Hemophilia Pedigree – Father has hemophilia, mother does not. What is the outcome for their kids?
His daughters would be carriers. This is x-link recessive.
Autosomal:
Dominant:
Autosomal: males and females equally affected.
Dominant: non-carrier parents
polymerase chain reaction (PCR)
The process of copying DNA in the lab. Uses Template DNA, Nucleotides (dNTPS), DNA Polymerase, and DNA primers.
3 Steps of PCR
- Denaturation: DNA is heated to 95C to separate it.
- Annealing: reaction is cooled to 50C; primers stick to the DNA you want to copy and add DNA polymerase.
- Elongation: reaction heated to 70C and DNA polymerase, adding nucleotides building a new DNA strand.
Base Excision Repair (BER)
How you repair a mutation. BER is used to repair damage to a base caused by harmful molecules. You remove the base that is damaged and replace it. BER removes a single nucleotide
DNA glycolsylase – sees damaged DNA and removes it.
DNA polymerase-puts the right one back in while DNA ligase seals it.
Mismatch repair (MMR) occurs during:
replication. DNA polymerase proofreads but sometimes a mismatch pair gets through. MMR removes a large section of the nucleotides from the new DNA and DNA polymerase tries again. (Ex: C-T instead of C-A)
Mismatch Repair corrects what kind of DNA damage?
When a base is mismatched due to errors in replication. Such as G-T instead of G-C. DNA polymerase comes by and fixes it.
What happens when DNA polymerase binds to DNA to make RNA?
TRANSCRIPTION! DNA polymerase takes the individual nucleotides and matches them to the parental sequences to ensure a correct pair. It must bind with RNA primer to work.
What is needed for DNA replication?
DNA polymerase
Nonsense Mutation
Change in 1 nucleotide produces a STOP codon Stop= nonsense because it is no more.
Silent Mutation
Change in 1 nucleotide but codes for the same amino acid. Silent= the change doesn’t change the name of the protein
Missense Mutation
Change in 1 nucleotide leads to a code for a different amino acid. Missense = mistake was made.
What happends during RNA splicing?
During RNA splicing introns are cut out, the remaining exons are joined together.
5’ATG AGT CTC TCT 3′
Find the DNA template strand.
3’TAC TCA GAG AGA 5′
The DNA template strand is complimentary. So start with the opposite number, then go L-R with the complimentary letter.
5’ATG AGT CTC TCT 3′
What is the corresonding mRNA sequence?
5’AUG AGU CUC UCU 3′
This sequence is the same as the coding strand except T changes to U because it is RNA. RNA doesn’t have T.
How would a mutation from CTC to ATC affect the protein sequence? (CTC/ATC – coding strand, AUC – mRNA strand)
This will make a missense mutation because it changes the name of the protein. (look at the chart provided.) missense = mistake
DNA replication process
DNA ->Transcription -> RNA -> Translation -> Polypeptide
Describe how you would find what ionized Alanine looks like.
This is an amino acid. Look for the “R” group. Alanine is a hydrophobic amino acid that has CH3. It is a weak interaction. An ionized acid will have a + or – charge.
Describe what causes the misfolding of protein in Alzheimer’s Disease.
Protein misfolding is caused by intracellular tangles and extracellular plaques (senile plaques) caused by abnormal protein aggregation.
TAU is fibrous material inside cells where the connections are lost. This becomes defective and forms filaments in the neuron.
Amyloid-Beta is a large precursor protein in the cell. Excess amyloid-beta creates senile plaques. This starts in the hippocampus and moves up.
Describe the process of neurodegenerative protein aggregation.
Alzheimer’s is the most common neurodegenerative disease. The formation of aggregated amyloid-beta fibers is another characterisitc of Alzheimer’s. However, neurodegeneration and memory loss can be detected before amyloid fibers accumulate in the brain.
What are the molecules that help denatured proteins with folding?
Molecular chaperones are protein helpers. They bind to the newly made polypeptide and enable proper folding. Proper protein folding is vital b/c proteins that do not fold properly can lead to a variety of diseases. Normally, the chaperones that help new proteins fold can also help misfolded proteins refold into the correct structure.
Genetic mutations that substitute one amino acid for another can cause incorrect folding.
What are the 4 levels of protein structure?
- Primary-chain of amino acids. PEPTIDE bonds form a polypeptide chain. This is a covalent bond (very strong) and does not denature.
- Secondary-alpha helix and beta sheet. HYDROGEN bonds that contain the carboxyl group and amino groups. Denatured by salt and pH change.
- Tertiary-side chain interaction (R group). Changes are seen with high temp, salt, change in pH, and reducing agents. (ex: sickle cell, arthritis, hemophilia)
- Quarternary-more than 1 polypeptide. Change seen with increased temp. (Ex: Hgb)
Hydrogen bonds are formed from
2 polar amino acids.
(Contains Oxygen and nitrogen-OH, NH, NH2. On exterior surface)
What structure would be unaffected by complete denaturation of its multi-subunit?
PRIMARY. Peptide bonds are strong and covalent. The primary structure is located at the backbone and does not denature.
What is the simplest way to denature a protein?
Heat it up. The tertiary structure is hydrophobic.
The tertiary structure is a protein structure stabilized primarily by the hydrophobic effect.
What is the secondary structure made up of?
Alpha helixes and beta sheets
Describe what is meant by “induced fit” of a substrate and enzyme.
The substrate and active site are somewhat complementary prior to substrate binding. Many enzymes will adjust their active site conformation slightly as the substrate binds to improve the fit. When the molecule is recognized as the substrate, the enzyme will adjust to form itself around the substrate more tightly to facilitate the reaction it catalyzes.
Describe the Substrate-enzyme complex.
Each substrate binds to an active site, producing an enzyme-substrate complex. The geometric and chemical complement between the enzyme and substrate depend on noncovalent forces.
Describe how the substrate and enzyme react with each other.
Substrate- molecule that an enzyme will bind to preferentially to any other molecule. Each enzyme is specific for that substrate. It will not react with molecules that are not its substrate.
Active site- serves as the binding platform on the enzyme for its specific substrate and acts as the site of the chemical reaction.
Competitive vs Non-competitive Enzyme Inhibition
Competitive inhibitor-usually a molecule similar in structure to a substrate that can bind to an enzyme’s active site even though the molecule is unable to react.
Non-competitive-attach to the enzyme at an ALLOSTERIC site, which is a site other than the active site.
Feed back inhibition
Non-competitive inhibition. Once the end product builds up, it will bind to the alloteric site on the first enzyme and stop the pathway. It binds to the enzyme, slowing the product.
How would you find which amino acid is non-polar?
It will contain carbons and hydrogens (CH, CH2, CH3) These are weak interactions that tend to aggregate in the middle of the protein. They will be affected by temperature change.
What part of the phospholipid is hydrophobic?
The tail
Describe peptide bonds.
Peptide bonds form between 2 amino acids by a dehydration reaction. During dehydration, a water molecule forms from the oxygen of a carboxyl group and 2 hydrogens from an amino group. As water forms, the carbon atom of the carboxyl group and the nitrogen atom of the amino group become bonded together. It is the bond b/w 2 amino acids.
How does cooperative binding on hemoglobin occur?
The four subunits of hgb work together. When one molecule of oxygen leaves, the other 3 tend to leave too. When one picks up oxygen, the others tend to pick it up also. (Think of the table and chairs.) This is how oxygen is picked up in the lungs and dropped off in the tissues.
Oxygen will bind quicker to hgb when…
there is another oxygen molecule already binding. This is known as Cooperative Binding.
Explain Carbon Monoxide’s affinity for hgb.
CO binds to the same group as oxygen, but binds more strongly. If CO is there, it will pick up the O2 but it will not drop it off. This is why CO poisoning is so harmful. The pt will be very pink in color. CO stabilizes the R-state by binding to the same iron in Hgb and changing the heme shape.
Describe fetal 2,3 BPG and oxygen affinity.
The fetus has a higher affinity for oxygen than mom. The mother’s 2,3 BPG is higher so their afinity for oxygen is lower. The mom becomes deoxygenated.
Affinity-stickiness for oxygen.
How is a HGB structure affected by the absence of oxygen?
The structure becomes tense. The heme is dome shaped. pH will be lower. This is found in the muscles.
Describe Hemoglobin
- Low affinity for oxygen.
- Transports oxygen to the tissues.
- Acts as a buffer and controls pH by binding to H+ ions.
- 4 protein, 4 Iron/Heme, 4 Oxygen
- Binds to oxygen at high pH and releases at low pH
- High affinity for CO
- Quarternary structure
Describe Myoglobin
- High affinity for oxygen
- Stores oxygen in muscle and releases it when oxygen levels get low
- Not affected by change in pH
- 1 protein, 1 iron/heme, 1 oxygen
- Tertiary structure
How does pH influence the oxygen saturation of hemoglobin?
Left shift: increased affinity for oxygen, increased pH (acidic), weak bond
Right shift: decreased affinity for oxygen, decreased pH, strong bond
Bohr Effect: increase in pH->increased affinity for oxygen->increased Hgb saturation->reach 100% sooner. Oxygen will be distributed better, delivering more or less where we need it.
Cholesterol
- 4 Ring structure
- AKA sterols (cholesterol, cortisol, testosterone)
- Needed for membrane fluidity (expansion)
- Increases temp to solidify
- Needed to synthesize Vitamin D in the skin, cholic acid (component of bile), and steroid hormones.
Steroid Hormones
synthesized by cholesterol;
testosterone and estrogen-promote growth and development of sex characteristics;
cortisol-released in response to stress and promotes glucose synthesis in liver.
How could myoglobin indicate an MI?
Myoglobin is a protein with a single subunit containing both heme and iron. While myoglobin is normally contained only in the muscles, it can be released into the bloodstream if there is muscle damage. For this reason, measuring the levels of myoglobin in the blood can provide evidence of rhabdomyolysis, a mild heart attack, or a muscular degenerative disease.
Describe the Anabolic/Anaerobic Pathway.
Occurs when there is no oxygen. The ETC cannot work. Requires energy to synthesize larger molecules.
NAD+ runs out->fermentation regenerates the NADH to NAD+ ->small amounts of ATP and lactate are made->Cori Cycle in liver
Ends in -GENESIS-
Describe the Catabolic Pathway.
generates energy by breaking down larger molecules.
Ends in -LYSIS-
What do the Anabolic and Catabolic pathways have in common?
They are both required for maintaining the cell’s energy balance.
Describe the Cori Cycle.
The Cori Cycle is part of the anabolic pathway. It uses the lactate made by fermentation in the liver and uses gluconeogenesis to convert 2 lactate to glucose. 2 ATP are made with each cycle, but it uses 6. The net loss is -4 ATP.
Describe fermentation.
Fermentation is the formation of lactate by regenerating the NAD+ from NADH that was used during glycolysis to make small amounts of ATP and lactate. It allows glycolysis to continue in the absence of oxygen.
What does the Cori Cycle supply for red blood cells?
The Cori Cycle supplies glucose for RBCs.
The Cori Cycle takes up lactate from the blood and uses the gluconeogenesis pathway to convert 2 molecules of lactate back to glucose. As the byproduct of anaerobic glycolysis, lactate diffuses into the blood and is taken up by the liver where it is converted back into pyruvate by the enzyme dehydrogenase. The newly formed glucose is released into the blood to be used again for energy by the red blood cells and muscles.
Because there is no oxygen present during the Cori Cycle, pyruvate from glycolysis is converted to lactate. What happens to this lactate?
The lactate made from glycolysis is put into the blood. The liver picks up the lactate and uses gluconeogenesis to convert 2 molecules of lactate into glucose.
Which molecule starts the citric acid cycle?
Acetyl-coA.
Describe the Citric Acid Cycle.
AKA Kreb’s Cycle.
Takes in Acetyl CoA, NAD, FAD, and GDP.
Puts out CO2, NADH, FADH2, and GTP.
Takes place in mitrochondria.
A defect in this cycle will cause low levels of ATP.
It can be inhibited by increased levels of NADH d/t feedback inhibition.
What is needed in the Citric Acid Cycle to continue aerobic metabolism?
NADH and FADH2
What is the effect of glucagon on carbohydrate metabolism?
Converts glucose into glycogen for later use during hyopoglycemia. Glycogenesis: the formation of glycogen from sugar.
If oxygen is scarce (anaerobic conditions, ie: exercise), what happens to pyruvate?
Pyruvate will be reduced via an anaerobic pathway by the addition of 2 hydrogen atoms to form lactic acid (lactate). This process is known as fermentation. The formation of lactate regenerates the NAD+ that was used during glycolysis, thus allowing glycolysis to continue making small amounts of ATP for the cell.
RBC rely on _ as their sole pathway for producing ATP.
glycolysis.
This is because they lack mitochondria (and therefore the citric acid cycle and electron transport chain). They are an example of fermentation.
When there is no more NAD+, fermentation________
takes NADH from glycolysis to make lactate and NAD+ to put the NAD+ back into glycolysis.
How does insulin manage glucose?
It moves Glut 4 to the membrane of the cell allowing glucose into the cell through facilitated diffusion and active transport.
How does Metform work to decrease glucose levels?
Metformin decreases efficiency of transferring electrons in the electron transport chain, decreasing the overall production of ATP. Metformin exerts its anti-hyperglycemic effect mainly by inhibiting liver glucose output.
Both gluconeogenesis and glycogenolysis are reduced by metformin.
Metformin can cause lactic acidosis because it lowers the blood pH.
How does carb loading help a long distance runner?
The body can store about 500g (~1.1lb) of glycogen, roughly 75% in skeletal muscle fibers and the rest in liver cells. Glycogenesis is the synthesis of glycogen. Glycogen is a polysaccharide that is the only stored form of carbohydrate in the body. Insulin stimulates liver and skeletal muscle cells to tap into glycogen stores and stimulate glycolysis.
Glucagon
activates when blood sugar is low
Gluconeogenesis
*makes glucose from non-carbs. (pyruvate, lactate, glycerol)
*NADH is oxydized into NAD+ for glycolysis.
(glu=glucose, neo=new, genesis=make)
*done via anabolic pathway with a peptide bond
Glucogenesis
Makes glycogen
Gluconeolysis
Breaks down glycogen to release glucose (fasting)
Glycolysis
Triggered by carb intake during exercise
Glycation
*Caused by increased blood sugar.
*Leads to AGEs (Advanced Glycogen End Products)
*Causes proteins to shrink
Where does Beta Oxidation take place?
in the mitochondria
(Occurs more often in a fasting state)
In Beta Oxidation, Co-enzyme A is added to
make fatty acetyl -CoA
What are the products of Beta Oxidation?
ATP, NADH, FADH2
C14:
How many Acetyl CoA are made per fatty acid?
How many rounds of beta oxidation did it take?
7 Acetyl CoA after 6 rounds
carbon atoms/2 = number of Acetyl CoA
(#carbon atoms/2) -1 = number of beta oxidation
rounds
MCADD: disease of fatty acid metabolism (beta oxidation)
- Cannot utilize adipose tissue for ATP production effectively.
- A “fat” problem, not a “carb”/glucose problem
- Can be fatal
- Must avoid fasting
- Eat diets rich in slow-release carbs (complex carbs)
- Avoid fats
- Enzyme used to oxidize medium chains is defective.
What would an ionized alanine look like?
It will be charged. Look for a pos or neg sign.
This is a hydrophobic amino acid.
The sidechain is made up of CH.
How would you identify an Omega-3 fatty acid?
The first double bond occurs between the third and fourth carbons.
How would you identify an Omega-6 fatty acid?
The first double bond occurs between the sixth and seventh carbons.
Where is the alpha bond located?
The alpha carbon is the last C before the Carboxyl Group. The bond connects the carboxyl group.
Where is the beta bond located?
The beta carbon is the next to last carbon. It is right before the alpha carbon.
*Beta oxidation is the breaking of the beta bond.
The Omega bond is found _
farthest away from the Carboxyl group.
Unsaturated bonds are most likely to be liquid at _
room temperature.
They are loosely packed, don’t stack well, and have a lower melting point. ie: olive oil
Where are fatty acids catabolized?
The fatty acetyl CoA molecules enter the mitochondrial matrix and begin the cyclical pathway of beta oxidation. ie: triglycerides
What is the process of fatty acid synthesis?
It is the building up of fatty acid from Acetyl CoA to make fatty Acetyl CoA.
Produces 2 carbon atoms at a time.
Takes place in the Cytoplasm (cytosol).
Produces ACP.
Cytosol= Acetyl CoA -> mitochondria -> cytosol using citrate. Acetyl CoA combines with CO2 and Biotin enzyme -> Malonyl ACP
Trans fatty acids
*The hydrogens are on opposite sides of the double bond (H-C=C-H)
*the carbon chain is straighter
*pack tightly together, so have a high melting point
*occurs in margarines and manufactured cooking oils as a result of hydrogenation process
Cis Fatty Acid Configuration
*Both hydrogens are on the same side.
*Takes less heat to melt b/c it is not packed tightly.
*The asymmetry forces a kink or bend in the carbon chain, making it difficult for the fatty acids to pack together.
What is the greatest reserve of energy?
Triglycerides
*glylcerol backbone with 3 fatty acid chains
Describe the mosaic fluid model.
*Lipid bilayer
*triglycerides – leaky membrane
*fatty acids-leaky membrane (d/t spaces)
*Phospholipids-tightly packed, impermeable membrane
What molecule fuels the activity of our bodies?
ATP
What are the 3 major steps of aerobic metabolism?
- Glycolysis
- Citric Acid Cycle
- Electron Transport Chain
What are needed as inputs for the overall process of cellular respiration?
Sugar, oxygen
What are the outputs of cellular respiration?
ATP (energy), CO2, H2O
C6H12O6 + 6O2 -> 6CO2+6H2O+30ATP
Disulfide bonds-
Ionic bonds-
Hydrogen bonds-
Peptide bonds-
Disulfide bonds- use cysteine
Ionic bonds- charged bonds (pos/neg)
Hydrogen bonds- non charged bonds
Peptide bonds- between amino acids
Fatty acid catabolism occurs during
Beta Oxidation
DNA pairing:
A-
C-
A-T
C-G
RNA pairing:
A-
C-
A-U
C-G
5′ ATG AGT CTC TCT 3′
What would be the template strand?
3′ TAC TCA GAG AGA 5′
5′ ATG AGT CTC TCT 3′
What would be the mRNA sequence?
5′ AUG AGU CUC UCU 3′
5′ AAG CGG TAC GTA 3′
What would be complimentary strand?
5′ TAC GTA CCG CTT 3′
Structure of the Amino Group
H-N+-H
l
H
Abbreviated structure of Amino Acids
COO-
I
H – C – R
I
NH3
Hydrophobic amino acids
- Come together in middle to strengthen core
- Contains carbons and hydrogens (CH, CH2, CH3) in R group
- AWAY from water
- Contribute to tertiary protein structure
- Non polar (inside the cell)
- Protein aggregation d/t hydrophobic interactions
- Weak interactions affected by change in temp.
Polar amino acids
- Contain oxygen and nitrogen (Oh, NH, Nh2) in R group
- Hydrogen bond on exterior surface connects to an oxygen bond or nitrogen
- Moderately weak interaction affected by salt or changes in temp or pH
Amino acids form _ by loss of water to make __.
Amino acids form peptide bonds by dehydration to make protein.
Charged amino acids
- positive/negative charge
- ionic bonds on exterior surface
- moderately strong interaction affected by salt or change in pH. (increased salt -> increased ions)
When pH is outside normal range, enzyme activity will _.
decrease.
A misfolded protein:
- causes protein aggregation
- can result from denaturation
- can be degraded by the cell
- will lose its normal function
Mutation of an active amino acid changes __
an enzyme’s ability to bind a substrate.
A dehydration reaction a polypeptide, whereas a hydrolysis reaction _ a polypeptide.
A dehydration reaction builds a polypeptide, whereas a hydrolysis reaction breaks a polypeptide.
During feedback inhibition, a molecule acts as an _ for an enzyme in order to_____.
During feedback inhibition, a molecule acts as an inhibitor for an enzyme in order to prevent over production of a product.
Replacing a polar amino acid with a non-polar amino acid will likely cause __.
a neurodegenerative disease.
Characteristics of hemoglobin in the lung:
- Relaxed, planar state
- Oxygenated – high affinity for O2
- high pH, low CO2, low H+ ions
Characteristics of hemoglobin in the muscle:
- tense, domed state
- low affinity for O2
- low pH, High CO2, High H+ ions
Hemoglobin _ to O2 at high pH and ___ O2 at low pH.
Hemoglobin binds to O2 at high pH and releases O2 at low pH.
(It binds at high pH in lung to pick up oxygen and carry it tissues and release it at low pH.)
These 3 things can be catabolized into Acetyl CoA
- fatty acids
- amino acids
- glucose
How many ATP are produced for every molecule of glucose that is aerobically metabolized?
30
What occurs in an exercising muscle under anaerobic conditions?
Pyruvate from glycolysis is turned into lactate in order to regenerate NAD+ for further rounds of glycolysis, yielding 2 ATP per round for muscle use. The Cori Cycle allows lactate to be turned into glucose via gluconeogenesis in the liver at the expense of 6 ATP. Overall, the Cori Cycle creates a deficit of 4 ATP.
What happens if cyanide is consumed?
ADP will build up, protons will not pump into intermembrane, and oxygen will not be consumed by ETC.
What happens to pyruvate in the absence of oxygen?
In the absence of oxygen, pyruvate is transformed to lactate by fermentation.
The Cori Cycle occurs during __.
exercise.
During the Cori Cycle, lactate produced by fermentation leaves the cell and enters the blood. The liver cells take up the lactate from the blood and use the gluconeogensis pathway to convert 2 molecules of lactate back to glucose.
3 functions of insulin:
- stimulates gluclose uptake
- inhibits glycogen breakdown
- stimulates fatty acid production and storage
Glucogenolysis is stimulated when __
Glucogenolysis is stimulated when glucagon enters the bloodstream.
Where is the largest store of energy in the human body located?
triglycerides in adipose tissue
If pH is low, Hgb will _ oxygen.
release
(muscles,tissues)
T/F: Essential fatty acids are polyunsaturated.
True. Examples include Omega-3 and Omega-6.
Essential fatty acids must be consumed.
4 steps of Beta Oxidation:
- FAD -> FADH2
- H2O
- NAD+ -> NADH
- CoA
Nucleotide excision repair is used to:
Nucleotide excision repair is used to repair deletions, insertions, and helix distorting lesions, such as thymine dimers. (cigarette smoke, benzopyrene.)