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Biology 111 > Exam 2 Study Guide > Flashcards

Exam 2 Study Guide Flashcards

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1
Q

What are genetic markers?

A

Particular sequences of DNA that correlate with disease

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2
Q

What are Genome Wide Association Studies (GWAS)?

A

Correlative studies of DNA sequence variants to see if they are associated with a human disease

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3
Q

What are anonymous markers?

A

Sequences of DNA not associated with disease or trait (no phenotypic affect)

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4
Q

What are some traits of anonymous markers?

A

Highly variable (polymorphic), multiple alleles, high degree of heterozygosity

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5
Q

What is single nucleotide polymorphism (SNP)?

A

One base difference between individuals; 7 million+

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6
Q

What are the two types of SNPs?

A

Coding and noncoding

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7
Q

What are the two types of coding SNPs?

A

Synonymous and non-synonymous

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8
Q

What does synonymous coding do?

A

Doesn’t change protein the gene codes for

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9
Q

What does non-synonymous coding do?

A

Changes the protein the gene codes for

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10
Q

What are Variable Nucleotide Tandem Repeats (VNTRs)?

A

Short repeated DNA sequences that vary in length (10-100 bp) and number of repeats (3-50) among individuals; thousands of VNTR loci in human genome

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11
Q

What demonstrates VNTR length?

A

DNA fingerprint, amplified in polymerase chain reaction analyzed through gel electrophoresis

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12
Q

What is identity matching?

A

Matching a suspect’s DNA with DNA at a crime scene. To match two samples , they must show the same allele pattern. (CODIS uses 15 VNTR loci)

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13
Q

What is inheritance matching?

A

VNTR alleles must follow rules of inheritance. In matching an individual with his parents or children, a person must have a VNTR allele that matches one from each parent

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14
Q

What is gene expression?

A

How genotype is converted into phenotype

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15
Q

What is the Central Dogma of Molecular Biology (CDMB)?

A

Unifying concept of molecular biology; describes information flow within cells

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16
Q

According to the CDMB, what is the information flow within cells?

A

DNA stores info and is replicated, RNA contains information in DNA, RNA is used to direct synthesis of proteins

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17
Q

What is the Updated Central Dogma?

A

Adds additional step that DNA can be made from RNA through reverse transcription (e.g. retroviruses like HIV have reverse transcriptase that can be used to make complementary DNA (cDNA) from RNA)

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18
Q

What did Beadle and Tatum do?

A

Studied synthesis of arginine in Neurospora (bread mold), exposed bread mold to x-rays which would cause mutations

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19
Q

What are the putative precursors of arginine?

A

Ornithine and citruline

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20
Q

What is the conclusion about each gene Beadle and Tatum mutated?

A

Each mutated gene encoded a single enzyme in the Arg synthesis pathway

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21
Q

Why is “one gene-one polypeptide” more correct than Beadle and Tatum’s original “one gene-one enzyme”?

A

An enzyme may be made up of multiple polypeptides; also, a polypeptide may not be an enzyme at all (a structural protein)

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22
Q

What may happen if alternative splicing occurs?

A

One gene may code for multiple proteins

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23
Q

How does a DNA sequence specify amino acids in a protein?

A

The genetic code

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24
Q

What was a milestone of the 20th century?

A

Cracking the code by identifying three base codons

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25
Q

What combination of scientific specialties identify codons and the role of RNAs in protein synthesis?

A

Genetics, biochemistry, and organic chemistry

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26
Q

How many naturally occuring amino acids are there?

A

20

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27
Q

How many DNA bases are there?

A

4

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28
Q

How many amino acids can 1 base code for?

A

4

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29
Q

How many amino acids can 2 bases code for?

A

16

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30
Q

How many amino acids can 3 bases code for?

A

64

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31
Q

Who first proposed the DNA base-amino acid logic and who later verified it experimentally?

A

Gamow; Nirenberg

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32
Q

What was the first-made synthetic RNA polymer?

A

PolyU

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33
Q

When translating RNA polymer with cell extract, what is made?

A

Proteins

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34
Q

What protein does PolyU make?

A

Phe-Phe-Phe-Phe (PolyPhe)

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35
Q

What is the 3-base equivalent of PolyPhe?

A

UUU

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36
Q

What is the 3-base equivalent of lysine?

A

AAA

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37
Q

What is the 3-base equivalent of proline?

A

CCC

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38
Q

What are copolymers?

A

Polymers with more than one base

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39
Q

After translating copolymers with cell extract and varying the ratio of bases, what is induced?

A

Frameshift rotations

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40
Q

The nature of code is universal. What does that mean?

A

Virtually the same in all organisms on the planet (rare exceptions exist in some mitochondria, protozoans and mycoplasma)

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41
Q

What is the equivalence ratio of bases to codons to amino acids?

A

3 : 1 : 1

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42
Q

How is coding redundant?

A

61 codons encode amino acids, more than one codon for some amino acids, redundancy usually in 3rd position

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43
Q

Code has how many start codons?

A

1 (AUG, Met)

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44
Q

Code has how many stop codons?

A

3 (UGA, UAG, UAA)

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45
Q

Is there any punctuation other than start/stop?

A

No

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46
Q

At its most basic, what is RNA?

A

Single stranded and only synthesized 5’ to 3’

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47
Q

What is messenger RNA (mRNA)?

A

Contain genetic information in the form of RNA and is used to direct the synthesis of a protein

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48
Q

What is ribosomal RNA (rRNA)?

A

Combine with ribosomal proteins to form the ribosome; not translated

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49
Q

What is transfer RNA (tRNA)?

A

Carry amino acids to the ribosome for incorporation into a polypeptide

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50
Q

What is micro RNA (miRNA)?

A

Very small RNAs that interact with mRNA to ‘silence’ them by preventing their translation into proteins

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51
Q

What is small nuclear RNA (snRNA)?

A

RNAs of ~150 nucleotides in length, involved in the regulation of mRNA splicing, and the regulation of gene transcription

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52
Q

Essentially, what is transcription?

A

How all RNAs are made

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53
Q

What enzyme carries out transcription?

A

RNA Polymerase

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54
Q

In transcription, the RNA is complementary to what?

A

The DNA ‘Template’ or antisense strand

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55
Q

In transcription, the RNA sequence is essentially what?

A

A copy of the ‘Coding’ or sense strand

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56
Q

Prokaryotic transcription and translation happen at the same time and place in the cell; what is this called?

A

Spatial and temporal coupling

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57
Q

When is a prokaryotictranscript (mRNA) translated?

A

As soon as it is made

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58
Q

In prokaryotic RNA transcript, are any additional modifications made?

A

No

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59
Q

Where does prokaryotic gene expression occur?

A

It all occurs in the cytoplasm (no nucleus)

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60
Q

In prokaryotic gene expression, what does single RNA Polymerase do?

A

Coordinate regulation of genes with similar function (Gene clusters called operons)

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61
Q

What is a promotor sequence?

A

Typically upstream (5’ end) of gene, where RNA polymerase binds

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62
Q

What is the TATA Box?

A

A conserved sequence in the promoter of archaea and eukaryotes (TATAAT in eubacteria)

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63
Q

What tells RNA Polymerase to stop?

A

Termination sequence

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64
Q

Are the promotor and termination regions transcribed?

A

No

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65
Q

What are the three stages of transcription?

A

Initiation, elongation, and termination

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66
Q

What is prokaryotic RNA Polymerase made up of?

A

Subunits that assemble for initiation

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67
Q

What do core enzymes do?

A

Synthesize RNA; 2 alpha and 2 beta

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68
Q

What do sigma factors do?

A

Recognize promotor region and disrupts hydrogen bonds

Binds the core enzyme to the promoter region, helps in the initial unwinding of the DNA so transcription can begin

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69
Q

What is RNA Polymerase?

A

A large multisubunit enzyme

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70
Q

What is a promotor?

A

Where RNA Polymerase attaches to the gene

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71
Q

What are holoenzymes?

A

Necessary for the accurate initiation of transcription; core + sigma factor; recognizes promotor

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72
Q

In prokaryotes, are additional proteins required such as transcription factors in eukaryotes?

A

No

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73
Q

Which was does prokaryotic transcription run?

A

Synthesized 5’ to 3’

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74
Q

What is required in prokaryotic transcription?

A

DNA template and RNA monomers (ribonucleoside tri-phosphate (rNTP’s) A, U, G, and C)

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75
Q

What does core polymerase do?

A

Carries out transcription elongation

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76
Q

What happens once transcription begins?

A

Sigma factor dissociates from the core enzyme

Core enzyme continues transcription until termination

Sigma factor can go associate with other core enzymes

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77
Q

What happens during prokaryotic initiation?

A

Requires a specific site on DNA

Promotors are recognized by RNA holoenzyme

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78
Q

What is prokaryotic elongation?

A

Similar to DNA synthesis except:

Only one strand is being transcribed

Only a small section of DNA is unwound at any one time (transcription bubble)

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79
Q

What is prokaryotic termination?

A

Requires specific sequences on DNA

Terminator is recognized by core enzyme

Core enzyme releases from the DNA and RNA transcript

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80
Q

Many prokaryotic mRNA transcripts in bacteria are polycistronic, meaning what?

A

More than one gene is included in one mRNA transcript

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81
Q

What do operons usually contain?

A

Genes involved in similar biochemical pathways

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82
Q

What are lac operons?

A

Clusters of genes involved in the transport and metabolism of lactose into glucose and galactose for energy

Three proteins are made from one mRNA transcript

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83
Q

When do transcription and translation occur in prokaryotes?

A

Simultaneously

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84
Q

In eukaryotes, are transcription and translation coupled?

A

No

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85
Q

Where does eukaryotic transcription take place?

A

Nucleus

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86
Q

Where does eukaryotic translation take place?

A

Cytoplasm

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87
Q

How many RNA Polymerases are involved in eukaryotic gene expression?

A

Three

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88
Q

Eukaryotic transcript is processed (additionally modified) to make what?

A

A mature mRNA

5’ Methyl Cap

3’ Poly A Tail

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89
Q

What is spliced to make a mature mRNA?

A

RNA primary transcript

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90
Q

What does RNA Polymerase I do?

A

Transcribes rRNA

91
Q

What does RNA Polymerase II do?

A

Transcribes mRNA (and snRNA, miRNA)

92
Q

What does RNA Polymerase III do?

A

Transcribes tRNA, rRNA

93
Q

What are the initial and final products of mRNA transcription?

A

Initial product transcribed by Pol II: primary transcript called (heteronuclear RNA = hnRNA) or pre-mRNA

Final product: mature mRNA, after processing

94
Q

Why is eukaryotic initiation more complex than in bacteria?

A

Pol II has no sigma factor

Instead other proteins are involved in getting Pol II to bind the promoter region

95
Q

How does eukaryotic elongation compare to prokaryotic elongation?

A

Similar; 5’ methyl cap is also added

96
Q

How is eukaryotic termination different from prokaryotic termination?

A

RNA modification

A Poly A tail will be added to the 3’ end of the newly transcribed mRNA

97
Q

Eukaryotic initiation requires transcription factors; what are the general ones?

A

Necessary for basal level of transcription; form initiation complex and attract RNA pol II to the promoter (these are common in all cell types).

98
Q

Eukaryotic initiation requires transcription factors; what are the specific ones?

A

Specific to certain cell types or produced in cells only under certain conditions to raise the transcription level of particular genes

99
Q

In eukaryotic initiation, what are promotor regions?

A

Binding site of general factors

100
Q

In eukaryotic initiation, what are enhancer regions?

A

Binding site of specific factors; may act over long distances so may be far away from promoter

Human genome contains 100,000s

101
Q

In eukaryotes, what is the initiation complex?

A

Consists of transcription factors plus RNA Polymerase II

102
Q

What can silencer sequences do in eukaryotes?

A

Decrease transcription

103
Q

What happens during eukaryotic elongation/termination?

A

mRNA is capped at 5’ end with methyl-G-Cap with aid of methyl transferase while elongation is in progress.

104
Q

How is eukaryotic elongation similar to that of prokaryotes?

A

5’ to 3’ (about 20 bases per second)

Occurs in transcription bubble

105
Q

How does eukaryotic termination differ from that of prokaryotes?

A

Have terminator sites but end of message is not end of transcript

mRNA is cleaved at the 3’ end after transcription

~200 A’s added by PolyA Polymerase to produce 3’ poly A tail

3’ end of mRNA not created by Polymerase II

106
Q

Why is there no no 5’ methyl cap or Poly A tail in prokaryotes?

A

RNA splicing

107
Q

In RNA splicing, what does an exonic mRNA sequence do?

A

Encodes a protein

108
Q

In RNA splicing, what does an intronic mRNA sequence do?

A

Noncoding

109
Q

RNA transcript starts off as containing what?

A

Both introns and exons, heteronuclear RNA (hnRNA)

110
Q

What does the 3’ Poly-A tail do?

A

Prevents mRNA from being degraded

111
Q

What does the 5’ mG Cap do?

A

Prevents degradation and is important for positioning of the mRNA on the ribosome

112
Q

What is splicing?

A

Removal of introns and ligation of exons

Must be exact or mRNA will not be properly translated

113
Q

What is the splicing enzyme?

A

Spliceosome

114
Q

What is the spliceosome?

A

Enzyme made up of snRNA and snRNP ‘snurps’

115
Q

How many snRNAs are in the spliceosome complex?

A

6 types (uridine rich): U1, U2, U3, U4, U5, and U6

116
Q

What are snRNPs (small nuclear ribonucleoproteins)?

A

Proteins complexed with uridines (an RNA base similar to uracil)

117
Q

What happens during splicing?

A
  1. snRNAs bind to specific RNA sequences at the 5’ and 3’ ends of the intron (Branch point A)(adenine nucleotide)
  2. snRNPs associate with other factors to form the spliceosome
  3. Intron is cleaved out and attached to itself forming a lariat structure
  4. Exons are joined (spliced together)
118
Q

What is alternative splicing?

A

Exons can be joined together in different combinations to generate multiple mRNA and multiple proteins

Can be cell type or sex specific or developmentally specific (i.e. time specific)

119
Q

What is an example of alternative splicing in humans?

A

Tyrosinase in melanocytes (5 combinations); dystrophin protein in muscle (79 exons, 18 combinations)

120
Q

How many mRNAs can one gene have?

A

Multiple that code for multiple proteins

121
Q

Does alternative splicing alter gene products?

A

Yes

122
Q

What percentage of human genes are alternatively spliced?

A

40%

(25,000 genes can produce 80,000 different mRNAs)

123
Q

What can Misregulated or aberrant RNA splicing lead to?

A

Disease (i.e. autism, cancer)

124
Q

What are cancer-associated splicing changes (CASCs)?

A

In proteins, they are known to be involved in oncogenesis, could represent an important new mechanism in how cells become cancerous

125
Q

What is the most energy-expensive step in gene expression?

A

Protein synthesis/translation

126
Q

Protein synthesis/translation uses information in mRNA to produce what?

A

A polypeptide

127
Q

What are the necessary components of protein synthesis/translation?

A

‘Charged’ tRNA (tRNA carrying an amino acid)

Ribosomal platform (mRNA)

Ribosomal complex

128
Q

What is a “charging reaction”?

A

How amino acids become covalently bound to tRNAs

129
Q

What is aminoacyl-tRNA synthetase?

A

The enzyme that catalyzes the charging reaction

There are 20 aminoacyl-tRNA synthetases, one for each of the 20 amino acids

Reaction requires energy (ATP)

130
Q

How do ribosomes play a role in gene expression?

A

Factory floor for translation

Huge macromolecular structure composed of rRNA and proteins

Organized into large and small subunits

Minor structural, but not functional, differences between prokaryotic and eukaryotic ribosomes

131
Q

When do large and small ribosomal subunits come together?

A

AFTER mRNA has been positioned on the small subunit

132
Q

What was the original view of ribosome function?

A

rRNA was “structural” and the proteins “active”

133
Q

What is the new view of ribosome function?

A

Ribosomes contain enzymatic RNA (ribozymes). Ribozymes catalyze the reactions that form the peptide bonds and release the finished peptide

134
Q

What are the functions of the large and small ribosome subunits?

A

Positioning of the mRNA (small subunit)

Binding 2 charged tRNAs (both subunits)

Peptidyl transferase activity (large subunit)

Recognition of the stop codon and peptide release (large subunit + a protein release factor)

135
Q

What are the phases of translation?

A

Initiation: assemble ribosome/mRNA/charged-tRNAs

Elongation: form successive peptide bonds and add amino acids to growing polypeptide chain

Termination: cleave peptide from last tRNA, release protein and mRNA, disassemble the ribosome

136
Q

What happens during prokaryotic initiation (translation)?

A

Small ribosomal subunit + other factors bind the mRNA at the 5’ ribosomal binding sequence

The initiator tRNA binds to the start codon (AUG)

The large ribosomal subunit joins and initiation is complete

137
Q

What happens during eukaryotic intitiation (translation)?

A

The small ribosomal subunit + initiator Met tRNA and other factors bind to the 5’ cap

The complex scans the mRNA until it finds the start codon (AUG)

The large ribosomal subunit joins the complex and initiation is complete

138
Q

In genetic code, how many possible codon sequences are there?

A

64

139
Q

Which sequences are stop codons?

A

UAA, UAG, UGA

140
Q

What is the Codon/Anticodon Conundrum in Translation?

A

In the genetic code, there are 64 possible codon sequences (UAA, UAG, UGA) are stop codons

If there were a different tRNA to pair up with each possible codon combination, there would be 61 tRNAs

However msot organisms only have 45 different tRNAs

So, there are 16 codons that specify an amino acid but have no tRNA to match them

141
Q

What is Wobble Base Pairing?

A

Base pairing in the 3rd position of a codon is weaker and more flexible than base pairing in the first 2 positions; allows 1 tRNA to read (or pair with) more than 1 codon

142
Q

What joins AAs?

A

Covalent bonds

143
Q

Where does peptide bond formation occur?

A

On the ribosome

144
Q

What happens in elongation (translation)?

A
  • The first charged tRNA binds to the P site
  1. A new charged tRNA binds to the A site
  2. Formation of the peptide bond
    • Growing aa chain now is transferred from the tRNA in the P site to the tRNA in the A site
    • tRNA in P site now has no aa (uncharged)
  3. The ribosome moves relative to mRNA. This is called TRANSLOCATION
    • Shifts the uncharged tRNA in P site to the E site (ejected)
    • A new charged tRNA binds to the codon in the A site
145
Q

What happens as release factors are recruited by a stop codon in the A site?

A
  1. break the covalent bond between the polypeptide and the acceptor stem of the tRNA in the P site, and
  2. cause the ribosomal subunits to dissociate
146
Q

After release factors are recruited by a stop codon in the A site, now what happens to the protein?

A

The protein will be transported to its proper location in the cell, or the protein will be exported out of the cell

Locational markers are present in the protein itself in parts of the protein called signal sequences (SS)

SS: are 16-30 amino acids long and act as an address or zip code for the protein

147
Q

What happens during the post-translational processing of proteins?

A
  1. Proteins may be cleaved after synthesis (proteolysis)
    1. Example: zymogens: enzymes that are not active until they are cleaved
  2. Glycosylation: the addition of sugars to a protein
    1. Many membrane-bound organelles are glycoproteins
  3. Phosphorylation: addition of PO4 group(s) to a protein
    1. The activity of many proteins are controlled by phosphorylation (cell cycle)
      1. Phosphotases and kisases: enzymes that control phosphorylation
      2. Phosphorylation can activate or deactivate the activity of a protein
  4. Ubiquitination: addition of ubiquitin (itself a small protein)
    1. Targets protein for destruction in the proteosome
      1. Addition of 4 ubiquitins is required for destruction
148
Q

What is the main rule of protein structure?

A

To be functional, proteins must be properly folded

149
Q

What characteristics denote primary structure?

A

The sequence of amino acids, which is determined by the gene that codes for the protein

All higher levels of structure are dependent on primary structure

Peptide bonds present

150
Q

What characteristics denote secondary structure?

A

Arises through hydrogen bonding between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone

Does not involve R group interactions

Alpha-helix

Beta-pleated sheets: consists of two or more hydrogen bonded beta-strands (Hydrogen bonds, although weak, provide structure stability due to the large number of them present)

151
Q

What are motifs?

A

The next level of secondary structure

Different combinations of beta-pleated sheets and/or alpha-helices form motifs

A beta-barrel is a large beta-sheet that twists and coils to form a closed tube that resembles a barrel

Often found in proteins that form pores in plasma membranes

152
Q

What characteristics denote tertiary structure?

A

3D shape of the entire protein; includes the secondary structure and arises through interactions between the R groups of the amino acids

153
Q

What R-group interactions exist in tertiary structures?

A

Electrostatic (H-bonding and ionic): attraction of positive and negatively charged R groups

Disulfide bridges: cysteine have sulfhydryl (SH) groups, which react to form covalent bond: disulfide (S-S)

Van der Waals Interaction: attraction of nonpolar groups for each other (a weak attractive force between the two nonpolar atoms due to small fleeting changes in atomic charge

Hydrophobic exclusion interactions: hydrophobic side chains will prefer to be in the interior of the protein to avoid contact with the aqueous environment

154
Q

What are domains?

A

Functional units of the protein within a tertiary structure

If amino acids are the letters of a protein, secondary structures and motifs are the words and phrases of a protein and domains are the chapters of a protein

Most have multiple domains

If a protein is only one polypeptide, this is the highest level of structure

155
Q

What are some examples of protein domains?

A

DNA binding domain (DBD): any protein that directly binds to DNA (transcription factor) will need a DNA binding domain

Any protein that activates transcription of a gene will need Transcriptional Activation Domain (TAD) to recruit RNA Polymerase

Scientists can deduce the function of a protein by what domains it has

156
Q

What characteristics denote quaternary structure?

A

Relevant for proteins made up of multiple polypeptides (highest level of structure)

Example: hemoglobin protein in RBC’s; Consists of two alpha and two beta chains

4 polypeptides=tetramer

157
Q

What is denaturation?

A

Occurs in response to changes in temperature, pH, and/or ionic concentrations

All of these alter chemical interactions and change protein shape

158
Q

What are chaperone proteins?

A

Enzymes that help proteins fold and/or refold

Chaperone proteins provide an optimal environment for the protein to fold in

Once thought that all newly-made proteins folded spontaneously, now know that chaperones assist in folding and/or refolding

159
Q

What can misfolded proteins cause?

A

Disease, as proper folding is crucial to cellular function

160
Q

What is cystic fibrosis?

A

An inherited disease in which abnormally thick mucus blocks airways causing difficulty breathing

A mutation in the CF transmembrane conductance regulator (CFTR) gene.

This mutation blocks the binding of CFTR protein with chaperone protein (causes CFTR misfolding)

161
Q

How is Alzheimer’s Disease related to misfolding?

A

Misfolded beta-amyloid proteins clump together to form plaques that collect between neurons and disrupt communications between neurons and cause cell death

Misfolded Tau proteins clump together to form tangles that collect inside the neuron and cause cell death

162
Q

What are therapeutic strategies for misfolded proteins?

A

It’s known that Tau proteins are hyperphosphorylated in Alzheimer’s

Inhibit tau protein kinases

Activate tau phosphatases

Promote the clearance of the abnormally hyperphosphorylated tau by targeting it for destruction using the ubiquitin proteasome system

163
Q

Protein misfolding is believed to be the primary cause of:

A

Parkinson’s disease

Huntington’s disease

Creutzfeldt-Jakob disease

Many other degenerative and neurodegenerative disorders

164
Q

What are ligands?

A

The signaling molecule sent out by cells that are talking

165
Q

What cells receive the ligand with a receptor?

A

Cells that are listening

166
Q

What does the ligand/receptor interaction do?

A

Conveys information across the membrane into the cell

167
Q

What is autocrine signaling?

A

Cell signaling to itself

168
Q

What are examples of autocrine signaling?

A

Immune cells: respond to wounds and infections by producing ligands that stimulate their own activation (amplifies the immune response)

Cancer cells: produce ligands that stimulate their own growth and mobility (contributes to tumor growth and metastasis)

169
Q

What is direct cell-cell contact?

A

Communicate via gap junctions or surface receptors

170
Q

What are examples of direct cell-cell contact?

A

Cell-cell interactions play a critical role during embryonic development, wound healing and the maintenance/repair of organs, muscles and other tissues of the body

171
Q

What is paracrine signaling?

A

Cell signaling to nearby cells

172
Q

What are examples of paracrine signaling?

A

Eicosanoids: signaling molecules secreted by cells that stimulate a variety of responses in their target cells, including the inflammation at sites of injury and smooth-muscle contractions

173
Q

What is endocrine signaling?

A

Systemic signaling via the circulatory system

174
Q

What are examples of endocrine signaling?

A

Hormones: produced by the gonads of males and females; stimulate development and maintenance of the reproductive system and secondary sexual characteristics

175
Q

What is synaptic signaling?

A

Similar to paracrine, but there is a synapse between the signaling nerve cell, and the cell receiving the signal

176
Q

What are examples of synaptic signaling?

A

Neurotransmitters: signaling molecules sent between a neuron and another neuron or a muscle that is controlled by neural activity

177
Q

Can ligands be hydrophobic or hydrophilic?

A

They can be both!

178
Q

Are cytoplasmic receptors intercellular or intracellular?

A

Intracellular

179
Q

What do hydrophobic ligands do?

A

Hydrophobic ligands such as hormones diffuse across the plasma membrane and bind to intracellular receptors

Intracellular receptors then transmit the signal to the nucleus causing a cellular response

180
Q

What can cytoplasmic hormone receptors double as?

A

Transcription factors

181
Q

What happens to receptors with no hormone?

A

They become inactive transcription factors

182
Q

How do hormones interact with their receptors?

A

Hormones bind to hormone receptors in the cytoplasm

Activated hormone receptor complex moves into the nucleus

Binds directly to enhancers, changes patterns of gene expression

183
Q

What happens with membrane receptors?

A

Signals cannot pass plasma membrane

Hydrophilic ligands bind to transmembrane receptors

Ligand-bound receptor transmit the sigmal across the membrane causing a cellular response

184
Q

What are ion channel-linked receptors that double as ion channels?

A

Found in nerve synpases; ligand binds and then ligand bonding opens an ion channel across the membrane

Allows ions such as Na+, K+, and Ca2+ to pass through the membrane in response to the binding of ligands

185
Q

What are enzymatic (catalytic) receptors?

A

Binding of an extracellular ligand causes enzymatic activity on the intracellular side of the receptor

Many growth factor receptors are catalytic receptors

Enzymatic receptors are usually kinases (enzymes that phosphorylate other proteins)

Example: Receptor Tyrosine Kinase (RTK): adds PO4 to amino acid tyrosine residues in proteins; can autophosphorylate (add PO4 to itself) and to other proteins

186
Q

What are kinase cascades?

A

When multiple kinases activate eachother in a particular order and ultimately alter the expression of genes

Ultimately, leads to the activation of transcription factors in the nucleus that alter gene expression

187
Q

G Protein-Coupled Receptors (GPCRs)?

A

Receprots that interact with a G protein

G proteins bind GTP and hydrolyze it to GDP

The G protein is active when bound to GTP, inactive after it hydrolyzes the GTP to GDP

When bound to a ligand, GPCRs activate G proteins by helping them exchange GDP for a new GTP

Important in many signaling pathways; effector proteins produce second messenger molecules that mediate the cellular responses

188
Q

What are 2nd messengers?

A

Ligand (1st messenger) interacts with GPCRs, leads to the activation of an effector molecule that produces a 2nd messenger

Short-lived intracellular signaling molecules

Elevated concentration of second messenger leads to rapid alteration in the activity of one or more cellula enzymes

Removal or degradation of second messenger terminate the cellular response

189
Q

What are common 2nd messengers?

A

Inositol triphosphate (IP3): binds channel-linked receptor in the ER; causes release of intracellular ions and important for muscle function

cAMP made from ATP: involved in the activation of protein kinases. In addition, cAMP binds to and regulates the function of ion channels

190
Q

What are agonists?

A

Pharmaceuticals that mimic action of ligand (activate receptor)

191
Q

What are antagonists?

A

Pharmaceuticals that bind to but do not activate a receptor

192
Q

Which drugs are commonly abused?

A

Drugs that activate the opioid receptor (GPCR)

193
Q

What is Naloxone/Narcan?

A

Opiate receptor antagonist

Outcompetes agonists from binding to the opioid receptor

No agonistic activity (does not activate receptor)

Administered intravenously, intramuscularly blocks the effects of drugs such as heroine

194
Q

What are epigenetic modifications?

A

Change gene expression without changing the DNA sequence; may be heritable; can change how strongly DNA and histones bind together

195
Q

How do classic epigenetic modifications work?

A

By changing chromatin structure

196
Q

What is chromatin?

A

DNA associated with histone proteins

197
Q

What is a nucleosome?

A

146 bp of DNA wrapped around 8 histone proteins

198
Q

What are the two types of chromatin in the cell?

A

Euchromatin and heterochromatin

199
Q

What is euchromatin?

A

DNA and histones are loosely associated and DNA is available to transcription factors; can be expressed

200
Q

What is heterochromatin?

A

DNA and histones are tightly associated and DNA is not accessible to transcription factors; cannot be expressed

201
Q

What is chromatin remodeling?

A

Changing chromatin state between euchromatin and heterochromatin

202
Q

What is the makeup of histone proteins?

A

Have amino terminal tails that extend out from the nucleosome core

203
Q

What is histone acetylation?

A

Changes the positively charged lysine residues to negatively charged lysine residues

This change in histone charge reduces how tightly DNA binds to the histones; provides a more euchromatin structure for transcription factors

Involves the attachment of acetyl groups to lysine residues in the N-terminal tails of histones

204
Q

What two types of enzymes control histone association

A

HATs and HDACs

205
Q

What are Histone Acetyl Transferases (HATs)?

A

Carry out histone acetylation

206
Q

What is hyperacetylation?

A

(histones more - charged)=relaxed chromatin, gene transcription is active

207
Q

What are Histone Deacetylases (HDACs)?

A

Carry out histone deacetylation

208
Q

What is hypoacetylation?

A

(histones more + charged)=closed chromatin, gene transcription is inhibited

209
Q

What is DNA Methylation?

A

Methyl group is added to cytosine in DNA to form 5-methylcytosine

210
Q

In DNA Methylation, what does the methyl group do?

A

Interferes with transcription factor binding to DNA (inhibits gene transcription)

211
Q

What carries out cytosine methylation?

A

DNA Methyl Transferases (DNMTs)

212
Q

What carries out cytosine demethylation?

A

DNA Demethylases

213
Q

Where does DNA methylation occur?

A

Cytosines that are followed by a guanine (5’ CG 3’)

214
Q

What are CpG islands?

A

CG-rich regions of DNA sequence within genes; C phosphodiester bonded to G

215
Q

Where are CpG islands located?

A

Around the promoter and enhancer regions of genes

216
Q

Different cell types have different methylation patterns which contribute to what?

A

The differences in gene expression in different cell types

217
Q

What combines to remodel chromatin and affect gene transcription

A

Histone acetylation/deacetylation and DNA methylation/demethylation

218
Q

What increases secretion of dopamine in the brain area affecting wants and desires and increases drug-seeking behavior?

A

Drug-altered methylation

219
Q

What is genomic imprinting?

A

Specific example of gene methylation that is inherited by the offspring

220
Q

Genes that are paternally imprinted are only expressed on which chromosome?

A

Maternal chromosomes

221
Q

Genes that are maternally imprinted are expressed on which chromosome?

A

Paternal chromosomes

222
Q

What is parental conflict theory?

A

Genes that promote growth: paternally-expressed

Mutants show growth retardation

Genes that supress growth: maternally-expressed

Mutants have enhanced growth

Some imprinted genes affect the behavior of offspring

223
Q

What are other imprinting effects?

A

Early-life stresses can imprint the stress response of an organism into the offspring; results in increased reactivity of the hypothalamus-pituitary-adrenal axis (HPA axis)

Prenatal and early-life stress can cause offspring to suffer from chronic stress, anxiety, and depression through altered imprinting of genes critical to controlling the stress response

224
Q

What are the generational effects of early prenatal care?

A

Rats raised by attentive mothers were, as adults, able to deal with stress better than rats raised by negligent mothers

Levels of a receptor that regulates the reaction to stress hormones (glucocorticoids), were different in these two groups

A mother rat’s level of maternal care leads to altered methylation patterns in the brains of rat pups

Methylation changes lead to the gene for the glucocorticoid receptor more accessible to transcription factos (excess expression)

Biology 111 (8 decks)

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