Week 1

Does K_m depend on enzyme concentration? 

Not with michealis kinetics ([S] way larger than [E]). 

How does salinity affect enzymes 

increasing levels of salt can disrupt hydrogen and ionic bonds, causing a partial change in conformation or denaturation

Relative speed of enzyme regulation (fastest to slowest)

allosteric, covalent (phosphorylation), transcriptional 

at concentrations much higher than Km, reaction rate will be 

about V_max (concentration of 100 times Km would be about vmax) 

Myosin composition 

Each subunit has single head and neck, movement at neck is responsible for power stroke of sarcomere contraction 

kinesin and dynein composition 

two heads, one remains attached to tubulin at all times

Are Km and Vmax also applicable to transporters?

yes, Km is solute concentration at which transporter is at half of max transport capacity. 

cation vs anion exchange chromatography 

cation has negative beads, holds positive charge. lets negative go. anion has positive beads, holds negative, lets positive go 

what property of protein-digesting enzymes allows for a sequence to be determined without fully degrading the protein?

selectivity- selective cleavage creates recognizable endpoints on segments so you dont have to fully digest

naming of sugars 

six carbon with aldehyde= aldohexose

five carbon with ketone= ketopentose

How to calculate number of stereoisomers with common backbone 

2ⁿ where n= number of chiral carbons in the molecule 

Five forces of tertiary structure 

1. Covalent disulfide bonds between cysteines to form the dimer cystine

 2. electrostatic interactions (between acidic and basic) (salt bridges)

 3. hydrogen bonds

4. van der Waals

5. hydrophobic forces

aldoses form cyclic

hemiacetals

Coenzymes are 

small organic groups, vast majority are derivatives of vitamins such as NAD+, FAD, coenzyme A

reason for conjugating proteins 

1. direct delivery to an organelle 

2. direct delivery to cell membrane 

3. add cofactor necessary for activity (heme in hemoglobin) 

a six membered sugar ring is a _____ring and a five membered sugar ring is a ______ ring 

pyranose, furanose 

V_max relation to K_cat

V_max=[E]K_cat

_{Works under saturated  conditions} 

how does one test specifically for glucose 

glucose oxidase because it doesn't react with other reducing sugars

glycosides derived from furanose rings are referred to as _____, and those derived from pyranose rings are refered to as_____

furanosides, pyranosides 

ranks

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

MNEMONIC: Kids Play Cod On Fuzzy Green Sofas

cell envelope

the name for all of the layers of the cell extending outward from the plasma membrane.

In gram positive bacteria, includes the PMb and cell wall

In gram negative bacteria, includes the PMb, cell wall (less thick vs g+), and outer membrane

centriole

- Structure: hollow structure composed of nine triplets of microtubules.

- Location: centrosome

- Function: mitotic spindle formation

What are the two types of bacterial cell wall?

1. Gram Positive

2. Gram Negative

What are the four steps of a Gram Stain?

1. Crystal violet basic dye is added, staining all cells deep purple

2. Mordant is added, typically iodine/iodide, which fixes the crystal violet to the peptidoglycan cell wall by forming a complex.

3. ETOH is added to dissolve the crystal violet iodide complex and washes it from thin cell walls (G- bact.) G+ bacteria retain the crystal violet iodide complex due to thick layer of peptidoglycan.

4. Safranin, a pink counterstain, is added and stains all cells. G+ bacteria are bound by both crystal violet and safranin and appear deep purple while G- bacteria are bound to safranin and appear pink

What are the characteristics and 3 roles of Microfilaments?

- Characteristics: Solid polymerized rods of Actin.  

- Functions: 

(1) Provide resistance to compression and fracture for the cell when organized into bundles and networks.

(2) Generate force for movement by interacting with Myosin.

(3) Formation of the cleavage furrow for cytokinesis in mitosis/meiosis.  This is accomplished by an actin ring which forms at the site of division between cells.  The ring contracts, and the cell gets pinched into two.

What color do Gram Positive and Gram Negative bacterium appear after Gram Staining?

Positive - Purple 

Negative - Pink

Describe the cell wall in gram positive cells

consist of a thick layer of peptidoglycan and lipoteichoic acid.

Describe the cell walls in Gram Negative bacteria

Gram Negative bacteria have a thin layer of peptidoglycan.  They also have an outer membrane beyond the peptidoglycan which is studded with lipopolysaccharides. Note periplasmic space in diagram 

What is chemotaxis?

The ability of a cell to detect chemical gradients and move towards or away from chemical stimuli.  

What are the three components of bacterial flagella?

1.  The Filament

2. The hook  
3.The Basal Body (Apparatus)

What is the bacterial flagellum filament?

The filament is a long hollow helical structure composed of flagellin.

When spun, produces propulsion

What is the basal body?

a complex structure that anchors the flagellum to the membrane and provides the motor force (torque) necessary to spin the flagellum.

organelle

An organelle is any specific sub unit within the cell that has a specialized function. These functions range from generating energy, protecting the cell, digesting things, transporting stuff, etc.

hook

Adaptor, translates the torque from the basal body to the filament

The hook connects the filament and the basal body in order to facilitate the motion in the filament that propels the bacterium forward.

What is a plasmid?

Plasmids are small pieces of circular accessory DNA separate from the genome, usually acquired from the environment.  Plasmids don't carry critical genetic information, but can sometimes carry genes that provide the bacterium an evolutionary advantage, e.g. antibiotic resistance.

How do prokaryotic ribosomes contrast with eukaryotic ribosomes?

Prokaryotic ribosomes are made of a 30S and a 50S subunit, while eukaryotic ribosomes are made of a 40S and a 60S subunit.

What are the 9 main differences between Eukaryotes and Prokaryotes?

Describe the timing of steroid hormone signals

Steroid hormones directly affect DNA, which takes longer to do, but leads to longer lasting changes in the cell by affecting gene expression.  Therefore, steroid hormones effects activate slowly, but stick around for a while. Water insoluable.

What are the 5 hypothalmic hormones? tropic or direct? 

1.  Gonadotropin-Releasing Hormone (GnRH)

2.  Growth Hormone Releasing Hormone (GHRH)

3.  Thyrotropin-Releasing Hormone (TRH)

4.  Corticotropin-Releasing Hormone (CRH)

5.  Prolactin-inhibiting factor (dopamine)

Tropic except dopamine

What is the route taken by hypothalmic hormones after they are secreted?

Hypothalmic hormones travel directly through the capillary beds of the hypothalamus to the capillary beds of the anterior pituitary due to the portal system that connects them.

The 4 tropic hypothalmic hormones are all subject to [what kind of feedback?]

hypothalamus

crf

anterior pituitary

acth

adrenal cortex

cortisol

NEGATIVE FEEDBACK

What are amino acid derivative hormones?

hormones that are made from a few modifications of one or two amino acids.

What is an axis in the context of the endocrine system?

Axis is the term used to refer to the common three-organ pathways the endocrine system takes to exert its effects.  For example, the HPA axis refers to the communication between the Hypothalamus, the Anterior Pituitary, and the Adrenal glands.  The HPO Axis refers to the communication between the Hypothalamus, the Anterior Pituitary, and the Ovaries.  

How does the hypothalamus exert its effects on the pituitary? What type of signaling? 

The hypothalamus releases hormones that travel through a portal system to affect the pituitary.  This is an example of paracrine signalling.

What effect does TRH have?

TRH (Thyrotropin-Releasing Hormone) stimulates the anterior pituitary to release TSH (Thyroid Stimulating Hormone).

What effect does CRH have?

CRH (Corticotropin-Releasing Hormone) stimulates the anterior pituitary to release ACTH (Adrenocorticotropic hormone).

What effect does Dopamine have?

Dopamine inhibits the anterior pituitary from releasing Prolactin. 

Dopamine also has various effects on motivation/feelings of accomplishment/happiness

What two hormones does the posterior pituitary release?

1.  Oxytocin

2.  Antidiuretic Hormone (ADH or Vasopressin)

Mnemonic: OPPA Gangnam style! Oxytocin Post. Pit. ADH

What are the 3 functions of Oxytocin?

1.  Stimulate uterine contractions during child labor

2.  Stimulate milk ejection due to baby latching

3.  Stimulate the formation of emotional bonds

What is the function of Antiduretic hormone (ADH)?

ADH increases re-absorption of water in the collecting ducts of the kidneys in response to increased plasma osmolarity or increased concentration of solutes in blood or low blood volume. 

This increases blood volume and decreases osmolarity

What are the two divisions of the pituitary?

Anterior and posterior

What are the 7 hormones of the Anterior Pituitary?

1.  Follicle Stimulating Hormone (FSH)

2.  Luteinizing Hormone (LH)

3.  Adrenocorticotropic Hormone (ACTH)

4.  Thyroid Stimulating Hormone (TSH)

5.  Prolactin

6.  Endorphins

7.  Growth Hormones

MNEMONIC:  FLAT PEG  of note, the FLAT hormones are tropic and the PEG hormones are direct.

What is the function of Prolactin?

Prolactin stimulates the production of milk in the mammary glands.

What is the route taken by hypothalmic hormones after they are secreted?

Hypothalmic hormones travel directly through the capillary beds of the hypothalamus to the capillary beds of the anterior pituitary due to the portal system that connects them.

What is the function of Growth Hormone and how does it carry this out?

Growth hormone promotes the growth of bone and muscle. stimulates breakdown of fatty acids and prevents glucose uptake in tissues not growing, thus increasing glucose availability for tissues that are growing 

What happens if you have excess Growth Hormone as an adult?

Your long bones only grow for a defined section of time, after which they will stop growing.  If you take Growth Hormone after this period of time passes, various small bones in your hands, feet, and head will grow, but the long bones in your arms, legs, chest, etc. will not.

change in Entropy of universe is equal to 

delta S system plus delta S surroundings which is greater than 0 

In an adiabatic compression process, the internal energy of the gas 

increases because work done on gas is positive. 

U=Q-W

Q is 0 in adiabatic and W is negative because work done by the gas is neg. (compression) neg times neg equals positive 

What is the equivalent weight of a compound 

the mass  that provides one mole of the particle of interest

Interested in Hydrogen, what is equivalent weight of H2SO4? It is one half the molar mass of the compound since that will give one mole of H 

Equations that arise from Pascals principle 

W=(F₁/A₁)(A₁d₁)=(F₂/A₂)(A₂d₂)=F₁d₁=F₂d₂

Whats an inviscid fluid 

no viscosity

What is the boundary layer in turbulent flow

thin layer of fluid adjacent to the wall has laminar flow even when rest is turbulant. flow speed at wall is 0 and increases throughout layer

What do streamlines do 

indicate the pathways followed by fluid particles as they move

Venturi flow application to bernoullis 

Height as compared to a datum remains constant at both points, so rho(g)(h) portion of eq is constant on bpth sides. flow rate is higher at point two, which means dynamic pressure is higher(1/2 rho v²), which means absolute pressure needs to be lower at point 2! thus column of fluid is lower

pitot tubes 

determine speed of fluid flow by determining difference between static and dynamic pressure of fluid at given points along tube

How much work is done in uniform circular motion 

None, force vector is perpidicular to displacement 

Value of G

6.67E-11

fluids and the circulatory system 

-closed loop with non constat flow rate (so no continuity equation, use poisseuilis in isolated segments) Actually tho you can use continuity equation 

-blood volume entering heart=exiting during pump cycle

-each vessel has higher resistence when flowing away from heart, but total resistence of system decreases because they are in parallel (equivalent resistence is lower for capillaries thnan aorta) 

- heart murmers cause turbulent flow 

-arterial circulation is motivated by heart, venous circulation is motivated by skeletal muscle contraction and expansion of heart and is three times volume of arterial 

-flow slower in capillaries than in aorta because lots of small cross setional areas added are larger than aorta cross secrional 

fluids and respiratory system 

-negative pressure gradient moves air into lungs and vice versa for exhalation 

-air has no speed when it reaches alveoli 

-resistence increases as it leaves body because fewer airways in parallel 

Gauge pressure for fluids stacked 

gauge for top fluid would just be pressure inside minus atm 

gauge for  bottom fluid would be pressure inside minus atm minus gauge pressure of top fluid 

If ignoring non conservative forces, whate are the relative peak velocities of two vehicles with different horsepower 

unlimited for both. HP is a measure of power (energy change over time) and with no friction both will continously increase kinetic energy (although at different rates, higher power will reach higher speeds faster) 

Bernoullis relation to flight

speed on top of wing greater (longer to travel up and around curved wing), so pressure lower. this means greater pressure below wing and thus lift. 

Big idea: Higher speed, lower pressure (higher v means the P term needs to be lower to stay equal to other side) Same applies to venturi effect

neopentyl

Maximum number of electrons within a shell 

2n²

n=principle quantum #

ethylene glycol - describe the structure

Shielding effect trend 

increases down (more elctrons blocking valence from nucleus)  

methylvinylketone

Methyl formate 

secretion

when the body either actively or passively transports waste products into the nephron that were too big to pass through the glomerular pores. Occurs anyhwhere besides bowmans capsule 

What are the major waste productes excreted in the urine?

H+ ions, Urea, NH3, and K+

MNEMONIC:  DUMP the HUNK

What is the interstitium?

The interstitium is the area surrounding the nephron that the nephron exchanges solutes with. Solutes in interstitium can be picked up by the vasa recta to return to bloodstream

What is an efferent arteriole, in the context of the kidney?

The efferent arterioles are the arterioles moving blood away from the glomerulus and towards the loop of henle. Feed into renal vein 

isotonic

An isotonic solution is a solution that is as concentrated as the interior of the cell/tubule/etc.  Isotonic solutions lose as much water to their surroundings as they gain, resulting in no net change in the amount of water inside or outside the cell. Doesn't stop movement of water, theres just no net change

What does it mean to be in a hypotonic solution?

Hypotonic solutions are less concentrated than the interior of the cell/tubule/etc in question.  Water follows the concentration of solutes and rushes into the cells, causing them to swell with water and potentially burst.

What does it mean to be Hypertonic?

A Hyper tonic solution is a solution that is more concentrated than the interior of the cell/tubule/etc.  Water follows the concentration of solutes and rushes out of the cell, causing it to dry out and shrivel.  

What happens in the descending loop of Henle?

The descending loop of Henle is only permeable to water.  As it descends into the medulla, the concentration of the interstitium increases, which favors the outflow of water, which can be reabsorbed by the vasa recta.  This is exactly what the descending loop of Henle does, remove water from the filtrate.

Note, if the body has a lot of water and does not need to reabsorb it, the interstitium's concentration will change to reduce the outflow of water from the filtrate back into the blood i.e. decrease medullar interstitial concentration.

What happens in the ascending loop of Henle?

The ascending loop of Henle is only permeable to salts, and is impermeable to water.  As the ascending loop ascends, the interstitium becomes less and less concentrated, favoring the removal of salts from the filtrate and back into the interstitium (and blood).

What is the Diluting Segment of the Nephron?

Site of active salt reabsorption.

The Diluting segment is the thicker part of the ascending loop of henle near the top of its ascension. The thickening is due to greater cell body volume, which is a consequence of increased mitochondria count in these cells.

 If for some reason the passive ascending loop of Henle was not able to reabsorb enough salts, this last segment of the ascending loop of henle will actively transport out salts to further dilute the urine.

Note, that because this is an active process, it won't stop when the interstitium and the filtrate equilibrate.  Energy can keep being spent to make it so that salts go against the concentration gradient into the filtrate.  This means that the Diluting Segment is the only structure in the kidney that can make filtrate even more dilute then blood itself.

What happens in the Distal Convoluted Tubule?

The DCT responds to Aldosterone, which promotes sodium Reabsorption.  

Sodium reabsorption will also lead to an increase in water reabsorption (because water follows the sodium molecules, i.e. osmosis/osmotic pressure).

The DCT is also a site of waste product secretion, like the PCT.

What is an afferent arteriole, in the context of the kidney?

The afferent arterioles are the arterioles moving blood away from the heart and towards the kidney (specifically, the capillary bed known as the glomerulus) supplied by renal artery

What molecules are responsible for the timing of the cell cycle?

Cyclins and Cyclin Dependent Kinases

How do cyclins control the timing of the cell cycle?

1. Cyclin concentration is cyclical.
2. Cyclins selectively activate their CDK
3. CDKs PO4 TFs, activating genes whose products are necessary for cell cycle progression

What is the invasion of distant tissues by cancer cells through the blood and lymphatic vessels called?

Metastasis

What 3 important things happen in Prophase?

1. Chromatin condenses into chromosomes, kinetochores at centromeres appear
2. Nucleolus disappears
3. Centrioles form spindle fibers. Polar MTs meet in the middle and push against each other; centrosomes migrate towards poles. Astral MTs anchor spindles to cell cortex at poles.

Kinetochore microtubules attach kinetochores between prophase and metaphase (prometaphase)

What are spindle fibers?

Spindle fibers are the names of the long microtubules that centrioles use to exert their effects during mitosis.

What is an aster?

Aster refers to the microtubules that radiate outward from the centrioles during mitosis and anchor the centrioles to the opposite sides of the cell membrane.  Asters are so named because they radiate outwards in all directions, and make the centrioles look like stars.

What is a kinetochore?

Kinetochores are protein structures located at the centromere that serve as attachment points for specific fibers of the spindle apparatus.

Telophase

Telophase is essentially the reverse of prophase.  A nuclei reforms around each of the copies of genetic information.  The chromosomes uncoil back into chromatin.  The spindle dissappears and the centrioles return to their normal location.