errors

sound waves are

longitudinal - they move from side to side to travel longitudinally.

light waves are transverse- they are perpendicular (trans perpendicular)

reduction potentials (E)

• tells you how readily something reduces or oxidizes

• if +-reduced, if negative-oxidize

electrons in a galvanic cell move

from anode to cathode

• cathode is where oxidation occurs

• anode is where reduction occurs

Positive E cell indicates a thermodynamically favorable reaction.

Ecell equation

Ecathode-Eanode

dG from E

dG = -nFE

relationship between wave speed, frequency and wavelength

f ~ v ~ sqrtT

• we know c=lambdaf

• speed of sound is 343 m/s

• double freq = 2*sqrtT1

upward buoyant force

• =weight fluid displaced (mg)

• To find, F=mg, where F is buoyancy force and g is acceleration constant

• irrelevant of how much water displaced

diffraction

bending of light - isn’t too significant between water and air

dispersion

spreading of light into different frequencies due to differences in index fraction

polarization

alignment of EM radiation along orientation

free fatty acids

• one line of fatty acid - carboxyl group and hydrocarbon tail

• exists as triglyceride or phospholipid in plasma- hydrolyze = free it

saponification

• hydrolysis of ester bonds with a strong base

• one equivalent of base is needed to hydrolyze one ester linkage

• catalytic amount is not enough to hydrolyze an ester

gas chromatography separates

• geometric isomers (cis/trans)

• they have different boiling points

Kirchoff’s loop rule

• sum of voltage drop around close loop is 0

• current going through series doesn’t change.

• Using V=IR, we know that if R decreases, V increases across the final resistor before closing the circuit

something feels colder when

• heat travels from your body to the object faster

  • this causes it to have a faster KE.

retro aldol reaction

• steps- first hydration with base then dehydration product is hydrated into the product

• produces either 2 ketones, 2 aldehydes, or one of each based on the structure of the original compound

superheating

• when liquid is heated above boiling point but doesn’t boil

• surface tension- could inhibit formation of bubbles, increasing vapor pressure

• boiling chips prevent superheatin

TLC

more nonpolar moves further up plate - higher Rf

stationary phase is polar- if silica -so polar binds quicker and can’t move as far

alpha emission

• release of He equivalent particle - 4 / 2 a

beta emission

• - means you gain protons, no effect on the mass number

• + means you lose protons, no effect on mass number

gamma

release of high energy photon that occurs when the protons and neutrons in nucleus change config from higher energy state

flow rate

Volumetric flow rate- Q =Av

• if your v increases and you want to decrease it, you have to make v less. THis means that A has to increase

venturi effect

• based on Bernoulli’s principle- says that if diameter decreases, speed increases

• says that if speed increases, pressure decreases

H2PO4 -

has 2 equivalent points, so 2 buffer zones

• equiv points ~ how many H+ you can remove

atoms in same column have

• same valence config so they have similar chemical properties but different physical properties

buffers

• mixture of weak acid and salt of conjugate base or weak base and conjugate acid

• each can neutralize either any added base or acid

strong acids

HI, HBr, HCl, HClO4, H2SO4, HNO3

• everything else is weak

strong bases

• group 1 hydroxides, oxides

• Ba(OH)2, Sr(OH)2, Ca(OH)2

• Metal amids

weak bases

• NH3

• amines

• conjugate of weak acids

when your cell is discharging

• spontaneous reaction occurs, electrons will flow in the oposite direction (so cathode to anode)

• This means that anode is where oxidation occurs while cathode is where reduction occurs.

k cat

catalytic constant- rate constant of reaction when enzyme is saturated with substrate

• first order rate constant

  • is like the max number of molecules transformed by an enzyme

catalytic efficiency

• effectiveness of enzyme - depends on how it binds and converts

  • Kcat/Km

  • catalytic perfection- overall rate of diffusion is controlled

diffusion controlled limit

maximum rate that 2 freely diffusing molecules can collide in an aqueous solution

lineweaver burk plot equation

1/vo = (Km/Vmax) (1/S) + (1/Vmax)

Slope- Km/Vmax

cooperativity

• subunits are linked to each other (allosteric/regulatory enzymes)

• sigmoidal curve

competitive inhibition

• inhibitor directly competes with substrate for binding to enzyme active site

• Causes Km to increase while Vmax stays

noncompetitive inhibitors

• inhibitor binds to allosteric site but NO confirmational change occurs, so the substrate can still bind, but the enzyme doesn’t work

• Causes V max to decrease because your enzymes are less effective, but Km isn’t affected because substrate can still bind

transition state analogs

compounds that mimix the transition state to take advantage of active site, making it a better competitive inhibitor

mixed inhibition

• inhibitor binds, altering the conformation

• Vmax decreases because the inhibitor makes it work less. Km increases because you need more substrate to combat the inhibitor’s binding

uncompetitive inhibition

• inhibitor binds to the enzyme after substrate already is bound, causing reaction to not go

• Vmax decreases because the enzymes are less effective. Km decreases because the substrates are going to stay bound longer—the problem isn’t with competing for binding.

monosaccharides

• aldose (3 carbon)- glyceraldehyde

• ketose (# carbon)- dihyroxyacetone

Sugar structures

D-glucose- middle finger

D-galactose- middle 2 fingers

D-mannose- gun

d-ribose- 5 carbon thumbs up

d-deoxyribose- 5 carbon thumbs up without index finger (you lose OH)

d-fructose- 5 carbon, lose 1 middle OH finger from mannose

a anomer

• C1 config of OH

• hydoxyl group lies on opposite side of ring from CH2OH group of chrial carbon that determines D or L

• down (usually)- draw out boat form

B anomer

• C1 config of OH

• hydroxyl group points up due to hydroxyl group lying in same side of right from CH2OH group of chiral carbon

• up (usually)

lactose

a- galactose + b- glucose connected by glycosidic bond

sucrose

a-glucose + a-fructose

most abundant disaccharide

a(1,4) vs a(1,6)

• a-1,4 extends, a-1,6 creates a branch point

amylose

• only a 1,4

amylopectin

a (1,6)

Oligosaccharides

• hydrophilic

• conformationally flexible

• stabilize protein structure

• intracellular addressing system

_ABO

• Type A- terminal N-acetylated galactose group. Antibodies against B- Can receive Type O

• Type B- terminal galactose- antibodies against A- can receive Type O

• Type O- no terminal groups - antibodies against A and B- can receive only Type O

• Type AB- doesn’t develop antibodies, can receive anything

mouth digestion enzymes

• amylase- starch break down

• protease- trypsin, chymotrypsin, elastase- in stomach and pancreas- for protein

• lipase- in pancreas going into small intestines- release FA by breaking down big chains

proteasome vs lysosome

• lysosome breaks down within a vesicle, proteasome breaks on its active sites

• lysosomes break down proteins, proteasomes break down proteins

• proteasomes require a tag of ubiquitin, it llinks C-terminus to a Lys side chain (contains at least 4 ubiquitins)

NAD+ vs NADP+

NAD+ is for catabolic reactions - break down

NADP+ s for anabolic reactions- build up

ubiquinone

• lipid soluble carrier that moves up to 2 e- at a time

Vitamins

• B3- niacin- precursor for NAD+

• B2- riboflavin- precursor for FAD2+

• Vitamin C- hydroxylation reaction precursor (for proline and lysine in collagen)

mRNA is synthesized from

5’ to 3’

protein is synthesized from

N-terminus to C-terminus

mRNA

• messenger of genetic information - how to code protein

• translated in ribosome

• RNA polymerase translates

• monocistronic- only one product is created- in euk

• polycistronic in prok

tRNA

• converts nucleic acids to amino acids and peptide

• cytoplasm

• pairs correct codon on mRNA

rRNA

• synthesized in nucleolus, used in protein synthesis in cytoplasm

• catalyze formation of peptide bonds and is also important in splicing out its own introns within nucelus

missense mutation

one amino acid changes for another

nonsense mutation

codon encodes for premature stop codon

frameshift mutation

1 nucleotide changes entire sequence

transcription

• RNA polymerase find promoter regions

• RNA polymerase II transcribes mRNA after binding to TATA box

• transcription always from 5’ to 3’

RNA pol

• 1- nucleolus and synthesizes rRNA

• 2- in nucleus and synthesizes hnRNA and some small nuclear RNA

• 3- in nucleus and synthesizes tRNA and rRNA

introns

noncoding sequences

exons

coding sequences

small nuclear RNA (snRNA)

couple with snRNPs that recognize the splice sites of introns, forming the lariat

5’ cap

• at 5’ end of hnRNA, 7-methylguanylate triphosphate cap added

• cap added during transcription and is recognized by ribosome as binding site

• protects mRNA from degradation in cytoplasm

3’ poly-A tail

• added to 3’ end of mRNA transcript to protect against rapid degredation

• as soon as it leaves nucleus, it is degraded from 3’

• longer poly A = longer mRNA survival before being digested in cytoplasm

• helps export mRNA from nucleu

alternative splicing

• primary transcript of hnRNA is spliced together to make variants of protein

translation steps general

• initiation- Initiation factors

• elongation- elongation factors

• termination- release factors

translation prokaryote initiation steps

1. small subunit binds to Shine-Dalgarno seq in 5’ untranslated region of mRNA

2. initiator tRNA binds to AUG codon through base pairing (fMet is start codon)

3. large subunit binds

translation initiation euk steps

1. small subunit binds to 5’ cap

2. initiator tRNA binds to AUG start codon (met)

3. large subunit binds

elongation steps

• ribosome moves in 5’ to 3’ direction to synthesize from N-term to C-term

1. A site takes in aminoacyl tRNA with the amino acid

2. P site- holds the tRNA that carries growing polypeptide chain, where Met binds to start. Peptide bond formed with peptidyl transferase

3. E-site- inactivated tRNA pauses before exiting

EF- recruit aminoacyl tRNA

termination steps

• release factor binds to termination codon - causes water molecule to be added to polypeptide chain

• hydrolyze the completed polypeptide chain

proper folding

• posttranslational processing, final step of synthesis

• chaperones- helps protein folding process

prenylation

addition of lipid groups to certain membrane bound enzymes

operon

• genes that regulates gene expression

• transcribed as single mRNA

Jacob Monod model

• describes structure and function of operons

• operons contain structural genes (codes for protein of interest), operator site (ipstream part binding represor), promoter site (further upstream, binds RNA polymerase), and regulator gene (codes for repressor)

inducible systems

• repressor binds tightly to the operator system so RNA pol can’t leave

• negative control mechanism

• to remove- inducer binds to repressor protein, polymerase moves downstream

positive control

• binding of protein to DNA increases transcription

repressible system

system is turned off even though it’s normally on

• repressor made by regulator gene is inactive until it binds to the repressor

• complex then binds to operator to prevent further transcription

catabolite activator protein (CAP)

• transcriptional activator used by Ecoli when glucose levels are low

• Binds cAMP, which allows it to bind promoter region of operon

transcription factors

• transcription activating proteins that search DNA looking for specific DNA binding motifs

• have 2 domains- DNA binding domain- binds to specific nucleotide sequence in promoter region or to DNA response element- sequence of DNA that binds only specific transcription factors

activation domain

• allows for binding of several transcription factors and other important regulator proteins

enhancer

controls of one gene’s expression with multiple signals

cell-cell junctions

• composed of cell adhesion molecules- cells recognize each other and contribute to cell differentiation

gap junctions

• allow for cell-cell communication and are often found in small bunches together

• called connexons

tight junctions

• prevents solutes from leaking into space beteween cells

• paracellular route

• in epithelial cells

desmosomes

• bind adjacent cells by anchoring to their cytoskeletons

• formed by interactions between transmembrane proteins associated with intermediate filaments inside adjacent cells

• between epithelial tissue

sodium potassium pump

maintains low concentration of sodium ions and high potassium concentration in the cell

Pumps 3 Na+ out, 2 K+ in

mitochondrial membrane

• outer- highly permeable due to many large pores- ions and small proteins pass

• inner- more restricted permeability, encloses mitochondrial matrix.

chylomicrons

transport dietary triacylglycerols, cholesterol, and cholesteryl esters from intestine to tissues

VLDL

transports triacylglycerols and fatty acids from liver to tissues

IDL

• remnants of VLDL ( transition state between VLDL and LDL)

• picks up cholesteryl esters from HDL to become LDL picked up by the liver

LDL

delivers cholesterol into cells

HDL

• picks up cholesterol accumulating in blood vessels

• delivers cholesterol to liver and steroidogenic tissues

• transfers apolipoproteins to other lipoproteins

apolipoproteins

• form protein component of lipoproteins

• receptor molecules and involved in signaling