize the polymerization -Long hemoglobin polymers form, causing RBCs to change to ___ shape -Damage cellular membrane and promote ___ of membrane proteins and cell ___ -Affected cells adhere to endothelial cells of capillaries, occluding vessels: leads to cellular damage, ___ pain, and even death

beta glutamate 6 valine 6 hydrophobic irregular aggregation dehydration ischemic

Eukaryotic Promoters sequences in DNA that determine the start point and the frequency of transcription (often composed of smaller sequences called ___ or elements).

boxes

The Bicarbonate Buffer System and Henderson-Hasselbalch Equation expresses the relationship between pH and components of the ___ Plasma bicarbonate is controlled by the ___ and ___, the metabolic component The denominator in the HH equation (pCO2) is controlled by the ___, the respiratory component

buffer kidneys and erythrocyte lung

Body Buffer Systems-Key Concepts -Body ___=hemoglobin, proteins, phosphate buffer, bicarbonate -Acid-base balance involves the lungs (CO2 out), ___ (CO2 to lungs), and kidneys (regulate H2CO3 and excrete H+). -Lungs=respiratory component, kidneys/RBCs=metabolic component of the system. -Blood pH is dependent on the ratio of ___- to pCO2. -The bicarbonate buffer system is a system of equilibrium between ___ and H+. -CO2 is a tissue byproduct of cell/tissue metabolism. -CO2 diffuses into red blood cells (RBCs). -In RBCs, carbonic ___ catalyzes the reaction of dissolved CO2. with H2O to form H2CO3. -H2CO3 dissociates into H+ and a bicarbonate anion (HCO3-). -H+ is buffered by intracellular phosphate buffer or hemoglobin while the HCO3- leaves the RBC and reforms as ___ in the blood and then absorbed by the kidney.

buffers erythrocytes HCO3 CO2 anhydrase H2CO3

Metabolic Acidosis An increase in metabolic acid production or an inability to remove acid/reabsorb base in the kidneys. May also result from a ___ in bicarb production or an increase in bicarb elimination ___ in blood pH. Diarrhea, severe renal failure, lactic ___, ___, and drug intoxication. Acute compensation -the bicarbonate buffering system to drive the production of CO2 which can be eliminated through ___ ventilation. -The increased acid is also intrinsically buffered by proteins, ___, and carbonate in the ___. Chronic compensation, the renal system increases the secretion of ___+ -Sodium-hydrogen exchanger in the kidney is ___: sodium flows down its gradient into the cell and ___ flows out of the cell and is excreted -___ expression of the sodium-driven chloride bicarbonate transporter -Protect the cell from ___ overload Upregulate acid extruders ___ is to increase expression of a transporter. ___ is to decrease expression of a transporter

decrease Decrease acidosis ketoacidosis increased phosphates bone H upregulated hydrogen Increased acid Upregulate Downregulate

Respiratory Alkalosis Caused by a ___ in pCO2 Compensated by a ___ in renal bicarbonate resorption and decrease in plasma ___ Associated with hyperventilation, salicylate poisoning, anemia

decrease decrease bicarbonate

Metabolic Acidosis Caused by a ___ in plasma bicarbonate or increase acids Compensated by respiratory facilitated ___ in pCO2 (hyperventilation) Associated with diabetes ___ (ketoacidosis), ___ acidosis, severed ___, ___ failure

decrease decrease mellitus lactic diarrhea renal

Metabolic Alkalosis Caused by an increase in plasma bicarbonate or ___ acids Compensated by respiratory facilitated ___ in pCO2 (hypoventilation) Associated with vomiting, hypokalemia, administration of IV bicarbonate, prolonged vomiting

decrease increase

Respiratory Acidosis Chronic Elevation of pCO2 results in ___ pH Therefore increase expression of acid extruders such as the ___ exchanger to rid the cell of Intracellular H+ Or bring in ___- to counter act the acidosis

decreased Na-H+ HCO3

Addition of a Poly(A) Tail to mRNA A protein-binding site that protects the mRNA from ___ Poly(A) Polymerase recognizes the poly (A) signal and ___ the primary transcript forming the ___' end. Then, the enzyme catalyzes the sequential addition of ___ nucleotides from ATP at the 3' end. No ___(dT) signal in the DNA template (post-transcriptional modification)

degradation cleaves 3 adenine poly

Action Potential Stimulus: Distance of Response Depolarizing Stimulus: -When threshold is reached an action potential develops -Once the action potential is developed, the action potential remains constant as it travels in distance away from the stimulus -The only change that occurs is the ___ between stimulus. The delay between stimulus and response increases with distance -Bottom FIGURE -Delay is 0 seconds in first panel -Delay is 1 second in second panel -Delay is 2 seconds in third panel -Delay is 3 seconds in fourth panel

delay next slide

Protein folding Every molecule of the same protein folds into the same stable 3-D structure Known as ___ conformation +Primary structure (aa sequence) determines ___ ___ and assembly of subunits into quaternary structure +Sometimes denatured proteins can ___ into native conformation As proteins fold and refold looking for native state, pass through many ___-energy conformations that ___ the process (___ barriers) ___-shock proteins can help overcome kinetic barriers +Use ___ to assist in folding process

native 3-D conformation refold high slow kinetic Heat ATPlow

Voltage-Gated Potassium Channel -Once a stimulus is received and threshold is reached, the voltage-gated potassium channel is activated but has a delayed opening -After this initial delay, the potassium channel fully opens and potassium ions can move down its concentration gradient bringing the Vm more ___ -Potassium conductance through this channel occurs in the ___ phase and ___ phase

negative repolarization hyperpolarization

LIPID-SOLUBLE SUBSTANCES Small ___-___ molecules Lipid-soluble molecules

non-charged

Facts about the Genetic Code The code is almost universal Same in humans, plants, bacteria, etc. Three minor changes in mitochondria The code is ___ Each codon is distinct and adjacent to next codon The code is degenerate and ___ Multiple codons for each amino acid, but only one amino acid per codon!

nonoverlapping unambiguous

Ways Genes Go Bad -Mutations may not just make a protein lose function -More may be made than normal, disrupt balance or flow in pathway -Less may be made -Abnormal protein may interact with ___, destroy function of complex

normal

Chromatin Remodeling Displacement of the ___ from specific DNA sequences to allow for gene transcription. Occurs by two mechanisms. ATP-driven ___ ___ ___: energy from ATP is used to unwind a section of DNA from the nucleosome core. Histone Acetylation of Histone Tails -Histone acetyl transferases (HATs) adds ___ groups to ___ residues (removes + charge; DNA can ___) -___ can remove acetyl groups

nucleosome Chromatin Remodeling Complex acetyl lysine unwind Histone Deacetylases (HDACs)

Translation Translates the genetic message from the ___ language of nucleic acids to the ___ acid language of proteins

nucleotide amino

DNA polymerase

replication

Primer needed in ___

replication

DNA codes for its own synthesis by the process of ___ and codes for protein synthesis through ___ and ___

replication transcription and translation

Resting Membrane Potential -Created when the voltage (charge) difference across the cell membrane when the cell is at ___ -Exists in both ___ and non-excitable cells i is ___.

rest excitable current

Thyroid Hormone Receptors -form heterodimers with ___ X receptor (RXR) -binds to thyroid hormone response elements constitutively in absence of ligand and ___ transcription through interaction with ___. -When thyroid hormone binds, the receptor dimer changes conformation allowing the ___ domain to bind coactivators, thereby ___ transcription.

retinoid retinoid corepressors transactivation initiating

Post-translational Modifications Changes to proteins after they emerge from the ___ that modify function activity, or help target protein to sub-cellular components The initial ___ is removed by specific proteases; methionine is not the ___-terminal amino acid for all mature proteins. Functional groups can be added enzymatically -changes the ___ on the proteins Ex) collagen is ___ to stabilize the protein

ribosome methionine N charge hydroxylated

Targeting of Proteins to Subcellular and Extracellular Locations Secreted Proteins are synthesized on ___ bound the rough endoplasmic reticulum (RER) Translation begins in the cytosol; a signal peptide is recognized by the ___ ___ ___ (SRP). The SRP binds its receptor

ribosomes signal-recognition particle