Mcat Flashcards

Adenine

- Purine- 2 rings aromatic- 5 donors ~ 4 Nitrogens + H on NH- 1 acceptor ~ NH2- Binds to Uracil in RNA and Thymine in DNA

Guanine

- Purine- 2 rings aromatic- 6 donors & acceptors- Binds to Cytosine

Cytosine

- Pyrimidines- Aromatic- Binds to Guanine

Uracil

- Pyrimidines- Aromatic- Only in RNA- Binds to Adenine

Thymine

- Pyrimidines- Aromatic- Only in DNA- Binds to Adenine

Beta Glycosidic Link

- Linked to N9 of Purine- N 1 of Pyramidine

Phosphodiester Bond

- What is broken/formed during replication - P-O

General Features of DNA

1) 2 Helical polynucleotide strands, - Coiled, common axis- Right hand screw sense- Anti parallel - 5' --> 3' - 3' --> 5'2) Sugar(polar) /Phosphate (charged) - outside the helix (hydrophilic) - nitrogenous base - inside the helix (aromatic, NP)3) Helix repeats ~34 Ã - 10 bases/turn of helix

On average, how many bases are there per turn ofthe DNA double helix?A.5 B. 10 C. 15 D. 20

- distance between base pairs = 0.34 nm. - The helix undergoes one complete turn (twist) every 3.4 nm. - This tells us that there are 10 base pairs (3.4 nm/0.34 nm = 10) per turn of the DNA double helix. - Remember, it is 10 base pairs per turn. - A base pair is composed of two bases held together by hydrogen bonds. - The question specifically asks for the number of bases (not base pairs) per turn of the DNA double helix. - The correct choice is D.

Which of the following base pairs is NOT usually associated with DNA?A. Uracil hydrogen bondingto adenineB. Adenine hydrogen bonding to thymineC. Guanine hydrogen bonding to cytosineD. Thymine hydrogen bonding to uracil

- The classical hydrogen bonding between base pairs in DNA occurs between adenine and thymine (two hydrogen bonds) and between guanine and cytosine (three hydrogen bonds) - This allows us to immediately eliminate choices B and C.- What about choices A and D? Both answers contain bases (adenine and thymine) found in the DNA double helix. Both answers also contain uracil, a base found in RNA. - Consider choice A. Can uracil hydrogen bond to adenine? If it can, that base pair associated with DNA? The answer to both of these questions is, yes. - As the DNA double helix unwinds and forms a transcription bubble, two single strands of DNA are exposed. One of those strands is used as a template to make messenger RNA (mRNA). As the mRNA is synthesized, it is hydrogen-bonded to the DNA. During transcription, a DNA-RNA hybrid is temporarily formed- If these is a cytosine (C) in the DNA template, then in the mRNA a guanine (G) is incorporated. If there is a thymine (T) in the DNA template, then in the mRNA an adenine (A) is incorporated. If there is an A in the DNA template, then a uracil (U) is called for in the mRNA

DNA is the carrier of genetic information during cell growth and division. Which of the following characteristics of DNA is NOT essential for the accurate transmission of this information?A. A genetic code that is degenerateB. A mechanism for self-replicationC. A low mutation rateD. A conformationally variable molecule

- D is correct - In order to transmit information accurately from one cell to the next, there must be an alphabet that makes the communication possible.- In DNA, this alphabet is composed of the bases adenine (A), guanine (G), cytosine (C), and thymine (T). - A triplet of these bases represents a codon, and a codon specifies a single amino acid. - There are 64 different codons (from 43 = 64), and among these 64 codons there is redundancy. - More than one codon can code for the same amino acid. - Because of this, the genetic code is referred to as being degenerate. - If there were no mechanism that would allow DNA to replicate itself, then the information contained in these codons would not be passed to the next generation. Thus, a means of self-replication is crucial. - As the information is replicated, the fidelity must be maintained. If a mutation were to be incorporated into the next generation of DNA, then it could have deleterious consequences. Therefore, a very low mutation rate is essential. - DNA can exist as either a single strand or a double strand. In the doubled-stranded form, it can exist in a number of different states (e.g., A-DNA, B-DNA, or Z-DNA). DNA is said to have variable conformations. - The information passed on to the next generation is still contained in these different forms of DNA. It is just a matter of having the appropriate mechanism to transmit that information. - DNA, as a conformationally variable molecule, would not pose a problem for the transmission of genetic information.

Denatured DNA shows an increase in ultraviolet absorbance. The temperature at which one-half the maximum absorbance is reached is called the melting temperature, Tm.All of the following factors will lead to an increase in the Tm of DNA EXCEPT:A. a lower mole fraction of A«T base pairs.B. a higher concentration of Mg2e.C. a lower concentration of histones.D. a higher mole fraction of G»C base pairs

C is correct. - If there is an increase in Tm, it means that it takes a higher temperature to melt (denature) the DNA. - This must mean that the DNA is stabler. - What would make the DNA stabler? If there were more hydrogen bonds between the base pairs, then the stability of the double helix would increase slightly. - Since there are three hydrogen bonds between G C base pairs and two hydrogen bonds between A»T base pairs, we would want an increase in the amount of G»C base pairs and/or a decrease in the amount of A»T base pairs. Both of these factors lead to an increased stability of the DNA duplex. We can eliminate choices A and D.- What about the divalent Mg2+ ion? DNA is quite negatively charged. If these negative charges were not shielded from one another, they would tend to blow the duplex apart (i.e., make it less stable). The result is a decrease in the Tm. - However, if there is a higher concentration of Mg2+ ions in the medium, there is also a greater chance of these magnesium ions associating with the negatively charged phosphate groups and shielding those negative charges from one another. The DNA double helix becomes slightly stabler. We can eliminate choice B.- Histones are proteins that bind to DNA. These proteins have a large proportion of the amino acid residues arginine (Arg) and lysine (Lys). Both of these amino acids have side chains that are positively charged at physiological pH. These positively charged residues ionically bind DNA's negatively charged phosphates and help stabilize the molecule. Histones can be dissociated from their interaction with DNA by using a sufficiently concentrated salt solution that interferes with these ionic interactions. The DNA becomes slightly less stable (due to the deshielding of the negatively charged phosphates) and easier to melt. The correct choice is C.

In a human cell, protein transport does NOT move from cytosol to:A. mitochondria.B. peroxisome.C. nucleus.D. chloroplast.

- Human cells do not have chloroplasts as organelles.- Therefore, there should be no protein transport from the cytosol into the chloroplast. - There is protein transport from the cytosol to the mitochondria, nucleus, and peroxisome. - A peroxisome is an organelle that carries out oxidative reactions. - The correct choice is D.

Which of the following is LEAST likely to be associated with the mitochondrial genome?A. Distinct promoter regionsB. RNA polymerase proteinC. DNA polymerase proteinD. Histone protein complex

- From the passage, we learn that the mitochondrial genome is very similar to that of the bacterial genome. - Bacterial genome does not have its DNA packaged with histone proteins- The mitochondrial genome has distinct promoters and must have both DNA polymerase and RNA polymerase in order to replicate and transcribe its genome. - Thus, the mitochondrial genome lacks histone proteins. The correct choice is D.

The codon AUG is used as a start codon in the genetic code of the mitochondria. This codon codes for which of the following amino acids?A . L eucineB. HistidineC. MethionineD. N-formyl methionine

- This problem requires the we know which amino acid is called for by a start codon.- It is neither histidine or leucine. - the modified amino acid used in prokaryotes?- The mitochondrial genome is very similar to the prokaryotic genome.- tHE mitochondria use N-formylmethionine instead of methionine. - The nuclear genome uses methionine.

As stated in the passage, every nucleotide in the mitochondrial genome is part of a coding sequence. A probable result of this is that compared to the nuclear genome, there would be:A. fewer mRNA molecules transcribed.B. more mRNA molecules transcribed.C. more room for regulatory DNA sequences.D. less room for regulatory DNA sequences.

- If every nucleotide is used for coding purposes, this leaves little room for any regulatory sequences in the mitochondrial genome. - Choice A is a true statement. There will be fewer RNA molecules coming from the mitochondrial genome. - However, the reason is not because every nucleotide in the mitochondrial genome is a coding nucleotide. The reason is simply the size of the respective genomes. - Therefore, choice A can be eliminated. Choice B is a false statement and can be eliminated. - It is D

Which of the following statements offers a reasonable explanation for the different genetic code found in mitochondria?A. The drift responsible for changes in the genetic code occurs only in mitochondria.B. The small number of proteins encoded in the mitochondrial genome makes changes in the meaning of the code tolerable.C. The mitochondria has unique tRNAs, which correct for the different genetic code.D. In mitochondria, the primary structure of a protein has no effect on the function of the molecule.

- The question is asking why we see a different genetic code in the mitochondria. - The answer lies in the volume of proteins that are produced by the genome. There is a small number of proteins produced by the mitochondrial genome. Thus, a change in the genetic code is not very far-reaching. - In other words, the change is tolerable because more likely than not, a small number of proteins would be affected. - There is no evidence that genetic drift occurs only in mitochondria. Therefore, we can eliminate choice A. For choice C, we have no reason to believe that the tRNAs in the mitochondria have any special correcting function. - We have codon-to-anticodon base-pairings, and the mitochondrial tRNAs do not change those base-pairing rules to accommodate a different genetic code. - Finally, like proteins anywhere else, the primary structure definitely affects the function by dictating the final shape of the molecule. Therefore, we can eliminate choice D. - The correct choice is B.

The DNA that codes for the light strand is also known as the:A. antisense strand, because the light chain is complementary.B. antisense strand, because the light chain is nearly identical.C. sense strand, because the heavy chain is complementary.D. sense strand, because the heavy chain is nearly identical.

- We are told from the passage that the heavy strand of RNA is responsible for encoding many proteins, while the light chain of RNA is over 90% nonsense. - One should realize that the heavy chain of RNA is nearly identical to the strand of DNA that gave rise to the light chain of RNA. - The only difference is that the thymines in the DNA have been replaced by uracils. - Since the heavy chain of RNA contains all of these functional codons, the strand that is nearly identical to it is called the sense strand. - The piece of DNA that actually gave rise to the heavy strand of DNA is called the antisense strand. The correct choice is D.

Velocity Formula

vf = v0+at (no displacement)Δx= v0t + 0.5at^2 (no final velocity)v​f^2​​ =v0^2 + 2aΔx (no time)

The following base sequence is given:123456789ATCGGTATAIf the genetic code is overlapping, a mutation in the base cytosine (C) may alter how many amino acids?A.1 B.2 C.3 D.4

To answer this question, one has to know what is meant by an overlapping genetic code. As in the question, let us assume the base sequence is ATCGGTATA. If this genetic code is overlapping, the first three amino acids come from ATC, TCG, and CGG respectively. If the code is nonoverlapping, the first three amino acids come from ATC, GGT, and ATA respectively. Since the question asks about the products of an overlapping code (the code is, of course, non-overlapping), as many as three amino acids may be affected.

Steps in the Beta oxidation of a fatty acid

1. FATTY ACID IN THE CYTOPLASM2. ACTIVATION OF FATTY ACID BY JOINING TO COA3. REACTION WITH CARNITINE4. ACYL COA IN MITOCHONDRION5. FAD-LINKED OXIDATION6. HYDRATION7. NAD+-LINKED OXIDATION8. CLEAVAGE (THIOLYSIS)

Compare the ATP yields from palmitic acid and palmitoleic acid.

- Palmitic acid has 106 molecules of ATP- Palmitoleic acid has a double bond so it makes less ATP, 104.5 molecules

STEARIC ACID IS A C18 FATTY ACID. SUPPOSE YOU HAD A DEPRESSING DAY AND GORGED ON CHOCOLATE. HOW MUCH ATP WOULD YOU DERIVE FROM THE COMPLETE OXIDATION OF STEARIC ACID TO CO2?

8 ROUNDS OF B OXIDATION IS 124 ATP- 2 ATP FOR ACTIVATIONTOTAL = 122 ATP.

How many nucleotides long is the gene that codes for the hormone leptin (167 Amino acids)

1. Central dogma of molecular biology, each AA in a polypeptide is coded for by a 3 nucleotide sequence in the gene that codes for the polypeptide.2. Eukaryotic genes contain a start codon, which codes for an AA (methionine), and a stop codon, which does not.3. Eukaryotic genes contain introns, sequences of nucleotides within genes that do not correspond to amino acids in the functional protein.4. The leptin gene is greater than [(167*3)+3] nucleotides long.

Gamma Rays

- Nothing past 10^-11- Everything up to 10^-11- Small wavelength = high frequency

X Rays

10^-11 to 10^-8

UV Rays

10^-8 to 10^-7

Visible Spectrum

400 to 750 nmViolet to Red410^-7 to 7.5 10^-7

Infrared

7.5*10^-7 to 10^-4

Microwaves

10^-4 to 10^-1

Radio Waves

Anything above 10^-1Large wavelengths = small frequency

C = Frequency * wavelength (lambda)

C = 3 *10^8 (speed of light)Ex. what is the frequency of UV rays?F=C/wavelengthF = (310^8)/(110^-8) = 3*10^16F = (310^8)/110^-7) = 3*10^15you have to take the upper and lower limits

ROY G BIV

- Red: 700-630 nm- Orange: 630-600 nm- Yellow: 600-560 nm- Green: 560-480 nm- Blue: 480-440 nm- Violet: 440 - 400 nmnano = 10^-9

E = hf = (hc)/lambda

E: energy in joulesH: planck's constant = 6.62610^-34 JSC: speed of light = 3 * 10^8Lambda: wavelength in meters

Avogadro's Number

6.02 * 10^23

Periodic Table Trends

Z-effective: increases from left to rightValence shell: bigger down a columnAtomic size: decreases bottom left to top rightIonization: increases bottom left to top rightElectron affinity: increases bottom left to top rightElectronegativity: increases bottom left to top right

Thompson Experiment

- Used to determine the signs of charges- Demonstrated existence of oppositely charged particles in an atom- Charge is a fixed quantity

Milikan's Oil Drop Experiment

- Used to determine the magnitude of charges- If the charged oil drop falls at a constant speed the force acting upwards = force acting downwards Q = -(MG)/E

Rutherform Experiment

- Location of dense particles -Atoms have dense nuclei with nearly all atomic mass concentrated in centre - Atom is a lot of empty space- Mass is in the middle

Synthesis of Cholesterol

1. Synthesis of isopentyl pryophosphate* activated isoprene is the building block2. Condensation of 6 isopentyl pyrophosphate to squalene3. Squalene cyclizes 4. Lanosterol shifts 19 times until you get cholesterol

Hormones of Cholesterol

Cholesterol (C27) becomes:1. Progestogens (C21)Splits to becomea. Glucocorticoids (C21)b. Mineralocorticoids (C21)c. Androgens (C19) i. Estrogens (C18)

Benzene

What is this molecule?

Phenol

What is this molecule?

Benzoquinone

What is this molecule?

Hydroquinone

What is this molecule?

Disubstituted Benzenes

- ORTHO: two methyl groups right next to each other- META: the two methyls are one carbon away from each other- PARA: the two methyls are on opposite sides from each other

Criteria for Aromaticity

1. Has to be a ring2. Planar, overlapping p orbitals (sp2)3. Molecule must have Huckel # (4n+2)π electrons

Huckel Number

Possible numbers: 2, 6, 10, 14, 18* (4n+2)π- Extra stability forming aromaticity

Anti-Aromatic molecules

Possible number: 4, 8, 12, 16- Unstable- Ex. square ring with two double bonds * 4n not 4n+2- Gives off a lot of energy

Amine

- Base - nucleophiles- Acts as a base before a nucleophile

Hydrazine

Imine

Oxime

T/F: Amine can reaction with an ether

F: Amines cannot react with an ether- Ether does not have a leaving group- It can react with an anhydride, benzoic acid, and alkyl halide

Law of reflection

Theta incidence = theta reflection- The angle the light comes in at is reflected with the same value

Index of Refraction

n = C/V = V(vacuum)/V(medium)- n is unitless - c is speed of light- v is speed of mediumn(air) = 1 n(water) = 1.333

Snell's Law

n1(sin theta 1) = n2(sin theta 2)light refracts from one medium into another mediumEx. going from air to water (two different mediums)- if n2 > n1, light ray bends toward the normal (horizontal line)- if n2 < n1, light ray bends away from the normal

Critical Angle

- Angle required for the theta to be 90 degrees- When coming out of a medium into a new one, it has to be come out at a specific angle n1 (sin theta critical angle) = n2 sin(90) [sin 90 = 1]sin (theta critical angle) = n1/n2- Smallest ratio of indices of refraction = smallest Theta Critical- Biggest ratio of indices of refraction = biggest Theta Critical

Total Internal Reflection

Any angle greater than the critical angle, the line will reflect back into the medium

A glass fiber carries a light digital signal long distances with a minimum loss of amplitude. What optical property of glass allows this phenomenon?A. DispersionB. RefractionC. ReflectionD. Diffraction

B. Refraction- Instead of escaping out into the air it is staying in the cable because of total internal reflection

Dispersion

Take white light (combo of all colors) shine it into a prism, it gets split into the individual colors that make up the visible spectrum - The top of the prism = red, longest wavelength- Bottom = purple, shortest wavelengthshorter wavelengths = greater bending

Magnification

M < 0 = Inverted imageM > 0 = Upright image| M | > 1 = Enlarged image| M | = 1 = Same size| M | < 1 = Smaller size

Thin Lens Equation

1/focal length = 1/distance of object + 1/distance of image- Focal length (+) = converging mirror- Focal length (-) = diverging mirror- Distance objection (left) = (+)- Distance of objection (right) = (-)- Distance of images (-) = virtual image- Distance of images (+) = real image

Plane Mirror

- Straight mirror, not convexed or concaved - Image is always: upright, virtual, and same sizeDistance of object = - distance of image

Convex (Diverging) Mirror

- Mirror is curved out towards you- Image is always: upright, virtual, smaller Pneumonic: Diverging SUV

Concave (converging) Mirror

1. Object beyond radius of curvature (roc)- Image is: real, inverted, smaller 2. Object at ROC- Image: real, inverted, same size3. Object between ROC and focal length- Image is: real, inverted, larger4. Object at focal point - No image forms because parallel lines5. Object inside the focal point- Image: virtual, upright, largerFocal point (f) = ROC/2

Distillation

Removing a liquid from another liquid or from a solute by using differences in boiling points

Fractional distillation

- Column with more surface area * allows vapors to condense and re-evaporate- Greater purity - Small differences in boiling points (less than ~30C)

Simple Distillation

- Used when there are very large differences in boiling points- Remove solvent from solute - Faster - Generates higher yields

Vacuum Distillation

- Attach to a vacuum at a point after the condensate has been collected- Reduce pressure in apparatus = lower BP

Extractions

- Based on big differences in solubility compounds

Partitioning

- A compound has different solubility in every solvent - Ratio of its max solubility in one solvent to the max solubility in another solvent = partition coefficient

Acid/Base Extraction

- One solvent is water - Properties of solutes change upon change in pH- Separating compounds by their pKa values * loss of charge, solute will go into organic layer (hydrophobic) * Gain of charge, solute will go into aqueous layer (hydrophilic)

Brine Solution

If you want to increase the difference between the two layers, add salt to the aqueous layer

Recrystallization

Dissolving something in water or a solvent and then precipitate it

Lenses

- Two curved, non-parallel reflecting surfaces- Real and virtual sides are flipped compared to mirrors

Converging Lens

- Allows parallel lights rays to bend towards an axis - Bends towards the focal point - Focal length: distance from the middle of the lens to the focal point, (+)- Convex

Diverging Lens

- Allows parallel light rays to move apart as they pass through the lens- Focal length = (-)- Concave

Real Image (Lens)

- Can only be cast upon a screen, photographic negative, retina- Only lenses in cameras and eyes have focal lengths that produce this

Virtual image (Lens)

- Place object between focal point and lens- Image forms to the left of the object and is larger

Magnification of Image

M = Height of image / Height of objectORM = Distance of image / Distance of object1. Identify if it is converging or diverging 2. Diverging ~ image is between focal length and lens, small, upright, virtual (SUV)3. image = (object distance * -focal length) / (object distance- [-focal length])

Vitreous Humor

- Transparent gel like substance inside the eye- Index of refraction (n) = 1.337

Light entering the eye

1. Light enters the cornea goes through aqueous humor to the lens (n=1.336)2. Iris, diaphragm that controls the amount of light that enters the eye by constricting/dilating the pupil3. Retina is the curved rear surface of the eye. Rods and cones change the light to electrical signals

Lens of the eye

- n = 1.386-1.406- Does little bending of light rays - Most refraction is done by the cornea- Ciliary muscles change the curvature of the lens

Nearsightedness

- Myopia- Far point is not at infinity but some shorter distance so it focuses before the retina - Distant objects cannot be seen clearly- Eyeball is too long - Curvature of cornea is too great - Solution: diverging lens forces the focal point to be on the retina

Farsighted

- Hyperopia- Eye cannot focus on nearby objects- Near point is greater than 25 cm so it hits behind the retina- Eyeball is too short and cornea not curved enough- Solution: converging lens

Astigmatism

- Out of round cornea or lens- Point of objects are focused as short lines- Blurs the image- Solution: use a cylinder to bring all the lines together onto the focal point

Alcohol IR

- Always Hydrogen bonding- Thumbprint around 3600-3200

Carbonyl IR

~ 1720 nm

Ester IR

~ 1740

Conjugated Ketone

- Conjugation lowers the peak- Less than 1720

Aldehyde IR

Carbonyl (C = 0) ~ 1720 + double peak at 2900, 2700

Carboxylic Acid

- Giant peak because of hydrogen bonding- Resembles a beard- Spans the 3000

NMR

- Where a peak is found (electronegativity & shielding)- Area under a peak (how many H's on a carbon)- How a peak is split (how many H's next to a C)

NMR Peaks

* C-H (methyls) are near 0-1 * C-O (Carbonyl) are downfield * O-H with a broad peak is near 4-5 * Benzenes are 7-8 * Aldehydes are at 10 * Carboxylic acid is 12 * Acetone is equivalent (singlet, int = 6)

Vision

- Absorption of light by photoreceptors within the eye - Cells are sensitive to light in a specific spectrum * wavelength between 390-750nm

Cones

- Function in bright light- Responsible for color vision- Contributing amino acids: phenoalanine, tyrisine, trypsine

Rods

- Function in dim light- Do not perceive color- Outer segment stack of ~1000 discs- Membrane enclosed sacs with photoreceptor molecules

Rhodopsin

- Consists of protein opsin * enables the detection of different colors * 7 transmembrane domain receptor- 11 Cis retinal * conjugated to Lysine

Innate Immune System

- All animals have it- Recognition of traits shared by broad ranges of pathogens using a small # of receptors- Rapid Response

Acquired Immune System

- Vertebrates only- Recognition of traits specific to a particular pathogen using wide variety of receptors- Humoral response (antibody mediated)- Cell response (T cell mediated)- Adaptive response- Relies on T-cells/B-cells

Barrier Defenses

- Barriers that block the entrances of pathogens- Mammalian Vertebrates: * Epithelial tissues (skin, mucous membrane), cells that produce mucus (viscous fluid that enhances defense by trapping pathogens * Secretions (saliva, tears, sweat etc) washing action to prevent bacterial colonization * tears/saliva have lysozyme = bacterial cell wall destruction * Oil/sweat glands given skin pH 3-5 (prevent bacteria growth)

Cellular Innate Defenses

- Pathogens entering mammalian body are risk for phagocytosis- Phagocytic cells detect fungi/bacterial invaders via Toll-like receptors * bind to fragments of molecules characteristic to pathogens Ex. TLR3 detects double stranded RNA = viruses TLR4 detects lipopolysaccharides = cell wall

Eosinophils

* low phagocytic activity* secrete destructive enzymes * important for multicellular pathogens (worms)

Neutrophils

* circulate in blood* attracted by signals from infected tissues* engulf and destroy tissue

Macrophages

* larger cells* circulate but primarily reside in lymph organs- Highest rate of endocytosis

Dendritic Cells

* populate tissue that have contact with the environment* adaptive immunity

Antimicrobial Peptides/proteins

- Viral infected cells produce interferons * signal to nearby cells to produce substances that prevent viral infection- Interferons provide innate defenses against viruses

Complement System

~ 30 proteins in blood plasma- Circulate in inactive state- Activated by substances on the surface of microbes * Biochemical reactions = lysis of infected and invading cells

Inflammatory Response

- At site of injury there are: * Mast cells release histamine * Macrophages release cytokines- Signaling molecules cause capillaries to dilate * Fluid with antimicrobial peptides flows out * Neutrophils come out and eat the pathogens= Swelling and Redness

Sound Basic

- Wave: wavelength * frequency = velocity- Speed in different media * in air v = 340 m/s (changes with temperature) * Velocity in solid > V liquid > V gas ^greater restoring force = faster sound travels

Pitch

- Individual's impression of the frequency of a particular sound - High pitch = high frequency- Low pitch = low frequency- Human ears perceive sounds waves: 20-20,000 Hz

Loudness

- Subjective, Perception of intensity (I)- Amplitude of the wave * If it is large = big amplitude * If it is quiet = small amplitudeI = Energy / (Area * Time) = Power / Area units: J/sm^2 or W/m^2 * Reference sound = 10^-12 w/m^2 ^minimum sound intensity humans detect

Change in Intensity

Difference in decibel = 10 log (I final/I initial)

Human Reproductive Hormones

- Coordinated action of hormones from hypothalamus, anterior pituitary, and gonads* hypothalamus: gondatropin releasing hormone* GnRH tells anterior pituitary to secrete FSH, LH* FSH and LH regulate sex hormone production

Androgens

Male sex hormones - testosterone

Estrogens

Female sex hormones- Estradiol, progesterone

Female Reproductive Hormone

1. hypothalamus secrets GnRH --> ant. pituitary * tropic hormone2. Small amounts of FSH/LH * FSH = stimulates follicle growth (aided by LH)3. Follicle grows-> secretes increasing amts of estrogen4. Estrogen stimulates hypothalamus to secrete more GnRH = more LH & FSH * Positive Feedback5. Surge in FSH/LH = follicle to rupture = egg release (ovulation) 6. Ruptured follicle = corpus luteum --> secretes progesterone and estrogen. promotes thickening of endometrium for implantation7. Corpus luteum stops secreting, big dip = drop in FSH/LH * Lows levels of FSH/LH = menstruation

Male Reproductive Hormones

1. hypothalamus secrets GnRH --> ant. pituitary * tropic hormone2. FSH and LH are secreted * FSH acts on Sertoli cells (nourish baby sperm) * LH acts on Leydig cells (produce androgens)3. Leydig cells produce testosterone, which encourage spermatogenosis - Sertoli cells release inhibin * Inhibin, testosterone are negative feedback

Lymphocytes

- Stem cells in bone marrow- B cells: stay in bone marrow- T cells: migrate to thymus

Antigen

- Substance that elicits a response from B-cell/T-cell- Epitope: portion of antigen bound to TCR & BCR * Bind to B & T cell via receptors

B-cell

- Y shaped molecule- 4 polypeptide chains * 2 identical heavy chains * 2 identical light chains - Receptor binds antibody w/o transmembrane helix

T Cell Receptor

- 2 chains: alpha and beta linked by disulfide

Immune Response

1. Leukocyte engulfs and chews up a pathogen2. Puts the pieces onto MHC II proteins3. Recognized by helper T cells (CD4+ cells [co receptor])4. Helper T cells promote secretion of cytokines by antigen presenting cell - cytokines (+) feedback on helper T cell = proliferation5. Helper T cell secretes other cytokines = activate B cell and Cytotoxic T cells

Cytotoxic T cells

Responsible for recognizing infected body cells and destroying them- Every cell in body (except for RBC) has MHC I * putting fragments of proteins onto MHC I- If cell is infected, pathogen proteins go on MHC I * Tc recognizes MHCI/antigen complex and targets for destruction ^Tc recognizes via TCR receptor/CD8 co-receptor- Tc cell releases perforin molecules * forms pores in membrane of cell

Perforin

- Tc cell recognizes infected cells- Secretes molecules to form pores in cell membrane - Inside of cell is hypertonic to outside so there is an influx of H20= Cell lysis

Humeral Response

Mediated by B-Cells in 2 ways1. Antigen presenting cells (macrophage) - MCHII/antigen2. Helper T cell via MHC II/antigen- Activated B cell colonies expand rapidly * Memory B cell (immunological memory) * Plasma cell (secrete its B-cell receptor in an antibody)- Antibodies bind to extracellular antigens * if antigens are running around it will be surrounded by the specific antibody that neutralizes it so a leukocyte can eat and destroy it

MHC I vs. MCH II (immune response)

- MHC II is only on macrophages and neutrophils * cells that eat pathogens- MHC I is on every cell except for RBC

Doppler Effect

Change in pitch of a sound from high frequency as it approaches an observer to lower frequency as it moves away from an observer- One or both sources get closer = higher pitch/freq- One or both sources far apart = low pitch/freq.F listener = [(V +/- V listener) / (V +/- V stationary)]Fs

Light Chain (B cell)

3 gene segments:1. Variable (V)2. Joining (J)3. Constant (C)1 + 2 = encode variable region of receptor- 1 C gene- 40 V genes- 5 J genesFunctional gene is made up of 1 V, 1 J, 1C ^ 40 5 1 = 200 diffrent combinations

VDJ Recombination

Recombinase randomly deletes DNA between V and J genes in the light chain of the B cell- Happens at DNA level during differentiation so it becomes unique with 1 V, 1 J, and 1 C 1.65 10^6 different combinations

T-Cell Development/Maturation

- Develop in thymus1. Pre Tcell Progenitor express surrogate chain * looks like a receptor * rearrangement of DNA via recombinase * develops into alpha and beta chain = Pre Tcell2. Two rounds of selection a) Positive selection: * occurs in cortex of thymus * Allows select Tcells to bind MHC * If affinity for MHC is too low, cell dies (apoptosis) b) Negative selection: * occurs in thymus medulla * eliminates T-cells whose receptor strongly recognizes self-MHC/self-antigen * Die via apoptosis

Standing Wave

- Wave that can be produced by waves traveling in opposite directions- Wave does not appear to move transverse- Looks like moves up/down

Standing Wave Characteristics

- Nodes: points where the line looks stationary- Antinodes: maximum displacement for a wave

Open/Closed Pipe

Pipe closed at one end, closed at the otherOnly observed odd harmonic third harmonics- Lambda = 4L/n- Frequency = n(V/4L)

Open/Open Pipe

Pipe is open at both endsEx. strings- Lambda = 2L/n- Frequency = n(V/2L) Frequency x lambda = velocity

D. 2.0 mFundamental = first harmonic --> n =1Lambda = 2(1)/2 = 2m

The fundamental resonant wavelength of a pipe open at both ends that is 1 m long and 0.1 m in diameter is?

Carbohydrate Digestion

Oral cavity/esophagus: polysaccharides (starch, glycogen)- salivary amylase breaks down to smaller polysaccharidesStomach: no formal digestion- acidity of stomach, protonates ether bondsSmall intestine (enzymes from pancreas): pancreatic amylase breaks down polysaccharides to disaccharidesSmall intestine (enzymes from epithelium):breaks disaccharides down to monosaccharides

Protein Digestion

Oral cavity/esophagus: noneStomach: pepsins break down proteins into smaller polypeptides- pepsin is a protease that uses water to cleave hydrogen bonds (hydrolase)Small intestine (enzyme from pancreas): trypsin and chymotrypsin breaks down small polypeptides into smaller polypeptides- pancreatic carboxy-peptidases Small intestine (enzymes from epithelium): dipeptidases, carboxypeptidases, aminopeptidase break down the small poplypeptides into digestible amino acids

Nucleic Acid Digestion

Mouth/esophagus: noneStomach: noneSmall intestine (enzyme from pancreas): DNA, RNA is disgested by pancreatic nucleases into nucleotidesSmall intestine (enzyme from epithelium): nucleotidases breaks down nucleotides into nucleosidesnucleosides are broken down into nitrogenous bases, sugar by nucleosidases

Fat digestion

Mouth: noneStomach: noneSmall intestine (enzymes from pancreas:) fat (triglyceride) coated with bile salts Smaller intestine (enzymes from epithelium): pancreatic lipases break down into glycerol, fatty acid, monoglycerides

Chemical Digestion (stomach)

- interior surface is highly folded- Gastric gland cells:1. Mucous cells secrete mucous to protect stomach lining 2. Chief cells secrete pepsinogen (inactive)3. Parietal cells secrete hydrochloric acid HCL converts pepsinogen to pepsinPepsin begins chemical digestion of proteins

Digestion in Small Intestine

- Different organs contribute to absorption1. Pancreas produces basic solution rich in bicarbonate (HCO3-) to neutralize stomach acid2. Bile mixture of substances made in the liver that has lots of salts. It is an emulsifier.Stored and concentrated in gallbladder

Pancreatic Enzymes

1. Proteases (chymotrypsin, trypsin) are secreted as zymogens * activated when they enter the small intestine

Hepatic Portal Vein

- Leads directly to liver- Blood travels to the heart and other tissue- Liver regulates distribution of nutrients- Liver removes anything that can be toxic

Absorption of fats

- Lumen of SI triglycerides are being broken down- Monoglyceride is transported across brush border to epithelial cells- In the cell the triglycerides are reconstructed- Emulsified by bile salts into fat droplets (chylomicrons)- Chylomicrons are exocytosized (Active transport) from the cell into lacteals- Lacteals (vessels of lymphatic system) carry away lymph to larger veins

Large Intestine

Reabsorption of water to prevent dehydration

lymphatic system

- circulatory + immune system - returns lost fluid and proteins to blood- network of tiny vessels intermingled among the capillaries

Lymph

- fluid = lymph - composition = ISFDrain into large veins of circulatory system at base of neck

Disruptions in movement of lymph

Causes edema from excessive fluid in tissueextremely swollen limbs (elephantiasis)

Lymph Nodes

- Important to immune system - Filter lymph- House T cells and Macrophages that attack bacteria, virusesDuring infection:- T cells divide rapidly = swollen

Electrical Power

Rate of conversion of electrical potential energy into some other type of energyPower = IV (current x voltage) = V^2/R= I^2/RUnit: 1 watt = 1 J/S

Capacitors

Formed when two conductors are separated by an insulator When you connect it to a battery, there is an accumulation of charge on each side

Insulator

Material that impedes the movement of chargeEx. rubber and air

Capacitance

Amount of charge (q) that can be stored per voltage or potential difference voltage (v) across parallel platesDepends on area of the conducting plates, distance between plates, dielectric constantC = q/vUnits: 1 F = 1 C /1 V

Dielectric

Non-conducting material between conducting plates of a capacitorCapacitance increases by a factor of k

Electrical Potential Energy

Needed to charge the capacitor Difference PE = q x Vavg = 0.5v x q

Ohm's Law

Voltage (V) = Current (I) x Resistance (R)

Conductor

Material that allows for movement of chargeElectric Force =Charge x Strength electric fieldF = qEEx. Metals (metallic bonding)

Current

Flow of charge from one point to another in a certain amount of timeFlow in same direction as positive chargeI = change in charge / change in timeUnits: Amperes = 1 coloumb / Second

Resistivity (p)

Measure of how difficult it is for charges to conduct through materialHigher = better electrical insulatorsLower = better electrical conductors p = Electric field / densityunits: ohms x meters

Conductivity (sigma)

Measure of how well a material conducts charge sigma = 1/p = current density / electric field

Electrical Resistance

Considers both the materials conductivity and dimensions of the deviceR = p (length/amperes)

Aldose

- Free aldehyde = reducing sugar * can be oxidized to carboxylic acid * Ag2O (Silver Mirror Test)

Chiral Center (glucose)

Fischer Projection:- If OH is on the right = D sugar- If OH is on the left = L sugarCyclized sugar:- CH2OH is up = D sugar* all substiutients in a ring are equitorial- CH2OH is down = L sugarGlucose - 6 carbons = aldohexose- 5 carbons = aldopentose- 4 carbons = aldotetrose- 3 carbons = aldotriose

Carbohydrate

Empirical formula = CH2OEx. Dihydroxyacetone: C3H6O3

Carboxylation

fatty acid and gluconeogenesis - When you add a CO2 to form a carboxylic acid- De is when you lose a CO2 from a carboxylic acid

Isomerization

Maintain the same amount of atoms but bonds rearrangeCannot for carboxylic acid

Cofactors

FAD: C-C double bond formation*Succinate to Fumarate NAD: C-O bond*2.5 ATP

Heme

- Porphyrin ring with an iron atom in the middle- Coordinated by four Nitrogens- Condensation of glycine + succinylCoA * SuccinylCoA comes from Acetyl CoA from the TCA cycle- Ferrous +2 when unbound to O2 in Hb

Biosynthesis of Heme

1. Succinyl CoA (4C) + glycine = condensation*Enzyme cofactor: PLP (conjugated to lysine)* mitochondria2. Combine four groups and cyclizes 3. Iron inserts in ferrous (Fe2+) form*Enzyme is ferrochelatase4. Transported in plasma by transferrin, binds 2 ferric ions

Breakdown of Heme

- Heme is reduced- NADPH is oxidizedColored because of network of conjugated pi system and absorb in the UV

Integumentary System

Skin, hair, nails, subcutaneous tissue bellow skin and assorted glandsFunctions:- Protection for injury/infection- Regulates body temp. - Sensory perception- Regulates water loss- Chemical synthesis

Layers of skin

1. Epidermis2. Dermis3. Subcutaneous tissue- fat, collagen, fibroblastsThroughout the skin are capillaries, hair follicles, sweat glands, and nerve endings

Physical Protection (Skin)

- Continuity of skin and hardiness of keratinized cells - Water proofing of glycolipids to protect from bacteria and abrasion- Glycolipids prevent diffusion of H2O and H2O soluble substances btwn cells

Skin Penetrating Substances

- Lipid soluble substances: CO2, steroids, O2, fat soluble vitamins- Poison oak/ivy- Organic solvents (acetone)- Salt of heavy metals (leads)

Chemical Protection (Skin)

Skin secretions: - Defensins antimicrobial peptides- Acidic environment will retard bacterial growth- Melanin protects from UV damage

Temperature Regulation (Skin)

- Produce sweat to dissipate heat1. body temp rises and is hotter than external environment2. blood vessels in dermis dilate and stimulate sweat glands3. evaporating sweat helps dissipate heat- Constriction of dermal blood vessels to retain heat1. Constricting blood vessels 2. Pull blood away from skin towards body3. Protects internal organs

Sensory Sensation

1. Meissner's Corpuscle & Merkel Disks respond to light touch2. Pascinian Receptors detect deep pressure contacts3. Hair Follicle Receptors movement across skin

Vmax (enzyme)

Maximal velocity of an enzymeDependent on [enzyme]Vmax = Kcat x [E]- Kcat: turnover #

Km (enzyme)

Concentration of substrate that gives half VmaxMeasure of affinity of enzyme for substrate

Line Weaver Burke Plot

X-intercept: -1/KmY-intercept: 1/VmaxSlope: Km/Vmax

Catalytic Efficiency

Kcat/Km --> turnover #/affinityRatio of how fast something is turned over/how fast something bindsRate cannot be faster than diffusion.10^8-10^9* Higher Kcat/Km = better enzyme* Lower ratio = worse enzyme

Competitive Inhibitors (enzyme)

- Vmax = not changing- Km = increasing

Uncompetitive Inhibitor (enzyme)

- Vmax = decreasing- Km = increasing- Ratio Km/Vmax = same *slope has not changed

Noncompetitive (enzyme)

- Vmax = decreasing * y-int is above original line - Km = same

Oxidation

Loss of electronsGain of bonds to oxygen, less to H Catabolic (+)Increase in oxidation state

Reduction

Gain of electrons Loss of bonds to oxygen, more to HAnabolic (-)Decrease in oxidation state

Modifying DNA

1. Isolate DNA from cell expressing GOI2. PCR amplify GOI *Amplifying 1 gene from the rest of DNA3. Isolate plasmid from bacteria4. Cut the GOI and plasmid with enzymes * restriction enzymes, very specific * Restriction sites where restriction enzymes cut GOI5. Ligate the plasmid and GOI together6. Transform bacteria so it can express protein of interest- GOI = Gene of Interest- Ligate = join together

Recombinant

Adding something foreign into the organisms DNA- Foreign gene added to a bacterial plasmid

Engineer Primers

At ends of primer need a region rich in G,COne goes in a forward direction5'-GC Region-Restriction site-Start gene-3'One goes in the reverse direction3'-End of gene-Restriction site-GC region-5'

Polymerase Chain Reaction (PCR)

1. 95 F - denature DNA2. 55 F - anneal primers to DNA3. 72F - elongate (DNA replication)4. Do this 30 times5. GOI of interest has been marked by restriction sites- Geometric amplification of gene- Important stuff to add: * Template * Primers * Nucleotides * MG, Tag pol.

Restriction Site

- Always a Palindrone *Reads the same forwards and backwards5'-GAATTC-3'3'-CTTAAG-5' } complementary strand

Gel Electrophoresis

Separates by size- Native electrophoresis: preserves struc.- Denaturing: disrupts secondary struc.- Bigger things get stuck at the top- Smaller things make it to the bottom