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1

Cells acquire nucleotides through two processes:

de novo synthesis and
salvage pathways.

2

De novo synthesis of purines results in the synthesis of

inosine that can be
converted into adenosine and guanosine.

3

Atoms in a newly synthesized purine are derived from

several sources
including the amino acids aspartate, glutamine and glycine, methyl groups
supplied by folic acid and carbon dioxide.

4

ADP and GDP regulate de novo synthesis of

purines at multiple points in the
pathway.

5

Hypoxanthine and guanine can be recycled through

the salvage pathway
with Hypoxanthine guanine phosphoribosyl transferase (HGPRT).

6

Xanthine oxidase catalyzes a

hydroxylase type reaction leading to the
formation of uric acid that can be excreted.

7

Excess uric acid is the cause of

gout

8

Gout is most often caused by

low levels of secretion of uric acid, but can
also be caused by excess production.

9

Crystallization of Sodium urate in the joints leads to

a localized inflammatory
response.

10

Allopurinol, a purine analog, is used to treat

gout. It inhibits Xanthine
oxidase preventing the formation of uric acid.

11

A HGPRT deficiency causes

Lesch-Nyhan syndrome that results in severe
retardation, crippling gouty arthritis and self-mutilation.

12

Lesch-Nyhan occurs in males only because

the HGPRT gene is located on
the X chromosome.

13

The breakdown of purines can replenish TCA cycle intermediates through

the production of fumarate.

14

The atoms in a pyrimidine ring are derived from

aspartate and carbamoyl
phosphate.

15

The first 3 enzymes in the synthesis of pyrimidines are

located on the same
protein (CAD protein).

16

The pyrimidines U and C can be

interconverted

17

dUMP is converted to TMP by

thymidylate synthase, an enzyme requiring
the transfer of a methyl group from tetrahydrofolate.

18

Inhibitors of tetrahydrofolate production are used as

as therapeutic agents for
treating cancer and bacterial infections.

19

Fluro substituted pyrimidine analogs that inhibit thymidylate synthase are

used as anticancer agents.

20

Ribonucleotide reductase converts

ribonucleotides to deoxyribonucleotides

21

Base-pairing in DNA is

A-T and G-C. In RNA it’s A-U and G-C.

22

Homologous regions of DNA can be compared among different species to
determine

phylogenetic relationships

23

Closely related organisms contain

similar DNA compliments, however they
are often arranged differently on the chromosomes of each species

24

The living world is made up of 3 divisions, or domains

: bacteria, archaea and
eukaryotes.

25

There are 4 main processes for generating change in a genome

intragenic
mutation (single base change), gene duplication, DNA segment shuffling,
horizontal transfer (from one cell to another).

26

Bacterial genes are usually clustered into groups (operons) that are

transcribed as a single unit.

27

Eukaryotic genes are often broken up with regions of

noncoding DNA or
introns between regions of coding DNA (exons).

28

In a comparison of the same gene in several closely related species,

exons will generally be very similar (conserved), while the introns will vary in
size and content.

29

Bacterial chromosomes are densely packed with genes leaving very little

DNA that is non-coding.

30

Most of the DNA in higher eukaryotes including humans does not code for

proteins. Most of the human genome is made up of repeated sequences. Many of those sequences are mobile elements that can move around in the genome.

31

Bacterial chromosomes are

circular and eukaryotic chromosomes are linear

32

In addition to the human genome, the entire genomes of a
large number organisms have been completed including several bacteria that
are found in the oral cavity.

a

33

It is possible to construct metabolic pathways and compare them with other
organisms by examining their

entire genome content

34

Genes can be grouped into families bases on similar (homologous)
sequences found in different organisms. Homologous sequences can be
found in

genes of the same organism that carry out different but similar
functions. Genes that have similar functions in very distantly related
organisms can have similar sequences (homology).

35

The phylogenetic relationships of different organisms can be compared by

comparing the DNA sequence of similar genes in the two organisms.

36

DNA polymerase is a

a DNA dependent (uses DNA as a template) DNA
synthesizing enzyme.

37

RNA polymerase is a

DNA dependent RNA synthesizing enzyme.

38

Reverse transcriptase is an

RNA dependent DNA synthesizing enzyme

39

Primase is a

DNA dependent RNA polymerase.

40

Primase synthesizes a

small RNA “primer” that can be used by the DNA
polymerase to elongate the chain.

41

DNA polymerase minimizes the number of mistakes

by using a 3’ to 5’ exonuclease (or proofreading) activity that is
part of the same protein.

42

DNA polymerase as well as all other nucleic acid polymerases synthesize
DNA in the

5’ to 3’ direction only.

43

During replication, each new nucleotide is added to the

3’ carbon on the last
nucleotide of the new DNA chain.

44

The base component of each nucleotide is connected to the sugar at the 1’
carbon. The adjacent nucleotides in a DNA chain are

attached at the 5’ and
3’ carbons. And the 2’ carbon differs between RNA and DNA. (see figure
below, you should be able to recognize each carbon from the figure)

45

DNA polymerase is an

elongating enzyme; it cannot initiate synthesis.
Therefore a primer is required for elongation of a new stand using the DNA
polymerase.

46

Bacterial chromosomes contain

one origin of replication

47

DNA synthesis proceeds in both directions away from the

origin until the two
replication forks meet at a specific sequence on the other side of the
chromosome.

48

In bacteria new rounds of DNA replication can begin

before the previous
round is completed.

49

Eukaryotic chromosomes contain many

origins of replication that may change
during the development of the organism.

50

In eukaryotes, each entire chromosome is replicated only

once each cell
division and new rounds of replication do not start until after the cell divides.

51

Eukaryotic chromosomes are

linear and special structures called telomeres
are placed on each end.

52

Telomeres are constructed with the enzyme

telomerase that uses an RNA
template to synthesize a short repeated DNA sequence at the ends of
chromosomes.

53

Because the polymerase must synthesize new DNA in the 5’ to 3’ direction,
the two polymerase molecules on opposite strands move

away from each
other.

54

Helicase

unwinds (separates) the 2 DNA strands before polymerization of the
new strands.

55

Single-stranded binding proteins keep the

two complementary strands for
reforming a double helix.

56

The polymerase on the leading strand moves toward

the replication fork and
the polymerase on the lagging strand moves away from it.

57

The lagging strand is synthesized in short

Okizaki) fragments

58

Primase initiates synthesis of each

Okizaki fragment by making a short RNA
primer.

59

The leading strand is synthesized by the

continuous movement of the DNA
polymerase along the template.

60

Methylation of the DNA signals that the DNA is

unreplicated and is ready to
be used as a template for the next round of synthesis.

61

New or modified genes can be generated by one or a combination of 4
events:

1) point mutations in the coding region that change the amino acid
composition of the protein. 2) duplication of the entire gene. 3) Mixing of
segments of one gene with segments of another gene – segment shuffling. 4)
Acquisition of new activities by transfer of genes between two organisms –
horizontal gene transfer.

62

Many genes belong to gene families that share

homologous regions. These
regions usually code for proteins that carry out similar functions.

63

Breaks in the DNA (especially double stranded breaks) facilitate

the initiation
of recombination.

64

A defect in DNA ligase, that affects

joining together of adjacent segment of
DNA on a chromosome, can cause abnormal amounts of recombination.

65

Recombination is the

reciprocal exchange of genetic information

66

Recombination can be the result OF

1) reciprocal exchange during cell
division. 2) DNA damage, e.g. X-ray damage. 3) Introduction of foreign DNA.
4) Programmed recombination during the development or maturation of a cell
type, e.g. antibody producing genes during B-cell maturation.

67

Gene conversion is the

non-reciprocal exchange of genetic information.

68

Recombination between

direct repeated sequences on the same
chromosome causes the loss of DNA that was between the two repeated
segments.

69

Circular DNA can be inserted in a

chromosome by recombination between a
region on of circular molecule and an homologous region on the
chromosome. (The reverse of #53).

70

X-rays and other agents that cause breaks in DNA induce

recombination

71

Transposable elements are found in

all species from bacteria to human

72

Transposable elements move from one

location in the DNA to another
location within that cell.

73

Transposable elements can cause changes

in the DNA at the site of
insertion.

74

There are two major types of transposable elements

one type that contains
inverted repeated sequences at the ends and causes a short region of the
genome to be duplicated at the site of insertion and a second type that is
structurally similar to a retrovirus and transposes through an RNA
intermediate.

75

Unequal crossing-over is

recombination that resulted from imprecise pairing
of tandemly repeated sequences.

76

Unequal crossing over results in

the loss or gain of gene copies.

77

There are two types of mutations

DNA rearrangements and base
substitutions.

78

There are many mechanisms in each cell for repairing

DNA

79

Damage to a nucleotide (e.g. deamination) can either be

repaired or lead to a
permanent mutation.

80

Mutations can be caused by either

errors during replication or by injury to the
DNA from chemicals or radiation.

81

A small fraction of every genome (about 3% in humans) is made up of

segmental duplications or large regions of DNA that are present in more than
one copy.

82

The duplicated DNA is generated by a process called

gene amplification

83

Gene amplification can result in

resistance to drugs, transformation into
cancerous cells or other changes in the cell phenotype.

84

Several human diseases are due to

defects in DNA repair enzymes.

85

The differences between fat-soluble and water-soluble vitamins.

Vitamins are classified into two groups: water-soluble and fat-soluble. Water-soluble vitamins, which include all of the B vitamins, are easily absorbed into the body. If you consume more of a water-soluble vitamin than you need, the excess will be excreted, not stored.

86


Measurements of vitamin levels in the blood relate more to

recent intake than to overall body status.

87

Water-soluble vitamins act as

coenzymes in many metabolic pathways

88

The body has no storage capacity for water-soluble vitamins– except

B12

89

Evidence is emerging that suggests an excess of some

B vitamins can be toxic

90

Most vitamins are modified before

they become active

91

B Vitamins are

co-enzymes in different types of reactions:

B1 – carboxylations
B2/B3 – oxidoreductases
B6 – transaminases
Biotin – carboxylases
Folic acid/B12 – single carbon transfers

92

B1

carboxylations

93

B2/B3

oxidoreductases

94

B6

transaminases

95

Biotin

carboxylases

96

Folic acid/B12

Single carbon transfers

97

Lack of riboflavin causes

angular stomatitis

98

Eating raw egg whites can cause

Biotin deficiency

99

Folic acid is

needed, indirectly, for DNA synthesis

100

Inhibitors of folate reduction are used as

as antibiotics (trimethoprim) and cancer therapy (methotrexate).

101

There is an increased demand for

folic acid during pregnancy

102

Folic acid deficiency is one of the most

common vitamin deficiencies

103

The functions of

B12 and folic acid are interrelated

104

B12 is concentrated in the

liver

105

Vitamin C deficiency causes

scurvy resulting in defective collagen synthesis

106

Lack of vitamin C also

impairs immune function

107

Fat-soluble vitamins are not as readily

absorbed as water-soluble vitamins, but can be stored in tissues

108

Some fat-soluble vitamins

(A and D) can be toxic in excess

109

Vitamin A is

teratogenic and should be avoided during pregnancy

110

Retinoic acid is a

signaling molecule that interacts with ligand-activated transcription factors

111

Deficiency of vitamin A causes

Night blindness

112

Vitamin D regulates

calcium and phosphorous homeostasis

113

The majority of vitamin D is

produced by UV exposure of skin

114

3People in northern climates have a

difficult time getting sufficient vitamin D in the winter

115

Deficiency of vitamin D causes

demineralization of bones with increased susceptibility to fractures

116

Vitamin D deficiency is

linked to early childhood caries

117

Vitamin K is necessary for

blood coagulation

118

Know the structure of lactic acid

C3H6O3 (carbon, carbon-OH, carboxyl group)

119

1. There are close to 3 billion bases of the human genome, but only

1. 20,000-25,000 protein-coding genes.

120

1. Alternative splicing and alternative gene promoters result in

in 4-6 different mRNAs from a single gene.

121

1. Number of protein-coding mRNAs (transcriptome) may be as large as

100k

122

1. The original Human Genome Project used

'clone-by-clone' and ‘shotgun’ approaches for sequencing.

123

1. There are 250 gaps remaining in the Human genome

(compared to 150,000 in draft)

124

1. Since the completion of the human genome, sequencing capacity has

increased dramatically while costs have declined.

125

1. Online Mendelian Inheritance in Man (OMIM) database

has >10,000 entries that associate human genes with inherited diseases

126

1. SNPs or single nucleotide polymorphisms are

mapped base positions in the genome where the nucleotide varies among people.

127

1. Companies (e.g. 23 and me) are offering full

genome scans to individuals for less than $100. This analysis is based on SNP (single nucleotide polymorphism analysis).

128

Chromosomal Microarray Analysis (CMA):

Labeled DNA hybridized to array of several million oligonucleotide on chips. This can be used for prenatal screening for early detection of chromosomal defects.

129

1. Transcriptome =

complement of mRNAs, containing protein-coding sequences but there are also other RNAs produced that play structural or regulatory functions (miRNA, siRNA, etc.)

130

The transcriptome can be studied using

Microarrays, a collection of complementary (cDNA) made from mRNA or synthetic oligonucleotides arranged on a solid phase slide in a defined order

131

Generally, several oligonucleotide probes per

gene are used

132

Two samples can be compared by labeling each with a different

fluorescent dye and hybridizing them to the same array. (e.g. Two-color arrays can compare normal and cancer cells).

133

1. With advances in sequencing technology,

RNAseq or sequencing the entire compliment of RNA in a sample is rapidly replacing microarray approaches.

134

Data analysis is

bioinformatics intensive and requires stringent statistical analysis.

135

1. Proteomics is the study of

the protein complement of a cell.

136

1. Comparative proteomics is the analysis of

protein profiles from two or more samples (e.g., diseased vs. healthy cells) to identify quantitative differences that could be responsible for observed phenotypes.

137

1. Proteomics can identify

posttranslational modifications that cannot be detected by transcriptome analysis.

138

1. Proteins can be separated by

two dimensional polyacrylamide gel electrophoresis (PAGE) or by Liquid chromatography (FPLC, HPLC).

139

Proteins are id'd by

Mass spec.

140

Metabolomics is the

identification and quantification of steady-state levels of intracellular metabolites (sugars, amino acids, lipids, nucleotides etc.)

141

1. Because the technology to identify every metabolite in a biological sample is

not available, targeted metabolomics is often carried out, where a few specific metabolites are measured.

142

Definition of genetics

the study of heredity and the variation of inherited characteristics

143

Monohybrid Cross

A monohybrid cross is a mating between two individuals with different alleles at one genetic locus of interest. The character(s) being studied in a monohybrid cross are governed by two or multiple alleles for a single locus.

4 squares

144

Phenotype

the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.

145

Genotype

the genetic constitution of an individual organism.

146

F1 cross

Cross of two heterozygotes - 25:50:25

147

Unit factor

a gene; a sequence of nucleotides that functions as the hereditary unit for a single character.

148

Dominance/Recessiveness

Duh

149

Segregation

He discovered that the traits in the offspring of his crosses did not always match the traits in the parental plants. This meant that the pair of alleles encoding the traits in each parental plant had separated or segregated from one another during the formation of the reproductive cells.

150

Punnett Squares

Duh

151

Dihybrid cross

4x4 square- using 2 different alleles at once - 2 orgs crossed that differ in 2 diff traits.

152

Gene

the basic physical and functional unit of heredity.

153

Gene locus

A locus (plural loci) in genetics is the position of a gene on a chromosome. Each chromosome carries many genes; humans' estimated 'haploid' protein coding genes are 19,000-20,000, on the 23 different chromosomes. A variant of the similar DNA sequence located at a given locus is called an allele.

154

Allele

one of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome.

155

Homologue

A homologous gene (or homolog) is a gene inherited in two species by a common ancestor. While homologous genes can be similar in sequence, similar sequences are not necessarily homologous. Orthologous are homologous genes where a gene is found in two different species, but the origin of the gene is a common ancestor.

156

Divisions in Meiosis

Anaphase I = 2n to n, Anaphase II = n to n (mitosis like)

157

Independent assortment

the principle, originated by Gregor Mendel, stating that when two or more characteristics are inherited, individual hereditary factors assort independently during gamete production, giving different traits an equal opportunity of occurring together. Expand. Also called Mendel's second law, Mendel's law.

158

Incomplete dominance

(also called partial dominance or semi-dominance) occurs when the phenotype of the heterozygous phenotype is distinct from and often intermediate to the phenotypes of the homozygous phenotypes. For example, the snapdragon flower color is either homozygous for red or white. Heterozygotes are pink.

159

Co-dominance

A genetic scenario where neither allele is dominant or recessive and both get expressed is known as codominance (spots on flowers)

160

Polymorphism

A gene is said to be polymorphic if more than one allele occupies that gene’s locus within a population.[1] For example in dogs the E locus, which controls coat pattern, can have any of five different alleles, known as E, Em, Eg, Eh, and e.[2

161

Epistasis

the interaction of genes that are not alleles, in particular the suppression of the effect of one such gene by another.

162

Lethal Allele

Duh.

163

Sex linkage

Sex linkage is the phenotypic expression of an allele that is dependent on the gender of the individual and is directly tied to the sex chromosomes. In such cases there is a homogametic sex and a heterogametic sex.

164

Crossover

Chromosomal crossover. Crossing over occurs between prophase 1 and metaphase 1 and is the process where homologous chromosomes pair up with each other and exchange different segments of their genetic material to form recombinant chromosomes.

165

Penetrance

Penetrance in genetics is the proportion of individuals carrying a particular variant of a gene (allele or genotype) that also expresses an associated trait (phenotype). In medical genetics, the penetrance of a disease-causing mutation is the proportion of individuals with the mutation who exhibit clinical symptoms.

166

Restriction enzymes

an enzyme produced chiefly by certain bacteria, having the property of cleaving DNA molecules at or near a specific sequence of bases.

167

Blunt end vs. adhesive end

Duh

168

End –labeling

There are two ways to label a DNA molecular; by the ends or all along the molecule. End labeling can be performed at the 3'- or 5'-end. Labeling at the 3' end is performed by filling 3'-end recessed ends with a mixture or labeled and unlabeled dNTPs using Klenow or T4 DNA polymerases. Both reactions are template dependent. Terminal deoxynucleotide transferase incorporates dNTPs at the 3' end of any kind of DNA molecule or RNA. Labels incorporated at the 3'-end of the DNA molecule prevent any further extension or ligation to any other molecule, but this can be overcome by labeling the 5'-end of the desired DNA molecule. 5'-end labeling is performed by enzymatic methods (T4 polynucleotide kinase exchange and forward reactions), by chemical modification of sensitized oligonucleotides with phosphoroamidite, or by combined methods. Probe cleanup is recommended when high background problems occur, but caution should be taken not to damage the attached probe with harsh chemicals or by light exposure.

169

In situ hybridization

In situ hybridization (ISH) is a type of hybridization that uses a labeled complementary DNA, RNA or modified nucleic acids strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ), or, if the tissue is small enough (e.g., plant seeds, Drosophila embryos), in the entire tissue (whole mount ISH), in cells, and in circulating tumor cells (CTCs). This is distinct from immunohistochemistry, which usually localizes proteins in tissue sections.

170

Insertion of DNA into a bacterial plasmid

Duh

171

Plasmid

a genetic structure in a cell that can replicate independently of the chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium or protozoan. Plasmids are much used in the laboratory manipulation of genes.

172

Ligase

an enzyme that brings about ligation of DNA or another substance.

173

Genomic DNA library

A genomic library is a collection of the total genomic DNA from a single organism.

174

Synthesis of cDNA

complementary DNA (cDNA) is double-stranded DNA synthesized from a single stranded RNA (e.g., messenger RNA (mRNA) or microRNA (microRNA)) template in a reaction catalysed by the enzyme reverse transcriptase. cDNA is often used to clone eukaryotic genes in prokaryotes.

175

DNA foot printing

DNA footprinting is a method of investigating the sequence specificity of DNA-binding proteins in vitro. This technique can be used to study protein-DNA interactions both outside and within cells.

176

Site-directed mutagenesis

The basic procedure requires the synthesis of a short DNA primer. This synthetic primer contains the desired mutation and is complementary to the template DNA around the mutation site so it can hybridize with the DNA in the gene of interest. The mutation may be a single base change (a point mutation), multiple base changes, deletion, or insertion. The single-strand primer is then extended using a DNA polymerase, which copies the rest of the gene. The gene thus copied contains the mutated site, and is then introduced into a host cell as a vector and cloned. Finally, mutants are selected by DNA sequencing to check that they contain the desired mutation.

The original method using single-primer extension was inefficient due to a low yield of mutants. This resulting mixture contains both the original unmutated template as well as the mutant strand, producing a mixed population of mutant and non-mutant progenies. Furthermore, the template used is methylated while the mutant strand is unmethylated, and the mutants may be counter-selected due to presence of mismatch repair system that favors the methylated template DNA, resulting in fewer mutants. Many approaches have since been developed to improve the efficiency of mutagenesis.

177

Gene targeting

a genetic technique that uses homologous recombination to change an endogenous gene. The method can be used to delete a gene, remove exons, add a gene, and introduce point mutations. Gene targeting can be permanent or conditional.

178

Three phases of transcription

1. Initiation:
RNA polymerase binds to DNA at a specific sequence of nucleotides called the promoter.
The promoter contains an initiation site where transcription of the gene begins.
RNA polymerase than unwinds DNA at the beginning of the gene.
2.Elongation:
Only one of the unmound DNA strands acts as a template for the RNA synthesis.
RNA polymerase can only add nucleotids to the 3' end of the strand so like DNA, RNA must be synthesized in the 5' to 3' direction.
Free ribonucleotides triphosphates from the cytoplasm are paired up with their commplementary base on the exposed DNA template.
RNA polymerase joins the ribonucleoside triphosphates to form an mRNA strand.
As RNA polymerase advances, the process continues.
The DNA that has been transcribed, re-winds to form a double helix.
Termination:
RNA polymerase continues to elongate until it reaches the terminator, a specific sequence of nucleotides that signals the end of transcription.
Transcription stops and mRNA polymerase and the new mRNA transcript are released from DNA.
The DNA double helix reforms.
The termination sequence usually consists of a series of adjancent adenines preceded by a nucleotide palindrome.
This gives an RNA molecule that assumes a stem-and loop configuration.
This configuration stops RNA polymerase from transcribing any further.

179

Promoter

In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 5' region of the sense strand).

180

Template vs. coding strand of DNA

The term template strand refers to the sequence of DNA that is copied during the synthesis of mRNA.
Coding is the other strand.

181

Function of Sigma factor

A sigma factor (σ factor) is a protein needed only for initiation of RNA synthesis. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters.

182

Consensus regions in a promoter

For example, many transcription factors recognize particular patterns in the promoters of the genes they regulate. In the same way restriction enzymes usually have palindromic consensus sequences, usually corresponding to the site where they cut the DNA

183

Structure of transcription termination in prokaryotes

Rho-dependent terminators: RNA helicase like activity that disrupt transcriptional complex.
Rho-independent terminators: Rho-independent terminators require the formation of a self-annealing hairpin structure on the elongating transcript, which results in the disruption of the mRNA-DNA-RNA polymerase ternary complex.

184

Polycistronic vs Monocistronic transcription

An mRNA molecule is said to be monocistronic when it contains the genetic information to translate only a single protein. This is the case for most of the eukaryotic mRNAs.[5][6] On the other hand, polycistronic mRNA carries the information of several genes, which are translated into several proteins. These proteins usually have a related function and are grouped and regulated together in an operon. Most of the mRNA found in bacteria and archea are polycistronic

185

Operon

a functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter.[1]

186

Repressor

a repressor is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers

187

Operator

a segment of DNA to which a transcription factor binds to regulate gene expression. The transcription factor is a repressor, which can bind to the operator to prevent transcription. The main operator (O2) in the classically defined lac operon is located slightly downstream of the promoter.

188

Regulation of lac operon

Review lac operon function***

189

Components of chromatin

DNA + histone = chromatin definition: The DNA double helix in the cell nucleus is packaged by special proteins termed histones. The formed protein/DNA complex is called chromatin. The basic structural unit of chromatin is the nucleosome.

190

Heterochromatin

chromosome material of different density from normal (usually greater), in which the activity of the genes is modified or suppressed.

191

euchromatin

Euchromatin is a lightly packed form of chromatin (DNA, RNA and protein) that is enriched in genes, and is often (but not always) under active transcription.

192

Transcriptional regulation by chromatin modification

Duh.

193

Which polymerase transcribes mRNA?

RNA pol II

194

General transcription factor

a class of protein transcription factors that bind to specific sites (promoter) on DNA to activate transcription of genetic information from DNA to messenger RNA.

195

Location of enhancers

Far or near depending on DNA folding/coiling (Silencers are the same way) - can be upstream or downstream.
Enhancers do not act on the promoter region itself, but are bound by activator proteins

196

Function of insulator

An insulator is a genetic boundary element that blocks the interaction between enhancers and promoters. It is thought that an insulator must reside between the enhancer and promoter to inhibit their subsequent interactions. Insulators therefore determine the set of genes an enhancer can influence.

197

DNA binding domain

an independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA. A DBD can recognize a specific DNA sequence (a recognition sequence) or have a general affinity to DNA.

198

RNA processing

5' cap: involves the addition of 7-methylguanosine (m7G) to the 5' end.

3' Processing: The pre-mRNA processing at the 3' end of the RNA molecule involves cleavage of its 3' end and then the addition of about 250 adenine residues to form a poly(A) tail. Polyadenylation signal near end of mRNA initiates this.

RNA splicing: removal of introns, rearrangement of exons
Histone processing as well.

199

Intercellular vs. intracellular signaling

Intercellular: Cell junction allows signaling molecules to pass from one cell to another.

Intracellular: Most receptors are on the plasma membrane but some are inside the cell.

Estrogen example
*Passes through membrane and binds to receptor in
nucleus.
*Dimer of estrogen-receptor complexes binds to DNA to
activate transcription of specific genes. (transcription
factors regulate transcription of specific genes)

200

Functions of intercellular signaling

For several types of intercellular signaling molecules that are unable to permeate the hydrophobic cell membrane due to their hydrophilic nature, the target receptor is expressed on the membrane. When such signaling molecule activates its receptor, the signal is carried into the cell usually by means of a second messenger such as cAMP.


*** look into this one***

201

Locations of receptors

Intracellular receptors are located in the cytoplasm of the cell and are activated by hydrophobic ligand molecules that can pass through the plasma membrane. Cell-surface receptors bind to an external ligand molecule and convert an extracellular signal into an intracellular signal.

202

Different forms of intercellular signaling


Intracrine signals are produced by the target cell that stay within the target cell. (intracellular***)
Autocrine signals are produced by the target cell, are secreted, and affect the target cell itself via receptors. Sometimes autocrine cells can target cells close by if they are the same type of cell as the emitting cell. An example of this are immune cells.
Juxtacrine signals target adjacent (touching) cells. These signals are transmitted along cell membranes via protein or lipid components integral to the membrane and are capable of affecting either the emitting cell or cells immediately adjacent.
Paracrine signals target cells in the vicinity of the emitting cell. Neurotransmitters represent an example.
Endocrine signals target distant cells. Endocrine cells produce hormones that travel through the blood to reach all parts of the body.

203

Can one signaling molecule perform multiple functions?

yes.

204

How signaling occurs through cascade of intermediate signaling complexes

*** look this up***

205

Type of ligands interact with intracellular receptors

*** look this up***

206

Ionotropic receptors

Ionotropic receptors form an ion channel pore.

207

Metabotropic receptors

metabotropic receptors are indirectly linked with ion channels on the plasma membrane of the cell through signal transduction mechanisms, often G proteins. Hence, G protein-coupled receptors are inherently metabotropic.

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Receptor inactivation

removal of the ligand by degradation or sequestration, and desensitization of the target cell.

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G-protein coupled receptors

sense molecules outside the cell and activate interior signal transduction pathways and, ultimately, cellular responses

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Dissociation of G-protein subunits

GTP binding changes the conformation of switch regions within the alpha subunit, which allows the bound trimeric G protein (inactive) to be released from the receptor, and to dissociate into active alpha subunit (GTP-bound) and beta/gamma dimer.

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Review how G-proteins really work

***

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The cyclic AMP cascade

*** review this

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protein kinase A (PKA)

vated only when cAMP is present. Hormones such as glucagon and epinephrine begin the activation cascade (that triggers protein kinase A) by binding to a G protein–coupled receptor (GPCR) on the target cell. When a GPCR is activated by its extracellular ligand, a conformational change is induced in the receptor that is transmitted to an attached intracellular heterotrimeric G protein complex by protein domain dynamics. The Gs alpha subunit of the stimulated G protein complex exchanges GDP for GTP and is released from the complex. The activated Gs alpha subunit binds to and activates an enzyme called adenylyl cyclase, which, in turn, catalyzes the conversion of ATP into cyclic adenosine monophosphate (cAMP) – increasing cAMP levels. Four cAMP molecules are required to activate a single PKA enzyme. This is done by two cAMP molecules binding to each of the two cAMP binding sites (CNB-B and CNB-A) which produces a conformational change in the regulatory subunits on a PKA enzyme causing the subunits to detach exposing the two (now activated) catalytic subunits.[2] Next the catalytic subunits can go on to phosphorylate other proteins.[3]

Below is a list of the steps involved in PKA activation:

Cytosolic cAMP increases
Two cAMP molecules bind to each PKA regulatory subunit
The regulatory subunits move out of the active sites of the catalytic subunits and the R2C2 complex dissociates
The free catalytic subunits interact with proteins to phosphorylate Ser or Thr residues.

Protein kinase A has several functions in the cell, including regulation of glycogen, sugar, and lipid metabolism.

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IP3 and DAG (also Ca++)

Inositol triphosphate (IP3) and diacylglycerol (DAG) are important second messengers. Their formation begins with the binding of an extracellular regulatory molecule to a membrane receptor that activates a trimeric G protein. The alpha subunit of this G protein then activates phospholipase C, which acts on a membrane phospholipid. (What other membrane phospholipase have we discussed this quarter?)

Acting on a membrane phospholipid, phospholipase C cleaves off IP3, which is a small polar molecule. Remaining in the membrane is the DAG, which consists of glycerol and two fatty acids

The IP3 diffuses to the endoplasmic reticulum, which stores Ca++. The IP3 binds to and opens a ligand gated ion channel that allows Ca++ to move out into the cytosol, where the Ca++ activates various cellular processes. This is discussed further under calmodulin page. (Note that in muscle, the Ca++ is stored in the sarcoplasmic reticulum.)

Meanwhile, the DAG in the membrane activates protein kinase C, which in turn activates proteins inside the cell by phosphorylation.

Thus the initial binding of the extracellular regulatory molecule to the membrane receptor turns on an integrated repertoire of cellular events.

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Enzyme-linked receptors

An enzyme-linked receptor, also known as a catalytic receptor, is a transmembrane receptor, where the binding of an extracellular ligand causes enzymatic activity on the intracellular side.

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Receptor dimerization

The principle underlying signal transduction by a tyrosine kinase receptor is that ligand binding to the extracellular domain triggers dimerization; this causes a conformational change in the cytoplasmic domain that activates the tyrosine kinase catalytic activity.

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Ras

When Ras is 'switched on' by incoming signals, it subsequently switches on other proteins, which ultimately turn on genes involved in cell growth, differentiation and survival. Mutations in ras genes can lead to the production of permanently activated Ras proteins. As a result, this can cause unintended and overactive signaling inside the cell, even in the absence of incoming signals.

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The phosphorylation cascade

A phosphorylation cascade is a sequence of events where one enzyme phosphorylates another, causing a chain reaction leading to the phosphorylation of thousands of proteins. This can be seen in signal transduction of hormone messages.

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NF-kB pathway

** look this up**

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Start codon

The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and a modified Met (fMet) in prokaryotes. The most common start codon is AUG. The start codon is often preceded by a 5' untranslated region (5' UTR).

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Reading frame

In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons.

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Structure of transfer RNA

Transfer RNA (tRNA) have a primary, secondary, and tertiary (L-shaped) structure. tRNA bonds to activated amino acids and transfers them to the ribosomes. Once at the ribosome, an initiator tRNA binds the amino acid to the ribosome to start translation.

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Aminoacyl-tRNA

Aminoacyl-tRNA (also aa-tRNA or charged tRNA) is tRNA to which its cognated amino acid is chemically bonded (charged). The aa-tRNA, along with some elongation factors, deliver the amino acid to the ribosome for incorporation into the polypeptide chain that is being produced.

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Ribosome domains

50S includes the activity that catalyzes peptide bond formation (peptidyl transfer reaction), prevents premature polypeptide hydrolysis, provides a binding site for the G-protein factors (assists initiation, elongation, and termination), and helps protein folding after synthesis.

30S subunit is the site of inhibition for antibiotics such as tetracycline and aminoglycosides.

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Stop codon

UAG
UAA
UGA

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Function of proteasome

The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. In eukaryotes, proteasomes are located in the nucleus and the cytoplasm.

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Ubiquitin

a compound found in living cells that plays a role in the degradation of defective and superfluous proteins. It is a single-chain polypeptide.