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From Flashcardlet > Cell Bio 1 > Flashcards

Cell Bio 1 Flashcards

1
Q

Transcription

A

DNA to RNA

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2
Q

Translation

A

RNA to protein

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3
Q

Phospholipids

A

amphipathic, hydrophobic hydrocarbon chains and hydrophilic head groups

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4
Q

Prokaryotes characteristics

A 
Diameter: 1-10um
DNA: 0.6 mil – 5 mil base pairs		~5000 different proteins
No nucleus or nuclear envelope
Circular DNA	
bacteria or archaebacteria
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5
Q

5 tissue/cell types of eukaryotes

A

epithelial, connective, blood, nervous, muscle

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6
Q

nucleus

A

control center, site of transcription

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7
Q

chloroplasts

A

site of photosynthesis

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8
Q

Vacuoles

A

in plant cells; perform a variety of functions, including digestion of macromolecules and storage of waste products and nutrients

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9
Q

Lysosomes and peroxisomes

A

specialized metabolic compartments for the digestion of macromolecules and for various oxidative reactions

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10
Q

ER

A

network of intracellular membranes, extend from nuclear membrane through the cytoplasm.
• Rough- where ribosomes assemble many proteins
• Smooth- synthesis of lipids
It functions in processing and transport of proteins and lipid synthesis

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11
Q

Golgi apparatus

A

proteins are further processed and sorted for transport to their final destinations. The Golgi apparatus is also a site of lipid synthesis; and (in plant cells) synthesis of some polysaccharides that compose the cell wall.

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12
Q

Cytoskeleton

A

¥ Provides structural framework
¥ Determines cell shape and organization
¥ Involved in movement of whole cells, organelles, and chromosomes during cell division

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13
Q

typical resolution of biological species

A

1-2 nm

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14
Q

2 types of light microscopy

A

phase contrast and bright field

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15
Q

GFP

A

jellyfish protein, can be fused to any protein of interest with recombinant DNA

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16
Q

Electron microscopy

A

much greater resolution (0.2 nm) because of short wavelength of electrons
• Transmission EM- fixed cells, add salts of heavy metals to a stain to give contrast
o Positive- darker sections are denser
o Negative- background is stained
o Metal shadowing-
• Scanning EM- gives 3D image, electron beams do not pass through, instead give outside

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17
Q

what does Subcellular fractionation do

A

isolate organelles from the cell

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18
Q

what does Differential centrifugation

A

separate cell components by size and density

  • Larger, denser organelles pellet out at lower speeds
  • Smaller, less dense organelles pellet out at faster speeds
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19
Q

what does density gradient centrifugation do and what are 2 ways

A

organelles separated through a dense material gradient (glucose)

  1. Velocity- starting material is layered on top of the glucose, slower material stays on top
  2. Equilibrium- separated on basis of buoyant density, parts will move until they match the density of the gradient which they are in
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20
Q

Embryonic stem cells

A

maintain ability to differentiate into all cell types in adult, can study gene function and offers possibility of treating diseases

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21
Q

HeLa cell line

A

first human cell line, 1951, cervical cancer cell line from Henrietta Lacks, most widely used cell line to study cancer

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22
Q

Viruses

A

intracellular parasites that cannot replicate on their own, instead they infect host cells and use the host cell machinery to survive, consist of DNA or RNA with protein coating

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23
Q

Bacteriophages

A

bacterial viruses, for example T4 infects E. coli, we study T4 instead of E. coli because it has a smaller genome and is easier to study

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24
Q

Retroviruses

A

have RNA genomes but synthesize a DNA copy of their genome in the infected cells, first demonstrated synthesis of DNA from RNA templates
- Some viruses convert normal cells to cancer cells for example HPV, studying these give an understanding of cancer, growth and differentiation

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25
Q

what is most abundant in cells

A

water

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26
Q

inorganic ions like ____ constitute less than __% of body mass

A

Na, K, Mg, Ca, HPO4, Cl, HCO3

1%

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27
Q

glycosidic bonds

A

link monosaccharides, formed by dehydration reaction

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28
Q

Fatty acids

A

long hydrocarbons chains that end with COO- (acid), unsaturated means 1+ DB

  • Stored are triglycerides or fats, 3 FA linked together to a glycerol
  • Insoluble in water, are fat droplets in cytoplasm
  • Can be broken down in an energy reaction
  • More efficient energy storage than carbs, by 2x
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29
Q

Phospholipids

A

2 fatty acids with polar head group, part of cell membranes

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30
Q

Sphingomyelin

A

nonglycerol fatty acid, has a serine polar head group

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31
Q

Glycolipids

A

2 hydrocarbon chains and a carbohydrate polar head group

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32
Q

Cholesterol

A

4 hydrophobic hydrocarbon rings and a polar hydroxyl (OH) group

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33
Q

Steroid hormones

A

(e.g., estrogens and testosterone): derivatives of cholesterol
- act as chemical messengers
derivatives of phospholipids serve as messenger molecules within cells

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34
Q

A binds with ___ and G binds with ___

A

T (U in RNA) 2 bonds

C 3 bonds

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35
Q

Phosphodiester bonds

A

form between the 5′ phosphate of one and the 3′ hydroxyl of another

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36
Q

Polynucleotides are synthesized in the ____ direction

A

5′ to 3′ direction

- one end terminates in a 5′ phosphate group and the other in a 3′ hydroxyl group

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37
Q

why is cysteine special

A

forms disulfide bonds/bridges

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38
Q

primary protein structure

A

the sequence of amino acids in the polypeptide chain

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39
Q

secondary structure

A

regular arrangement of amino acids within localized regions.

¥ α helix and β sheet - both are held together by hydrogen bonds between the CO and NH groups of peptide bonds

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40
Q

tertiary structure

A

the polypeptide chain folds due to interactions between side chains of amino acids in different regions of the chain.
¥ In most proteins this results in domains, the basic units of tertiary structure.
¥ Critical determinant- placement of hydrophobic amino acids in the interior of the protein and hydrophilic amino acids on the surface

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41
Q

quaternary structure

A

interactions between different polypeptide chains in proteins composed of more than one polypeptide

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42
Q

Sickle cell disease

A

first case of a genetic disease that could be localized to a defect in the structure of a specific protein molecule; Incomplete dominance - intermediate phenotype between the homozygous dominant and homozygous recessive conditions, 1 in 12 African Americans carry sickle cell, survival advantage over malaria
Symptoms: Anemia -spleen – sickled RBCs trapped and disposed of -RBCs live 120 days, Sickle cells 10-20 days; Clogged blood vessels lead to pain, oxygen deprivation of tissues, organs, eye problems stroke and infections (result of damage to the spleen)

  • HbAHbA- Homozygous dominant, normal individual (hemoglobin molecules consist of 2 alpha and 2 beta chains)
  • HbAHbS- Heterozygous, individual with sickle cell trait (Half the individual’s hemoglobin molecules consist of 2 alpha and 2 beta chains, and half consist of 2 alpha and 2 S-chains), usually asymptomatic
  • HbSHbS- Homozygous recessive individual with sickle cell disease/sickle cell anemia (All hemoglobin molecules consist of 2 alpha and 2 S-chains)
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43
Q

Enzymes

A

catalyst that increases the rate of a chemical reaction in cells that is not consumed or altered, and does not change the equilibrium of the reaction; not all enzymes are proteins!

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44
Q

Active site

A

substrate binds to this on enzyme, clefts or grooves on enzyme surface formed by 3* structure, substrate initally binds with H bonds, ionic bonds and hydrophobic intereactions

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45
Q

Serine Proteases

A

The active sites of serine proteases contain serine, histidine, and aspartate.
Substrates bind by insertion of the amino acid adjacent to the cleavage site into a pocket at the active site. The nature of the pocket determines the substrate specificity of the different ones.

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46
Q

Prosthetic groups and an example

A

small molecules bound to proteins
that have critical functional roles
eg. in myoglobin and hemoglobin, the prosthetic group
is heme, which carries O2

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47
Q

key features of enzymatic catalysis (3)

A

¥ Specificity of enzyme-substrate interactions.
¥ Positioning of substrate molecules in the active site.
¥ Involvement of active-site residues in formation
and stabilization of the transition state.

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48
Q

Co-factors-

A

Metal ions (e.g., zinc or iron) can be bound to enzymes and play a role in the catalysis

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49
Q

Co-enzymes-

A

small organic molecules that work with
enzymes to enhance reaction rates, not altered by rxn
- act as electron carriers
- involved in the transfer of a variety of groups.
- closely related to vitamins, which contribute part or all of the structure of the coenzyme

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50
Q

Allosteric regulation

A

enzyme activity is controlled by the binding

of small molecules to regulatory sites on the enzyme; changes the conformation of the enzyme and alters the active site

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51
Q

Phosphorylation

A
  • common mechanism of enzyme regulation, phosphate groups are added to the side-chain OH groups of serine, threonine, or tyrosine, can either stimulate or inhibit the activities of many enzymes
52
Q

what do kinases do

A

phosphorylate

53
Q

what do phosphotases do

A

dephosphorylate

54
Q

Phospholipid bilayer

A 
the basic 
structure of all biological 
membranes form a stable 
barrier between two 
aqueous compartments
55
Q

mammalian membrane fluidity is determined by

A

temperature and lipid composition

56
Q

unsaturated fatty acids result in

A

kinks

57
Q

Cholesterol at cool temperature

A

maintains fluidity by tight packing

58
Q

Cholesterol at high temperature

A

restrains movement, rigid

59
Q

Cholesterol at normal conc

A

the interaction of the steroid ring with the long hydrophobic tails of phospholipids tends to immobilize these lipids and thus decrease biomembrane fluidity

60
Q

Cholesterol at low conc

A

the steroid ring separates and disperses phospholipid tails, causing the inner regions of the membrane to become slightly more fluid

61
Q

Freeze fracturing

A

specimens are frozen in liquid nitrogen, fractured with a knife blade, then shadowed with platinum, splits the lipid bilayer, revealing the interior faces of a cell membrane

62
Q

Integral membrane proteins

A

embedded directly in the lipid bilayer

63
Q

Peripheral membrane proteins

A
  • associated with the membrane indirectly, generally by interactions with integral membrane proteins
64
Q

Transmembrane proteins

A

span the lipid bilayer, with portions exposed on both sides; usually α-helical regions of 20 to 25 nonpolar amino acids; some (n some bacteria, chloroplasts, and mitochondria) have a β-barrel, formed by folding of β sheets into a barrel-like structure

65
Q

Selective permeablitity; which can pass and which cannot

A

allows a cell to control its internal composition

  • Small, nonpolar molecules can diffuse across the lipid bilayer: CO2, O2, H2O
  • Ions and larger uncharged molecules, such as glucose, cannot diffuse across
66
Q

Channel proteins

A

form open pores across the membrane, selectively opened and closed in response to extracellular signals, Ex: ion channels allow the passage of inorganic ions

67
Q

Passive transport

A

molecule movement across the membrane is determined by concentration and electrochemical gradients

68
Q

Active transport

A

molecules can be transported against a concentration gradient if coupled to ATP hydrolysis as a source of energy

69
Q

RNA processing

A

before mRNA can exit the nucleus, it is called pre-mRNA, to exit needs a 5’ cap and 3’ Poly (A) tail, and interanlly, the mRNA gets spliced and modified, introns are removed, exons are spliced together, then finally the mRNA can leave and attach to the ribosomes

70
Q

Translation (long definition)

A
  • the synthesis of proteins as directed by mRNA templates, the first step in the formation of functional proteins
  • polypeptide chains must fold into appropriate conformations and often undergo various processing steps, sorting, and transport
  • gene expression is regulated by this
  • carried out on ribosomes, with tRNAs serving as adaptors
  • each amino acid is specified by three bases (a codon) in the mRNA
  • interactions between the three types of RNA (mRNA, tRNA, rRNA), plus other proteins
71
Q

tRNAS

A

align amino acids with corresponding codons on the mRNA template, are 70–80 nucleotides long, characteristic cloverleaf structures from base pairing between different regions

72
Q

Structure of tRNAs

A

All tRNAs fold into compact L shapes, to fit onto ribosomes during translation
They have the sequence CCA at the 3′ end, and amino acids are covalently attached HERE, to the ribose of the terminal adenosine
Anticodon loop binds to the appropriate codon by complementary base pairing

73
Q

Aminoacyl tRNA synthetases

A

enzymes that mediate the attachment of amino acids to specific tRNAs, each of these 20 enzymes recognizes a single amino acid, as well as the correct tRNA to which it should attach

74
Q

Wobble

A

nonstandard base pairing at third condon position= some tRNAs can recognize more than one mRNA codon; allows G to pair with U, and inosine (I) to pair with U, C, or A. (Guanosine is modified to inosine in the anticodons of some tRNAs.)

75
Q

Ribosomes

A

site of protein synthesis; 70S for bacterial and 80S for eukaryotic; cells have many ribosomes, bc protein synthesis is important

76
Q

rRNAs

A

form characteristic secondary structures by complementary base pairing with itself, folding results in distinct 3D structures

77
Q

mRNA

A
  • have noncoding untranslated regions (UTRs) at the ends
  • most eukaryotic mRNAs are mono-cistronic, encoding a single protein
  • prokaryotic mRNAs are often poly-cistronic, encoding multiple proteins, each of which is translated from an independent start site
  • translation always starts with methionine, usually encoded by AUG
  • signals that identify initiation codons are different in prokaryotic and eukaryotic cells
78
Q

translation starts with

A

methionine (AUG)

79
Q

Shine-Dalgarno sequence

A

aligns the mRNA on the ribosome, preceeds initiation codons in bacterial mRNAs

  • They can initiate translation at the 5′ end of an mRNA and at internal initiation sites of polycistronic mRNAs.
  • Eukaryotic mRNAs are recognized by the 7-methylguanosine cap at the 5′ end.
  • The ribosomes then scan downstream of this cap until they encounter the initiation codon.
80
Q

eukaryotic mRNA are recognized by

A

7-methylguanosine cap at the 5′ end

81
Q

3 stages of translation

A

initiation, elongation, and termination

82
Q

Methionyl tRNA

A

a specific initiator, and the mRNA bind to the small ribosomal subunit.
The large ribosomal unit then joins, forming a functional ribosome

83
Q

what is on the 5’ end for IF recognition

A

5’ methyl cap

84
Q

what is on 3’

A

poly-A-binding-protein

85
Q

Binding of SRS to LRS is____ rxn

A

hydrolysis

86
Q

binding sites of ribosomes

A

P (peptidyl) – methionyl tRNA binds here
A (aminoacyl)
E (exit)

87
Q

Elongation factor

A

EF-Tu in prokaryotes, eEF1α in

eukaryotes) complexed to GTP brings the aminoacyl tRNA to the ribosome

88
Q

what determines the accuracy of protein synthesis

A

Selection of the correct aminoacyl tRNA

89
Q

can base pairing account for accuracy of protein synthesis? if not what does?

A

no; “decoding center” in the small ribosomal subunit recognizes correct codon-anticodon base pairs and discriminates against mismatches; can fix any errors, very accurate

90
Q

eIF2B

A

eIF2B regenerates another GTP (active) to keep hydrolyzing the tRNA after GTP hydrolysis leaves with a GDP

91
Q

Stopping protein synthesis

A
  • Elongation continues until a stop codon (UAA, UAG, or UGA) is translocated into the A site
  • Release factors recognize these signals and terminate protein synthesis
  • In prokaryotic cells RF1 recognizes UAA or UAG, RF2 recognizes UAA or UGA
    In eukaryotic cells eRF1 recognizes all three stop codons
92
Q

what are the 3 stop codons

A

UAA, UAG, or UGA

93
Q

Polysome or polyribosome

A

group of ribosomes bound to an mRNA molecule

94
Q

regulation of translation

A

translational repressor proteins and noncoding microRNAs

95
Q

Chaperones

A

proteins that facilitate folding of other proteins
¥ catalysts that assist the self-assembly process without becoming part of the folded protein
¥ bind to polypeptide chains that are still being translated on ribosomes
¥ stabilize unfolded or partially folded polypeptides during transport into organelles

96
Q

Hsps and Hsp70

A

heat shock proteins; what chaperones were initially thought to be, expressed in cells exposed to high temperatures
¥ Hsp70 stabilize during translation and transport by binding to short hydrophobic segments

97
Q

Chaperonin

A

where folding takes place; consist of subunits arranged in 2 stacked rings to form a double-chambered structure which isolates protein from the cytosol and other unfolded proteins

98
Q

Protein misfolding diseases

A

caused by defects in protein folding

99
Q

Cystic fibrosis

A

caused by a mutation that results in one amino acid deletion that leads to improper folding of protein CFTR- transports Cl‒ ions across epithelial cell membranes, so Cl can’t pass, so water can’t pass, build up of mucous= congestion and bacterial growth

100
Q

examples of protein misfolding diseases

A

Alzheimer’s, Parkinson’s and Type 2 Diabetes

101
Q

Alzheimer’s Disease

A

a common disorder that strikes as many as 10% of individuals who are at least 65 years of age and perhaps 40% of individuals who are 80 years or older.
Symptoms: memory loss, confusion and a loss of reasoning ability

102
Q

AD is characterized by two aggregate types in brain tissue:

A
  1. Neurofibrillary tangles (misfolded tau proteins)- consist of insoluble twisted fibers that are found inside of the brain’s cells, consist of a protein called tau, which forms part of a structure called a microtubule
  2. Amyloid plaques (aggregates of misfolded amyloid-β protein [Aβ])- main cause of AD
    ¥ Amyloid precursor protein (APP) – spans the nerve cell membrane from outside to inside; cleaved by two enzymes, β-secretase and g-secretase; to release Aβ
103
Q

Amyloid

A

general term for protein fragments that the body produces normally

104
Q

β-Amyloid

A

fragment of a protein that is snipped from another protein called amyloid precursor protein (APP). In a healthy brain, these protein fragments would be broken down and eliminated. In Alzheimer’s disease, the fragments accumulate to form hard, insoluble plaques

105
Q

Microtubule

A

transport nutrients and other important substances from one part of the nerve cell to another. In AD the tau protein is abnormal and the microtubule structures collapse

106
Q

what are domains and the critical determinant of 3* structure

A

domains- the basic units of tertiary structure, what protein folding results in
Critical determinant- placement of hydrophobic amino acids in the interior of the protein and hydrophilic amino acids on the surface

107
Q

what does RNA need before it exits nucleus

A

5’ cap and 3’ Poly (A) tail

108
Q

PABP

A

poly-A-binding protein; binds to poly-A-tail on 3’ end, stimulates translation

109
Q

α-secretase releases

A

sAPPα, which is good and harmless, and then P3

110
Q

β-secretase releases

A

sAPPβ and Aβ40 and Aβ42 which are BAD

111
Q

Inherited form of AD

A

mutation leads to an increased production of the Aβ42 peptide
Ð Mutation in the APP gene
Ð Mutation in the genes, PS1 and PS2, that encode subunits of g-secretase
Ð Symptoms of the disease are exhibited at an early age (50’s)

112
Q

Therapies for AD

A

Prevent formation of β amyloid or clear it from the brain once it has been deposited

113
Q

phase 1 is focused on

A

safety

114
Q

phase 2 is focused on

A

effectiveness

115
Q

phase 3 is focused on

A

Comparing the effectiveness of the new treatment with standard approaches

116
Q

prion diseases

A

called spongiform encephalopathies (SE) because of the post mortem appearance of the brain with large vacuoles in the cortex

117
Q

prion

A

misfolded proteins that can self-replicate; defined as a small proteinaceous infectious particle, which resists inactivation

118
Q

Prion protein is encoded by

A

PRNP gene within cells own chromosomes

119
Q

normal prion protein

A

PrPc

120
Q

abnormal prion protein

A

PrPSc

121
Q

Similarities between AD and CJD

A

Ð Fatal neurodegenerative diseases that can occur in either an inherited or sporadic form
Ð Brains contain amyloid plaques and neurofibrillary tangles that are thought to contribute to the degradation of the neurons
Ð The toxic fibrillar deposits result from the self-association of a polypeptide composed predominantly of β sheets

122
Q

Differences between CJD and AD:

A

Ð The proteins that form the disease-causing aggregates are totally unrelated
Ð The parts of the brain that are affected are distinct/different
Ð The protein(s) responsible for AD does not act like an infectious agent (nontransmissable)

123
Q

Two enzymes act as chaperones by catalyzing protein folding

A

Protein disulfide isomerase

Peptidyl prolyl isomerase

124
Q

Peptidyl prolyl isomerase

A

catalyzes isomerization of peptide bonds that involve proline residues
proline- rigid, found in both cis and trans form
Isomerization between the cis and trans configurations of prolyl-peptide bonds could otherwise be a rate-limiting step in protein folding

125
Q
  1. Protein disulfide isomerase (PDI):
A

catalyzes disulfide bond formation, abundant in the ER, where an oxidizing environment allows (S—S) linkages, help to stablize protein

126
Q

Proteolysis

A

cleavage of a polypeptide chain removes portions such as the initiator methionine from the amino terminus

From Flashcardlet (34 decks)

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