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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
which amino acid does not have a chiral center
glycine
26
what is unusual about proline
since it is a five member ring amino acid, it causes kinks
27
what is unusual about glycine
it has no side chain making it very flexible
28
what is unusual about cysteine
it can form disulfide bonds because of its sulfhydryl group as a side chain
29
what are the four types of secondary structures
beta strand alpha helix beta turn random coil
30
what are the super secondary structures
``` beta-alpha-beta beta hairpin alpha alpha coiled coils zinc finger ```
31
characteristics of a beta strand
held together by backbone binding can be parallel or anti-parallel perpendicular to backbone
32
characteristics of an alpha helix
3.6 residues per turn held together by hydrogen bonding no prolines allowed- form kinks
33
characteristics of a beta turn
found in most proteins small structured loop stabilized by hydrogen bonding
34
characteristics of a random coil
anything that is not a helix, turn or strand
35
what are chaperones
help in protein folding | required for larger proteins to fold correctly
36
what are heat shock proteins
reduce to help refold proteins damaged during heating process
37
what are some post translational modifications of proteins
proteolytic processing, glycosylation, lipid attachment, sulfation, carboxylation, hydroxylation, acetylation, phosphorylation
38
what is myoglobin
``` 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
what is hemoglobin
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
how is oxygen carried
it does not bind to protein, it binds to prothetic group, specifically the nitrogens on the Heme group
41
what are the two forms of hemoglobin
oxyhemoglobin: relaxed, high affinity for oxygen deoxyhemoglobin: tense, low affinity for oxygen
42
what is the Bohr effect
an acidic environment or addition of CO2 to the blood reduced the affinity for oxygen to bind to the heme group
43
what is the carbon monoxide effect
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
what are the properties of enzymes
biological catalysts that accelerate reactions without being consumed by the reaction
45
what is the importance of enzymes
``` metabolic pathways clinical measurements diagnostic use hereditary diseases drug targets ```
46
how are enzymes different from other catalysts
chemical structure enormous rate accelerations high degree of specificity
47
how do enzymes lower activation energy
binding to the active site
48
explain the lock and key hypothesis
active site of enzyme is rigid, explains enzyme specificity
49
explained induced fit hypothesis
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
what is a holoenzyme (conjugated enzyme)
contain a prosthetic group and allow a reaction to occur even when it is not favorable
51
what is an apoenzyme
catalytically inactive holoenzyme
52
what is a coenzyme
function as organic prosthetic groups and assist enzymes in catalyzing difficult reactions
53
examples of coenzymes
Riboflavin NAD (acceptor of electrons) Magnesium
54
how are enzymes regulated competitively
competitive inhibitors bing to enzymes do not affect Vmax increase Km
55
how are enzymes regulated non competitively
non competitive inhibitors do not bind directly to enzymes, they bind somewhere else on the substrate decreases Vmax doesn't affect Km
56
Bait-Prey strategy to identify interaction partners in vitro
Co-immunoprecipiation: bind antibody to antigen then mix with cell extracts to see which protein binds to the antigen
57
Bait-Prey strategy to identify interaction partners in vivo
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
driving forces of protein interactions
non-covalent interactions like hydrogen bonds, disulfide bonds, salt bridges, etc.
59
which nucleic acids are purines
adenine and guanine
60
which nucleic acids are pyrimidines
cysteine, uracil and thymine | *you can't CUT pyramids*
61
difference between nucleoside and nucleotide
``` nucleoside = sugar and base nucleotide = phosphate, sugar and base ```
62
what are the major force that stabilizes DNA double helix
hydrogen bonding between the purine and pyrimidines and base stacking
63
most common form of DNA
B form
64
describe the sequence specific interactions of DNA-binding proteins
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
What is the TATA-binding protein
it induces a large conformational change when binds to DNA | binds exclusively to the minor groove
66
how is DNA packing in eukaryotes
with the help of positively charges histone that bind to DNA tightly
67
what groove does DAPI bind to
minor groove
68
why is the B form unfavorable for RNA
there are steric clashes with 2' OH groups
69
what is the major driving force of RNA folding
base stacking, interaction between aromatic rings van Der Waals and electron cloud
70
what are riboswitches
RNA molecules that sense metabolites and regulate gene expression in bacteria

Pre-Lim (2 decks)

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