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Exam 1 Notes > The Cell > Flashcards

The Cell Flashcards

1
Q

What are the three major classes of lipids that make up the plasma membrane?

A

Phospholipids, cholesterol, and glycolipids.

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2
Q

What are the two major classes of proteins that make up the plasma membrane?

A

Integral-embedded in or pass through the lipid bilayer

Peripheral-associate noncovalently with the membrane proteins. Basically just chill on the surface of the bilayer.

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3
Q

What does cholesterol do in the plasma membrane?

A

Intercalates (gets between} phospholipids in order to reduce membrane fluidity.

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4
Q

Glycolipids

A

Contain sugar. Found exclusively in the outer monolayer and help with cell recognition, self v non self, etc.

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5
Q

What are the 6 general categories of integral membrane proteins?

A

1) Pumps/carriers/transporters (transport ions or metabolic precursors)
2) Channels (passive defusion, etc)
3) Receptors
4) Linkers (anchor proteins)
5) Enzymes
6) Structural proteins (hold cells together)

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6
Q

What are the three types of endocytosis?

A

Receptor medicated, pinocytosis, and phagocytosis.

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7
Q

Regulated vs. constitutive exocytosis

A

Regulated is in response to a stimulus and constitutive is a substance that is continuously delivered to the plasma membrane for export.

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8
Q

Receptor Mediated Endocytosis

A

Selective uptake of large molecules, depends on Cathrin to make a Cathrin coated pit which drives the vehicle formations. Then dynamin causes the visible to pinch off from the plasma membrane.

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9
Q

Endosomes

A

Membrane enclosed structure associated with the Endocytosic pathway

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10
Q

Early endosome

A

Functions to sort and recycle proteins

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11
Q

Late endosome

A

Receives proteins for degradation and matures into a lysosome with help from the Golgi (Golgi gives it lysosomal enzymes).

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12
Q

Pinocytosis

A

Cell drinking, non specific ingestion of small vesicles. Constitutive, clathrin independent, found a lot in smooth muscle.

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13
Q

Phagocytosis

A

Ingestion of large particles, generally performed by specialized phagocytes, dependent on action and independent of clathrin.

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14
Q

Glycocalyx

A

Carbohydrate rich zone on the cell surface (sugar coating) that helps to establish the micro environment of the cell surface. It provides protection from mechanical and chemical damage, cell recognition, and cell to cell interactions. Made up of glycolipids attached to a glycoprotein.

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15
Q

Neoplasm

A

New growth, usually a tumor, abnormal mass of cells

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16
Q

What are some characteristics of malignant neoplasms?

A

Grow rapidly and may invade invade other areas, ignore restraints on cell division, unregulated growth

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17
Q

How are malignant neoplasms classified?

A

Based on the cell type from which they originate, usually the epithelium or connective tissue

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18
Q

Carcinoma

A

Malignant tumor of the epithelium

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19
Q

Sarcoma

A

Malignant tumor growing from connective tissue

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20
Q

Leukemia

A

Cancer of the blood/bone marrow

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21
Q

Sarcoma

A

Naming used for connective tissue tumors

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22
Q

Metastasis

A

When tumors are invasive and can spread into other tissues

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23
Q

Why are carcinomas so prevalent?

A

The epithelial tissue covers a lot of area and is constantly reproducing so there is greater chance of it mutating. It is also frequently exposed to physical and chemical damage.

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24
Q

Clonal Evolution theory

A

idea that tumors develop through repeated rounds of mutation and proliferation and eventually take over neighbor cells

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25
Q

Stem Cell Theory

A

Tumors contain their own set of stem cells so they can reproduce indefinitely and can’t truly be killed

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26
Q

karyotype

A

Chart showing the organization of chromosomes according to size, shape, and fluorescent colors

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27
Q

Necrosis

A

Cell death is a pathological and chaotic way in which the cell swells, bursts, and spills its member and everywhere

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28
Q

Apoptosis

A

Programmed cell death, orderly, normal, cells shrinks and maintains membrane

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29
Q

What is the central dogma of molecular biology?

A

DNA–>RNA–>Protein

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30
Q

What are the monomeric units that make up the DNA polymer?

A

Nitrogenous base, pentose sugar, and phosphoric acid group

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31
Q

Ribose

A

Hydroxyl group attached to the 2’ carbon

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32
Q

Deoxyribose

A

The hydroxyl group attached to the 2’ carbon in ribose is replaced by a hydrogen group

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33
Q

Nucleosides

A

Nitrogenous base and a ribose or deoxyribose sugar

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34
Q

Nucleotides

A

Nitrogenous base, sugar, and a phosphate group

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35
Q

Phosphodiester Bond

A

Bond between the 3’ OH group of the sugar and the 5’ phosphate on the nucleoside triphosphate

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36
Q

How many bonds are between C and G?

A

3

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37
Q

B-DNA

A

Basis of Watson and Crock model. Right hand helix

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38
Q

Z-DNA

A

Left hand helix, found in sequences where pyrimidines and purines alternate

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39
Q

A-DNA

A

Right hand sequence of dehydrated DNA, very compact

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40
Q

Primary Structure

A

Sequence of nucleotides (AGTACA)

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41
Q

Secondary Structure

A

3-D structure-double helix of DNA

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42
Q

Tertiary Structure

A

Supercoiling of secondary structure

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43
Q

Quarternary Structure

A

Interaction of nucleic acids with proteins (DNA wrapped around a histone)

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44
Q

mRNA

A

Single stranded, carries codon information for translation

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45
Q

tRNA

A

Folded stem loop system that carries amino acid to ribosome

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46
Q

rRNA

A

Linear, single stranded, folded molecule, helps form ribosome

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47
Q

snRNA

A

Small nuclear RNA that is involved in generation of mature mRNA transcripts and are an essential part of splicing

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48
Q

miRNA

A

Micro RNA is responsible for the regulation of gene expression and can either silence of express mRNAs

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49
Q

Negative Supercoiling

A

Promotes strand separation (good for DNA Replication) . Introduced behind the protein.

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50
Q

Positive Supercoiling

A

Unwanted side effect of negative super coiling and must be corrected so DNA can be separated. Introduced ahead of the protein.

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51
Q

What is the function of topoisomerase I?

A

Forms a single covalent bong with DNA, breaking phosphodiester bonds, allowing the DNA to rotate and relieve stress from supercoiling

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52
Q

What is the function of topoisomerase II?

A

Topoisomerase II (DNA grade in bacteria) is activated when two double helices cross over each other. It bonds to both ends of the strand, breaking the backbone, and allowing the second DNA helix is pass through the first. Requires ATP

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53
Q

Chromatin

A

Complex of DNA and chromosomal proteins

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54
Q

What are the 5 major types of histones?

A

H1, H2A, H2B, H3, and H4

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55
Q

Nucleosome Structure

A

Core of histones (2 molecules of each type) around which DNA is wrapped, and linker DNA

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56
Q

Euchromatin

A

Decondensed and transcriptionally active

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57
Q

heterochromatin

A

Condensed and transcriptionally inactive

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58
Q

How does chromatin form?

A

DNA methylation occurs which tags a region of the genome for his tone modification that causes the formation of heterochromatin (by deacetlyting) The acetylation removes the positive charge and reduces the affinity between histones and DNA which increases transcription.

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59
Q

What is the central dogma of molecular biology?

A

DNA–>RNA–>Protein

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60
Q

What are the monomeric units that make up the DNA polymer?

A

Nitrogenous base, pentose sugar, and phosphoric acid group

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61
Q

Ribose

A

Hydroxyl group attached to the 2’ carbon

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62
Q

Deoxyribose

A

The hydroxyl group attached to the 2’ carbon in ribose is replaced by a hydrogen group

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63
Q

Nucleosides

A

Nitrogenous base and a ribose or deoxyribose sugar

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64
Q

Nucleotides

A

Nitrogenous base, sugar, and a phosphate group

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65
Q

Phosphodiester Bond

A

Bond between the 3’ OH group of the sugar and the 5’ phosphate on the nucleoside triphosphate

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66
Q

How many bonds are between C and G?

A

3

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67
Q

B-DNA

A

Basis of Watson and Crock model. Right hand helix

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68
Q

Z-DNA

A

Left hand helix, found in sequences where pyrimidines and purines alternate

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69
Q

A-DNA

A

Right hand sequence of dehydrated DNA, very compact

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70
Q

Primary Structure

A

Sequence of nucleotides (AGTACA)

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71
Q

Secondary Structure

A

3-D structure-double helix of DNA

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72
Q

Tertiary Structure

A

Supercoiling of secondary structure

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73
Q

Quarternary Structure

A

Interaction of nucleic acids with proteins (DNA wrapped around a histone)

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74
Q

mRNA

A

Single stranded, carries codon information for translation

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75
Q

tRNA

A

Folded stem loop system that carries amino acid to ribosome

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76
Q

rRNA

A

Linear, single stranded, folded molecule, helps form ribosome

77
Q

snRNA

A

Small nuclear RNA that is involved in generation of mature mRNA transcripts and are an essential part of splicing

78
Q

miRNA

A

Micro RNA is responsible for the regulation of gene expression and can either silence of express mRNAs

79
Q

Negative Supercoiling

A

Promotes strand separation (good for DNA Replication) . Introduced behind the protein.

80
Q

Positive Supercoiling

A

Unwanted side effect of negative super coiling and must be corrected so DNA can be separated. Introduced ahead of the protein.

81
Q

What is the function of topoisomerase I?

A

Forms a single covalent bong with DNA, breaking phosphodiester bonds, allowing the DNA to rotate and relieve stress from supercoiling

82
Q

What is the function of topoisomerase II?

A

Topoisomerase II (DNA grade in bacteria) is activated when two double helices cross over each other. It bonds to both ends of the strand, breaking the backbone, and allowing the second DNA helix is pass through the first. Requires ATP

83
Q

Chromatin

A

Complex of DNA and chromosomal proteins

84
Q

What are the 5 major types of histones?

A

H1, H2A, H2B, H3, and H4

85
Q

Nucleosome Structure

A

Core of histones (2 molecules of each type) around which DNA is wrapped, and linker DNA

86
Q

Euchromatin

A

Decondensed and transcriptionally active

87
Q

heterochromatin

A

Condensed and transcriptionally inactive

88
Q

How does chromatin form?

A

DNA methylation occurs which tags a region of the genome for his tone modification that causes the formation of heterochromatin (by deacetlyting) The acetylation removes the positive charge and reduces the affinity between histones and DNA which increases transcription.

89
Q

DNA A Proteins

A

Binds to the origins of replication and breaks hydrogen bones between bases

90
Q

DNA B

A

Helicase , opens and binds primase

91
Q

Single copy genes

A

unique sequences in the genome that code for a proteins

92
Q

Multigene Families

A

Genes with similar functions that have arisen by gene duplication

93
Q

Classic gene families

A

Multicopy genes that show a high degree of homologous (HOX, globin, etc)

94
Q

Gene super families

A

Not so closely related as classic gene families, but have similar function.

95
Q

Extragenic DNA

A

Mostly transcriptionally inactive, might regulate gene expression

96
Q

Tandem DNA

A

Tandem repeats of DNA sequences that are non coding and are inherited in a co-dominant fashion

97
Q

SNP

A

Single nucleotide polymorphism where there is a single base pair change in individuals. Fairly common!

98
Q

SSR

A

Simple Sequence repeat. Most simple of the repetitive sequences and most polymorphic. repeats of 2-4 base pairs.

99
Q

VNTR

A

Variable and tandem repeats- longer than the SSR (5-100 bp) repeating many times

100
Q

LINE

A

Long intersperses nuclear elements-make RNA and include genes that encode reverse transcriptase and integrates LINE into genome

101
Q

SINES

A

Short interspersed nuclear elements. Short RNAs that were converted to DNA by reverse transcriptase that they stole from a LINE. Most common is the Alu sequence

102
Q

Rare variants

A

Not usually found, but thought to contribute to human disease more than SNP.

103
Q

Pseudogenes

A

Look like real genes, but don’t code for a product (gene that used to allow us to make vitamin C, but is now inactive)

104
Q

When is the chromosome maximally condensed?

A

At metaphase (this is when karyotyping occurs)

105
Q

Metacentric chromosome

A

Centromere in the middle

106
Q

Submetacentric Chromosome

A

Centromere closer to the top (p arm shorter than q arm)

107
Q

Acrocentric Chromosome

A

Centromere very close to the top and p arm contains little genetic information. Involved in robertsonion translocation.

108
Q

Uniparental Disomy

A

When both the chromosomes are derived from the same parent

109
Q

Lyonization

A

X-inactivation. One of the X chromosomes is condensed into the Barr body and is inactive. Random event-either X from mom or dad could be inactivated. regulated by X-inactivation center that has the XIST gene.

110
Q

Asymmetric X inactivation

A

When more than 50% of the cells from either the father or mother is active

111
Q

How does XIST work?

A

Produces an RNA that coats the X chromosome, causing it to condense into heterochromatin. Methylation of cytosine bases and histone deacteylation results in transcriptional repression.

112
Q

What is the Huntington gene locus?

A

4p

113
Q

In which direction is protein written?

A

N-terminus to C-terminus

114
Q

What is the start codon?

A

AUG

115
Q

How many reading frames are there per RNA?

A

3

116
Q

What frame shift mutation does CF have?

A

F508

117
Q

P site

A

Holds the tRNA that carries the growing polypeptide chain

118
Q

A site

A

Holds the tRNA that carries the next amino acid to be added to the chain

119
Q

E site

A

Exit site, where discharged tRNAs leave the ribosome

120
Q

where on the tRNA do amino acids attach?

A

The 3’ end

121
Q

What is the wobble baby hypothesis?

A

Base pairing is less strict for the third base, allowing tRNA to read more than one codon.

122
Q

how is tRNA activated?

A

Amino acid is bound by amino acid adenylate, forming aminoacyl-tRNA. This requires the hydrolysis of pyrophosphate.

123
Q

N-formylmethionine:

A

First amino acid that is recognized. By the ribosome allowing initiation. Usually two tRNAs, one which recognized fMET and other recognized AUG. Not formylated in eukaryotes.

124
Q

In eukaryotes, where does the small ribosome bind? In prokaryotes?

A

Close to the 5’ cap (scans until it finds a start codon) and at the Shine Dalgarno sequence.

125
Q

Chaperones

A

Help to regulate the number of folds in a newly synthesized protein.

126
Q

Differences between prokaryotic and eukaryotic translation:

A

In eukaryotes: first MET is not formylate, monocistroni, start at first AUG (don’t internally pick), transcription and translation occur in different membranes.

127
Q

Diphtheria toxin

A

Inactivation of EF-2 by ADP ribosylation

128
Q

Streptomycin (aminoglycoside)

A

Binds to 30s and prevents assembly of ribosome

129
Q

Tetracycline

A

Four ring structure that blocks elongation by reverting aminoacytRNA-access to A site

130
Q

Erythromycin

A

Binds to the 50s subunit of the complete ribosome and blocks translocation

131
Q

Chloramphenicol

A

Inhibits peptidyl transferase activity in prokaryotes and may inhibit mitochondrial translation

132
Q

cycoheximide

A

Inhibits eukaryotic peptidyl transferase activity

133
Q

Puromycin

A

Causes premature termination of translation in both prokaryotes and eukaryotes

134
Q

EF-g

A

Prokaryotic protein, EF-2 in eukaryotes.

135
Q

Zymogen Activation

A

Zymogen (pro enzyme) is an inactive enzyme precursor that can be activated by enzymatic cleavage of peptide bonds. Can lead to active apoptosis, blood coagulation, digestion of proteins.

136
Q

Protein phosphorylation by a kinase

A

Phosphate is transferred from ATP to a protein on a SER/THR residue of a protein

137
Q

Insulin Receptor

A

Tyrosine kinase that transfers a phosphate from ATP to a protein on a Tyr residue of a protein

138
Q

O-linked glycosylation

A

Glycosylation on the OH group of the SER/THR. Often found as extra cellular proteins or as membrane bound proteins.

139
Q

N-linked glycosylation

A

On the Asn residue. Can be high mannose or complex.

140
Q

Lipid anchoring

A

Adding a farnesyl (15 carbon isoprenoid) group to the cysteine to anchor amino acid into the membrane. Anchors Ras to inner leaflet.

141
Q

Totipotent

A

Give rise to all tissues in the body. Both embryonic and extra embryonic.

142
Q

Pluripotent

A

Ability to develop into all cells and tissues

143
Q

Multipotent

A

Develop into a small number of cell types

144
Q

Unipotent

A

Develop into one cell type

145
Q

Morula

A

Totipotent

146
Q

Blastocyst

A

Inner cell mass that is pluripotent and gives rise to all derivative of the 3 primary germ layers

147
Q

What are the three primary germ layers?

A

Ectoderm, endoderm, and mesoderm

148
Q

Mesoderm

A

Gives rise to muscles and lining of organs

149
Q

Endoderm

A

Gives rise to the epithelia

150
Q

Ectoderm

A

Skin

151
Q

Hematopoietic

A

RBCs and immune cells

152
Q

Mesenchymal

A

Bone marrow stromal cells. Create bone cells, cartilage cells, fat cells, and other CT cells

153
Q

Neural

A

Nerve and glial cells

154
Q

Epithelial

A

Lining of the digestive tract

155
Q

Skin

A

Basal layer of the epidermis, keratinocytes, hair follicles

156
Q

Stem Cell Plasticity

A

Ability of adult stem cells to form specialized cell types of other tissues

157
Q

Asymmetric Cell division

A

Mechanism to maintain the stem cell population while generating differentiated cells. 2 daughter cells and 2 distinct cell fates

158
Q

Stem Cell Niche

A

Microenvironment that regulates the self-renewal and maintenance of stem cells

159
Q

Extrinsic Signaling

A

External cues that control the proliferation of stem cells. Cell to cell interactions (Cadherins) and cell to EC matrix (integrins), and growth factors.

160
Q

Intrinsic Mechanism

A

Preferential serration of molecules prior to cell division. Maintain one daughter cell as a stem cell and other daughter cell differentiates.

161
Q

Transcription Factors

A

Proteins that work together to activate pathways needed for stem cell identity. Include Oct4, Sox2, and Nanog.

162
Q

Epigenetic Modification of DNA

A

Chromatin structure of stem cells is very different compared to differentiated cells. More relaxed and ready for transcription.

163
Q

Polycomb proteins

A

Family of proteins that function to modify chromatin structure. May function to silence genes associated with stem cells.

164
Q

Progenitor Cell

A

Intermediate between stem cells and differentiated cells

165
Q

SCNT

A

Somatic Cell Nuclear Transfer. Creating a cloned embryo with a donor nucleus. Can be reproductive or therapeutic.

166
Q

Therapeutic Cloning

A

Used to make new embryonic stem cells which can generate an organ and have the same genetic markers as the patient.

167
Q

Induced Pluripotent Stem cells

A

Adult stem cells that are reprogrammed into a pulripotent state. Requires vectors and can lead to tumors.

168
Q

Cloudy Swelling

A

First sign of cell injury. Organelles swell and give off a cloudy appearance when stained.

169
Q

Hydropoic Degeneration

A

Continued swelling of the organelles, vacuoles appear in the cytoplasm.

170
Q

Steatosis

A

Fatty acid change in response to cell injury. The cytoplasm gains lipid dots. Frequently seen in the liver.

171
Q

Atrophy

A

Decrease in cell size. Reduction in functional cell mass. Reversible. Caused by decreased functional demand or blood supply. Also caused by loss of stimulation and aging. Commonly affects the testis in elderly, skeletal muscle, and the brain.

172
Q

Hypertrophy

A

Increase in cell size resulting in increased organ size. Reversible. No change in cell number. Caused by increased functional demand or hormone stimulation. Seen frequently in cardiac muscle, skeletal muscle, and uterus.

173
Q

Hyperplasia

A

Increase in cell number. Reversible. Caused by increased function demand or hormone stimulation. Commonly affects the endometrium, prostrate gland, RBC s, glandular epithelium of the breast, and uterine enlargement (pregnancy).

174
Q

Metaplasia

A

Change in differentiation (change in cell type). Reversible, seen in reprogrammed stem cells and other cells. It is an adaptive response to environmental stimuli (cigarette smoke, acid reflux). Typically affects the epithelium of the respiratory tract, cervix, and esophagus. Puts you at increased risk for dysphasia and neoplasia.

175
Q

Involution

A

When the cell turns in on itself and shrinks.

176
Q

Kidney Atrophy

A

Caused by decreased blood flow to kidney from the narrowing of the renal artery. Often due to atherosclerosis.

177
Q

Dysplasia

A

Failure of differentiation and maturation. Persistently atypical cells. Caused by rapid multiplication of cells. Affects the cervix and skin. Increased risk of neoplasia.

178
Q

Neoplasia

A

Cellular growth and proliferation in absence of external stimulus. Can be benign or malignant.

179
Q

Cloudy Swelling

A

First sign of cell injury. Organelles swell and give off a cloudy appearance when stained.

180
Q

Hydropoic Degeneration

A

Continued swelling of the organelles, vacuoles appear in the cytoplasm.

181
Q

Steatosis

A

Fatty acid change in response to cell injury. The cytoplasm gains lipid dots. Frequently seen in the liver.

182
Q

Atrophy

A

Decrease in cell size. Reduction in functional cell mass. Reversible. Caused by decreased functional demand or blood supply. Also caused by loss of stimulation and aging. Commonly affects the testis in elderly, skeletal muscle, and the brain.

183
Q

Hypertrophy

A

Increase in cell size resulting in increased organ size. Reversible. No change in cell number. Caused by increased functional demand or hormone stimulation. Seen frequently in cardiac muscle, skeletal muscle, and uterus.

184
Q

Hyperplasia

A

Increase in cell number. Reversible. Caused by increased function demand or hormone stimulation. Commonly affects the endometrium, prostrate gland, RBC s, glandular epithelium of the breast, and uterine enlargement (pregnancy).

185
Q

Metaplasia

A

Change in differentiation (change in cell type). Reversible, seen in reprogrammed stem cells and other cells. It is an adaptive response to environmental stimuli (cigarette smoke, acid reflux). Typically affects the epithelium of the respiratory tract, cervix, and esophagus. Puts you at increased risk for dysphasia and neoplasia.

186
Q

Involution

A

When the cell turns in on itself and shrinks.

187
Q

Kidney Atrophy

A

Caused by decreased blood flow to kidney from the narrowing of the renal artery. Often due to atherosclerosis.

188
Q

Dysplasia

A

Failure of differentiation and maturation. Persistently atypical cells. Caused by rapid multiplication of cells. Affects the cervix and skin. Increased risk of neoplasia.

189
Q

Neoplasia

A

Cellular growth and proliferation in absence of external stimulus. Can be benign or malignant.

Exam 1 Notes (10 decks)

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