Biochemistry

Question 1

Amino acids

Answer 1

molecules that contain 2 functional groups, amino group (-NH2) and carboxyl group (COOH), and another grou pcalled a side chain or R group specific to each amino acid

Question 2

for carboxylic acids, the alpha carbon is the carbon ____ to the carboxyl carbon

Answer 2

adjacent

Question 3

all aminoacids are chiral at the alpha carbon except for….

Answer 3

…glycine, which has 2 hydrogens

Question 4

L amino acids

Answer 4

the only kind of amino acid found in eukaryotes, and are drawn with the amino group on the left in a fischer projection

Question 5

nonpolar, nonaromatic side chain amino acids (7)

Answer 5

glycine, alanine, valine, leucine, and isoleucine, methionine, and proline

Question 6

methionine is unique because

Answer 6

it contains a sulfer with a methyl group attached and is nonpolar relatively

Question 7

proline is unique because

Answer 7

it forms a cyclic amino acid, the amino nitrogen becomes part of the side chain forming a 5 membered ring

Question 8

aromatic side chain amino acids (3)

Answer 8

tryptophan, phenylalanine, and tyrosine

Question 9

polar non-aromatic side chain amino acids (5)

Answer 9

serine, threonine, asparagine, glutamine, cysteine

Question 10

negatively charged acidic side chain amino acids (2)

Answer 10

aspartate and glutamate (depronated form of aspartic acid and glutamic acid respectively)

Question 11

positively charged (basic) side chain amino acids (3)

Answer 11

lysine, arginine, and histidine

Question 12

why can histidine have a positive charge?

Answer 12

pKa of side chain relatively close to 7.4, about 6, so at physiologic pH one nitrogen atom is protonated and the other isn’t, inder more acidic conditions a 2nd nitrogen atom can become protonated giving a positive charge

Question 13

hydrophobic amino acids

Answer 13

alanine, isoleucine, leucine, valine, and phenylalanine

Question 14

hydrophilic amino acids

Answer 14

histidine, arginine, and lysine, plus neg charged glutamate and asparate

Question 15

charged amino acids tend to be on the ___ of a protein, while hydrophobic tend to be on the ___

Answer 15

outside, inside

Question 16

alanine abbreviation

Answer 16

Ala, A

Question 17

arginine abbreviation

Answer 17

Arg, R

Question 18

Asparagine abbreviation

Answer 18

Asn, N

Question 19

Aspartic acid abbreviation

Answer 19

ASP, D

Question 20

Cysteine abbreviation

Answer 20

Cys, C

Question 21

Glutamic acid abbreviation

Answer 21

Glu, E

Question 22

Glutamine abbreviation

Answer 22

Gln, Q

Question 23

Glycine abbreviation

Answer 23

Gly, G

Question 24

Histidine abbreviation

Answer 24

His, H

Question 25

Isoleucine abbreviation

Answer 25

Ile, I

Question 26

Leucine abbreviation

Answer 26

Leu, L

Question 27

Lysine abbreviation

Answer 27

Lys, K

Question 28

Methionine abbreviation

Answer 28

Met, M

Question 29

Phenylalanine abbreviation

Answer 29

Phe, F

Question 30

Proline abbreviation

Answer 30

Pro, P

Question 31

Serine abbreviation

Answer 31

Ser, S

Question 32

Threonine abbreviation

Answer 32

Thr, T

Question 33

Tryptophan abbreviation

Answer 33

Trp, W

Question 34

Tyrosine abbreviation

Answer 34

Tyr, Y

Question 35

Valine abbreviation

Answer 35

Val, V

Question 36

Ionizable groups tend to ___ protons under acidic conditions and ___ them under basic

Answer 36

gain, lose

Question 37

Remember, pKa is when ___=___

Answer 37

deprotonated version of ionizable group equals protnated version of ionizable group

Question 38

If pH <pKa, then majority of species is ___, and vise versa

Answer 38

protonated

Question 39

all amino acids have ___ pKa groups

Answer 39

at least 2

Question 40

zwitterions

Answer 40

dipolar ions often at a physiologic middle of the road pH where the carboxylate group tends to be unprotonated and negative and the amino group tends to be protonated thus have a molecule with a negative and positive charge but overall electrically neutral

Question 41

when pH of a solution is approx equal to the pKa of a solution, then….

Answer 41

….the solution is acting as a buffer and the titration curve is relatively flat

Question 42

isolelectric point (pI) definition and formula

Answer 42

pH at which a molecule is electrically neutral
(pKa NH group + pKa COOH group) /2

Question 43

Isoelectric points for amino acids with charged side chains

Answer 43

for acidic, do the pKa of the R group + pKa COOH group /2 and for basic do the pKa of the NH group + pKA r group /2

Question 44

Peptide

Answer 44

composed of amino acid subunits also called residues formed by a peptide bond that is a specialized form of an amide bonde that is a dehydration reaction removing H2o from it

Question 45

steps in formation of a peptide bond

Answer 45

electrophilic carbonyl carbon on first amino acid attacked by nucleophillic amino group on second, then hydroxyl group of carboxylic acid is kicked off

Question 46

why is the rotation of the protein backbone around it’s C-N amide bond restricted?

Answer 46

resonance between the C-N bond having partial double bond character

Question 47

4 strucutres of protein

Answer 47

primary structure is linear arrangement of amino acids from encoded DNA, covalent peptide bonds between each amino acid, it is energentically favorable to adopt higher structure levels
secondary structure is hydrogen bonding between near amino acids, alpha helices and beta pleated sheets
tertiary structure is a 3d shape determiend by hdrophilic and hydrophobic interactions between R groups, and electro statin interactions that further stabilize the protein from the inside and disulfide bonds between two cysteine molecules that create loops in a protein chain
quaternary is optional, for proteins with more than one polypeptide chain combining these subunits to functional protein

Question 48

oxidoreductase

Answer 48

catalyze oxidataion reduction reactions, often enzymes will have name dehdrogenase or reductase in their name, often have a donor reductant and an acceptor oxidant

Question 49

transferase

Answer 49

catalyze movement of functional groups from one molecule to another, includes kinases which catalyze transfer of a phosphate group to another molecule

Question 50

hydrolase

Answer 50

catalyze breaking a compound into 2 molecules using the addition of water, for example phosphatase, peptidase, nuclease, lipase

Question 51

lysases

Answer 51

catalyze cleavage of a single molecule into 2 products without water as a substrate or oxidoreductases, because most enzymes can also catalyze the reverse of their specific reactions, may also synthesize a single molecule, known as a synthase during this activity

Question 52

isomerase

Answer 52

catalyze rearrangement of bonds within a molecule, for eample reaction between stereoisomers as well as constitutional isomers

Question 53

ligase

Answer 53

catalyze addition or synthesis rxn, generally between similar molecules, and often require ATP,

Question 54

enzymes do NOT change these about rxns, they do impact ___

Answer 54

the overall free energy change, or the equilibrium, they do impact the kinetics or rate that equilibrium is reached

Question 55

lock and key vs induced fit model

Answer 55

lock and key proposes enzymes active site is already in appropriate conformation for a substrate to fit perfectly with no alteration of tertiary or quaternary structure, vs induced fit which is more likely, where the substrate has induced change in shape to the enzyme in an endergonic phase then upon release a desired product is formed that is exergonic and released, the enzyme returns to its original shape

Question 56

apoenzymes and holoenzyme

Answer 56

enzyme lacking a cofactor vs enzyme containing one

Question 57

cofactor/coenzyme

Answer 57

nonprotein molecules small in size that bind to the active site of n enzyme usually participating in catalysis of rxn through carrying charge thru ionization, protonation, or deprotonation, generally inorganic moleculse or metal ions are cofactors, coenzymes are small organic groups mostly vitamins or derivatives of vitamins

Question 58

enzyme saturation

Answer 58

when all availabel enzymes are occupied and adding more substrate will not change the rate of rxn, reaching maximum velocity

Question 59

michaelis menten equation

Answer 59

V = Vmax (S)/Km + (S) where s is substrate and Km is michaelis constant which is substrate concentration at which half the enzymesactive sites are full

Question 60

the enzyme with the lower Km has the…

Answer 60

….higher affinity for its substrate because it requires less substrate concentration to be half saturated

Question 61

lineweaver burk plots

Answer 61

double reciprocal graph of michaellis menten equation, where the intercept of the x axis is the value of -1/Km, and the intercept of the y axis is the value of 1/vmax

Question 62

cooperativity in enzymes

Answer 62

some enzymes have sigmoidal kinetics owing to cooperative enzymes that have multiple subunits and multiple active sites, that can be in a low affinity tense state (T) or high affinity relaxed state (R), binding of the substrate encourages the transition of other subunits from the T state to the R state which increases the likelihood of substrate binding by these other subunits,

Question 63

3 effect of different local conditions on enzyme activity

Answer 63

temp - rxns tend to double in velocity for every 10 degree C increase in temp until optimum temp reached (in human body 37 degree C) after this activity falls off sharply as enzyme denatures at higher temps
pH - physiologic pH of 7.4 in athe blood for enzymes that circulate in the body, vs in the digestive tract might see optimal activity at a pH of 2 because of the acid
salinity - can interupt hydrogen and ionic bonds

Question 64

competitive inhibition

Answer 64

occupancy of the active site so substrates cannot access enzymatic binding sites if there is an inhibitor in the way, can be overcome by adding more substrate so the substrate to inhibitor ratio is higher, increases value of Km but not Vmax

Question 65

noncompetitive inhibition

Answer 65

binding to an allosteric site instead of active site which induces change in enzyme conformation, allosteric are noncatalytic regions of enzyme, cannot be overcome by adding more substrate, decreases value of v max because less enzyme available but not the km because same affinity

Question 66

mixed inhibition

Answer 66

when an inhibitor can bind either the enzyme or the enzyme substrate complex, but has different affinity for each, bind an allosteric site, alters experminetal value of Km depending on preference of inhibitor for the enzyme vs enzyme substrate complex, if prefers the enzyme increases Km value and if prefers complex lowers km value

Question 67

uncompetitive inhibition

Answer 67

binds only to the enzyme substrate complex to lock the substrate in the enzyme preventing its release by increasing afinity between the enzyme and the substrate, because the complex has already formed upon binding, uncompetitive inhibitors must bind at an allosteric site, lowers km and vmax

Question 68

irreversible inhibition

Answer 68

a type of inhibition where active site is made unavailable for prlonged period of time or the enzyme is permanently altered, can only be overcome by producing new enzyme

Question 69

allosteric enzymes

Answer 69

enzymes that have multiple binding sites, active site but also at least one other site that can regulate availability of the active site known as allosteric sites

Question 70

covalently modified enzymes

Answer 70

enzymes subject to covalent modifications can be activated or deactivated by phosphorylation or glycosylation or otherwise

Question 71

zymogens

Answer 71

enzymes that contain the catalytic active domain and a regulatory domain that must be removed or altered to expose the active site as a control measure (think the pancreatic enzymes digesting the pancreas iteslf if activated in there

Question 72

cell adhesion molecuels (CAMs)

Answer 72

proteins found on the surface of most cells and aid in binding the cell to the extracellular matrix or to other cells, they are all integral membrane proteins, with 3 major family of cadherins, integrins, and selectins

Question 73

cadherins

Answer 73

glycoproteins that hold similar cell types together such as epithelial cells specific to the type of cell

Question 74

integrins

Answer 74

groups of proteins that have 2 membrane spanning chains called alpha and beta, these chains are important in binding and communicating with extracellular matrix, also play a role in cell signaling

Question 75

selectins

Answer 75

bind to carbohydrate molecules that project from other cell surfaces, weakest bonds formed by cella dhesion molecules,

Question 76

antibodies are produced by ___ cells and serve 3 functions

Answer 76

B cells, using their antigen binding sites to neutralize the antigen, mark the pathogen for destruction (opsonization) and clump togther (agglutination) the antigen and antibody into insoluble protein complexes that can be phagocytosed by macrophages

Question 77

ion channels

Answer 77

create pathway for charged molecules, all utilize facilitated diffusion down a concentration gradient through a transmembrane protein, 3 typpes ungated, voltage gated, and ligand gated

Question 78

ungated channels

Answer 78

unregulated ion channel that allows for diffusion

Question 79

voltage gated channels

Answer 79

regulated by membrane potential change near the channel, closed under resting conditions but depoarization causes protein conformation change that allows them to open quicly and close as the voltage increases

Question 80

ligand gated channels

Answer 80

binding of specific substances or ligand to the channel causes opening or closing

Question 81

enzyme linked receptors

Answer 81

membrane receptors that display catalytic activity in response to a ligand binding with 3 primary protein domains, a membrane spanning domain anchoring it to the cell membrane, a ligand binding domain allowing appropriate ligand and when bonded induces conformation change so this acivates the catalytic domain, this often induces initioatn of a 2ndary messenger cascade

Question 82

g protein coupled receptors

Answer 82

large family of integral membrane proteins involved in signal transduction characterized by 7 membrane spanning alpha helices, binding of the ligand increases affinity of the receptor for the G protein, the binding of this represents a switch to the active state and affects the intracellular signaling pathway, Gs which increases levels of cAMP in a cell and Gi which decreases

Question 83

g protein pathway

Answer 83

inactive alpha cubunit with GDP is bound with B and gamma components, then a ligand binds the receptor becomes activated, GTP is present causing dissociation of the beta and gamma subuintis which then activate adenylate cyclase, lose the phosphate and become GDP again and rebinds the beta and gamma subunits inactivating it again

Question 84

electrophoresis

Answer 84

method of separating proteins bys ubjecting compounds to an electric field which moves them according to their net charge and zie, negatively charged will migrate to the positivly charged anote, and positiveily charged with migrate toward the negativelycharged cathode, the velocity of the migration v is directly proportional to the electric field strength E and to the net charge of the molecule z, and inverse to the frictional coefficient f which depends ont he mass and shape of the molecule v=ExZ/f

Question 85

cathodes are ___ charged, anodes are ___

Answer 85

negatively, positively

Question 86

polyacrylamide gel

Answer 86

standard medium for protein electrophoresis, allowing small particles to pass more easily, molecules will migrae slower or not at all if they are larger or electrically neutral

Question 87

native PAGE

Answer 87

method for analyzing proteins in their native state, limited by the varying mass to charge and mass to size ratios of cellular proteins because different proteins may display the same level of migration, most useful to compare molecular size or charge of proteins known to be similar in size from other analytic methods, does not denature the protein unless stained

Question 88

SDS PAGE

Answer 88

sodium dodecryl sulfate separates proteins on basis of mass alone, SDS is a detergent that disrups all noncovalent interactions, binds to proteins creates large chains with net negative charges neutralizing the proteins original charge and denaturing the protein

Question 89

isolectric focusing

Answer 89

method of separating protein on basis of isoelectri point pI, mixture of proteins placed in a gel with a pH gradient, acidic at the psotive cathode, basic at the negative cathode, and neutral in the middle

Question 90

chromatography

Answer 90

tool to separate and identify compounds from a complex mixure, refers to a variety of techniques that require the homogenized protein mixture to be fracctionated thru a porous matrix, preferred over electrophoresis when large amounts of protein are being separated, steps include placing a sample onto a solid medium called the stationary phase or adsorbent, next step is to run the mobile phase thru the staitonary phase, dependingon the relative affinity of the sample for the stationary or mobile phases, different substances will migrate at different speeds,

Question 91

retention time

Answer 91

amount of time a compound spends in the stationary phase on chromatography

Question 92

column chromatography

Answer 92

column filled with silica or alumina beads as adsorbent, and gravity moves solven and compoudns down the column, size and polarity have role in determining how quickly a compound moves, less polar, the more it can elute thru the column

Question 93

ion exchange chromatography

Answer 93

beads in column coated with cahrged substances so theya tract or bind compounds of the opposite charge, so a positive charged colummn will attract and hold a negatively charged protein

Question 94

size exclusion chromatography

Answer 94

beads used in column contain tiny pores of varying sizes, these tiny pores allow small compounds to enter the beads thus slowing them down, large can’t fit into the pores so they move around them and travel thru faster, the smaller compounds are slowed down,

Question 95

affinity chromatography

Answer 95

coating beads with receptors that bind the protein or a specific antibody to the protein, retaining it in the column,

Question 96

2 methods of protein structure determination

Answer 96

x ray crystallography to measure electron density on high resolution scale which is the majority, and minority done thru nuclear magnetic resonance spectroscopy

Question 97

edman degradation

Answer 97

analysis best for small prteins which uses cleavage to sequence proteins of about 70 amino acids, selectively and sequentially removes n terminal amino acid of protein which can tehn be analyze via mass spectroscopy

Question 98

carbohydrates with an aldehyde group as their most oxidized function group are called ____, those with ketone group as most oxidized are called ___

Answer 98

aldoses, ketoses

Question 99

a chiral carbon atom is one that has

Answer 99

4 different groups attached to it

Question 100

D and L system

Answer 100

Same as R and S system for denoting enantiomers BUT they are not interchangable, some D are S and L are R

Question 101

how to determine number of steroisomers with a common back bone

Answer 101

2^n where n is number of chiral carbonds

Question 102

rule for D and L sugars

Answer 102

all D sugars have hydroide of their highest numbered chiral center on the right, and all L sugars have hydroxide on the left

Question 103

diastereomers

Answer 103

2 molecules of the same family either ketoses or aldoses and have same number of carbonds but are not identical and are NOT mirror images of each other, a molecule can have multiple of these

Question 104

epimers

Answer 104

subtype of diastereomers that differ in configuration at exactly 1 chiral center

Question 105

haworth projection

Answer 105

depicts cyclic sugars as planar 5 or 6 membered rings with top and bottom surfaces of the ring nearly perpendicular to the page, chari like configuration

Question 106

cellulose

Answer 106

homopolysaccharide, a chain of B-D-glucose moleculse linked by B1,4 glycosidic bonds, unable to be digested by humans due to lakck of cellulase enzyme

Question 107

starches

Answer 107

polysaccharides more digestible by humans because they are linked a-d-glucose monomers, typically amylose and amylopectin digested by the enzymes B amylase and alpha amylase

Question 108

glycogen

Answer 108

carb storage unit in animals, similar to startch but has more alpha 1,6 glycosidic bonds which makes it highly branched optimizing energy effiency

Question 109

glycogen phosphorylase

Answer 109

cleaves glucose from nonreducing end of a glycogen branch and phosphorylating it producing glucose 1 phosphate

Question 110

difference between liposome and micelle

Answer 110

liposome is double membrane layerphospholipid, micelle is single layer

Question 111

fully saturated fatty acid

Answer 111

tails have only single bonds, saturated fats, more stable and solid at room temp

Question 112

unsaturated fatty acid

Answer 112

includes one or more double bonds which introduce kinks into the fatty chain making it hard for them to stack and solidify, tend to be liquid at room temp

Question 113

glycerophospholipids

Answer 113

phospholipids that contain glycerol backbone bonded by ester linkages ot 2 fatty acids and by a phosphodiester linkage to a highly polar head group, head group determines name

Question 114

sphingolipids

Answer 114

have sphingosine or sphingoid backbones, have long chain, nonpolar fatty acid tails and polar head groups, 4 major subclasses differing by head group

Question 115

4 classes of sphingolipids

Answer 115

sphingomyelins - have either phosphatidylcholine or phosphatidylethanolamine as head group
glycosphingolipids - sugars bonded by glycosidic linkages on outer surface of plasma membrane foudn primarily
gangliosides - polar head groups composed of oligosaccharides with one or more N acetylneuraminic acid, negatively charged
ceramide - single hydrogen atom as its head group

Question 116

steroid structure

Answer 116

4 cycloalkane rings fused together, 3 cyclohexane and 1 cyclopentane

Question 117

cholesterol

Answer 117

major component of phospholipid bilayer responsible for mediating membrane fluidity, choelsterol, like a phospholipid, is an ampiphaathic molecule containing both hydrophilic and hydrophobic components

Question 118

prostaglandins

Answer 118

lipids that act as parapcrine or autocrine signaling molecules, regulate syntesis of cAMP which is a ubiquitous intracellular messenger

Question 119

lipids are excellent to store energy, as their carbonds are mor reduced than sugars which contain alcohol groups. Oxidation of triacylglycerols yields ____ the energy per gram as carbs

Answer 119

twice

Question 120

triacylglycerols are also known as… what is their composition

Answer 120

triglycerides, composed of 3 fatty acids bonded to ester linkages to glycerol they are nonpolar and hydrophobic

Question 121

saponification

Answer 121

ester hydrolysis of triacylglycerols using a strong base typically lye (sodium or potassium hydroxide)

Question 122

surfactant

Answer 122

lowers surface tension at the surface of a liquid serving as a detergent or emulsifier, for example soap

Question 123

nucleoside and nucleotides

Answer 123

nucleosides have a 5 carbon sugar (pentose) bonded to a nitrogenous base and are formed by covalent linking the base to c1 of the sugar, nucleotides are formed when 1 or more phosphate groups are attached to c5 of a nucleoside, named accoring to number of phosphates present (diphosphate, triphosphate)

Question 124

what carbon determines if a pentose is ribose or deoxyribose

Answer 124

the 2’ carbon having oh group or not,

Question 125

What is an exception to the rule that bond breaking is endothermic and bond making is exothermic?

Answer 125

ATP, due to all the negative charges inclse proximity removing the terminanl phosphate from atp actually releases energ

Question 126

DNA is read in the ____. Is it polar?

Answer 126

5’ to 3’ direction, it is polar

Question 127

list the purines and the pyrimidines and what is the difference?

Answer 127

Purines contain 2 rings in their structure, include adenine and guanine found both in DNA and RNA, pyrimidines contain 1 ring in their structure, include cytosine, uracil, and thymine and thymine is only in DNA and uracil only in RNA

Question 128

aromatic molecules

Answer 128

describes any molecule taht is an unusually stable ring system that is cyclic, planar, conjugated, follows huckels rule. They arevery stable because all carbon atoms tend to be sp2 hybridized and have overlap in their orbtitals making them fairly unreactive

Question 129

watson and crick model

Answer 129

double helix antiparalllel with complentary base pairing A to T via 2 hydrogen bonds and G to C with 3 hydrogen bonds which make that one stronger

Question 130

chargaff’s rules

Answer 130

in double stranded DNA, purines = pyrimidines, %A=%T, and %G=%C

Question 131

B DNA chracteristics

Answer 131

Helix makes turn every 3.4 nm and contains 10 bases in that span, with major and mino grooves often the site of protein bonding

Question 132

DNA denaturig and reannealling

Answer 132

heat will rip the hydrogen bonds apart first before affecting the backbone structure, if the heat denatured dna is slowly cooled the strands can become paired again

Question 133

DNA wrapped aroundhistones is called

Answer 133

chromatin

Question 134

how many histone proteins are found in eukaryotic cells and what is the complex formed called

Answer 134

5 histone proteins, the last one H1 seals off the DNA as it eneters the complex, which is called a nucleosome

Question 135

heterochromatin vs euchromatin

Answer 135

dark and transcriptionally silent, dispersed euchromatin is genetically active DNA

Question 136

telomeres

Answer 136

repeating unit at the end of DNA that can be replaced during replication by telomerase, help prevent unraveling and knkot off the end of a chromosome

Question 137

helicase

Answer 137

enzyme responsible for unwinding DNA creating two single stranded templates, in prokaryotes there is only 1 origin of replication but in eukaryotes there are many and in both cases they travel in both directions

Question 138

DNA topoisomerases

Answer 138

work ahead of helicase nicking one or both strands allowing for relaxation of the torsional pressure to prevent single stranded DNA from supercoiling ontot itself

Question 139

DNA polymerases alpha, epsilon, and zeta

Answer 139

repsonsible for reading parental DNA srand and synthesizing new daugheter strand, the leading strand is copied in continiuuous fashion and will read 3’ to 5’ with its complement synthesized in a 5’ to 3’ direction. The lagging strand is read also from a 3’ to 5’ template but creastes small strands called okazaki fragments working backward to produce a 5’ to 3’ daughter

Question 140

primase

Answer 140

synthesizes a short primer of RNA 10 nucleotides in the 5 to 3 direction to start repliciation on each strand, RNase H removes the RNA after then DNA polymerase epsilon adds DNA nucleoitides where the NRA primer had been

Question 141

DNA ligase

Answer 141

seals ends of DNA molecules together creating one continuous strand

Question 142

oncogenes

Answer 142

mutated genes that cause cancer, primarly encode cell cycle related proteins. Before they are mutated referred to as proto-oncogenes

Question 143

p53 is considered an antioncogene, and in order to be fully lost tumor suppresion activity requires…

Answer 143

….both alleles be inactivated

Question 144

how can DNA polymerase tell which strand is template when proofreading error in DNA

Answer 144

the parent is more heavily methylated because it is older

Question 145

recombinant DNA technology

Answer 145

allows for a a fragment of DNA from any source to be multipled by either gene cloning or PCR, this provides means of analyzing and altering genes and proteins, could be used for genetic testing, prenatal diagnosis, and gene therapy

Question 146

DNA cloning technique

Answer 146

often done thru ligating DNA of interest to a piece of nucleic acid called a vector forming a recombinant fector, usually these are bacterial plasmids that can b transferred to a host bacterium, then the bacteria is grown in colonies and a colony containing the recomibnant vector is isolated such as thru tying this to gene for antibiotic reisstance, the bacteria can then express the gene of interest or lysed and reisolated to be processed by restriction enzymes to release the DNA from the vector

Question 147

types of DNA libraries

Answer 147

Genomic libraries contianing large fragments of DNA including introns and exons, cDNA (complementary) libraries are constructed by reverse transcribing processed mRNA, thus removing introns and only genes that are expressed, sometimes called expression libraries

Question 148

PCR

Answer 148

automated process to produce millions of copies of DNA sequence without amplifying the DNA in bacteria, used in criminal cases, ancestry tracing, disease causing bacteria and viruses. Knowing the sequences that flank the desired region of DNA allows for the amplification of the sequence between, PCR requires primers that are complementary to the flanks of the DNA of interest, nucleotides, and DNA polymerase (isolated from thermus aquaticus as human can’t live at this temp), and heat,

Question 149

southern blot

Answer 149

used to detect presence and quantitiy of various DNA strands in a sample, DNA is cut by restriction enzymes then separated by gel electrophoresis, then transferred into a membrane retainint thir separation, the membrane is then probed with many copies of a single stranded DNA sequence, the probe will bind its complementary sequences, probes are labeled with radioisotopes or indicator proteins used to indicate presence of desired sequence

Question 150

transgenic and knockout mice

Answer 150

once dna has been isoalted, transgene can be introduced to an embryo to monitor disease process to adulthood, knockout mice, where a gene has had a gene deleted as well

Question 151

mRNA is synthesized in the ___ direction, and is complementary and antiparallel to the DNA template strand. The ribosome translates in the ___ direction, and synthesizes protein from ___ terminus to ____

Answer 151

5’-3’, 5’-3’, amino, carboxy

Question 152

the DNA ____ strand is identical to the mRNA

Answer 152

DNA coding strand

Question 153

mRNA

Answer 153

transcribed by RNA polymerase enzymes, then may undergo posttranscriptional moidifications prior to release from the nucleus

Question 154

mRNA in eukaryotes is monocistronic, meaining

Answer 154

each mRNA molecule translates into only 1 protein product, thus in eukaryotes, the cell has different mRNA molecule for each of the thousands of proteins, in prokaryotes may be polycistronic

Question 155

tRNA

Answer 155

transfer RNA responsible for converting the language of nucleic acids into the language of amino acids and peptides, each tRNA includes a 3 nucleotide anticodon, this recognizes and pairs with the appropriate codon on an mRNA molecule while it is in the ribosome, each amino acid is activated by a different aminoacyl-tRNA synthetase that requires 2 ATP bonds and transfers the activated amino acid to the 3’ end of the correct tRNA, each tRNA has a CCA sequences where the amino acid binds.

Question 156

rRNA

Answer 156

ribosomal, synthesized in the nucleolus and functions as integral part of the ribosomal machinery used during protein assembly in the cytoplasm, function as ribozymes, enzymes made of RNA molecules instad of peptides, help catalyze formation of peptide bonds and splice out its own introns within the nucleus

Question 157

codons

Answer 157

the 3 letter mRNA sequences that corresponds to a specific and only one amino acid, 64 total. Most amino acids are represented by multiple codons

Question 158

___ codons code for one of the 20 amino acids, while 3 codons code for….

Answer 158

61, termination or a stop codon of translation

Question 159

every eukaryotic protein starts withthe same amino acid:

Answer 159

methionine (AUG) the start codon

Question 160

3 stop codons

Answer 160

UGA
UAA
UAG

Question 161

wobble position

Answer 161

evoluationary development designed to protect against mutations in coding regions of DNA, where the third base of a codon is variable when the first two are usually the same to protect against mutation, called silent mutations

Question 162

missense mutation vs nonsense mutation

Answer 162

mutation where 1 amino acid substitutes for another, vs a mutation where a codon now encodes for a prematurestop codon

Question 163

frameshift mutation

Answer 163

when number of nucleotides are added or deleted from mRNA sequence, shifting the entire reading frame

Question 164

What synthesizes RNA

Answer 164

DNA dependent RNA polymerase II that lcoates genes by looking for regions called promoters, most often TATA box, does not require primer to start generating a transcript

Question 165

RNA polymerase I vs II vs III

Answer 165

I - nucleolus synthesizes rRNA
II - nucleus and synthesizes preprocessed mRNA (hnRNA)
III - tRNA and some rRNA

Question 166

Posttranscriptional processing (3)

Answer 166

before hnRNA can leave the nucleus to be translated into protein, it undergoes 3 processes
1) splicing out introns and lligating exons together in the spliceosome by small nuclear RNA coupled with proteins called small nuclear ribonucleoprotieins or snRPS which recognizes the 5’ and 3’ splice sites of introns
2) 5’ cap of hnRNA a 7 methylguanylate triphosphate cap is added whic protects against degradation in cytoplasm and is recognized by ribosome
3) 3’ poly A tail added to 3’ end of mRNA and protects against degradation,

Question 167

alternative splicing

Answer 167

primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene

Question 168

3 binding sits of ribosomes for tRNA and the order they bind in

Answer 168

A site - aminoacyl
P site - peptidyl
E site - exit

Question 169

4 strands of rRNA in eukaryotic ribosomes

Answer 169

28 S, 18S, 5.8 S, and 5S, the genes for these used to construct the ribosome are found in the nucleolus

Question 170

3 stages of translation

Answer 170

initiation - small ribosomal subunit binds the mRNA at the 5’ cap, the charged initiatior tRNA binds the AUG start codon through base pairing with its anticodon within the P site of the ribosome, the large subunit then binds the small unit with initiation factors
Elongation - ribosome moves in the 5’ to 3’ direction along the mRNA, synthesizing the protein, the A site holds the incoming aminoacyl tRNA complex, the P site holds the tRNA that carries the growing polypeptide chain,a peptide bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site requiring peptidyl transferase enzyme using GTP for energy, the E site is where the now inactivated tRNA pauses before exiting the ribosome ready to be recharged
Termination - stop codon moves in a proteinc alled a relase factor binds terminatino codon causing water moleculed to be added tot he polypeptide chain allowing peptidyl transferase and termiation factors to hydrolyze the completed polypeptide

Question 171

posttranslational processing

Answer 171

modifcations to polypeptide chain before becoming a functioning protein after translation, chaperones help with this

Question 172

operon (prokaryotes)

Answer 172

cluster of genes transcribed as a single mRNA, very common in prokaryotes, either inducible or repressible systems

Question 173

inducible systems

Answer 173

repressor bonded tightly to the operator system and acts as a roadblock so RNA polymerase is unable to get from the promoter to the structural gene, negative control,

Question 174

example in prokaryotes of inducible system

Answer 174

lac operon for the gene lactase, which bacteria can digest but is more energetically expensive than glucose, so only want to use in the presence of lactose and only transcribed when useful to the cell

Question 175

repressible systems

Answer 175

allow constant production of a protein product, the repressore is inactive until binds to a corepressor that then prevents further transcription, as a negative feedback where the final structural prodect serves as the corepressor

Question 176

transcription factors (eukaryotes)

Answer 176

transcription activating proteins that search the DNA looking for specific binding motifs, tend to have 2 domains a DNA binding domain and activation domain, the DNA binding domain binds to a specific nucleotide sequences int he promotor region the activation domain allows for the binding of several transcription factors and other regulatory proteins such as RNA polymerase and histone acetylases

Question 177

enahncer

Answer 177

group of response elemetns outside the normal promoter region recognized by specific transcription factors to ehance levles of transcription,

Question 178

types of transcription factors

Answer 178

cAMP, cortisol, estrogen

Question 179

DNA regulatory base sequences are ___ regulators, transcription factors are ___ regulators because

Answer 179

cis, trans because they are not located in the same area and have to travel back to the gene to their point of action

Question 180

euchromatin can be…

Answer 180

…accessible to transcription machinery such as promoters

Question 181

histone acetylases

Answer 181

proteins involved in chromatin remodeling, bid to the DNA and can recruit other coactivators, increases space between histones thru acetylation that decreases positive charge and weaknes interaction allowing for easy access of the transcriptional machienry, histone deacetylases also reverse this process

Question 182

DNA methylation

Answer 182

involved in chromatin remodeling and regulation of gene expression levels in cell, DNA methylases add methyl groups to cytosine and adenine nucleotides, heterochromatin tneds to be more heavily methylated hindering access of transcriptional machinery to the DNA

Question 183

fatty acids

Answer 183

carboxyclic acids that contain hydrocarbon chain and terminal carboxyl group

Question 184

2 important essential fatty acids for humans

Answer 184

a linolenic acid and linoleic acid

Question 185

saturated and trans fats impact when incorporated into phospholipid membrane

Answer 185

decraease overall membrane fluidity

Question 186

phospholipid or glycerophospholipid

Answer 186

substituted 1 fatty acid chain of trigs for a phosphate group

Question 187

cholesterol role in phospholiipid bilayer

Answer 187

occupies space preventing crystalization at lower temps and decreases fluidityy at higher temps

Question 188

2 types of integral proteins

Answer 188

transmembrane passing completely thru the bilayer and embedded proteins associated with only the interior or exterior surface of the cell membrane,

Question 189

gap junction

Answer 189

allow for direct cell to cell communication anda re found in small bunches toghther, permit movement of water ands ome solutes directly between cells

Question 190

tight junction

Answer 190

prevent solutes from leaking into space between cells via paracellular route

Question 191

desmosomes

Answer 191

formed by interactions between transmembrane proteins associated with intermediate filaments inside adjacent cells, bind adjacent cells by anchoring to their cytoskeletans

Question 192

simple diffusion

Answer 192

substrates moving down concentrationg radient directly across a cell membrane, only particles that are freely permeable to the membrane undergo this,

Question 193

osmosis

Answer 193

water will move from lower solute concentration to higher,, down gradient of higher water concentration (diluted) to lower water concentration (concentrated)h

Question 194

hypo, iso, and hypertonic solutions

Answer 194

if a cell is placed in a hypotonic solution, it will swell with water and then burst, if palced in isotonic it will have no net movement, hypertonic then it will shrivel

Question 195

osmotic pressure formula

Answer 195

II = i MRT (m is molarity of solution, R is ideal gas constant, T is absolute temp, i is van’t hoff factor which is # of particles obtained from the molecule when in solution (glucose =1, sodium chloride because it dissociates becomes 2)

Question 196

facilitated diffusion

Answer 196

diffusion for molecules large polar or charged that are impermeable to the membrane requuring integral proteins to serve as transporters or channels

Question 197

carriers vs channels

Answer 197

carrier proteins are only open on one side at a given point, requiring a substrate binding then a confirmational change, a channel is a tunnel

Question 198

active transport

Answer 198

movement of a solue against concentration gradient, primary uses ATP, secodnary uses energy released by another particle going down to drive a different particle up its gradient, symport is particles flowing same direciton antiport is opposite