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Flashcards in SM01 Mini 1 Deck (256):
1

Carbonic Acid System

 

 

 

H2O + CO2 ⇔ H2CO3 ⇔ HCO3- + H+

2

 

 

Branches of Chemistry

 

  1. Inorganic
  2. Organic
  3. Biochemical

3

Characteristics of Living Things

  1. complexity
  2. respond to environment
  3. precise replication
  4. extract, transform, and uses Energy from environment
  5. defined functions & regulation of functions

4

Viral Replication

RNA → DNA thru reverse transriptase

OR

RNA → RNA by RNA dependent RNA polymerase

5

Anabolism 

builds molecules 

uses ATP

6

Catabolism

 

breaks molecules

builds ATP

7

Henderson Hasselbach

pH=pKa + log([A-]/[HA])

8

Respiratory Acidosis

H2O + CO2 ⇔ H2CO3 ⇔ HCO3- + H+

  • shallow breathing or hampered gas exchange →
  • increase of CO2 (pCO2) →
  • shift to right of above equation 
  • AKA increase of H+
  • metabolic compensation by kidneys to retain HCO3- to attempt to restore normal pH

9

Respiratory Alkylosis

H2O + CO2 ⇔ H2CO3 ⇔ HCO3- + H+

  • hyperventilation →
  • decrease of CO2 (pCO2) →
  • shift to left of above equation 
  • AKA decrease of H+
  • metabolic compensation by kidneys to expel HCO3- to attempt to restore normal pH

10

Metabolic Acidosis

H2O + CO2 ⇔ H2CO3 ⇔ HCO3- + H+

  • excessive loss of HCO3- →
  • shift to right of above equation to regenerate HCO3-
  • AKA increase of H+
  • respiratory compensation by lungs to increase pCO2 (RR & delth increase)

11

Metabolic Alkylosis

H2O + CO2 ⇔ H2CO3 ⇔ HCO3- + H+

  • excess loss of alkaline material→
  • increased [HCO3-] →
  • shift to left of above equation 
  • AKA decrease of H+
  • metabolic compensation by lungs to decrease pCO2 (decrease RR and depth)

12

Biomolecules

chemical compounds found in living organisms

important eleemnts: C, H, N, O, S, P

mostly organic & macromolecules

function dependent on 3D structure

four classes: lipids, carbohydrates, proteins, & nucleic acids

made from monomeric subunits thru dehydration synthesis

degraded thru hydrosis

13

Hydrolysis

addition of water as a reactant in a chemical eqution

ex. dimer + H2O → monomer + monomer

14

Dehydration Synthesis

removal of water from two reactants in the formation of a product

ex. monomer + monomer → dimer + H2O

15

Isomer

coumpounds with the same chemical empirical formula, but have different structures

16

Constitutional Isomer

isomers have different connectivity

ex. H2C=O-NH2 v. H3C-O=NH

17

Stereoisomers

atoms are connected in the same order, but have different spatial orientation

broken down into diastereomers & enantiomers

18

Enantiomers

mirror images of each other

same physical properties, but different biological ones

19

Diastereomers

broken down into categories: cis/trans, conformers, & rotamers

20

cis

type of diastereomer formed around a double bond or rigid ring

substituents are on the same side

21

trans

type of diastereomer formed around a double bond or rigid ring

substituents are on the opposite side

22

Conformer

diastereomer that differ due to rotation around one or more σ bonds

types: gauche, anti, & eclipsed

23

Rotamer

type of conformer

diastereomer that differ due to rotation around only one σ bonds

types: gauche, anti, & eclipsed

24

Chirality

molecules whose mirror image is NOT superimposeable has a chiral center

25

Spearmint

R-carvone

26

caraway

S-carvone

27

Naproxen

R: liver toxicity

S: anti-inflammatory

28

Carbohydrate

Cx(H2O)y

classes: monosaccharide, oligosaccharides, polysaccharides

29

Monosaccharide

simplest subunit of a carbohydrate

classification: based on position of carboxyl group (aldose or ketone) & number of carbons atoms (numeric prefix)

all have one or more chiral centers

ALL biological relevant are in D configuration

4+ C exist mostly as cyclic structures

30

DL classification

based off of optical activity of glyceraldehyde ONLY

D(extrorotatory) turn to the right (-OH on right of 2nd carbon from bottom on Fischer projection)

L(evorotatory) turn to left (-OH on left of 2nd carbon from bottom on Fischer projection)

all others based on similarity to glyceraldehyde structurally NOT optically

ALL biologically relevant carbohydrates are in D

ALL biologically relevant proteins are in L

31

RS classification

based off of priority of substituent groups around chiral center 

R(ectus): if priority decreases in a clockwise direction

S(inistra): if priority decreases in a counter-clockwise direction

 

32

Epimers

diastereomers that differ by the configuration around one chiral center

ex. glucose & galactose

33

34

Furanose form

when  4+C forms a 5 membered heteocyclic ring

35

Pyranose form

when  4+C forms a 6 membered heteocyclic ring

36

Anomer

stereoisomers that differ in form straight v. ring structure

anomeric C: new chiral center formed when a the ring forms

alpha= when hydroxyl group of anomeric C is below plane of ring

beta= when hydroxyl group of anomeric C is above plane of ring

37

Mutatrotation

interconvertion of anomers

38

Reducing sugars

monosaccharides that act as reducing agents (deliver electrons) by their anomeric C hydroxyl group

 

39

Benedict's reagent

Cu containing reagent that changes brick red in the presence of reducing sugar (production of precipitate Cu2O)

40

Tollen's reagent

Ag containing reagent that produces silver-like mirror in aqueous solution with reducing sugars

Ag→ Ag

41

Aldonic Acid

oxidation of aldehyde of aldose sugar to produce a carboxyl group

42

Sugar phosphate esters

additionof phosphoryl (PO32-) group to monosaccharide

43

Uronic acid

oxidation of the 1º hydroxyl group of a monosaccharide to a carboxyl group

44

Lactones

internal esterifications of monosaccharide-derived acids to form 5 or 6 membered heterocyclic rings

45

Alditols

redution of an aldose or ketose carboxyl group to a hydroxyl group

46

Deoxy-sugars

when one hydroxyl group of a sugar is replaced with an H

47

Amino-sugar

when one hydroxyl group of a monosaccharide is replace with an amine group (NH2)

48

Disaccharide

two monosaccharides covalently bound together

49

Glycosidic bond

anomeric C of one sugar to a C of another

diether linkage (-O-)

specific notation (anomeric C# → bound C#)

50

Sucrose

table sugar

alpha-D-glucopyranosyl-(1→2)-beta-D-fructofuranose

nonreducing sugar b/c neither retains the -OH group on their anomeric C

51

Lactose

milk sugar

D-galactopyranosyl-beta(1→4)-D-glucopyranose

reducing sugar b/c glucose monomer retains the -OH group on its anomeric C

52

Cellobiose

from partial hydrolysis of cellulose

D-glucopyranosyl-beta(1→4)-D-glucopyranose

reducing sugar b/c the 2nd glucose monomer retains the -OH group on its anomeric C

53

Polysaccharides

AKA glycans

differ in: monomeric subunits, type of bond between subunits, degree of branching

mostly water insoluble

 

54

Oligosaccaride

2-20 monosaccharide units

55

Glucan

glycan/polysaccharide made up entirely of glucose monomers

56

Amylose

found in startch in plants

unbranched chain 300+

bound by alpha(1→4) glycosidic bonds

one reducing & one non-reducing end

57

Amylopectin

found in starch in plants

alpha(1→4) with branching 24-30 residues w/alpha(1→6)

one reducing end & many non-reducing ends

58

Glycogen

gluose storage in animals

alpha(1→4) with branching 8-12 residues w/alpha(1→6)

forms alpha helices stabilized with hydrogen bonds

stored in muscle and liver

regulated by pancreas thru insuilin & glycogen

59

Cellulose

most abundant biomarcomolecule on earth

found in plant cell walls

water insoluble

beta(1→4) binding glucan

forms sheets & stacks

cannot be digested b/c we lack cellulase

dietary fiber

60

Peptidoglycan

heteropolysaccharide found on bacterial cell walls

beta(1→4) bonds

peptide cross-linkers bind to cell (PCN prevents synthesis of these peptides)

broken down by lysozyme

61

Glycoaminoglycans

aka GAGs

unbranched heteropolysaccharides composed of repeating disaccharide unit (20-25,000 times)

major constituent of extracelluar matrix, holds cells together

examples: hyaluronan, chondroitin 4/6-sulfate, dermatan sulfate, keratan sulfate, & Heparin

62

Glycoconjugates

information carriers

3 classes: proteoglycan, glycoproteins, & glycolipids

63

Proteoglycans

molecules of the cell surface or ECM to which one or more GAGs are bound

major component of connective tissue

over 30 mammalian types

64

Glycoproteins

proteins with one or more oligosaccharides covalently linked to them 

outer face of cell membrane, ECM, blood, in some specialized organelles

many functions most in signaling & identification

65

Glycolipids

lipids with attached carbohydrate chain

all body tissue, esp. nervous

usually on outer leaflet of cell membrane

ex. glycoshingolipids, gangliosides, lipopolysaccharide

66

Glycobiology

study of structure & function of carbohydrates & glycoconjugates

67

"Sugar Code"

use of specific oligosaccharides as information carriers

68

Lectins

proteins that read the sugar code

69

HK RED

hydrophilic charged amino acids

Histidine (H), Lysine (K), & Arginine(R)= hydrophilic basic aa

Glutamate (E) & Aspartate (D)= hydrophilic acidic aa

70

Polar uncharged amino acids

Ser, Threonin (Thr), Asparagine (Asn), & Glutamine (Gln)

71

Nonpolar aliphatic amino acids

Ala, Val, Ile, Leu, Met

72

Nonpolar aromatic amino acids

phenylalanine (Phe), Tyrosine (Tyr), & Tryptophan (Trp)

absorb UV light

73

Special amino acids

Cys, Gly, & Pro

74

Protein

1º structural & functional bio-macromolecule

build from 20 different amino acids & their derivatives

complex 3D structures

75

Proteomics

study of proteins & their functions in an organism & their expression changes in response to the environment

76

Functions of Proteins

  1. forming structural elements of ECM
  2. catalyzing reactions
  3. carrying chemical information
  4. transporting other molecules w/in cell & the body
  5. general & specific functions of cell/tissue

77

Zwitterion

pH=7.0

both alpha-amino & alpha-carboxyl group of an amino acid are in ionized state

zwitter= hermaphrodite in german

78

Ampholyte

something that is amphoteric or can act as an acid or a base

79

Amino acids with Ionizable R groups

HK RED + Cys (sulfhydryl group) + Tyr (phenol group)

80

Isoelectric point

pH at which the aa has a net charge of 0

pI= (pKa1 + pKa2)

2

81

Amino Acids

subunits of proteins

20 different ones

all made by the body except: His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val

use as buffer +/-1pH unit around pKa: therefore all have 2 buffering ranges, those with ionizeable side chains have 3

82

Essential Amino Acids

His, Val, Ile, Leu, Lys, Phe, Trp, Thr, Met

83

Important Amino Acid Modifications

hydroxylation (+ an -OH)

Methylation (+ a -CH3)

Acetylation (+ a -COCH3)

Phosphorylation (+ a -PO32-)

 

 

84

N-formylmethionine

-COH addition to alpha-amino group 

first amino acid of all prokaryotic proteins & usually removed during maturation

85

Peptide bond

N-terminus to C-terminus 

amide bond made by dehydration synthesis (O from carboxyl group and 2H from amino group of following aa)

σ & π like properties due to resonance structure with carboxyl O therefore bond is rigid & planar

 

 

86

Phi angle

angle of free rotation around the peptide bond N & alpha C

87

Psi angle 

angle of free rotation around the peptide bond C & alpha C

88

Adrenocortotropic hormone

39 aa= polypeptide

stimulates function of adrenal glands

89

Bradykinin

nonapeptide (9aa)

smooth muscle relaxer & vasodialator

90

Creatine

Arg-Gly derivative

supplier of metabolic energy, mostly muscle 

91

Endorphins

various aa length

neuropeptides with analgesic effect

92

Gastrin

various aa length

stimulate gastric acid secretion

93

Glutathione

tripeptide Cys-Glu-Gly

antioxidant, reducing agent 

94

Glucagon

29aa polypeptide

stimulates glycogenolysis

secreted by pancreas

95

Oxytocin

nonapeptide (9aa)

stimulates lactation & uterine contraction

96

Vasopression

nonapeptide (9aa)

prevents water loss to control bp (raise it)

97

Native Protein

protein folded into its proper physiological structure

most thermodynamically stable (lowest G)

98

Denatured Protein

random coil, tangle of polypeptide chains, 3D structure not intact

NOT biologically active

  1. breaking of covalent bonds
  2. disruption of noncovalent bonds- heat, detergents, or acid/base
  3. high concentration of small hydrophilic molecules- break H bonds
  4. Heavy metal ions

99

1º Protein Structure

linear sequence of aa

exclusively covalent bonds

determines all other structure levels

changes occur from DNA mutation

100

2º Protein Structure

H bonding due to rotation around phi/psi angles

  • alpha helix: 3.6aa/turn, R groups face out of helix, Gly & Pro break helix
  • beta-pleated sheet: parallel & antiparallel varieties, up to 15aa in length, 2-22 sheets in a stack
  • Coil/loop: other organizational structures

101

3º Protein Structure

folding of 2º structures

H & disulfide bonds + ionic & hydrophobic interactions

made of motifs (supersecondary structures): helix-loop-helix, zinc finger, coiled-coil, beta-alpha-beta

motifs form domains

102

Motif

supersecondary structures: helix-loop-helix, zinc finger, coiled-coil, beta-alpha-beta

build domains

103

Domain

made up of motifs

globular clusters in protein, usually each has a different function

categorized by the 2º elements that they are made of: alpha, beta (stacks or barrels), alpha-beta

104

4º Protein Structure

multiple subunits (polypeptide chains) coming together

105

Fibrous Protein

highly elongated, determined by 2º structure

functions: motive or supportive

ex. keratin & collagen

106

Keratin

component of skin, hair, & nails

variety of types: 1 (acidic) 2 (basic)

more Cys the harder the Keratin

ex. hair: type 1 & 2 form coiled-coil, more cysteine=straighter

107

Globular Protein

higher order structural elements

functional elements of living organisms

water soluble: increased in low salt concentration

insoluble when pH=pI, b/c they are maximized for formation of intermolecular salt bridges

108

5º Protein Structure

loose term for when protein perform together (most do)

ex. protein complexes (mTOR), Metabolons, marcomolecular assemblies (molecular machines)

109

Metabolon

temporary functional complex of sequential enzymes in a metabolic pathway or cycle

110

Amyloidosis

usually a denatured globular protein that refolds incorrectly: normally loss of alpha helices

aggregate into fibrillar structures called amyloid

usually in ECM except in nervous tissue

ex. Alzheimer's, Parkinson's, type 2 diabetes mellitus

111

Prion Disease

Prion protein (PrPc) normal: abundant in nervous system, tethered to outer leaflet of plasma membrane by GPI-anchor

spontaneous refolding into PrPsc (scrapie)

PrPsc forms aggregates & causes diseased state

ex. Creutzfeldt-Jacob Disease (spongiform encephalopathy), Kuru is transmissible form (cannibalism), variant (vCJD)= mad cow

112

Specificity

ability of a protein to bind one molecule over another in preference to others

113

Affinity

tightness of binding

quantitative measure= Kd

K= ([P][L])/[PL] = Koff/Kon

as related by: P + L ⇔ PL

lower Kd, higher affinity 

114

Activator

ligand that binds in an allosteric site that increase P-L binding affinity

115

Inhibitor

ligand that binds in an allosteric site that decrease P-L binding affinity

substance that temporarily or permenantly reduces enzyme's activity

116

Rate of a Chemical Reaction

rate = k[A]x[B]y where A & B are reactants

x+y=0, then zero order reaction, etc.

understand how reaction rate depends on reactant concentration

117

Half-life

t1/2

time required for [reactant] to decrease to half of original

118

Transition State

temporary intermittant chemical species of reactants before they form product

typically higher G than reactants or products

very unstable

119

Activation Energy

minimum amount of energy to make a reaction occur

amount of energy required to form transition state

120

Equilibrium Constant

law of mass action derivative

for reversible rxn at equilibrium & constant T, 

aA + bB ⇔ cC + dD

Keq = ([C]c[D]d)/([A]a[B]b) = kf/kr

Keq>>1, then equilibrium lies left (reactants) → does NOT favor reaction

Keq<<1, then equilibrium lies right (products) → does favor reaction

Keq>>1, then equilibrium lies left (reactants) → does NOT favor reaction

Keq = 1, then [R]=[P=]

121

Catalysis

increasing the rate of a chemical reaction

122

Catalyst

substance that increases the rate of a chemical rxn w/o itself being consumed

typically works by bringing reactants in closer proximity, into the proper orientation, and/or lowering the activation energy

123

Enzyme

protein that functions as a biological catalyst

dramatically increases rate of reaction 106-1012

kcat measures catalytic power

traditional name or anmed by the reaction they catalyze + -ase

high specificity & affinity for substrate

124

catalytic rate constant

kcat turnover number

maxiaml number of substrate molecules an enzyme can convert to product in a second

 

125

Simple enzyme

composed of polypeptide(s)

126

Conjugated enzyme

polypeptide(s) and non-protein co-factor

127

Coenzyme

organic molecule cofactor, "co-substrate"

128

Prosthetic group

permenantly associated cofactor

ex. Heme group of hemoglobin

129

Apoenzyme

polypeptide portion of enzyme-cofactor complex

130

Holoenzyme

catalytically active enzyme-cofactor complex

131

Zymogen

proenzyme

synthesized in its inactive form, requires metabolic processing to beome active

protection to be used elsewhere in the body (trypsinogen made in pancreas, used in small intestine

132

Isozyme

different enzymes that perform the same function

133

Cofactor

linked to apoenzyme to form holoenzyme, required for enzyme to function

many are vitamins that must be consumed in the diet

important ex: NAD+ & NADP(derived from niacin, proton acceptor), Coenzyme A (CoA, acyl [R-C=O] carrier), FAD & FMN (amphoteric), cationic tranisition metals (Fe, Zn, Cu, Mn)

134

Lock & Key Model

substrate bind to active site with perfect complementarity

135

Induced-fit Model

substrate binding induces conformational change in enzyme

136

Enzymatic Mechanisms

  1. proximity & orientation of substrates
  2. aicd/base: partial proton transfer 
  3. covalent catalysis: formation of transient covalent bond between enzyme & substrate
    1. ex. lysozyme
  4. metal ion: 1/3 of enzymes use, bind substrate for proper orientation, mediate redox rxn, electrostatically stabilize
    1. ex. Mg2+ shield negative charge of terminal phosphate groups in ATP
  5. eletrostatic catalysis
  6. preferential binding of transition state

137

Metalloenzyme

contain tightly bound metal ions

usually transition metals: Fe2+, Fe3+, Cu2+, Zn2+, Mn2+, Co3+

138

Metal-activated enzymes

loosely bind metal ions in solution

usually alkali metals:K+, Na2+, Mg2+, Ca2+

139

Serine Proteases

family of peptide cleaving enzymes

ex. trypsin, chymotrypsin, & elastase

catalytic triad: Asp, His, Ser in active site

cleavage specificity through binding site aa characteristics

Ser: covalent catalysis with carbonyl C

His: takes H+ from Ser -OH group (acid/base)

Asp:stabilizes His trough electrostatic catalysis via hydrogen bond

axonion hole for carbonyl O hydrogen bonding

 

140

Michaelis-Menten Equation

v0= (vmax[S])/(KM + [S])

v0= initial velocity of rxn <10% substrate transformed (y axis)

vmax= maximum velocity of reaction, theoretical only

KM= Michaelis constant 

[S]= x axis

141

Michaelis constant

KM= (k-1 kcat)/k1

approximately = to Kd, but takes kcat into consideration

inversely proportionaly to affinitiy

if [S]=KM, then v0Vmax/2

142

Lineweaver-Burk Plot

graph of (1/v0)=(KM/Vmax) (1/[S]) + (1/Vmax)

y-axis= 1/v0

x-axis= 1/[S]

slope= KM/Vmax

y-intercept= 1/Vmax

x-intercept= -1/KM

143

Hyperthermia

increased body temperature

@ low levels, stimulates rate of enzymatic rxn thus facilitating immune response

>42ºC (107.6ºF), most enzymes are denatured & loose all function, can be fatal

144

Hypothermia

decreased body temperature

decreases rate of enzymatic rxn

slowdown of vital functions

tissues more resistant to hypoxia

useful ie. code chill or chilling transplant organs

145

Classical Competitive Inhibitior

binds to enzyme in substrate's binding site

overcome by increasing [S]

temporary & reversible, noncovalent interactions

No change in Vmax, increases KM​ ("apparent")

ex. Methanol poisoning treated with Ethanol

146

Allosteric Competitive Inhibitor

binds to enzyme at an allosteric binding site, but conformationally changes enzyme to block substrate binding

overcome by increasing [S]

temporary & reversible, noncovalent interactions

No change in Vmax, increases KM ("apparent")

147

Uncompetitive Inhibitor

binds enzyme-substrate complex thru noncovalent interactions at allosteric site, irrevesible

distorts active site NOT binding site

increasing [S] does NOT overcome

Vmax decreases (apparent), KM decreases (apparent)

ex. Lithium

148

Noncompetitive Inhibitor

binds allosteric site of enzyme thru noncovalent interactions

can bind ES or free E

increasing [S] does NOT overcome

Vmax decreases (apparent), KM does NOT change

ex. HIV drugs- reverse transcriptase

149

Irreversible Inhibitor

covalently binds inhibitor, irreversible

can bind ES or E

only way to overcome is synthesis new E

Vmax decreases (apparent), KM does NOT change

ex. Sarin gas (nerve gas)

 

150

Genetic Inhibition

gene mutation that can alter enzymatic activity

ex. neonatal diabetes mellitus, glucokinase enzyme

151

Enzyme Regulation

  1. substrate/cofactor availability
  2. Posttranslational modifications
  3. zymogen activation
  4. allosteric control

152

Allosteric Control

more than one active site: + or - cooperativity

more than on allosteric site: activators or inhibitors

usually irreversible reactions

do NOT follow Michaelis-Menten

ex. feedback inhibition

153

Promoter

region of DNA close to the start site of a gene where transcription is initiation proteins bind

CAAT & TATA boxes are sequences recognized by RNA polymerase II in this region

154

5' UTR

5' untranslated region is in the pre-mRNA & mature RNA at the 5' end upstream of initiation codon

DNA template for this region is after the START codon

function: regulation of transcript

155

Start Codon

three nucleotide sequence (codon) on the mRNA that signals where to start translation

always codes for Methionine in eukaryotes

156

Translated Region

portion of mature mRNA sequence that codes for amino acids in the translation of a protein

157

Exons

parts of DNA or pre-mRNA that code for protein

the translated region of the mature mRNA

158

Introns

part of gene that does not code for protein

found in DNA template & pre-mRNA

spliced out during RNA maturation process

159

Stop codon

three nucleotide sequence that codes for stop of translation

UAA, UAG, & UGA

160

3' UTR

3' untranslated region is on the mRNA immediately following the STOP codon

161

Enhancers

transcriptionally control region(s) on DNA template well before promotor

bind activators that stimulate transcription factors to make RNA polymerase more active at that gene

position (5' or 3' of gene) & orientation independent (forward or reverse)

162

mRNA

messenger RNA

product of transcription

translated by ribosomes into protein

matches coding strand DNA (except Thymine to Uracil) & is paired to the template strand

163

Coding Strand

DNA that codes for gene

match for RNA sequence

written on top when veiwing double stranded DNA in 5' → 3' direction

164

Template Strand

anneals to coding strand

transcribed into RNA sequence by base pairing

written on bottom when veiwing double stranded DNA in 3' → 5' direction

if single strand, will still be written in 5' → 3' direction

165

Transcription

mechanism for making RNA from DNA by copying template strand to match the coding strand

166

Transcription Start Site

referred to as +1

first nucleotide that is transcribed

167

pre-mRNA

unmodified mRNA transcript

168

mRNA Maturation

  1. 5' CAP: GTP sugar 5'C is bound to 5'C sugar of first nucleotide
  2. splicing out of introns
  3. addition of poly-A tail to the 3' end

169

CTD

carboxyl-terminal domain of largest subunit of RNA polymerase II

couples transcription w/processing

has tandem repeating 7 aa repeats, different phosphorylation sites signal for different modifications

all RNA machineries bind to it (capping, splicing, & adenylation factors), hop off CTD & onto RNA when they recognize their RNA signal

170

Spliceosome

combination of small nuclear RNAs (snRNAs) & proteins

  1. 2' -OH of A at branch site attacks the phosphate group at the 5' end of the intron
  2. 3' end of exon 1 then attacks 5' phosphate group at start of exon 2, splicing the intron out 

 

171

5' Cap

first post-translational modification

occurs in nucleus

5' C on mRNA is bound to the 5' C of GTP with a triphosphate linkage

methylation of 2' -OH group on first two nucleotides

function: mRNA stability & binding mRNA to ribosome

poly-A tail at 3' end stabilizes it

172

CBP

Cap binding proteins

bind to 5' cap of mRNA

173

Splicing

2nd post-translational modification of mRNA

introns are cut out of the mRNA by spliceosomes

174

5' Splice Site

consensus GU cut before G

175

3' Splice Site

consensus AG cut after G

176

Branch Site

 10-40 nucleotides upstream (5'-ward) of 3' splice site & polypyrimidine tract (C & U) at an A

binding site for Splicing Factor 1

177

Lariat

the lasso shaped spliced intron

178

Alternative Splicing

means we can get more than on protein from a single gene by combining the exons in different ways

74% of genes are involved in alternative splicing

179

Polyadenylation

  1.  pre-mRNA is cut 10-30 nucleotides downstream (3'-ward) of AAUAAA consensus
  2. 200 adenylate residues are added by poly(A) polymerase
  3. bound by poly(A) binding protein (PBP)
  4. PBP binds CBP 

function: stabilize mRNA

180

PBP

poly(A) binding protein

binds to poly A tail & CBP (cap binding protein

181

Rat1

ribonuclease that digests mRNA without 5' cap

when Rat1 catches up to the poymerase catalytic domain the whole RNA polymerase complex detaches from DNA

transcription termination factor

182

Wobble effect

one tRNA can match up with more than one mRNA codon

61 codons, but only 50 tRNA species

possible due to nontraditional base pairing between third nucleotide of codon & first nucleotide of anticodon

tRNA

mRNA

A

U

G

C, U

U

A, G

C

G

I (inosine)

U, C, A

183

Translation

protein synthesis 

reading of mRNA to make protein

AUG codon or Methionine aa is always the start

 

184

Characteristics of Genetic Code

  1. Specificity: codon always codes for same aa
  2. Universality: all organisms use same
  3. Redundancy: more than one aa/codon
  4. Nonoverlapping & commaless: read continuously, nothing innately marking start & finish of codon

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Mutation

change of one or more nucleotides

186

Silent Mutation

point mutation where codon still codes for the same amino acid

aka synonymous mutation

187

Missense Mutation

point mutation where codon codes for a different amino acid

188

Nonsense Mutation

point mutation where codon becomes a STOP codon

189

Point Mutation

when one nucleotide is exchanged for another

190

Frame-shift Mutation

addition or subtraction of nucleotide of any amount (except multiples of 3)

changes all codons after mutation site

creats nonsensical or nonsensical & truncated proteins

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Aminoacyl-tRNA synthetases

enzyme that attaches amino acids to tRNAs

VERY accurate enzyme

aa alpha-carboxyl group to 2' or 3' -OH of ribose of adenosine at 3' end of tRNA

ATP → AMP, 2 units of energy from 1 molecule

this is called charging the tRNA

192

Anticodon

base pair complement to mRNA codon found on tRNA

193

tRNA

transfer RNA, smallest of major RNAs (4S)

carries anticodon that antiparallel/complementarily binds to mRNA codon

attached to amino acid at 3' end adenosine

approx. 50 types, 74-95 nucleotides long

contain unusual nucleotides & extensice intrachain base pairing (hairpin cross)

194

Charge tRNA

tRNA bound to amino acid

195

Ribosome

80S (S=sedementation gradient in sucrose solution)

small subunit 40S

large subunit 60S

196

Initiation

  1. eIF4 initiation factors bind CBP on 5' end of mRNA
  2. PBP binds eIF4/cap complex activating translation
  3. small 40S ribosome unit binds eIF2/tRNAMET/GTP complex
  4. mRNA is pulled through subunit to find AUG start
  5. hydrolysis of GTP by eIF2
  6. release of initiation factors & binding of large ribosome subunit

197

eIF-4E

eukaryotic Initiation Factor 4E

binds to 5' cap of mRNA & attracts small ribosomal subunit

198

eIF-4G

eukaryotic Initiation Factor 4G

function: positioning of mRNA on ribosome

199

eIF-2

eukaryotic Initiation Factor 2

function: positions tRNAMET to P site on small ribosomal subunit

200

Elongation

  1. eEF1 guides aminoacyl tRNA to A site in ribosome
  2. peptide bond formation
  3. mRNA is moved three nucleotides down on ribosome by eEF2 (A tRNA → P site)
  4. repeat until STOP codon is in A site

201

eEF1

eukaryotic Elongation Factor 1

function: guide aminoacyl tRNA into A site of ribosome

requires GTP energy

202

eEF2

eukaryotic Elongation Factor 2

function: moves mRNA three nucleotides thru ribosome

requires GTP energy

203

Ricin

deadly poison from residue of castor oil production

ricin A (portion of heterodimer) depurinates specific Adenine (thought to be involved w/eEF1 & eEF2) of 28S rRNA in large ribosomal subunit

1 molecule inactivates 50,000 ribosomes → killing the cell

204

Peptidyl Transferase

function of 28S rRNA in large ribosomal subunit

peptide chain that is attached to tRNA in P site is transfered to the tRNA in the A site by formation of the peptide bond that is created by peptidyl transferase

does NOT require energy (no ATP or GTP)

205

Peptide Bond Formation

  1. N of Adenine on 28S rRNA hydrogen bonds H of alpha-amino group (accepts H) & amino nitrogen attacks carboxyl C attached to P site tRNA
  2. displaced H stabilizes O- of carboxyl thru hydrogen bonding but attacks O on tRNA 
  3. tRNA leaves, peptide bond is formed, & nascient protein is attached to tRNA in A site

206

Chloramphenicol

antibiotic that inhibits peptide bond formation in bacteria

no longer available as wrecking of the bone marrow is an effect of long term

207

Cyclohexamide

drug that inhibits peptide bond formation in eukaryotes

used as cancer drug

208

Ribozyme

RNA enzyme

ex. 28S rRNA in the large ribosomal subunit

209

Polysome

mRNA that are simultaneously being translated by more than one ribosome

210

Ferritin

cytosolic iron binding protein

expressed when iron is abundant (to sequester)

aconitase binding of IRE in 5' UTR of mRNA inhibits expression by blocking start codon

Fe binds to aconitase → ferritin expressed

211

Transferrin Receptor

membrane receptor for import of iron

expressed when iron is low

aconitase w/o Fe binding of IRE in 3' UTR of mRNA → blocks RNase from cleaing poly A tail→ transferrin receptor expressed 

Fe bound to aconitase → transferrin receptor NOT expressed

212

IRE

iron response elements foudn in UTRs of transferrin receptor & ferritin

213

eIF2B

eukaryotic Initiation Factor 2B

after eIF2 brings first tRNA into P site it is still tightly bound to GDP & can't be recycled until it is unbound

eIF2B is GEF (guanine exchange factor) removes the GDP

HOWEVER, many kinases can phosphorylate eIF2-GDP & peIF2-GDP complex tightly binds eIF2B→ no eIG2 GDP to GTP exchange→ most translation ceases

214

Interferon Translational Control

leukocyte→ alpha-IFN, fibroblast→ beta-IFN, lymphcyte→ gamma-IFN

induced by dsRNA (double stranded RNA-usually found as viral component)

induce RNA-dependent protein kinase that phosphorylates eIF2 turning off translation

induces synthesis of 2'-5'-oligoadenylate that activates preexisting RNase L

215

Polio Virus

  • viral protease 2A cleaves eIF4G so it can nolonger function as bridge between methyl cap binding subunit & 40S subunit→ stops cellular translation
  • viral translation occurs due to IRES (internal ribosomal entry site) of viral RNA→ cap-independent initiation from interanl AUG codons

216

Posttranslational Modification

  • phosphorylation: on -OH functional groups (ser, thr, & tyr)→ usually used as On/Off switch
  • addition of sugar to ser or asn→ esp. proteins going to plasma membrane or secreted
  • addition of -OH to pro or lys: to make them more reactive & able to form cross links
  • carboxylation: usually to clotting factors
  • addition of hydrophobic side chain to cys to be used as membrane anchor

217

Diptheria toxin

catalyzes ADP-ribosylation & inactivation of eEF-2

preventing translocation of mRNA

218

Termination

when STOP codon is positioned in A site of ribosome

tRNA-shaped protein enters A site→hydrolysis GTP →release of ribosomal subunits, mRNA, tRNA & associated proteins

219

snRNA

small nuclear RNA

fuction: splicing

220

miR

microRNA

avg. 22 nucleotides long

function: post-transcriptional regulation via binding of complementary sequenceson target mRNA

leads to translational repression, target degradation, & gene silencing

221

RNA polymerase I

found in nucleolus

produces 35-47S pre-rRNA

50-70% of cell's polymerase activity

relatively insensitive to alpha-amanitin

222

RNA polymerase II

 

found in nucleoplasm

produces mRNA precursors, U1-U5 snRNA, & miRs

relatively sensitive to alpha-amanitin

223

RNA polymerse III

found in nucleoplasm

produces 5S rRNA & tRNA

moderately sensitive to alpha-amanitin

224

alpha-amanitin

mushroom toxin

used to initially distinguish RNA polymerases

225

rRNA

28S, 5.8S. & 5S found in large ribosomal subunit & 18S found in small ribosomal subunit

produced via cleavage of 13kb transcript (in 40kb tandem repeat x80 on tips of acrocentric chromosomes [13, 14, 15, 21, &22])

226

227

Post-transriptional tRNA Modification

  1. RNase P cleaves 5' end
  2. some nucleotides removed (splicing of intron)
  3. uracil at 3' end is removed & CCA is added
  4. some nucleotides modified or changes
    1. hydrogenation, methylation, deamination, etc

228

MIDD

Maternal Inherited Diabetes & Deafness

sensoineural hearing loss

diabetes precedes deafness (early onset [38] type 2)

cardiomyopathy

tRNA mutation x3

229

MELAS

Mitochondrial Encephalopathy, Lactic Acidosis, Stroke-like Episodes

hemiparesis, hemianopia, cortical blindness, focal seizures

progressive encephalopathy, disability, death

diabetes

single tRNA mutation

230

Complex I

found in mitochondria, vital for electron transport chain→ effects amount of ATP is made

2 subunits are mtDNA w/ highest proportion of Leu residues translated by UUR codon

3243A→G tRNA mutation is most common repsiratory chain defect

deficiency results in: lower proton pumping, reduced elctrochemical potentail gradient, decrease respiration, lower rate of ATP synthesis

231

Topoisomerase

removed supercoils from DNA produced at either end of unwound site used for transcription

3'→ positive supercoil (clockwise)

5'→ negative supercoil (counter-clockwise)

232

Ciprofloxin

inhibits bacterial topoisomerase

233

Housekeeping Gene

efficiently & continuously transcribed

if product needed in high levels→ strong promoter

if products only needed in low levels→ weak promoter

 

234

Regulated Genes

expressed at different levels under different conditions, most genes

235

Silencer

opposite of enhancer

repressors bind to  them

236

Types of DNA Mutation

  1. single base substitution (point mutation)
  2. insertion/deletion (indel)
  3. translocation
  4. duplication
  5. abnormal chromosome number

237

Somatic Mutations

cause of aging & cancer

238

Germline Mutations

mutations in gametes passed on to offspring

can lead to genetic disease

239

Dominant Mutation

cause disease in homo & heterosygous state

240

Recessive Mutation

causes disease on lin homozygous state

241

Purifying Selection

detrimental mutations are weeded out of gene pool either by short lifespan or inability to procreate

242

Fitness

measure of selection ranging 0 to 1

average number of surviving offspring relative to the population mean

243

Genetic Lethal

condition that prevents reproduction

fitness=0

244

Causes of Mutations

  1. spontaneous tautomeric shifts
  2. ionizing radiation
  3. UV radiation
  4. Chemicals 

most sensitive during S phase of mitosis or meiosis

245

Parental Age Effects

  • advanced maternal age: risk for aberrations in chromosomal number
  • advanced paternal age: risk for point mutations

246

DNA Repair

  1. damage to top strand
  2. excision of damaged region 
  3. DNA polymerase uses bottom strand as template
  4. DNA Ligase seals nick

247

AP endonuclease

enzyme used in base excision repair 

repair damaged or mismatched nucleotides

248

Post-replication Mismatch Repair

  1. binding of mismatch repair proteins
  2. removal of newly synthesized strand 
  3. repair by DNA polymerase & ligase

249

Apurinic sites

depurination (loss of purine/pyrimidine)

AP endo nuclease, DNA polymerase B, & DNA ligase repair

250

Base Excision Repair

deamination of base

DAN glycosylase cuts improper base out

path then follows same as for apurinic

251

Nucleotide Excision Repair

used to fix pyrimidine dimers (C & T next to each other covalently bound)

Nuclease cuts out whole strip on one strand

DNA polymerase & ligase then base pair patch new in

252

Repair of Double-strand Break

nonhomologous end-joining: loss of nucleotides in between

homologous end-joing: involves copying process of from second chromosome

253

Lynch Syndrome

caused by post-replication mismatch repair

greater risk of colon, endometrial, & other cancers

autosomal dominant inheritance (heterozygous only)

if somatic mutation knocks out single intact copy of gene, then cell becomes mutator

 

254

Xerodermia pigmentosum

defect of genome-wide nucleotide excision repair

sunburn & skin cancer

autosomal recessive

7 types

255

Cockayne syndrome

defect of transcription-couples nucleotide excision repair

poor growth, neurological problems, early senility

autosomal recessive

2 types

256

Ataxia-telangiectasia

mutation in ATM protein kinase (signaling protein for DNA double-strand repair)

cerebellar atxia in early childhood

thymus hypoplasia, immunodificiency

lymphoreticular malignancies

dilatation of small blood vessels (telangiectasia)

extreme sensitivity to ionizing radiation