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Flashcards in Assessment 1 Deck (95):
1

basic structure of AA

- alpha carbon
- hydrogen
- amine
- carboxylic acid
- "R" group

2

Essential amino acids

PriVaTe TIM HALL

Phenylalanine
Valine
Threonine
Tryptophan
Isoleucine
Methionine
Histidine
Arginine
Leucine
Lysine

3

Non-essential amino acids

alanine
aspartate
glutamate
serine
cysteine
glutamine
asparagine
glycine
proline
tyrosine

4

which two aa's are only essential when cell growth demands exceed capacity to synthesize them (i.e. during childhood)

arginine & histidine

5

whats the difference between essential and non-essential aa's?

essential CANNOT be made de novo

non-essential CAN be made de novo

6

What does it mean to have a conditionally essential aa?

- synthesis pathway is defective
- precursor lacking in dietary intake

7

What aa is conditionally essential?

tyrosine

- synthesized from essential Phe
- defective Phe --> Tyr pathway or lack of dietary Phe, then Tyr becomes an essential aa

8

Aliphatic (non polar) aa's
(hydrophobic)

GAVLIP

Glycine
alanine
valine
Leucine
isoleucine
proline

9

Aromatic rings aa's
(hydrophobic)

PTT

phenylalanine
tyrosine
tryptophan

10

positive charge aa's
(hydrophilic)

positive people LAugH

lysine
arginine
histidine

11

negative charge aa's
(hydrophilic)

AG!! so negative!

aspartate
glutamate

12

polar aa's
(hydrophilic)

Santa Claus Me Three Annoying Grinches

serine
cysteine
Met
Thr
asparagine
glutamine

13

branched cain amino acids
(subgroup of aliphatic/nonpolar aa's)

valine
leucine
isoleucine

14

Phe -->

Tyr --> thyroid hormones T3 & T4
Or
Tyr --> catecholamines (dopamine, NE, E)

15

Trp -->

Serotonin (gut, pineal gland, & brain stem)

melatonin (pineal gland)

16

Where is serotonin made?

Gut, pineal gland, & Brian stem

17

Where is Melatonin Made?

Pineal gland

18

Gln-->

Glu --> GABA (CNS)

19

Define and utilize the terms Bmax, Kd and EC50

◦ EC50 - the [ ] of drug that produces 50% of maximal effect
◦ Bmax - the total [ ] of receptor sites
◦ Kd - represents the [ ] of free drug at which 1/2 maximal binding is observed

20

Describe the concept of spare receptors

◦ The more spare receptors you have, the less drug you would need
◦ Slight correlation b/w binding and effect, but remains within physiologic window
‣ Gives you failsafe - if you had toxicity you could still activate system
‣ Allow you to respond at low [ ] ligand

21

explain how Spare receptors' existence can be demonstrated experimentally.

◦ Spare receptors may be demonstrated by using irreversible antagonists to prevent binding of agonist to a proportion of available receptors and showing that high concentrations of agonist can still produce an undiminished maximal response

22

Agonist

‣ can also be the ligand
‣ bind to receptor and activate generation of a signal

23

Partial Agonist

‣ produces a lower response
‣ completely inhibit the responses produced by full agonists
‣ "agonist-antagonism" mix property

24

antagonist

‣ bind to receptors but do not activate generation of a signal
‣ interfere with ability of antagonist to activate receptor

25

inverse agonist

‣ reduce receptor activity below basal levels observed in the absence of any agonist at all

26

competitive

‣ competitive antagonist - progressively inhibit the agonist response
‣ can be overcome with high agonist
‣ fight for binding site

27

Noncompetitive

‣ reduces the max effect the agonist can achieve although may not change its EC50
‣ Once a receptor is bound by such a drug, agonst cannot surmount the inhibitory effect irrespective of their [ ]
‣ often bind irreversibly

28

Chemical Antagonist

‣ drugs used to counteract each other
‣ makes the other drug unavailable for interactions with proteins

29

Physiologic antagonism

‣ b/w endogenous regulatory pathways mediated by different receptors
‣ use of a drug as a physiologic antagonist produces effects that are less specific & less easy to control than are the effects of a receptor-specific antagonist

30

Potency vs. Efficacy

◦ Potency = amount of drug needed to produce effect
◦ efficacy = maximal effect a drug can produce

31

Describe the terms median effective dose, medium toxic dose, median lethal dose, and therapeutic index

Median Effective Dose (EC50)
‣ dose at which 50% of individuals exhibit the specified quantal effect

Median Toxic Dose (TD50)
‣ the dose required to produce a particular toxic effect in 50% of animals

Median Lethal dose (LD50)
‣ if toxic effect is death, LD50 may be experimentally defined

Therapeutic Index
‣ relates the dose of a drug required to produce desired effect to that which produces an undesired effect

32

Idiosyncratic Drug Response

one that is infrequently observed in pts

33

hypo/hyper reactive

a drug in that the intensity of effect of a given dose of drug is diminished or increased compared with the effect seen in most individuals

34

hypersensitivity

allergic or other immunologic responses to drugs

35

tolerance

responsiveness decreases as a consequence of continued drug administration, producing a state of relative tolerance to the drugs effects

36

tahyphylaxis

when responsiveness diminishes rapidly after administration of a drug

37

Explain the factors affecting the number of receptors present at a given time in a tissue

‣ can be caused by other hormones
‣ the agonist ligand induces a decrease in # or coupling efficiency of its receptors
‣ antagonist may inc. # of receptors in a critical cell or tissue by preventing down-regulation caused by endogenous agonist

38

Explain the impact of identical receptors in non-target tissue to overall drug safety

what may help a problem in one tissue could hurt something else in another

39

Discuss factors affecting the drug [ ] at a biological target

• alteration in [ ] of drug that reaches the receptor
• variation in [ ] of endogenous receptor ligand
• alterations in # or function of receptors
• changes in components of response distal to the receptor
• tolerance
• tachyphylaxis - rapid appearance of progressive decrease in response to a given dose after repetitive administration of a pharmacologically or physiologically active substance

40

DNA Methylation

• Diet/starvation can modify methylation patterns
• Takes place on cytosine residue in the 5 position
• Turns off genes
• The 5’methyl group is added to cytosine in a CpG pair (opposite strand also reads CpG)
• Conserved thru mitosis b/c maintenance DNA methyltransferase methylates any newly made strand to match the methylation on the original strand
• Mandatory for proper development
• daughter cells have same methylation pattern as parents
• Can lead to undesirable gene methylation/silencing

41

Histone Modification

• Can be modified by acetylation, deacetylation, phosphorylation, dephosphorylation, methylation, & demethylation
• Tails can be methylated, acetylated, or phosphorylated
• Affect DNA binding to histones & binding of other proteins to the chromatin
• Some alterations can be inherited (such as methylation)
• Effect expression of genes
◦ Methylation of histone H3 at Lys9, silences transcription of gene
◦ Methylation on other lysinces may serve as activators of transcription
◦ Histone acetylation – new class of drugs can activate tumor suppressor genes & turn off cancer

42

Comparison of DNA Methylation/Histone Modification vs. DNA sequence mutation

• DNA sequence mutation = change in DNA base pair
• Whereas DNA methylation & histone modification doesn't make a change in the DNA base pair

43

Summarize RNAi (RNA interference) and gene silencing.

• Posttranscriptional gene silencing
• Can knockdown a gene
◦ Reduction of gene expression

44

Appreciate the significance of DNA reprogramming (an epigenetic phenomenon) in mammalian development.

◦ Agouti gene
‣ Mice
‣ Methylation determines coat color, size, and disease resistance
‣ Can influence this by feeding the animal a different diet

45

Describe epigenetic therapy, where drugs are given to remove epigenetic marks to reactive tumor suppressor genes and thereby treat some cancers.

• Epigenetics can be given in the form of RNAi to inhibit the transcription/expression of a particular gene.
◦ This could be to silence a gene
◦ Or it could also be to amplify another gene or activate a gene (such as tumor suppressor genes)

46

Recognize tRNA structure

• short - only 72-76 nucleotides
• cruciform 2D structure
• left and right arms have open loops
◦ contain nucleotides w/ ability to form base triplets
‣ bonds w/ 2 other nucleotides which then form the final 3D structure
• anticodon loop
◦ contains the unpaired bases that recognize codons on mRNA
• Amino acid attachment site
◦ 3' end extends out unpaired

47

describe the tRNA charging reaction

• tRNA (cognate) + L-amino acid + ATP --> aminoacyl-tRNA + AMP
• the addition of amino acids to tRNA

48

identify the enzymes that catalyze tRNA charging reaction

aminoacyl-tRNA synthetases

49

Describe the role of the Shine-Dalgamo sequence in the initiation step of prokaryotic translation

• shine-dalgarno sequence is located on the 5' end of prokaryotic mRNA
• rRNA in small subunit contains a sequence that is complementary to the shine-dalgarno sequence on mRNAs
• small ribosomal subunits are recruited to bind prokaryotic mRNA by the base pairing of the shine-dalgarno sequence to its complement in the small subunit rRNA

50

Initiation Factors (eukaryotic)

eIF-2
eIF-4G
4IF-4E

51

Elongation Factors (eukaryotic)

eEF-1alpha
eEF-2

52

Elongation factors (prokaryotic)

EF-Tu
EF-G

53

role of EF-G

• has bound GTP
• uses the energy from hydrolyzing the GTP to push the mRNA through the ribosome precisely one codon

54

Role of EF-Tu

• escorts the charged tRNA whose anticodon loop is complementary to the 2nd codon on the mRNA

55

Role of eEF-2

• 2nd elongation factor
• has GTP bound to it & uses the energy from hydrolyzing the GTP to push the mRNA through the ribosome precisely on codon
◦ now theres room for a new charged tRNA coded by the third codon

56

Role of eIF-4E

• prepares the mRNA to participate in translation by binding to its 5' cap
• '4' opens the door

57

Role of eEF-1alpha

• escorts tRNA into ribosome

58

Role of eIF-4G

• large protein with many sites for binding other eIFs
• 'G' is for glue - the Glue that holds eIF4E & small ribosomal subunit together

59

Role of eIF-2

• important as the mandatory escort for the initiator methionyl-tRNA
• the initiation factor that escorts the charged initiator tRNA to the small ribosomal subunit.
• 't' is for tRNA & two

60

Cap-dependent eukaryotic translation initiation

• most common
• translation begin with ribosomes binding to the 5' cap on mRNA
• scans nucleotides looking for a start codon surrounded by Kozak consensus sequence
◦ PuNNAUGPu
‣ Pu = a purine (A or G) & N = any nucleotide
• Gets to Kozak consensus & stops & is rapidly joined by the large ribosomal subunit to complete the cap-dependent initiation

61

Cap-independent eukaryotic translation initiation

• begins with ribosome binding to a secondary structure on the mRNA & NOT by binding to the 5' cap
• only used by mRNA that have special secondary structure
• small ribosomal subunit binds to the eIFs & then with methionyl-tRNA
• additional eIFs join to complete preparation of small subunit for mRNA binding
• this small subunit complex binds directly to a secondary structure called the IRES (Internal Ribosome Entry Site) on the mRNA
• Ribosomes don't scan b/c the start AUG codon is immediately after the IRES & the large ribosomal subunit joins immediately after the small subunit complex binds the IRES
• initiation complete

62

differences b/w cap-depedent & cap-independent

• the part of the mRNA bound by the ribosome
• distance from first binding to the start codon AUG
• the need for eIF4E for mRNA binding

63

Identify the peptide transferase, the enzyme that catalyzes peptide bond formation

• peptide transferase is rRNA in the large subunit
• the energy comes from the ATP used to attach the aa to the tRNA

64

Describe the characteristics of RNA

• Amount of mRNA is based on amnt of protein made
• Ribose = sugar in sugar phosphate backbone (instead of deoxyribose in DNA)
• U instead of T
• Free 3' -OH end of RNA chain is where activated nucleoside triphosphates are added on the growing chain
• RNA can fold on itself with intrastrand base pairing to make 2° structure
• Complementary to 1 strand of DNA
• Coding strand (aka sense strand) of. DNA = same as RNA sequence; template strand = complementary sequence

65

role of RNA polymerase

• Transcribes DNA --> RNA
• Takes in ribonucleoside triphosphates, (NTPs) to polymerize them using 1 strand of DNA as template

66

]Describe the main RNA types involved in translation

• mRNA = code for proteins
• rRNA = form the core of the ribosome & catalyze proteins synthesis
• miRNA = regulate gene expression
• tRNA = serve as adaptors b/w mRNA & amino acids during protein synthesis
• Other small RNAs = used in RNA splicing, telomere maintenance & other processes

67

Describe a promoter, start site, terminator & stop site

• Promoter
◦ aka start site
• Terminator
◦ Aka stop site
◦ Often can form hairpins & have a A-T or U-A rich region

68

Explain what activator proteins do, what repressor proteins do:

• Activator Proteins
◦ Increase the number of transcription starts
◦ Inc. amount of gene transcribed
◦ CAP + cAMP = example of ligand activating an activator gene regulatory protein
• Repressor Proteins
◦ Decrease transcription of a gene
◦ Prevents polymerase from binding to promoter and starting transcription

69

What are gene regulatory proteins

• Activators & repressor proteins are aka gene regulatory proteins or transcription factors
• Act like gene switches to turn genes on/off
• Regulate amount of transcription of a gene

70

What do gene regulatory proteins have in common

• Transactivation Domain (TAD)
• DNA binding domain (DBD)
• Ligand Binding Domain (LBD)

71

What does the transactivation domain (TAD) do on gene regulatory proteins

- Binds to proteins that regulate transcription
- often causing assembly of protein complex

72

What does the DNA binding domain (DBD) do on gene regulatory proteins

◦ Bind to sequence of DNA that is associated with the gene of interest
◦ Identifies gene to be regulated

73

What does the Ligand Binding Domain (LBD) do on gene regulatory proteins

◦ Ligand binding regulates the activity of the gene switch protein

74

How do gene regulatory proteins work

• Glucocorticoid Receptor (GR) = gene regulatory proteins
• HSP - attaches to GR in cytosol which makes it inactive
• Cortisol binds to GR which makes HSP fall off --> GR dimerizes & exposes the DBD & TAD --> Nuclear Localization Signal (NLS) makes the active GR pass into nucleus thru nuclear pores --> DBD binds its specific DNA sequence & TAD binds to a coactivator complex of proteins that starts the basal transcription complex to increase transcription
• Gene has now been regulated by the hormone cortisol

75

How do gene regulatory proteins recognize a DNA sequence

• DNA binding domains interact within grooves of DNA to detect specific sequences of DNA
• DBD can see the DNA sequence by interacting with the edges of DNA in the grooves
• The DNA strands DO NOT have to be pulled apart to recognize the bases as in replication & transcription
• Contacts are H-bonds that require close proximity & correct spatial orientation
◦ H-bonds b/w side chains of aa's within a specific protein structure & a specific base pair sequences ithin the DNA

76

General Transcription factors

• `bind to the promoters to begin transcription
• mRNA synthesis requires many general transcription factors at the start site TATA Box to start transcription
• RNA poly II needs assembly of many General transcription factors to start transcription at TATA box with
• GRs can work on multiple genes to inc. transcription when activated

77

Activator

‣ Stimulates the binding and assembly of general transcription factors

78

Mediator

• Aka co-activator
• Molded like a puzzle piece b/w the activator and general transcription factor-polymerase complex

79

discuss how chromatin structure regulates gene expression

• Chromatin remodeling complexes
◦ Change the packing of nucleosomes (the spacing of nucleosomes)
◦ Creates looser structure of DNA
• Histone modifying enzymes
◦ Histone acetylases
‣ Enhance gene expression
‣ Histone H3 can have multiple modifications but acetylation at certain sties enhances gene expression
◦ Make a pattern of histone modifications that would encourage transcription

80

Be able to recognize the vocabulary of transcription & chromatin

◦ Gene regulatory proteins are influenced by several mechanisms: ligand binding, unmasking, nuclear entry

81

Describe 5' end capping of mRNA & its function

• End capping
◦ Important for processing, nuclear export and translation
◦ Caps with methyl guaninosine (MethylG cap)
• Function
◦ Recognized by cap-binding proteins (in nucleus & cytosol)

82

Describe mRNA termination & addition of poly A tail

• mRNA termination
◦ mRNA processing is in the nucleus
‣ Adds changes at 5' & 3' ends and removes non-coding sequences so that pre-mRNA becomes a functional mRNA in the cytosol
• Addition of poly A tail
◦ Important for. Translation initiation and nuclear export
◦ Aka polyadenyoaltion of 3' end
◦ 200 or more A's long
◦ Protected by poly A binding protein
◦ Added when factors recognized the AAUAAA sequence encoded at the 3' end of transcripts
◦ Bound by proteins

83

Describe mRNA splicing from a precursor pre-mRNA

• Introns
◦ Removed from transcript
◦ Special sequences signal beginning and end of intron

• Exons
◦ spliced together after introns are moved
◦ Sequences in mature mRNA

• Needed for translation and nuclear export

• Splicing is catalyze by snRNPs (U1, U2, ...) that assemble at consensus sequences to form a splisosome
◦ Ensure it occurs properly
◦ Assist with formation of lariat

84

Describe mRNA export of mRNA from the nucleus to cytosol

• mRNA export through the nuclear pore to cytoplasm
• Needs the modifications of capping, splicing and polyadenylation to GEB exported
• Transcripts are spliced, 5' ends capped and 3' ends polyadenylated before export to cytoplasm
• Proteins in nucleus make a mature mRNA as "export ready"
• mRNA can be delivered as "cargo" by a nuclear export system to the cytosol
◦ Cargo binds to Ran-GTP associated with nuclear export receptor --> travels to cytoplasm --> cytoplasmic GTPase activity causes release of cargo (mRNA) and Ran-GDP --< export receptor without bound Ran-GDP is carried into nucleus thru nuclear pores and cycle repeats as long as there is RAN-GTP

85

Discuss how signals in time can trigger new gene regulation

• Combinatorial control creates different cell types expressing unique gene regulatory genes
• Combinatorial = time & space
• Clock genes - cell division are signals of appropriate time for expression of gene
• The vertical direction - a new gene is turned on with each cell division

86

Discuss how cells can discern their spatial positioning in a developing embryo

• Special signals through morphogenetic gradients signal where the cell is relative to other cells
• Simplified to whether it divides to the right or left of the original cell
◦ Each right side dividing cell makes the next temporally expressed gene
• Spatial info comes from anterior, posterior, and dorsal ventral position signals
• Morphogens
◦ Inducer molecules
◦ Directs nearby cells along a developmental path
◦ Secreted outside teh cell & detected by cell surface receptors
◦ Examples: Hedgehog (HH), Indian Hedgehog (IHH), Sonic Hedgehog (SHH), & bone morphogenetic proteins (BMP-2,-3,-5, etc)
• Morphogenetic form a gradient of activity that specify positional information that allows cells to differentiate (aka morphogenic gradients)

87

Explain the idea of cell memory

• Aka commitment to lineage
◦ As they differentiate, they undergo a series of committed steps that they cannot reverse

88

Explain how cells keep gene on using cell memory

‣ Once expressed, a gene stays on through the process of cell memory
◦ Changes in chromatin structure can be inherited by daughter cells, which allow them to keep patterns of gene expression on/off

89

Explain how cells keep gene off using cell memory

‣ Chromatin structure can help keep a gene off once it is turned off
◦ Changes in chromatin structure can be inherited by daughter cells, which allow them to keep patterns of gene expression on/off

90

Explain how a gene regulatory event is recalled in the descendants of a differentiating cell

‣ Daughter cells remember the commitment of a precursor cell gene expression pattern (memory)
‣ Remember patterns of gene regulatory protein expression by positive feedback loops

91

Be able to discuss how new combinations of genes help increase gene & species diversity

• homologous genes from P & M often have minor differences in sequence
• alleles = variations in gene sequences
• children = combination of parents DNA

92

Be able to recall the result of homologous recombination in meiosis

• chromosome crossovers during meiosis to generate haploid gametes
• common in haploid gametes
• new combinations of paternal & maternal genes in sperm & egg

93

Be able to explain steps in the process of homologous recombination

• chromosome arms cross over --> DNA from paternal and maternal genes are reasserted
• equivalent homologous genes in long arms of chromosomes have exchanged
• there is a double strand break & Rejoining
• a single strand of DNA invades to start the process
• single strand invasion occurs in all homologous recombination sites

94

Be able to compare homologous recombination to effective repair of double strand breaks in DNA

• recombination process can be used as a template to repair broken DNA
• recombination i driven by base-pairing b/w nearly identical paternal & maternal sequences of DNA

95

Be able to explain steps in the process of homologous recombination

• homologous DNA is aligned
• double strand break is made in one
• Nuclease digests one strand leaving single strands at break
• single strand invades other copy (assisted by enzymes like RAD51)
• polymerase extends from the 3' end using the other parental strand as template
• precise cutting & DNA ligation
• 2 newly combined chromosomes