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Pre-Lim > Core 1- Section 1 > Flashcards

Core 1- Section 1 Flashcards

pass the prelim

1
Q

What is kinetic energy

A

energy that can be moved by heat.

increased heat = increased movement

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2
Q

what is potential energy

A

energy that will be releases when a process occurs

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3
Q

delta H of an exothermic reaction

A

negative

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4
Q

delta H of an endothermic reaction

A

positive

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5
Q

1st law of thermodynamics

A

energy is neither created nor destroyed

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6
Q

second law of thermodynamics

A

entropy is always increasing

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7
Q

difference between enthalpy and entropy

A

enthalpy is delta H and is measure of energy

entropy is delta S and measures randomness or disorder of a system

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8
Q

what is activation energy

A

the energy required to excite molecules into transition state

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9
Q

how does a catalyst work

A

a catalyst lowers the activation energy allowing a reaction to proceed quicker

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10
Q

what is the hydrophobic effect

A

non polar solutes cannot engage in polar interactions with water molecules therefore they do not dissolve in water. i.e. oil and water

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11
Q

what is amphipathic

A

a molecule that has both polar and non polar regions

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12
Q

what is the bronsted-lowry definition of acid and bases

A 
acid = proton donor 
base = proton acceptor
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13
Q

which isoform of amino acids is used to make proteins

A

L form

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14
Q

which amino acids are non polar

A

Glycine, alanine, phenylalanine, valine, leucine, isoleucine, trytophan, proline

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15
Q

which amino acids are polar with neutral charge

A

serine, threonine, tyrosine

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16
Q

what is a stereoisomer

A

molecules with the same formula but different conformation

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17
Q

what is enantiomers

A

molecules that are mirror images of one another

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18
Q

what are diastereomers

A

stereoisomers that are not mirror images

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19
Q

what are epimers

A

molecules that differ in stereochemistry in ONE position

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20
Q

what is the role of n-linked glycolsylation if proteins

A

aids in protein folding
increase stability of folded proteins
participate in specific recognition events
immune system evasion
targeting of proteins to different cellular compartments

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21
Q

what are lectins

A

proteins that can recognize mono and oligosaccharide structures and read the carbohydrate code

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22
Q

what is the function of lectins

A

cell-cell recognition
selective uptake of certain glycosylated protein
distinguishing self from non-self
host targeting by pathogens

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23
Q

what are GPI anchors

A

anchor proteins to lipids

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24
Q

what is the most common cross link of polypeptide chains

A

disulfide bond

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25
Q

which amino acid does not have a chiral center

A

glycine

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26
Q

what is unusual about proline

A

since it is a five member ring amino acid, it causes kinks

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27
Q

what is unusual about glycine

A

it has no side chain making it very flexible

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28
Q

what is unusual about cysteine

A

it can form disulfide bonds because of its sulfhydryl group as a side chain

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29
Q

what are the four types of secondary structures

A

beta strand
alpha helix
beta turn
random coil

30
Q

what are the super secondary structures

A 
beta-alpha-beta
beta hairpin 
alpha alpha
coiled coils 
zinc finger
31
Q

characteristics of a beta strand

A

held together by backbone binding
can be parallel or anti-parallel
perpendicular to backbone

32
Q

characteristics of an alpha helix

A

3.6 residues per turn
held together by hydrogen bonding
no prolines allowed- form kinks

33
Q

characteristics of a beta turn

A

found in most proteins
small structured loop
stabilized by hydrogen bonding

34
Q

characteristics of a random coil

A

anything that is not a helix, turn or strand

35
Q

what are chaperones

A

help in protein folding

required for larger proteins to fold correctly

36
Q

what are heat shock proteins

A

reduce to help refold proteins damaged during heating process

37
Q

what are some post translational modifications of proteins

A

proteolytic processing, glycosylation, lipid attachment, sulfation, carboxylation, hydroxylation, acetylation, phosphorylation

38
Q

what is myoglobin

A 
found in heart and skeletal muscle 
helps diffuse oxygen in the cell 
single polypeptide chain 
about 80% helix 
high concentration of Mb in muscle cells help organisms hold their breath longer
39
Q

what is hemoglobin

A

a tetrameric protein with 4 myoglobin-like chains

used to shuttle oxygen from the lungs to the tissues and return protons and carbon dioxide back to the lungs

40
Q

how is oxygen carried

A

it does not bind to protein, it binds to prothetic group, specifically the nitrogens on the Heme group

41
Q

what are the two forms of hemoglobin

A

oxyhemoglobin: relaxed, high affinity for oxygen
deoxyhemoglobin: tense, low affinity for oxygen

42
Q

what is the Bohr effect

A

an acidic environment or addition of CO2 to the blood reduced the affinity for oxygen to bind to the heme group

43
Q

what is the carbon monoxide effect

A

CO binds to the heme group and greatly increase its affinity for oxygen and forces it to stay in oxy conformation leading to carbon monoxide poisoning

44
Q

what are the properties of enzymes

A

biological catalysts that accelerate reactions without being consumed by the reaction

45
Q

what is the importance of enzymes

A 
metabolic pathways 
clinical measurements 
diagnostic use
hereditary diseases 
drug targets
46
Q

how are enzymes different from other catalysts

A

chemical structure
enormous rate accelerations
high degree of specificity

47
Q

how do enzymes lower activation energy

A

binding to the active site

48
Q

explain the lock and key hypothesis

A

active site of enzyme is rigid, explains enzyme specificity

49
Q

explained induced fit hypothesis

A

when a substrate binds, a conformation change of the enzyme allows them to bind, conformational change of enzyme causes

*most support comes for this hypothesis**

50
Q

what is a holoenzyme (conjugated enzyme)

A

contain a prosthetic group and allow a reaction to occur even when it is not favorable

51
Q

what is an apoenzyme

A

catalytically inactive holoenzyme

52
Q

what is a coenzyme

A

function as organic prosthetic groups and assist enzymes in catalyzing difficult reactions

53
Q

examples of coenzymes

A

Riboflavin
NAD (acceptor of electrons)
Magnesium

54
Q

how are enzymes regulated competitively

A

competitive inhibitors bing to enzymes
do not affect Vmax
increase Km

55
Q

how are enzymes regulated non competitively

A

non competitive inhibitors do not bind directly to enzymes, they bind somewhere else on the substrate
decreases Vmax
doesn’t affect Km

56
Q

Bait-Prey strategy to identify interaction partners in vitro

A

Co-immunoprecipiation: bind antibody to antigen then mix with cell extracts to see which protein binds to the antigen

57
Q

Bait-Prey strategy to identify interaction partners in vivo

A

yeast-two hybrid: protein is bound to DNA binding domain and prey is bound to a transcription activator, when they interact, transcription occurs and the reporter protein is expressed proving that the bait and prey interacted

58
Q

driving forces of protein interactions

A

non-covalent interactions like hydrogen bonds, disulfide bonds, salt bridges, etc.

59
Q

which nucleic acids are purines

A

adenine and guanine

60
Q

which nucleic acids are pyrimidines

A

cysteine, uracil and thymine

you can’t CUT pyramids

61
Q

difference between nucleoside and nucleotide

A 
nucleoside = sugar and base
nucleotide = phosphate, sugar and base
62
Q

what are the major force that stabilizes DNA double helix

A

hydrogen bonding between the purine and pyrimidines and base stacking

63
Q

most common form of DNA

A

B form

64
Q

describe the sequence specific interactions of DNA-binding proteins

A

base readout: proteins scan the DNA looking for patterns of potential hydrogen binding, can be in major or minor groove

shape readout: proteins scan DNA TO FIND WHERE TO BIND BASED ON DISTORTS

65
Q

What is the TATA-binding protein

A

it induces a large conformational change when binds to DNA

binds exclusively to the minor groove

66
Q

how is DNA packing in eukaryotes

A

with the help of positively charges histone that bind to DNA tightly

67
Q

what groove does DAPI bind to

A

minor groove

68
Q

why is the B form unfavorable for RNA

A

there are steric clashes with 2’ OH groups

69
Q

what is the major driving force of RNA folding

A

base stacking, interaction between aromatic rings van Der Waals and electron cloud

70
Q

what are riboswitches

A

RNA molecules that sense metabolites and regulate gene expression in bacteria

Pre-Lim (2 decks)

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