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Medical School > Week One > Flashcards

Week One Flashcards

1
Q

Describe how properties of amino acids affect protein structure

A

Structure determines Function

Sim structure may have sim function

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2
Q

Identify key structural features found in proteins

A

They are polymers built from 20 AA
Side chains affect the charge and polar interactions
Covalent peptide bonds join AA together
Hydrophobic and hydrogen bonds stabilize 3d structure
Covalent disulfide bonds contribute to 3d structure

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3
Q

Identify how posttranslational modifications and changes in the primary protein sequence can alter protein structure and function

A

heat light solvent and change in ph affect structure

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4
Q

Recognize that proteins with similar function will have similar tertiary structure but may have different primary sequences

A

Change in AA can change entire structure if it can not fold correctly, or makes a new protein

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5
Q

describe the chemical makeup of nucleic acids

A

Nitrogenous base, five carbon sugar and phosphate are the monomeric units of DNA and RNA

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6
Q

identify the 3 and 5 ends and know how it relates to dsDNA as being antiparallel

A

5 prime end has a phosphate group

3 prime end has the hydroxyl group

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7
Q

Watson crick base pairing

A

deoxyribose sugars and joined by hydrogen bonds with adenine paired with thymine and with cytosine paired with guanine

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8
Q

Compare features of eukaryotic and prokaryotic genomes

A
  1. They both have DNA as their genetic material.
  2. They are both membrane bound.
  3. They both have ribosomes
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9
Q

Contrast features of eu and pro genomes

A

Larger genome in Eu
Pro is typically single circular DNA
Pro, the DNA is supercoiled and attached to RNA core protein
Eu, chains of chromatin with links of nucleosomes

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10
Q

What is semi-conservative model of DNA replication and what are its implications for inheritance

A
  • each daughter chromosome contains one of the parental DNA strands and one newly sythesize complementary strand
  • replication is said to be semi conserved because both parental strands are still intact but are no longer together
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11
Q

DNA polymerase

A

enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA

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12
Q

Ligase and Pol1

A

Joins two polynucleotide chains together on DNA. The gaps between okazaki fragments have a OH and phosphate group which the ligase connects via phosphodiester bond.

Pol1 fills the gap once primer is removed

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13
Q

Primase

A

*Adds an OH group, which the polymerase attaches to and allows replication to begin.

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14
Q

single stranded DNA binding protein

A

prevent the strands from re-associating and protect them from enzymes that cleave single stranded DNA

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15
Q

Topoisomerase 1

A

Covalently binds to DNA phosphate. Breaks phospodiester bond and allows for DN strand to rotate, relieving stress.

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16
Q

Topoisomerase 2

A

*Largely confined to proliferating cells in eukaryotes

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17
Q

What mechanism prevents DNA from shortening and how it contributes to normal aging and cancer

A
  • Telomerase create and add DNA sequence from an RNA template to the 3’ end of replicated DNA strand. If this didnt happen cells would reach hayflick limit and undergo cell death. Cancer upregulates these enzymes to become immortal.
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18
Q

Given an antineoplastic or antiviral drug which targets DNA synthesis, predict the molecular and clinical consequences

A

*not sure

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19
Q

When does mammalian cell cycle DNA replication occur

A

S phase of

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20
Q

Helicases

A

Seperate DNA strands and unwind the parental duplex

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21
Q

Clamp proteins

A

Prevent DNA polymerase from falling off the template strand

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22
Q

Okazaki fragments

A

Short, newly synthesized DNA fragments that are formed on the lagging template strand during DNA replication

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23
Q

Describe chemical reactions by their energetics and kinetics, and predict how conditions such as pH, temperature, substrate and product concentration,

A

Delta G is energetics. Delta G = H-TS Prime is 25C pH7
Increase product = unfavorable
Increase substrate or decrease product = favor (-G)
Kinetics is speed

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24
Q

Use Michaelis-Menten plots to describe enzyme catalyzed reactions in the presence and absence of competitive, non-competitive, and allosteric inhibitors and activators

A

competitve = no change in Vmax. Increases Km
non competitve = decrease vmax, no change in Km

When it goes closer to 0 it increases

allosteric = can change both vmax and km. Change from hyperbola to sigmoidal curve

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25
Q

Describe how enzymes’ active sites interact with substrates to provide substrate specificity, proper orientation and spacing, and stereo-specificity for biological reactions to efficiently generate products.

A

punuske

Transition states are stabalized by interactinos with AA side chains and enzyme cofactors

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26
Q

Describe the structure of a gene, identifying the relative locations and functions of promoters, enhancers, transcriptional start site, introns and exons.

A

a

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27
Q

Describe DNA replication in prokaryotes and eukaryotes, leading and lagging strand synthesis, Okazaki fragments, role of polymerases, helicases, single stranded binding proteins, topoisomerases, telomerase, dysregulation in human diseases

A

pro =dnaA binds, brings in helicase and primase. Binds and goes bilateral in transcribing. pro uses 3 polymerases, does not need primer and can go both ways.

28
Q

Describe how RNAs are modified after transcription by capping, splicing, and polyadenylation, and understand how defects in these processes can cause disease (e.g. beta thallasemia)

A

i

29
Q

Compare transcription in prokaryotes and eukaryotes.

A

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30
Q

Understand the functions, structures, and synthesis of mRNAs, tRNAs, rRNAs, and miRNAs and lincRNAs.

A

k

31
Q

Given a wild type mRNA sequence, apply an understanding of the codon structure of mRNAs to predict changes in protein structure due to a specific mutation.

A

l

32
Q

Describe the structure and variation in the genetic code

A

m

33
Q

Describe the structure and function of tRNAs in the process of translation

A

n

34
Q

Understand wobble base pairing (will be on USMLE!

A

o

35
Q

Describe how mRNAs are translated to proteins, including the molecular mechanisms of initiation, elongation, and termination.

A

p

36
Q

Compare eukaryotic and prokaryotic translation, and describe the targets of antibiotics that target translation.

A

q

37
Q

Describe the structure and function of ribosomes in prokaryotes and eukaryotes

A

r

38
Q

Describe how defects in genes involved in translation are common causes of human diseases

A

s

39
Q

Learn that the Human Genome Project: found far fewer genes but greater complexity; that specific isoforms (mRNA, proteins, ncRNAs) are expressed in specific tissues, at specific times, and in specific diseases and that emerging technologies permit the dissection of this complexity - with important clinical implications

A

t

40
Q

Learn that cells in an organism can appear dramatically different in size, shape, function and stage of development; yet all nucleated cells contain the same DNA, this was proven by the generation of new adult cloned animals from the reprogramming of a single adult somatic cell - in amphibians and mammals, therefore, the difference in cell phenotypes must be based on differential regulation of gene expression, ie., different cell types make different sets of proteins (and also regulatory RNAs); a typical eukaryotic cell may express 10,000-20,000 of its ~ 20-30,000 genes but which of those genes that are expressed is critical to cell phenotype

A

u

41
Q

Learn that comparison of the genomes of diverse organisms, e.g., humans vs chimps or humans vs mice, indicate that many higher organisms share essentially the same set of genes, thus what distinguishes humans from mice or chimps is more complex regulation of its genome

A

v

42
Q

Know that cells can change the expression of its genes in response to external signals, e.g., if a liver cell is exposed to a glucacorticoid hormone the production of many specific proteins are dramatically increased; glucacorticoids are released in the body during starvation or intense exercise and signal the liver to produce glucose from amino acids and other molecules; when the hormone is no longer present production of target proteins drops to normal; another example are the response of cells to iron availability

A

w

43
Q

Learn that regulation of gene expression can occur at the level of genomic regulation, transcriptional regulation, post-transcriptional regulation, protein synthesis & stability and post-translational modifications

A

x

44
Q

Describe how transcription factor use zinc fingers, helix-turn-helix motifs, and leucine zippers to bind different DNA structural elements and recruit co-factors such as acetyl transferases, allowing RNA polymerase access to a DNA coding sequence and initiate transcription.

A

y

45
Q

Using bacterial models such as the lac operon, describe how promoter elements regulate transcription in response to environmental stimuli. Compare and contrast bacterial transcriptional regulation with a eukaryotic model, e.g. regulation of ferritin and transferrin receptor expression.

A

z

46
Q

Describe the concept of epigenetics, and describe how methylation of cytosine is responsible for, e.g. random X inactivation, imprinting, inactivation of tumor suppressor genes.

A

a

47
Q

Know that changes in the regulation of gene expression underlie much disease etiology and pathology; cancer cells are an excellent example

A

b

48
Q

Describe the relationship between vitamins, cofactors, apoenzymes and holoenzymes.

A

c

49
Q

Identify the major redox and activation transfer cofactors and describe their general biochemical functions and vitamin precursors (if applicable).

A

d

50
Q

Given a deficiency in a major redox or activation transfer cofactor, predict what pathways will be impacted, how concentrations of metabolites will be affected, and how the deficiency causes pathology. Describe the molecular pathophysiology of scurvy, beriberi, pellagra, riboflavin deficiency, pyridoxine oxidase deficiency, antiquitin deficiency (pyridoxine dependent epilipsy) and pernicious anemia.

A

e

51
Q

Describe the substrates, products, key regulatory enzymes, and relative energy yields of glycolysis and fatty acid beta oxidation. Describe the transport of fatty acids and reducing equivalents (e.g. reduced NADH) within the cell.

A

f

52
Q

Describe the biochemical basis for altered metabolism in cancer, lactic acidosis, Jamaican vomiting sickness, medium chain acyl-CoA-dehydrogenase deficiency (MCAD), and carnitine palmitoyl transferase – 1 deficiency.

A

g

53
Q

Given a physiologic or pathologic change in an enzyme, substrate or regulatory molecule in the glycolysis or beta-oxidation pathways, predict effects on other enzyme activities, other product/substrate/regulatory molecule concentrations, and physiology.

A

h

54
Q

Describe how and why metabolites divert from glycolysis and beta oxidation, such as 2,3-bisphosphoglycerate from glycolysis and ketone bodies from beta oxidation. Describe the significance of special cases of fatty acid catabolism: the breakdown of odd chain length and branched chain fatty acids, oxidation of unsaturated fatty acids, and peroxisomal oxidation.

A

i

55
Q

Understand that DNA’s structure allows the repair of replication errors and other damage, that cells expend great effort to repair DNA, and that defects in DNA repair enzymes can lead to increased susceptibility to diseases such as cancer.

A

jj

56
Q

Describe the chemical basis of common potential structures such as guanine adducts, thymine dimers, deamination, and depurination; describe cells’ repair mechanisms to prevent permanent damage from these insults.

A

kk

57
Q

Know the repair capabilities of the different DNA polymerases (high impact USMLE)

A

ii

58
Q

Know how double stranded DNA breaks are made physiologically and pathologically, and how double stranded breaks can be repaired by homologous or non-homologous end joining.

A

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59
Q

Describe how large scale DNA damage such as chromosomal dyslocations can result in diseases such as cancer and Downs.

A

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60
Q

Enzymes (catalysts)

A

provide proximity and orientation
ensure specificity of substrates and products
Stablize the transition complex

overall, lower activation energy

Can couple reactions to favor desired reaction

61
Q

Hexokinase

A

Links hydrolysis of atp (-7.3) to phosphyorylation of glucose (3.3) to favor production of glucose 6 phosphate

62
Q

v

A

= Vmax(S) / Km + S

Vmax is conc when all enzymes bound to substrate
Km is michaelis constant and is .5Vmax

units are product / time

63
Q

Pol III

A

Ecoli uses this to proofread and fix wrong base groups. DNA replication

64
Q

Pol II

A

DNA repair

65
Q

processivity

A

DNA polymerase remains attached to parent strand while it moves down chain

Medical School (1 decks)

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