Bio/Biochem

What is a totipotent cell?

Can differentiate into ANY cell type including embryonic/extraembryonic (aka placenta)

What is a pluripotent stem cell?

Can become any organismal cell but not a placental cell

What is a totipotent cell?

Can differentiate into ANY cell type including embryonic/extraembryonic (aka placenta)

What is a pluripotent stem cell?

Can become any organismal cell but not a placental cell

What is a multipotent stem cell?

Can differentiate into many cells within its same family (ie muscle can make many other muscle but not blood)

What is vasopressin aka ADH released in response to?

Increased blood osmolality aka low body water

What is osmolality?

Concentration of solute in water (opposite of osmolarity)

what does hybridization mean in relation to nucleotides?

It’s when single stranded nucleic acids (DNA or RNA) bind with another of their same single stranded nucleic acid to form a double strand or an RNA structure

What is passive immunity?

The transfer of antibodies from one individual to another

What produces antibodies?

B lymphocytes produce antibodies which are proteins

What is an erythrocyte

A red blood cell (don’t have DNA or membrane bound nucleus - so they can have more space to keep hemoglobin and carry oxygen through it)

What stimulates Protein Kinase A?

cAMP

What does aldosterone do?

increases sodium reabsorption in kidneys - it’s secreted in response to low blood pressure

what are the three main muscle tissue types and where are they found?

skeletal muscle - attached to bones

smooth muscle - attached to organs

cardiac muscle - attached to heart

what is the hardy weinberg equation for calculating allele frequency?

p + q = 1 (dom + recs)

What is the Hardy Weinberg equation for genotype frequency

p² +2pq + q² = 1

What is the mitotic spindle made of?

Microtubules

What filaments play a role in cell adhesion?

Intermediate filaments

What filaments play a role in muscle contraction?

Microfilaments

What are analogous structures?

Structures that evolved separately but serve the exact same function

What are homologous structures?

Structures that evolved from the same place but have different functions

How can you tell if two genes are located close together on a chromosome?

They will have very few recombinant offspring

What buffer system aids in maintaining blood pH

bicarbonate buffer system: CO2 + H20 —> HCO3- + H+

what does renal secretion and reabsorption mean?

secretion - into urine, reabsorption - back into bloodstream

How long is an amino acid?

.11 kDa = 110 Da

What does the esterification of cholesterol with a fatty acid do in terms of membrane binding and why?

It pushes the new molecule into the protein because the non polar fatty acid can’t interact with the bilayer like cholesterol can so it goes inside

What is a Hill coefficient and what do the various numbers indicate?

A measure of enzyme cooperativity

>1 = positive cooperativity

-1 = negative cooperativity

=1 no cooperativity

What is enzyme cooperativity?

A measure of how the efficiency of the enzyme is dependent on binding of other molecules (more binding - more cooperative or less?)

How does a plot look for a cooperative enzyme?

sigmoidal

What does a downward shift in LB mean in terms of enzyme concentration?

More efficient/concentration of enzyme results in a downward shift compared to without enzyme because it is 1/v

What is the makeup of the solvent phase on normal TLC?

non polar

What is the function of the colon?

to absorb water

What is the M phase of the cell cycle?

Mitosis

In the rate limiting step of glycolysis, what is the mechanism by which PFK-2 works and why does this mechanism exist?

Insulin and glucagon both control PFK-2 activity. PFK-2 works by converting a small amount of Fruc 1,6 BP to Fruc 2,6 BP which activates PFK-1. This is so that liver cells can make more ATP for storage than just the basic amount the cell needs to fucntion and bypasses the primary mechanism of inhibition

What are all of the steps in glycolysis and the Kreb’s cycle that contain the reduction of NAD+ to NADH or FADH to FADH₂ what enzymes catalyze them?

Glycolysis: Glyceraldeyhde 3P —> 1,3 Bisphosphoglycerate catalzyed by Glyceraldehyde 3P Dehydrogenase

Krebs Cycle:

Isocitrate —> a-ketoglutarate catalyzed by Isocitrate Dehydrogenase

a-ketoglutarate —> Succinyl - CoA catalyzed by a-ketoglutarate Dehydrogenase

(FADH) Succinate —> Fumarate catalyzed by Succinate Dehydrogenase

Malate —> Oxaloacetate catalyzed by Malate Dehydrogenase

What is DHAP and why is important?

DHAP is an intermediate of glycolysis and it is used for triacylglycerol synthesis in hepatic and adipose tissue

How does Acetyl - CoA play a role in gluconeogenesis and where does it come from?

It activates pyruvate carboxylase and it comes from fatty acid oxidation

What is the rate limiting enzyme in the Pentose Phosphate Pathway and what step does it catalyze? What is a byproduct of this step?

Glucose 6-P Dehydrogenase catalyzes the conversion of Glucose-6-Phosphate —> 6 Phosphogluconate

NADPH is a byproduct

What is the structure of Acetyl-CoA?

What does a dehydrogenase do and what is it a special kind of?

It reduces a molecule (usually NAD+ to NADH)

It is a special kind of oxidoreductase which catalyze REDOX reactions (ex ketone to alc)

What does a kinase do?

It phosphorylates a molecule using ATP

What does a phosphatase do?

It removes a phosphate group

What does a phosphorylase do?

It phosphorylates a molecule using inorganic phosphate instead of ATP

What step uses a synthetase in the Krebs cycle and what are its byproducts?

Succinyl - CoA —> Succinate using Succinyl - CoA synthetase and it powers GDP —> GTP

What is the FA pathway and where does it occur?

Acetyl - CoA —> Malonyl CoA — Palmitic Acid/Palmitate

1. Acetyl-CoA carboxylase

2. Fatty Acid/Palmitate synthase

occurs in cytoplasm of liver(hepatocytes) and fat (adipose) cells

What is the FA oxidation pathway?

Fatty acyl-CoA —> FA Carnitine —> transporter —> FA - CoA

1. Carnitine Acyltransferase - 1

2. Travels into mitochondria via carnitine transporter

What is the pathway for Ketogenesis?

Acetyl - CoA —> HMG - CoA —> Acetoacetate

1. HMG-COA synthase

acetyl CoA can be reduced to B-hydroxybutyrate

Where does Ketolysis occur?

In tissues outside the liver because the liver can’t catabolyze the ketone bodies it produces —> esp heart, brain, and muscle cells

What are the ketogenic AAs and what does that imply?

Leu and Lys as well as others and they can get converted to ketone bodies in times of extreme energy deprivation

What are the glucogenic AAs and what do they do?

All but Leu and Lys can act as glucogenic AAs and they can get converted to glucose through gluconeogenesis in extreme energy deprivation

What is the Urea Cycle and when does it occur?

The process of protein catabolism causes proteins to lose their amino groups which can cause toxic leftover ammonia in the blood and the Urea Cycle removes this waste product.

Occurs in in the liver

What is the Cori Cycle?

The process by which RBCs/erythrocytes bring lactate from muscle to liver cells to be converted to glucose through gluconeogenesis. They then take the glucose made from the liver back to the muscle cells to use as energy (anaerobic respiration) and convert to lactate once more.

Do valves exist in systemic veins or arteries? What happens if valves are damaged?

Valves exist in systemic veins and can cause backflow of blood in body (away from heart) when damaged

How does blood flow through the heart and when does it become oxygenated?

Deoxygenated blood enters at right atrium and goes to right ventricle.

From there it goes through pulmonary arteries to lungs and becomes oxygenated.

The now oxygenated blood enters through the pulmonary vein into the left atrium before going to the left ventricle which then pumps the oxygenated blood throughout the body

What is a protease?

Enzyme that digests a protein

What is an amidase?

An enzyme that cleaves amide bonds - like peptide bonds

What is an esterase?

An enzyme that either accelerates the breaking down or creation of esters

What is a hydrolase and what are some examples?

Catalyzes hydrolysis reactions

Examples: decarboxylase, phosphatases, GTPase, Protease

What is a lyase?

Breaks bonds NOT using water

What is the iron containing molecule in hemoglobin?

Heme - it is crucial for oxygen transportation

What is heme made up of and what is it’s structure called?

Four pyrrole rings and a central iron atom —> called a porphyrin ring

What is the structure of pyrrole?

What is the structure of imidazole and where is it found?

Found in Histidine (His, H)

What is the structure of glucose? (draw Fisher and Haworth)

middle finger!

What is the structure of galactose? (draw Fischer and Haworth)

two central fingers

What is the structure of fructose? (Draw the Fisher and Haworth projections)

first one after the carbonyl, only 5 membered ring!

What happens to substances people with elevated kidney function take?

They get drained faster from their body so in order to have an effect, more of the substance needs to be given

How do you calculate catalytic efficiency?

k_cat/k_m

When the slope of an LB plot increases what does that tell you about catalytic efficiency and why?

Catalytic efficiency has decreased because it is inversely proportional to the slope

What does a R shift on an LB plot for the x intercept tell you about Km?

Km has increased meaning there is a lower enzyme affinity

What is the equation for a 0 order reaction and how does it relate to substrate concentration?

r = k_cat and the rate is independent of substrate concentration

What is the equation for a first order reaction and how does it relate to substrate concentration?

r = k_cat[A] —> it is directly dependent on substrate concentration

What is the difference between an uncompetitive and a noncompetitive inhibitor

A non competitive inhibitor will NOT bind at the enzyme-substrate complex while an uncompetitive inhibitor will

What is alternative splicing?

When the SAME GENE/DNA SEQUENCE produces different protein products because of different mRNA molecules

What is conjugation?

It is the exchange of genetic information between prokaryotes (usually through plasmid DNA)

What is transformation?

The process by which prokaryotes acquire DNA from their surroundings

Describe gene duplication

It can occur through unequal crossing over and over time it can acquire mutations which cause very small variations in the gene

Which kind of muscle tissues are striated and which are not? What does striated mean?

Striated indicates the presence of sarcomeres (look like lines under a microscope)

Only smooth muscle isn’t striated

Which muscle tissues have gap junctions and which don’t?

Cardiac and smooth muscle have gap junctions while skeletal muscle doesn’t. This means that it is electrically isolated

How are each of the muscle tissues controlled? Is it voluntary or involuntary?

Cardiac and smooth muscle are controlled involuntarily and regulated by the ANS while skeletal muscle is controlled voluntarily through ACH

Which muscle tissue has intercalated disks and what are they?

Cardiac muscle has intercalated disks which is how each cell connects to the other and allows them to contract as a unit

Which muscle tissues have multiple nuclei?

Cardiac and skeletal

Cardiac will typically have up to 2 nuclei/cell while skeletal can have 100s

What bonds get broken in the process of denaturation?

H-bonds, hydrophobic interactions, disulfide bonds, but NOT peptide bonds meaning that the primary structure is still intact after denaturation

In amino acids, how do protonatable side chains act around their pKa?

They act through a buffer system meaning that near their pKa, there will never be 0 percent protonation or deprotonation. Hendersson-Hasselbach should be used to find the ratio of protonated to deprotonated residues

How do mechanically gated ion channels work?

They respond to forces like pressure or tension

How can voltage changes occur across a membrane to promote the opening of voltage gated ion channels?

The opening of ligand or pH based channels can allow ions to flow in that depolarize the cell and create a voltage difference across the membrane that promotes voltage gated channels to open

Describe the pathway of FADH₂ in the ETC

Complex II (Succinate Dehydrogenase —> Complex III —> Complex IV

Describe the pathway of NADH in the ETC

Complex I —> Complex III —> Complex IV

What is the final electron acceptor in the ETC?

O₂

Describe the process of the ETC/Oxidative Phosphorylation and how it generates ATP

High energy electron carries (NADH and FADH₂) carry electrons through their respective complex pathways which are highly exergonic reactions. The energy released powers the transfer of H⁺ into the intermembrane space. Finally, this high collection of H⁺ shoots down ATP synthase which spins and smashes ADP and P_i to make ATP

What is a parietal cell and where is it found?

found in the stomach and secretes HCl and intrinsic factor (aids in absorption of vit. B12 in small intestine)

Why is HCL important in the stomach?

The acidic environment does three very important things:

1) activates enzymes

2) defends against pathogens

3) denatures/breaks proteins (proteolytic environment)

What helps prevent the self destruction of stomach cell walls because of the acidic environment and what cells secrete these things?

Mucous and bicarbonate - secrete by mucous cells

What do chief cells do and why are they important?

Chief cells secrete pepsinogen which is the inactive form of pepsin - the enzyme that breaks down polypeptides

How does pepsin become activated from pepsinogen?

By low pH

What do G cells do and why are they important?

G cells secrete Gastrin —> regulates the secretion of HCl from parietal cells

(along w CCK) regulates release of Chyme

What are key features of the endoskeleton/bones (4)?

1) Has living and nonliving parts - living: osteocytes, osteoblasts, and osteoclasts, nonliving: Ca₃PO₄

2) Forms an internal scaffolding and attachment point for tissues

3) Grows as organism goes

4) Comes from the embryonic mesoderm

Describe the makeup/qualities of a virus

• made of DNA or RNA

• surrounded by protein coat/capsid

• need host cell to replicate

What is a prion?

Misfolded proteins that act as infectious agents —> modify host protein secondary structure and cause aggregation

Describe the makeup/qualities of a viroid

• only RNA

• no protein coat/capsid

• this RNA doesn’t code for protein

• can be self complimentary (form hairpin sections)

How do enzymes affect the ΔG of a reaction?

Enzymes have NO EFFECT on the ΔG of a rxn, enzymes only change E_a

What is circular dichroism?

Tells how much of a protein will change form alpha helices and beta sheets into random coils as temperature rises