A pairs with T in DNA

A pairs with U in RNA

G pairs with C

Level 1, the DNA double helix.

Level 2, DNA is wrapped around histone proteins, like “beads on a string”.

Level 3, DNA & histones are wrapped into a solenoid to form a chromatic fiber.

Level 4, solenoid loops attach to a non-histone scaffold.

Level 5, the scaffold is wrapped into a supercoil

AUG codes for methionine

(on the DNA sense strand, it's ATG; on the anti-sense/template strand, it's TAC) 

A DNA segment from the first transcribed base pair to the start codon; contains sequences that regulate mRNA’s stability or translation.

(the 5'untranslated region IS transcribed, just not translated.  Unlike the promoter, the 5'untranslated region is always contiguous with the translated region)

a hydrogen (H)

an amino group (--NH3+)

a carboxyl group (--COOH, or --COO-)

and a side chain (varies)

A connexon is a a hexagonal arrangement of 6 connexin protein subunits. Many hemichannels make up a gap junction.

A connexon is aka a hemichannel

Scanning Electron Microscope

(Scanning Electron Microscope scans the surface with a beam of electrons.  Transmission Electron Microscope transmits a thin beam of electrons through a very thin object) 

Scanning Electron Microscope 

The E-face is the outer leaflet of the membrane (you’re looking from the inside of the cell out). The E-face has significantly fewer proteins than the P-face.

Remember:  E is for Exterior. E is for Empty of proteins.

(P is for Private layer.  P is for protein-filled)

The P-face is the inner leaflet of the membrane (you’re looking from the outside of the cell in). The P-face has significantly more proteins than the E-face.

Remember:  P is for Private (the inside).  P is also for Protein!

(as opposed to the E-face, which is the Exterior face and is relatively Empty of protein)

collagen type IV

laminin 

Do nerves cross the basal membrane?  Do blood vessels?  Do epithelial cells?

Nerves may cross, but blood vessels don't (so epithelial cells get receive nutrients and discard wastes by diffusion across the basement membrane).

Healthy epithelial cells do not cross (cancerous cells may).

Endothelium lines ____, _______, and ______.  What kind of cells is endothelial tissue made of?

blood vessels, lymph vessels, and heart chambers

simple squamous

1. they have a high mitotic index (frequently divide)

2. they are exposed to many stresses

adenocarcinoma

the "top"

for an epithelial cell lining the lumen of a hollow organ, the apical domain faces into the lumen

for an epithelial cell lining the exterior of an organ, the apical domain faces out from the organ

epithelial cells have polarity, with apical, lateral, and basal domains

the "bottom" & "sides" of an epithelial cell

for an epithelial cell lining the lumen of a hollow organ, the basolateral domain is facing away from the lumen (and toward other epithelial cells)

for an epithelial cell lining the exterior of an organ, the basolateral domain is facing in toward the organ (and toward other epithelial cells)

What kind of epithelial cells line surfaces involved in passive diffusion of materials (e.g., air sacs of lungs, blood vessels, etc.)?

(that is simple, stratified, pseudostratified, squamous, cuboidal, columnar, transitional, ciliated, unciliated etc.) 

Describe the shape and location of the nucleus of a simple cuboidal epithelial cell.  

simple cuboidal:  nucleus is usually round & located in center of cell

simple columnar:  nuclei are elongated (oval) & may be located at the base, center, or (occasionally) apex of the cell 

What kind of epithelial cells primarily line the gut, and may have absorptive and/or secretory functions.

(that is simple, stratified, pseudostratified, squamous, cuboidal, columnar, transitional, ciliated, unciliated etc.) 

epithelium in which differing heights of nuclei make cells seem stratified (not all cells have their apical domains at the surface), but actually all the cells sit on the basal lamina

in the respiratory airways (pseudostratified ciliated columnar epithelia is aka respiratory epithelia)

ciliated cells move mucous (produced by goblet cells) & foreign particles trapped in the mucous up to throat.

The cells of transitional epithelia may look like _______ eptithelial cells, or like _______ epithelial cells.  

Describe the surface of transitional epithelium.  

squamous/cuboidal

surface has a thick, densely-stained outline with a scalloped edge of "umbrella cells" (so called because they are round on the exterior edge & may cover 2 or more cells beneath them)

1. can withstand toxicity of urine (low metabolic activity in transitional epithelium makes it better able to withstand toxicity of urine)

2. waterproof-->can protect underlying tissues form toxicity of urine (unlike, say, cuboidal or columnar eptihelium, which is not typically waterproof)

Name the parts in this single-cell reflex pathway

1. cell detects increased estrogen

2. estrogen/receptor complex enters cell, travels to…

3. cell nucleus

4. increased transcription & translation of proteins

5. cell grows

(options:  afferent pathway, effector, efferent pathway, integration center, receptor)

1. Receptor

2. Afferent pathway

3. Integration center

4. Efferent pathway

(mnemonic:  EFFERent-->EFFEctor)

5. Effector

About 2/3 of body water is ______ and 1/3 is ______

(location)

intracellular

extracellular

Na+ would flow into the cell

K+ would flow out of the cell

The Na+ K+ ATPase pump moves _________(# & ion) out of the cell and __________(# & ion) into the cell.

Is that active transport or facilitated diffusion?:

pumps 3 Na+ out of cell (up gradient)

pumps 2 K+ into cell (up gradient)

it's active transport--it requires energy from phosphorylation of ATP to make pump go

cells actively absorb glucose, and water passively follows after

(then the cell consumes or stores the glucose, leaving a higher concentration of water than before)

bone marrow (where naive B cells arise & mature & where naive T cells arise)

thymus (where naive T cells mature)

paracrine

(as opposed to autocrine cytokines, which act on the cell that synthesize it, either within the cell cytoplasm or excreted to work on surface molecules; 

endocrine cytokines, aka endocrine hormones, which are secreted directly into the bloodstream to work on distant cells;

exocrine cytokines, aka exocrine hormones, which are secreted into a duct) 

endocrine cytokines (aka endocrine hormones)

(as opposed to autocrine cytokines, which act on the cell that synthesize it, either within the cell cytoplasm or excreted to work on surface molecules; 

paracrine cytokines that work at very short range for cells near secretor cell;

and exocrine cytokines, aka exocrine hormones, which are secreted into a duct) 

1. don't express normal MHC class I surface molecules (invader cells or stressed self cells)

2. express a nonspecific activation signal

Natural Killer (NK) cells

(note:  Neutrophils are White Blood Cells, and they are part of the innate immune system, but they are not lymphocytes)

colonization

(microbiology)

colonization is establishment of a population of organisms which can live and multiply 

infection occurs occurs when colonized bacteria cause a host reponse (such as inflammation) that leads to signs and symptoms of disease

So, the healthy gut is colonized by many beneficial flora, but is not infected. 

positive--purple or blue

negative--pink

(the bacterial world is upside down

positive bacteria are blue

negative bacteria have a rosy outlook)

gram positive

The main function of teichoic acids is to provide rigidity to the cell-wall.  Lysis of Gram-positive bacteria and release of the teichoic acid into the bloodstream may cause fever, blood vessel dilation and possibly shock and subsequent death. Teichoic acid can also be used by bacteria to attach to mucosal membranes.

chitin

(A long-chain polysaccharide that also makes up the exosekeletons of arthropods) 

branch

(one exception to the rule is Nocardia, which is a branching filamentous bacterium)

yeast--a single-cell form of fungi

filamentous--a thread-like form of fungi

dimorphic--a form of fungi that can live in either yeast or filamentous forms

helical (a cylinder of coiled proteins)

icosahedral (having 20 faces of 1 or more proteins each; appears spherical)

other viral capsids have more complex shapes

tapeworms

flukes

roundworms

hypertrophy

(as opposed to hyperplasia, when a cell responds to stimulation by reproducing; hypertrophy may occur with hyperplasia)

hyperplasia

(Grk:  "beyond formation")

(as opposed to hypertrophy, when a cell responds to stimulation by increasing in size; hyperplasia & hypertrophy may occur together)

aplasia

(Grk:  "no formation")

(as opposed to atrophy, which is decrease in cell size)

Atrophy

(such as muscle atrophy--disused muscles decrease in size because cells are decreasing in size, not b/c cell are failing to reproduce--aplasia--b/c muscle cells don't typically reproduce anyway)

metaplasia

(Grk:  "change in formation")

heterolysis

apoptosis induced by enzymes from surrounding (usually inflammatory) cells 

(as opposed to autolysis, which is from the cell's own enzymes)

Apoptotic cells shrink and eventually fragment (b/c, as part of the death program, the cell pumps out ions & water follows; this may be advantageous b/c smaller fragments are easier to phagocytize).

Necrotic cells swell and eventually lyse (b/c when the cell has low energy, ion transporters stop working, ions flow into the cell, and water follows).

apoptotic cell membranes remain intact (though the surface molecules may change)--they gradually shrink (by actively exporting ions & letting water follow) until the cell membrane touches itself and they break up into well-contained fragments that are easy to phagocytise

necrotic cell membranes are disrupted (the cells lose the ability to actively transport ions, swell up, and burst)

apoptosis doesn't caused inflammation (b/c the cell contents are always contained by cell membrane until they're phagocytised)

necrosis usually does (b/c the cell swells up and bursts, releasing its contents into the extracellular fluid)

apoptosis is usually "housekeeping" but may be pathological (ex., due to viruses re-programming the cell)

necrosis is always pathological

Accumulation of carbon in the lungs from inhaled smoke or coal dust

(may be a type of pneumoconiosus, or occupational lung disease)

abnormal deposits of fat within a cell due to one of a variety of impairments of normal movement of triglyceride fat throughout the cell 

most commonly associated with fatty liver (b/c the liver is the primary organ of lipid metabolism), but can occur in a variety of organs 

coagulative necrosis

(note: ischemia leads to coagulative necrosis in most parts of the body, but in the brain it causes liquefactive necrosis b/c there's little structural framework in neural tissue)

a pale wedge (triangle) in the heart or kidney with the apex at the occluded vessel and the base at the periphery of the organ (the wedge corresponds to the area served by the occluded vessel)

caseous necrosis

(the white cheesy appearance is caused by a leftover mass of protein from dead cells when, unlike in coagulative necrosis, cell architecture is obliterated)

(Frequently, caseous necrosis is seen in the lungs of people with TB infection, but it can also be caused in other organs and by other types of infection)

adipose necrosis (fat necrosis)

(unlike coagulative necrosis, for instance, fat necrosis is not caused by a specific type of injury, though it's frequently associated with trauma.  The fact that adipose tissue has a distinctive appearance and structure b/4 death means that it has a distinctive structure & appearance after death)

liquefactive (ex., in preemies)

(in other tissues, ischemia causes coagulative necrosis, in which the cell dies and leaves its architecture behind, but the brain has little cell structure to leave behind and turns into mush, which turns into empty cavities)

toward the head (cephalad = "head" + "to")

antonym:  caudad

(sim. to rostral & caudal)

a plane that is perpendicular to the body's axis

(you typically look at a human transverse plane up from the feet, so left is right & right is left)

With the arm hanging at the side, a rotation of the forearm that moves the palm from an anterior-facing position to a posterior-facing position

pronation

(if the arm were flexed so that the palm started out facing up, pronation would turn it so that it faced down)

(mnemonic:  a SUPlicant has their palm up for begging, which is the SUPine position; the Prone position is the opposite)

supination

(mnemonic:  a SUPlicant has their palm turned SUPine for begging)

speed up by suspending in aqueous solution (since the extracellular fluid is aqueous, the drug can easily move from the aqueous solution to the extracellular fluid)

slow down by suspending in "depot solution" of non-aqueous liquid (such as polyethylene glycol), which forms a barrier between the drug and the aqueous extracellular fluid

Explain the following mnemonic: 

Acid Accepts Electrons (sometimes by donating a proton)

AH --> A- + H+

(note: A- is technically the conjugate base but strong acids typically exist in the conjugate base form so the conjugate base will sometimes be labeled with the acid's name.  For example COOH is carboxylic acid.  COO- is carboxylic acid's conjugate base, but COO- is sometimes labelled carboxylic acid.  The gods invented this system just to mess with your head) 

Base Picks up a Proton

B + H+ --> BH+

(the note above also applies) 

HA <--> H+ + A-

mnemonic: Acid Accepts Electrons (sometimes by donating a proton)

Base Picks uP a Proton

B + H+ <--> BH+

Mnemonic:  Acid Accepts Electrons (sometimes by donating a proton)

Base Picks uP a Proton 

Acidic, basic

Because acids are better absorbed in their uncharged, acidic form than in their charged, conjugate base form, and bases are better absorbed in their uncharged, basic form than in their uncharged, conjugate acid form 

AH <--> A- + H+

B + H+ <--> BH+

For a base 10 log,

log(x) = y

x =

x = 10^y

So, log(100) = 2 

Protonated

AH <--> A- + H+ 

the non-ionized form is the protonated form (AH, not A-), and is more absorbable by non-polar cell membranes:

Mnemonic: 

Acid Accepts Electrons (sometimes by donating a proton)

Base Picks uP a Proton 

non-protonated

B + H+ <-->BH+

Base Picks up a Proton, so the non-ionized (absorbable) form is non-protonated (B, not BH+)

[non]/[pro] = 10^(pH – pK)

where non = nonprotonated form (A- for acids, B for bases)

and pro = protonated form (AH for acids, BH+ for bases)

AH <--> A- + H+

B + H+ <--> BH+

(Acid Accepts Electrons, sometimes by donating a proton

Base Picks uP a Proton)

glycolysis

(1 glucose in, 2 pyruvates out, 2 ATP are made)

34

(17 per pyruvate; when added to the 2 ATP of glycolysis this gives 36 ATP for aerobic respiration of 1 molecule of glucose)

The circular metabolic pathway in which

muscles convert glucose to lactate via anaerobic respiration

and liver converts lactate to glucose (via gluconeogensis), which then returns to the muscles 

1. use for energy (feed into TCA/citric acId/Krebs cycle)

2. build into proteins

3. transform into other amino acids or other substances (ex., histamine from histidine, nitric oxide from arginine, neurotransmitters, etc.)

insulin

glucagon

lipases

Beta-oxidation:  Fatty acids-->acetyl CoA

can feed acetyl CoA into TCA /citric acid/Krebs cycle & electron transport

this can occur in many cells (ex., muscle cells)

(as opposed to the glycerol backbone, that can only be used for gluconeogenesis in the liver)

glycerol is used for gluconeogenesis by the liver only

(as opposed to fatty acids, that can be beta-oxidized into acetyl CoA and fed into the TCA/citric acid/Krebs cycle in many cells in the body) 

During fasting or carbohydrate starvation, oxaloacetate is depleted in liver because it is used for gluconeogenesis. This impedes entry of acetyl-CoA into Krebs cycle. Acetyl-CoA then is converted in liver mitochondria to ketone bodies, which are exported to the rest of the body to use for energy.

One of the ketones produced is acetone, which has a fruity smell.

An Ori is an origin of replication for DNA

each prokaryotic circular genome has one Ori, called an OriC

In eukaryotes, DNA Polymerase delta forms diester bonds between the 3' end of the last nucleotide in the chain & the 5' end of a free nucleotide.

(DNA polymerase delta is the main eukaryotic DNA polymerase.  DNA polymerase epsilon 

glycosaminoglycan (GAG)

GAGs form an important component of connective tissues. GAG chains may be covalently linked to a protein to form proteoglycans. Some examples of glycosaminoglycan uses in nature include heparin as an anticoagulant, hyaluronan as a component in the synovial fluid lubricant in body joints, and chondroitins, which can be found in connective tissues, cartilage, and tendons.

laminin

(LAMINin is the major protein in the LAMINa)

loose connective tissue

(If the tissue is spread out on a glass slide, it will appear more like a loose net of fibers)

Compare to dense regular connective tissue, which looks like many parallel straight or wavy fibers, or dense irregular connective tissue, which looks like wood grain (neither as swirly & marble-like as loose connective tissue, nor as organized as dense regular connective tissue)

dense regular connective tissue

(compare to loose connective tissue, which looks swirly, like marble, and dense irregular connective tissue which looks like wood grain)