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Midterm Flashcards

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Biology 101 flashcards
1
Q

Cell theory

A

cells are the basic unit of structure in all living things

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2
Q

Who first named the cell in 1665?

A

Robert Hooke

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3
Q

What did Hooke see?

A

Non-living cells from a cork

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4
Q

Who first witnessed a live cell under a microscope in 1674?

A

Anton Van Leeuwenhoek

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5
Q

Who first developed the cell theory in 1839?

A

Matthias Jakob Schleiden and Theodor Schwann

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6
Q

What does the cell theory state?

A

all organisms are composed of one ore more cells, all cells come from pre-existing cells, vital functions occur within cells, contain hereditary information

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7
Q

Exceptions to the cell theory

A

viruses are considered by some to be alive (not made up of cells), the first cell did not originate from a pre-existing cell

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8
Q

Conditions on Earth (evolution of cells)

A

little oxygen in the atmosphere, thought the environment was rich in hydrogen, methane, and ammonia

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9
Q

What did Stanley Miller demonstrate in the 1950’s?

A

the spontaneous formation of organic molecules

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10
Q

What was a critical characteristic of self-replication of RNA?

A

the ability to replicate itself

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11
Q

What was the discovery made from by Sid Altman and Tom Cech in the 1980’s?

A

the discovery of the ability of RNA to catalyze chemical reactions

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12
Q

What is unique about RNA?

A

it can serve as a template for and catalyze its own replication

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13
Q

What was RNA world?

A

though to have been an early stage of chemical evolution based on self-replicating RNA molecules

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14
Q

What were the first cellular life forms on Earth?

A

Proteinoid-based protocells enclosing RNA molecules

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15
Q

What do amphipathic molecules consist of and what does it form?

A

one portion that is soluble in water and another portion that is not. forms a stable barrier between interior of cells and external environment

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16
Q

What is glycolosis?

A

an anaerobic breakdown of glucose to lactic acid and occurs in the cytoplasm

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17
Q

What does photosynthesis allow the cell to do?

A

harness energy from sunlight

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18
Q

What is oxidative metabolism?

A

the principal source of energy for most present-day cells and utilizes highly reactive O2 to generate energy from organic moelcules

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19
Q

What do prokaryotes lack and what do eukaryotes have?

A

lack a nuclear envelope and have a nucleus in which the genetic material is separated from the cytoplasm

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20
Q

E. Coli is…

A

a prokaryotic cell and a common inhabitant of the human intestinal tract

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21
Q

What is E Coli surrounded by?

A

a rigid cell wall that is composed of polysaccharides and peptides (wall is porous and allows passage of molecules)

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22
Q

What is beneath E. Coli?

A

a plasma membrane that consists of a bilayer of phospholipids and associated proteins

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23
Q

DNA of E. Coli is a single circular molecule that resides in..

A

the organisms nucleoid

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24
Q

The mitochondria is the site of…

A

oxidative metabolism

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25
Q

Where are chloroplasts found and is the site of?

A

in the cells of plants and green algae and site of photosynthesis

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26
Q

What do lysosomes provide?

A

specialized metabolic compartments for the digestion of macromolecules

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27
Q

What do peroxisomes perform?

A

various oxidative reactions

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28
Q

What do vacuoles perform?

A

a variety of functions, including the digestion of macromolecules and the storage of both waste products and nutrients

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29
Q

What is the ER a network of?

A

intracellular membranes that functions not only in processing and transport of proteins, but also in the synthesis of lipids

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30
Q

What does the Golgi apparatus do?

A

sorts and transports proteins destined for secretion- site of lipid synthesis, (in plant cells- the site of synthesis of some of the polysaccharides that compose the cell wall)

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31
Q

The cytoskeleton is another level of internal organization. What does it provide?

A

the structural framework of the cell and is responsible for the movements of the entire cells- intracellular transport and positioning of organelles and other structures

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32
Q

What is endosymbiosis?

A

one cell living inside another

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33
Q

What does the endosymbiotic theory concern?

A

the origins of the mitochondria and chloroplasts

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34
Q

What does the endosymbiotic theory postulate?

A

the mitochondria evolved from aerobic bacteria living within their host cell and chloroplasts evolved from endosymbiotic photosynthetic cyanobacteria

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35
Q

What is Saccharomyces Cerevisiae?

A

commonly studied yeasts

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36
Q

What are Pseudopodia?

A

cytoplasmic extensions used for moving and engulfing other organisms- includes bacteria and yeasts

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37
Q

What is volvox?

A

a unicellular green alga and associates with other alga cells to form multicellular colonies (precursors of plants)

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38
Q

Yeast mutants have been important in…

A

understanding many fundamental processes in eukaryotes, including DNA replication, transcription, RNA processing, protein sorting, and the regulation of cell division.

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39
Q

Genetic analysis of Drosophila uncovered..

A

many genes that control development and differentiation, especially with respects to formation of body planes and multicellular organisms

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40
Q

Why is the frog an important model for studies of early vertebrate development?

A

its eggs develop outside the mother and all stages of development from egg to tadpole can be studied in the lab

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41
Q

Why are mice most useful for genetic analysis?

A

many mutations affecting mouse development have been identified -the development of genetically-engineered mice in which specific mutant genes have been introduced into the mouse germ cells, allowing the functions of these genes to be studied in the context of whole animals

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42
Q

What are viruses helpful in?

A

cellular research and human therapies

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43
Q

How to viruses work?

A

cannot replicate on their own-heed to hijack the replication machinery of a host organism- viral DNA or RNA is enclosed in a capsid protein coat

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44
Q

Anton Van Leeuwenhoek invented what in the 1670’s?

A

a microscope that magnified objects up to 300 times their size and was able to identify a variety of different cells

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45
Q

What does optical resolution decribe?

A

the ability of an imaging system to resolve detail in the object that is being imaged

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46
Q

What does resolution describe?

A

the ability of a microscope to distinguish objects separated by small distances

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47
Q

Bright-field microscopy

A

light passes through directly through the cell-used to study various aspects of cell structure because of its simplicity (cells are stained with dyes to enhance contrast)

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48
Q

Phase-Contrast Microscopy and DIC

A

use optical systems that convert variations in density or thickness between different parts of the cell to differences in contrast that can be seen in the final image

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49
Q

Fluorescence Microscopy

A

widely used and sensitive for studying the intracellular distribution of molecules

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50
Q

Fluorescent Microscope

A

light microscope used to study properties of organic/inorganic substances using the phenomena of fluorescence

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51
Q

Steps for fluorescent microscope

A

specimen is labeled with a fluorescent molecule called a fluorophore-then specimen is illuminated with light of a specific wavelength which is absorbed by the fluorophores, causing them to emit longer wavelengths of light

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52
Q

What is the green fluorescent protein (GFP) used for?

A

to visualize proteins within living cells

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53
Q

Fluorescence recovery after photobleaching (FRAP) is used to study

A

the movements of GFP-labeled proteins

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54
Q

Fluorescence resonance energy transfer (FRET) is used to study

A

the interactions of two proteins with one another within a cell - two GFP variants are used: the light emitted by one GFP excites the second- if the molecules interact (brought close), the first GFP will excite the second resulting in emission of the second GFP

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55
Q

Confocal Laser Scanning Microscopy

A

a technique for obtaining high-resolution optical images

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56
Q

what is a key feature of Confocal Laser Scanning Microscopy?

A

its ability to produce in-focus images of thick specimens , a process known as optical sectioning

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57
Q

Who developed the electron microscope in the 1940-50’s?

A

Albert Claude, Keith Porter, George Palade

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58
Q

What is an electron microscope and what does it use?

A

a type of microscope that uses electrons to illuminate and create an image of a specimen- uses electrostatic and electromagnetic lenses to control the illumination and imaging of the specimen

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59
Q

Transmission Electron microscopy

A

passes a beam of electrons through a specimen to form an image on a fluorescent screen

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60
Q

What does scanning electron microscopy provide

A

used to provide a 3D image of cells

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61
Q

What does differential centrifugation do?

A

separates and isolates eukaryotic cell organelles on the basis of their size and density for use in biochemical studies

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62
Q

What is density-gradient centrifugation?

A

separates and purifies organelle preparations by using sedimentation through a gradient of a dense substance (sucrose)

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63
Q

What do in vitro cell culture systems enable?

A

study cell growth and differentiation, as well as to perform genetic manipulations required to understand gene structure and function

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64
Q

What are primary cultures?

A

first cell cultures established from tissues

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65
Q

How are secondary cultures form?

A

the cells grow until they cover the culture dish surface- removed and replated

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66
Q

Permanent (or immortal) cell lines are

A

embryonic stem cells (and cells derived from tumors) that frequently proliferate and indefinitely in culture

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67
Q

What percent of water do molecules account for?

A

70%

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68
Q

Inorganic molecules (Na+, K+, Mg+, Ca++, Cl-, HPO4-,HCO3-) constitute what % of cell mass?

A

1% but play critical roles in cell function

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69
Q

What do organic molecules include?

A

carbohydrates, lipids, proteins, and nucleic acids

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70
Q

What % do macromolecules constitute of the dry weight of most cells?

A

80-90% (include proteins, nucleic acids, and most carbohydates)

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71
Q

What do carbohydrates include and what does the breakdown provide?

A

simple sugars & polysaccharides, provide both a source of cellular energy and the starting material for the synthesis of other cell constituents

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72
Q

What are the representative simple sugars?

A

Monosaccharides (CH2O)n

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73
Q

How do glycosidic bonds form?

A

links a small number of monosaccharides together to form an oligosaccharide

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74
Q

What is the structure of polysaccharides?

A

hundreds/thousands of monosaccharides linked together

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75
Q

What are common polysaccharides?

A

glycogen and starch

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76
Q

What do lipids provide?

A

energy storage, major components of cell membranes, and play an important role in cell signaling

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77
Q

What are fatty acids?

A

the simplest lipids and consist of long hydrocarbon chains

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78
Q

What do triacylglycerols consist of?

A

three fatty acids linked to glycerol molecule- can be broken down for use in energy-yielding reactions

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79
Q

Phospholipids are the principal compartment of what and consist of?

A

cell membranes and consist of two fatty acids joined to a polar head group

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80
Q

What does a glycerol phospholipid consist of?

A

two fatty acids and one phosphate group, which in turn frequently attached to another small polar molecule

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81
Q

What is sphingomyelin?

A

the only nonglycerol phospholipid in cell membrane, contains two hydrocarbon chains that are linked to a polar head group formed from serine rather then glycerol

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82
Q

What do cell membranes contain in addition to phospholipids?

A

glycolipids and cholesterol

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83
Q

What does cholesterol consist of?

A

four hydrocarbon rings which are strongly hydrophobic, and OH group which is weakly hydrophilic

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84
Q

What are steroid hormones?

A

estrogen and testosterone- derivatives of cholesterol and act as signaling molecules both within and between cells

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85
Q

DNA

A

one of the principal informational molecules of the cell and is located in the nucleus of eukaryotic cells

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86
Q

What does mRNA carry?

A

carries information from DNA to the ribosomes

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87
Q

What is rRNA and tRNA involved in?

A

involved in protein synthesis

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88
Q

DNA and RNA are polymers of…

A

nucleotides, which consist of purine and pyrimidine bases linked to phosphorylated sugars

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89
Q

DNA consists of ..

A

two purines- adenine, guanine, and two pyrimidines- cytosine and thymine

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90
Q

RNA consists of..

A

adenine, guanine, thymine, and uracil

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91
Q

2-deoxyribose (sugar) links..

A

bases in DNA to form nucleosides

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92
Q

Ribose sugar links..

A

bases in RNA to form nucleosides

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93
Q

Nucleotides contain..

A

one or more phosphate groups

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94
Q

What do phosphodiester bonds form?

A

the 5’ phosphate of one nucleotide and the 3’ hydroxyl of another

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95
Q

How are polynucleotides synthesized?

A

in the 5’ to 3’ directions, with a free nucleotide being added to the 3’ OH group of a growing chain

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96
Q

DNA is a double stranded molecule consisting of …

A

two polynucleotide chains running in opposite directions- the bases inside of the molecules are joined by hydrogen bonds between complimentary base pairs

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97
Q

What do proteins execute?

A

the tasks directed by the genetic information of the cell

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98
Q

What is the most fundamental property of proteins?

A

their ability to act as enzymes, which catalyze nearly all the chemical reactions in biological systems

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99
Q

What forms proteins?

A

polymers of 20 different amino acids

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100
Q

What are the 4 groups of amino acids?

A

nonpolar, basic, acidic, polar

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101
Q

Non polar amino acids

A

Glycine, Alanine, valine, leucine, isoleucine, proline, cysteine, methionine, phenylalanine, tryptophan

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102
Q

Polar amino acids

A

serine, threonine, tyrosine, asparagine, glutamine

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103
Q

Basic amino acids

A

lysine, arginine, histidine

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104
Q

Acidic amino acids

A

aspartic acid, glutamic acid

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105
Q

What do peptide bonds join?

A

amino acids together

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106
Q

Fredrick Sanger was first to determine what is 1953?

A

the complete amino acid sequence of the hormone insulin

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107
Q

Why types of chains join insulin together?

A

two polypeptide chains joined by disulfide bonds

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108
Q

Christian Anfisen first demonstrated what?

A

that the shapes of proteins are determined by their amino acid sequence (3D conformation is critical for protein function)

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109
Q

What is x-ray crystallography?

A

a high resolution technique that can determine the arrangement of individual atoms within a molecule

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110
Q

How does x-ray crystallography work?

A

a beam of x-ray is directed at crystals of the protein- the structure of the molecule can be deduced from the pattern of scattered x rays detected on x ray film

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111
Q

John Kendrew was the first to determine what in 1958?

A

the 3D structure of a protein, myoglobin

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112
Q

What is the primary structure of proteins?

A

the sequence of amino acids in the proteins polypeptide chain

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113
Q

What is the secondary structure of proteins?

A

the regular arrangement of amino acids within localized regions of the polypeptide

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114
Q

What are two types of secondary structures?

A

a helix and b sheet

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115
Q

What is the tertiary structure of proteins?

A

the 3rd level and consists of the folding of the polypeptide chain as a result of interactions between the side chains of amino acids that lie in different regions of the primary sequence

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116
Q

What is the quaternary structure of proteins?

A

the 4th level and consists of the interactions between different polypeptide chains in proteins composed of more than one polypeptide

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117
Q

Isoelectric points have a net charge of

A

0

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118
Q

Why is pL of basic proteins above 7?

A

NH2 group is basic and at neutral pH accepts proton and become NH3+

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119
Q

Why is pL of acidic proteins below 7?

A

COOH group is acidic and at neutral pH donates proton and becomes COO-

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120
Q

What is the first step in order to characterize a protein?

A

purify the protein by separating it from other components in complex biological mixtures

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121
Q

What are the sources of proteins?

A

blood, tissues, cell culture, bacteria, yeast

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122
Q

Cells are disrupted by…

A

grinding or homogenization

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123
Q

‘Crude extract’ containing organelles are fractionated by..

A

high-speed centrifugation or ultracentrifugation

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124
Q

What are protein separations based on?

A

size, charge, solubility, specific biological interaction

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125
Q

Solubility: (salting out)

A

proteins are less stable at high salt concentrations

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126
Q

What happens when the salt concentration is increased?

A

as a result of the increased demand for solvent molecules, the
protein-protein interactions become stronger; the protein molecules coagulate by forming hydrophobic
interactions with each other

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127
Q

Salt can be removed using ….

A

dialysis

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128
Q

What is dialysis?

A

used to remove small molecules, such as salts from proteins

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129
Q

What is the process of dialysis?

A

The protein-salt solution is added to a
semipermeable membrane tube
The tube is immersed in a dilute buffer
solution
small molecules will pass through
large protein molecules will be retained in the tube

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130
Q

What is the process of gel filtration chromatography?

A

based on size - Molecules move through a bed of porous
beads, diffusing into the beads to greater or lesser degrees.
Smaller molecules diffuse into the pores of the beads and therefore move through the bed more slowly
larger molecules enter less or not at all and thus move through the bed more quickly.

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131
Q

Charge: Ion-Exchange chromatography

A

The beads are attached to ionic (charged) functional groups that interact with analyte ions of opposite charge.
Cation exchange chromatography retains cations because the stationary phase displays a negatively charged functional group
Anion exchange chromatography retains anions using positively charged functional group

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132
Q

Specific Biologic interaction: Affinity chromatography

A

Affinity chromatography is a specific method for purification of proteins, based on a highly specific biologic interaction such as
between antigen and antibody
enzyme and substrate
receptor and ligand.
A column matrix is derivatized with a ligand that binds to a specific protein in a complex mixture. The other proteins wash through the column.

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133
Q

High-performance liquid chromatography

A

is a powerful chromatographic technique for high-resolution separation of proteins, peptides, and amino acids. Separation can based on different protein characteristics

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134
Q

What is the process of HPLC?

A

sample is forced at high pressure in stream of mobile phase through a column of the stationary phase, sample is retarded by specific chemical or physical interactions with the stationary phase- The time at which a specific analyte elutes (comes out of the end of
the column) is a unique identifying characteristic of a given analyte
The eluates are monitored by ultraviolet absorption, refractive index, or fluorescence.

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135
Q

What does HPLC give?

A

high-resolution separation with high specificity and high sensitivity and is the most common technique for purification of proteins and peptides

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136
Q

What is SDS-PAGE used to separate?

A

is used to separate proteins
in electric field on the basis of their molecular weights.

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137
Q

What does Polyacrylamide gel -cross-linked polymer form?

A

a net structure though which protein molecules travel. (the smaller molecules to be separated, the higher
percentage of polyacrylamide is used)

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138
Q

The solution of proteins to be analyzed is first mixed with SDS, an anionic detergent which:

A

1) denatures secondary and non–disulfide–linked tertiary
structures,
2) applies a negative charge to each protein in proportion
to its mass, so that they may be separated strictly by length
(or number of amino acids).

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139
Q

What is the reducing agent used to reduce disulfide bonds?

A

β-mercaptoethanol

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140
Q

Charge: Isoelectric Focusing

A

Separation of proteins on the basis of their pI by conducting electrophoresis in gel containing a pH gradient.

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141
Q

Upon application (in IEF) a protein will move towards…

A

the anode or cathode until it encounters that part of the system that corresponds to its pl, where the protein has no charge and will cease to migrate

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142
Q

2D Gel electrophoresis (IEF & SDS-PAGE) what is a proteome and what is proteomics?

A

proteome- defined as the full compartment of proteins produced by a particular genome
proteomics- defined as the qualitative and quantitative comparison of proteomes under different conditions with the goal of further unraveling biological processes

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143
Q

How do you analyze a proteome of a cell?

A

proteins from a cell
are extracted and subjected to 2 dimensional gel electrophoresis (IEF in one direction followed by
SDS-PAGE in another direction).
Gel spots identified on a 2D Gel are usually attributable to one protein. If the identity of the protein is desired, the gel spot can be excised, and digested proteolytically in order to analyze

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144
Q

How to determine a protein’s amino acid composition once purified?

A

a protein is subjected to hydrolysis, commonly in 6 mol/L HCl at 110°C in a sealed and evacuated tube for 24-48 h.

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145
Q

What happens after hydrolysis?

A

the free amino acids are separated on an automated amino acid analyzer using an ion-exchange column, or
by reversed-phase (HPLC). The amino acids are reacted with chromogenic or fluorogenic reagents and are separated by charge or hydrophobicity.

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146
Q

What is sequencing?

A

a stepwise process of identifying the specific amino acids at each position in the peptide chain

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147
Q

The cleaved peptides are sequenced using the..

A

Edman Degradation technique

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148
Q

How is a protein cleaved first?

A

by digestion by specific endoproteases, such as trypsin to obtain peptide fragments

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149
Q

What is the Edman degradation method?

A

sequentially removes one residue at a time from the amino end of a peptide. (PITC, Edman reagent) binds N-terminal amino acid and introduce instability in the N-terminal peptide bond that can be selectively hydrolyzed.

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150
Q

The sequences of overlapping peptides is used to obtain…

A

the primary structure of the protein

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151
Q

How can an unknown protein be identified?

A

mass spectrometry

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152
Q

What is the process of mass spectrometry?

A

The protein is first cleaved and masses and charges of proteolytic peptides are
used as input to a search of a database of predicted masses/charges that
would arise from digestion of a list of known proteins.

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153
Q

How to determine the 3D structure of proteins?

A

x-ray crystallography and nmR spectroscopy

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154
Q

What does x-ray crystallography involve?

A

the diffraction of X-rays by the electrons of the atoms constituting the molecule. Thus the location of atoms, in the crystal can be calculated to determine the structure of the protein

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155
Q

What is nmR spectroscopy used for?

A

structural analysis of small organic
compounds and is based upon the magnetic properties of an atom’s
nucleus.

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156
Q

What is allosteric regulation?

A

a process in which a regulatory molecule binds to a site on an enzyme that is distinct from the catalytic site

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157
Q

The regulation by GTP binding is a mechanism by which…

A

the activities of intracellular proteins are controlled

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158
Q

Ran/GTP-Ran/GDP

A

nuclear-cytoplasmic transport

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159
Q

Rab proteins

A

membrane fusion

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160
Q

Ras Proteins

A

activates a number of pathways which transmit signals downstream to other gene regulatory proteins

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161
Q

What is an activated or inactivated form?

A

RAS-GTP and RAS GDP

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162
Q

What is often deregulated in cancers and what does it lead to?

A

ras and ras related proteins, lead to increased invasion and metastasis and decreased apoptosis

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163
Q

What do protein kinases catalyze?

A

protein phosphorylation by transferring phosphate groups from ATP to the hydroxyl groups of the side chains of serine, threonine, or tyrosine residues

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164
Q

What do protein-serine/threonine kinases phosphorylate?

A

serine and threonine residues

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165
Q

What do protein-tyrosine kinases phosphorylate?

A

tyrosine residues

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166
Q

What do protein phosphatase reverse?

A

protein phosphorylation and catalyze the hydrolysis of phosphorylated amino acid residues

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167
Q

Many kinases consist of multiple subunits, each of which is an…

A

independent polypeptide chain

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168
Q

Many kinases are dependent on what and consist of?

A

cAMP-dependent protein kinase and consist of two regulatory subunits and two catalytic subunits

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169
Q

What does binding of cAMP to regulatory subunits induce?

A

a conformational change that leads to their dissociation from regulatory subunits

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170
Q

The free catalytical subunits are…

A

enzymatically active

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171
Q

Proteins can be modified by…

A

methylation and acetylation

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172
Q

Why are post-transitional modifications of histones are of special interest?

A

may regulate transcriptional activity of cells and regulate the level of different proteins in the cells

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173
Q

What do specific histone modifications result in?

A

more open (transcriptionally active) or condense (repressed) chromatin state

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174
Q

What happens when chromatin is open?

A

transcription factors can access DNA and initiate gene transcription

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175
Q

Where does histone phosphorylation occur?

A

serine residues and also correlates with transcriptional activation

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176
Q

Where does histone acetylation occur?

A

lysine residues and correlates with transcription activation

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177
Q

Where does methylation occur?

A

lysine and arginine residues and correlates with transcriptional repression

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178
Q

Specific histone modifications are recognized by what?

A

transcriptional factors or other proteins that regulate modification of chromatin and initiation of transcription-histone code

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179
Q

What is the histone code?

A

is a hypothesis that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications to histone proteins

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180
Q

Activity of genes can also be regulated by …

A

methylation of Cytosine residue on DNA molecule which would
usually inhibit the transcription

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181
Q

What is epigenetics?

A

is the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence (for example DNA methylation and histone
modification).

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182
Q

What does evidence supporting epigenetics show?

A

these mechanisms can enable the
effects of parents’ experiences to be passed down to subsequent generations

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183
Q

What is nitrosylation?

A

the addition of NO groups to the side chains of cysteine residues

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184
Q

The levels of proteins within cells are determined by…

A

rates of synthesis & rates of degradation

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185
Q

What happens with faulty or damaged proteins?

A

they are recognized and rapidly degraded within cells, thereby eliminating the consequences of mistakes made during protein synthesis

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186
Q

Ubiquitin is a marker that targets…

A

cytosolic and nuclear proteins for rapid proteolysis and recruit them to proteosome

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187
Q

What are proteasomes?

A

large multi-subunit protease complexes that recognize and degrade polyubiquinated proteins

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188
Q

Activation of ubiquitin and its conjugation to target protein through the series of enzymes. What are the proteins?

A

Activating protein, conjugating protein, ligating protein

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189
Q

What is monoubiquitination?

A

is not a marker for degradation but is away to modify a protein properties (regulation of transcription factor activities)

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190
Q

What is SUMO?

A

(small ubiquitin-related modifiers) were discovered based on their homology to ubiquitin

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191
Q

What does SUMO implicate?

A

don’t target proteins to degradation but are implicated in variety of cellular events including regulation of transcription

192
Q

Modifications of proteins with…

A

SUMO-sumoylaylation

193
Q

Ubiquitination and sumolaytion of histones may also constitute an element of the…

A

histone code

194
Q

What does the structure of a cell membrane functions to?

A

separate the interior of the cell from its environment and to define the internal compartments of eukaryotic cells, including the nucleus and cytoplasmic organelles

195
Q

What do all cell membranes share?

A

a common structural organization: bilayers of phospholipids with associated proteins

196
Q

What are the fundamental building blocks of all cell membranes?

A

phospholipids

197
Q

What do phospholipid bilayers form?

A

a stable barrier between two aqueous compartments and represent the basic structure of all biological membranes

198
Q

What do lipid bilayers behave as?

A

2D fluids in which individual molecules are free to rotate and move in lateral directions

199
Q

What is cholesterols distinct role?

A

determining membrane fluidity

200
Q

Jonathan Singer and Garth Nicolson gave what description to the cell?

A

“Fluid mosaic” when they observed that proteins are inserted into a lipid bilayer

201
Q

Where are integral membrane proteins embedded?

A

within the lipid bilayer

202
Q

What are transmembrane proteins?

A

integral membrane proteins that span the lipid bilayer

203
Q

What are peripheral membrane proteins?

A

not inserted into the lipid bilayer but associated with the membrane indirectly

204
Q

What does the selective permeability of biological membranes allow?

A

allows the cell to control and maintain its internal composition

205
Q

What cannot diffuse freely across a lipid bilayer?

A

charged (ions) and most large polar molecules

206
Q

What can cross the membrane?

A

small and uncharged molecules

207
Q

What are channel proteins?

A

form open pores through the membrane, allowing free passage of any molecule of the appropriate size

208
Q

What do carrier proteins do?

A

selectively bind and transport specific molecules such as glucose

209
Q

What is passive transport?

A

a process where molecules are transported by either channel or carrier
proteins across membranes in the energetically favorable direction

210
Q

What is active transport?

A

process where molecules are transported in an energetically unfavorable direction across a membrane if their transport is coupled to ATP hydrolysis as a source of
energy

211
Q

What is cell metabolism?

A

the sum of many ongoing individual processes by which living cells process nutrient molecules and maintain a living state

212
Q

Chemical reactions in biological systems are organized into sequences. What are the sequences called?

A

metabolic pathways

213
Q

Control of pathways is achieved via the … which do what?

A

enzymes which specifically catalyze each of the steps in a pathway

214
Q

How to organize the reactions into pathways?

A

-allows doe individual reactions to be stimulated or inhibited by changing the concentration of key compounds or by chemical modification of the enzyme
-prevents very large chemical bond energy releases which would be damaging to cells
-permits branch points which allows pathways to be directed (under different circumstances) to different end products

215
Q

What are inborn errors of metabolism?

A

mutation of a single gene results in the loss of function of the appropriate enzyme

216
Q

What do enzymes increase?

A

the rate of chemical reactions without themselves being consumed or permanently altered by the reaction, and increase reaction rates without altering the chemical equilibrium between reactants and products

217
Q

What is a substrate?

A

a molecule that is acted upon by an enzyme

218
Q

What is a product?

A

a result of the reaction between the enzyme and the substrate

219
Q

What is activation energy?

A

the energy required to reach the transition state, which constitutes a barrier to the progress of the reaction

220
Q

What does the substrate bind to?

A

a specific region of the enzyme called the active site

221
Q

What is a specific interaction?

A

the binding of a substrate to the active site of an enzyme

222
Q

What is the simplest model of enzyme-substrate interaaction?

A

lock and key model- the substrate fits precisely into the active site

223
Q

What is induced fit?

A

the process in which the configurations of both the enzyme and the substrate are modified by substrate binding

224
Q

What are prosthetic groups?

A

small molecules bound to proteins in which they play critical functional roles

225
Q

What are coenzymes?

A

low-molecular-weight organic molecules that participate in specific types of enzymatic reactions by working together with enzymes to enhance reactions rates

226
Q

What is an example of a coenzyme which functions as a carrier of electrons in oxidation-reduction reactions?

A

NAD+

227
Q

What are metabolic oxidation/reduction reactions catalyzed by?

A

a class of enzymes designated as dehydrogenases

228
Q

What do these enzymes (dehydrogenases) use?

A

one of a limited number of cofactors as electron acceptors or donors to complete the reaction as the metabolic substrate is reduced or oxidized

229
Q

What is oxidation?

A

loss of electrons from a molecule, accompanied by a loss of one or more hydrogen atoms from the molecule

230
Q

What is reduction?

A

gain of electrons by a molecule, accompanied by the gain of one or more hydrogen atoms from the molecule

231
Q

What is an important feature of most enzymes?

A

their activities are not constant but instead can be modulated

232
Q

What is feedback inhibition?

A

a type of enzyme regulation in which the product of a metabolic pathway inhibits the activity of an enzyme involved in its synthesis

233
Q

What is allosteric regulation?

A

the process wherein enzyme activity is controlled by the binding of small molecules to regulatory sites on the enzyme

234
Q

What is phosphorylation a mechanism for?

A

regulating enzyme activity- the addition of phosphate groups either stimulates or inhibits the activities of many different enzymes

235
Q

What are the two divisions of metabolism?

A

anabolism and catabolism

236
Q

What is anabolism?

A

the metabolic process that binds larger molecules from smaller ones

237
Q

What happens in anabolism?

A

energy is consumed to synthesize or combine simpler substances, such as amino acids or nucleotides, into more complex organic compounds such as enzymes and nucleic acids

238
Q

What is catabolism?

A

the metabolic process that breaks down molecules into smaller units

239
Q

What happens in catabolism?

A

Large polymeric molecules (polysaccharides, nucleic acids, and proteins) are processed into their constituent monomeric units (monosaccharides, nucleotides, and amino acids)

240
Q

Complex molecules are broken down to …

A

produce energy and reducing power

241
Q

Why does ATP need to be regenerated?

A

ATP molecule is used within a minute of its formation, during strenuous exercise, the rate of utilization of ATP is even higher

242
Q

The body utilizes energy from nutrients in the diet to produce what?

A

ATP through oxidation-reduction reactions

243
Q

What is chemical energy in our food converted to?

A

reducing agents (NADH and FADH2)

244
Q

What are the reducing agents used for?

A

to make ATP

245
Q

What does ATP store?

A

chemical energy so that it is available to the body in a readily accessible form

246
Q

3 groups of biological molecules are considered to be “fuels” for the body: Carbohydrates

A

glucose is the most abundant monomer in this group and animals- glucose is stored as glycogen

247
Q

3 groups of biological molecules are considered to be “fuels” for the body: Proteins

A

the monomers of proteins (amino acids) are a significant fuel for carnivores, but are a less significant component of out omnivorous diet- provide an important reserve of fuel molecules but are only used to a large extent in circumstances of prolonged starvation

248
Q

3 groups of biological molecules are considered to be “fuels” for the body: Fats

A

stored as triglycerides in adipose tissue and make up our major fuel store- the fatty acid components of triglycerides are readily oxidized to produce ATP

249
Q

What happens in carbohydrate catabolism?

A

(breakdown of sugars)- glycolysis breaks glucose down into pyruvate- in eukaryotes, pyruvate moves into the mitochondria, is converted into acetyl-coA and enters the citric acid cycle

250
Q

What happens in protein catabolism?

A

proteins are broken down by protease enzymes into their constituent amino acids- these amino acids are brought into the cells and can be a source of energy by being funneled into the citric acid cycle

251
Q

What happens in fat catabolism?

A

triglycerides are hydrolyzed to break them down into fatty acids and glycerol- in the liver, glycerol can be converted into glucose by way of gluconeogenesis. in many tissues (heart tissue) fatty acids are broken down through a process known as beta oxidation which results in acetyl-CoA which can then be used in the citric acid cycle

252
Q

What happens in stage 1 of catabolic processes?

A

breakdown of macromolecules occurs outside cells

253
Q

What happens in stage 2 of catabolic processes?

A

glucose to pyruvate (occurs in cytosol), pyruvate is transformed into acetyl-CoA which is the common intermediate in the energy metabolism of carbohydrates, lipids, and amino acids (happens in mitochondria)

254
Q

What happens in stage 3 of catabolic processes?

A

Acetyl-CoA enters the central metabolic engine of the cell (citric acid cycle) in the mitochondrial matrix- the citric acid cycle oxidizes acetyl-CoA to CO2 and reduces NAD+ to NADH & FAD to FADH2- the reduced nucleotides capture the energy from fuel oxidation and are the substrates for the final pathway (oxidative phosphorylation in the inner mitochondrion membrane which provides the energy for synthesis of ATP)

255
Q

What has enabled scientists to dissect complex eukaryotic genomes and probe the functions of genes?

A

gene cloning

256
Q

The presence of what is a general property of the genomes of complex eukaryotes?

A

large amounts of noncoding sequences

257
Q

What constitutes most of the DNA of higher eukaryotes?

A

non-coding sequences

258
Q

What is a gene?

A

a segment of DNA that is expressed to yield a functional product

259
Q

What are spacer sequences?

A

long DNA sequences that lie between genes

260
Q

What are exons?

A

segments of coding sequence

261
Q

What are introns?

A

(intervening sequences) are segments of noncoding sequences

262
Q

What is the entire gene transcribed to yield:?

A

a long RNA molecule and the introns are removed by splicing

263
Q

What does the gene encoding the adenovirus hexon consist of?

A

four exons interrupted by three introns

264
Q

What is RNA assembled from?

A

several distinct blocks of sequences originated from different parts of viral DNA

265
Q

What do introns not specify and what do they play a role in?

A

do not specify the synthesis of a cellular product but play a role in controlling gene expression

266
Q

When does alternative splicing occur?

A

when exons of a gene are joined in different combinations, resulting in the synthesis of different proteins from the same gene

267
Q

What are the complexes between eukaryotic DNA and proteins called?

A

chromatin- contain about twice as much protein as DNA

268
Q

What are histones?

A

small proteins containing a high proportion of the basic amino acids, arginine and lysine that facilitate binding to the negatively charged DNA molecule

269
Q

What are the 5 major types of histons?

A

H1, H2A, H2B, H3, H4

270
Q

What is the basic structural unit of chromatin and who first described it?

A

Nucleosome, Roger Kornbert in 1974

271
Q

What do nucleosome core particles contain?

A

145 base pairs of DNA wrapped around a histone octamer consisting of two molecules each of H2A, H2B, H3, H4

272
Q

What is bound to the DNA as it enters each nucleosome core particle?

A

H1

273
Q

What is euchromatin?

A

decondensed transcriptionally active interphase chromatin

274
Q

What is heterochromatin?

A

condensed transcriptionally inactive chromatin and contains highly repeated DNA sequences

275
Q

What is a centromere?

A

a specialized region of the chromosome that plays a critical role in ensuring the correct distribution of duplicated chromosomes to daughter cells during mitosis

276
Q

What is the kinetochore?

A

the protein structure in eukaryotes which assembles on the centromere and links that chromosome to microtubule polymers from the mitotic spindle during mitosis

277
Q

What are telomeres?

A

the sequences at the ends of eukaryotic chromosomes

278
Q

What do the telomere DNA sequences consist of?

A

repeats of a simple-sequence DNA containing clusters of G residues on one strand

279
Q

What did traditional biologists believe?

A

single gene and protein experiments –> understanding individual molecules and pathways

280
Q

What did systems biologists believe?

A

genome and proteome-wide experiments —> understanding integrated cell processes

281
Q

Large-scale screens based on RNA interference are being used to…

A

systematically dissect gene function in a variety of organisms

282
Q

The normal function of RNA interference inside the cells depends on the production of…

A

double stranded RNA

283
Q

How can complimentary RNA strands be produced?

A

by transcription of both template DNA strands of some genes

284
Q

What processes double-stranded RNA undergoes?

A

double stranded RNA is processed by dicer to small inhibitory RNA

285
Q

What is the function of siRNA?

A

siRNA can form a molecular complex with proteins (RISC) that strip away the sense strand of RNA, making the (iRNA) available for base pairing with mRNA

286
Q

What is the role of iRNA?

A

iRNA targets a specific mRNA for destruction, resulting in the inhibition of the biological function served by the protein coded for by the mRNA

287
Q

What must occur each time a cell divides?

A

its entire genome must be duplicated

288
Q

What is the enzyme that catalyzes the synthesis of DNA?

A

DNA polymerase

289
Q

What plays distinct roles in DNA replication and repair?

A

multiple different DNA polymerases

290
Q

How many known DNA polymerases are there in prokaryotes?

A

5

291
Q

What is the main polymerase in bacteria?

A

Pol III

292
Q

How many DNA polymerases are there in eukaryotes?

A

15

293
Q

What does Pol a complex contain?

A

primase which synthesizes an RNA primer

294
Q

What is Pol b implicated in?

A

repairing DNA

295
Q

What does Pol y replicate?

A

mitochondrial DNA

296
Q

Which polymerase is the main polymerase in eukaryotes?

A

Pol δ

297
Q

What is the structure of DNA?

A

a double helix with the bases on the inside and the sugar-phosphate backbones on the outside of the molecule

298
Q

What are bases on opposite strands paired by? (DNA)

A

hydrogen bonds between adenine and thymine and between guanine and cytosine- two DNA strands run in opposite directions, defined by the 5’ and 3’ groups of deoxyribose

299
Q

What initiates DNA replication?

A

partial unwinding of the double helix at the replication fork, facilitated by DNA helicase

300
Q

What enzyme moves into position as the DNA strands separate?

A

DNA polymerase

301
Q

In which direction do all polymerases synthesize DNA?

A

5’ to 3’ direction

302
Q

Where can DNA polymerases add a new deoxyribonucleotide?

A

a preformed primer strand that is hydrogen-bound to the template

303
Q

What is the start point for DNA polymerase?

A

a short segment of RNA primer, laid down complementary to the DNA template by an enzyme known as primase

304
Q

Why can only one new DNA strand begin at the 3’ end of the template DNA?

A

the original DNA strands are complementary and run antiparallel

305
Q

How does the other DNA strand grow?

A

opposite direction, resulting in discontinuous replication

306
Q

What are the short sections of new DNA called?

A

Okazaki fragments

307
Q

Who discovered Okazaki fragments?

A

Japanese researcher

308
Q

How are the Okazaki fragments joined together?

A

by the action of an enzyme called DNA ligase, which ligates the pieces together by forming the missing phosphodiester bonds

309
Q

How is the replication described when each new helix contains one old template strand and one newly synthesized strand?

A

semi-conservative

310
Q

What initiates the process of converting DNA information into proteins?

A

synthesis of mRNA molecules - known as transcription

311
Q

How is transcription similar to DNA replication?

A

involves unwinding a small section of the DNA double helix and exposing the bases on the two strands

312
Q

What is the difference between transcription and DNA replication regarding the copying of DNA strands?

A

transcription- only one of the two DNA strands is transcribed into mRNA
DNA replication- both strands are copied (transcribed DNA strand is called the template strand)

313
Q

How many nuclear RNA polymerases do eukaryotes have?

A

3

314
Q

What is the role of RNA polymerase I?

A

transcribes ribosomal RNA

315
Q

What is the role of RNA polymerase II?

A

transcribes messenger RNA and most small nuclear RNA

316
Q

What is the role of RNA polymerase III?

A

transcribes transfer RNA

317
Q

How are primary mRNA’S transcripts processed in eukaryotic cells?

A

synthesized as larger precursor RNA’s which are processed by splicing out introns and ligating exons into the mature mRNA

318
Q

What is the promotor site?

A

the starting point of a gene is marked by a certain base sequence

319
Q

What does the promotor of protein-encoding genes contain?

A

binding sites for the basal transcription complex and RNA polymerase II (normally within 50 bases upstream of the transcription initiation site)

320
Q

What is found in the core promotor for RNA polymerase II?

A

contains a TATA box- DNA recognition sequence for the TATA box binding protein

321
Q

What does binding of TBP to the TATA box initiate?

A

transcription complex assembly at the promotor

322
Q

What additional elements do some genes have?

A

enhancer elements which can be thousands of bases upstream or downstream of the transcription initiation site

323
Q

What is the role of enhancer elements?

A

in combination with upstream control elements, regulate and amplify the formation of the basal transcription complex

324
Q

Where does mRNA travel after it has the DNAs intructions?

A

out of the nucleus to the cytoplasm where protein synthesis takes place

325
Q

What is the next step after transcription?

A

translation- process of making proteins

326
Q

What is a ribosome made of?

A

a small subunit and a large subunits

327
Q

What is the role of tRNA?

A

transfer RNA- is responsible for bringing in the proper amino acids to the site of protein synthesis

328
Q

What is a series of three nucleotides bases on a DNA molecule called?

A

a triplet

329
Q

What is a set of three nucleotide bases on an mRNA molecule called?

A

a codon

330
Q

What is a set of three nucleotide bases on a tRNA molecule called?

A

an anticodon

331
Q

How is the anticodon related to mRNA codons?

A

the anticodon on tRNA is complementary to the mRNA codons

332
Q

What is found at the “other end” of the tRNA molecule?

A

there is an “acceptor” site where the tRNA’s specific amino acid will bind

333
Q

How many types of amino acids can each type of tRNA molecule be attached to?

A

each type of tRNA molecule can be attached to only one type of amino acid

334
Q

How many stages does protein synthesis occur in?

A

3 stages- initiation, elongation, and termination

335
Q

What happens during the initiation stage of protein synthesis?

A

the small unit of the ribosome encounters an mRNA in the cytoplasm and the mRNA message is positioned between the two ribosome subunits

336
Q

What acts as a “start” signal for the translation machinery during initiation?

A

the first A-U-G codon on the 5’ end of the mRNA acts as a ‘start’ signal

337
Q

What does the start codon (A-U-G) code for?

A

the introduction of a methionine amino acid

338
Q

Is the start codon always the same in all mRNA molecules?

A

Yes, the start codon (A-U-G) and the methionine amino acid - it codes for will always be the first in any and all mRNA molecules

339
Q

When is initiation complete?

A

when the methionine tRNA occupies one of the two binding sites on the ribosome

340
Q

What happens during elongation in protein synthesis?

A

incoming tRNA binds to the A site next to where the tRNA with the methionine attached is on the P site

341
Q

How does the correct tRNA attach during elongation?

A

attaches by having an anticodon that is complementary to the codon of the A site on the mRNA

342
Q

What enzyme forms the peptide bond during elongation?

A

peptidyl transferase forms the peptide bond between the two amino acids

343
Q

What happens after the peptide bond is formed?

A

the tRNA on the P site leaves and passes its amino acid on the tRNA on the A site

344
Q

Where does the tRNA with the two amino acids move to after passing the amino acid?

A

moves to the P site, holding the growing protein

345
Q

How does the ribosome expose a new A site during elongation?

A

the ribosomes slides down three bases (1 codon on the mRNA) exposing a new A site by the action of a translocase

346
Q

What happens during termination of protein synthesis?

A

a ‘stop’ codon signals the end of the process

347
Q

Why does protein synthesis stop at a stop codon?

A

there is no tRNA that is complementary to the stop codon, so protein synthesis stops

348
Q

What role does the releasing factor play in termination?

A

frees the newly made polypeptide chain from the last tRNA

349
Q

What happens to the mRNA molecule during termination?

A

the mRNA molecule is released from the ribosomes as the small and large subunits fall apart

350
Q

What determines the fate of the mRNA molecule after termination?

A

Depending on how much of that particular protein is needed, the mRNA can either be re-translated or degraded. All mRNA messages are eventually degraded when the protein is no longer needed.

351
Q

What does the presence of a nucleus allow?

A

gene expression to be regulated by post transcriptional mechanisms (such as alternative splicing) - enables genetic material to be protected (adding a layer of transcriptional control)

352
Q

What does the nuclear envelope separate?

A

the contents of the nucleus from the cytoplasm and provides the structural framework of the nucleus

353
Q

What does the nuclear envelope consist of?

A

complex structure- consists of two nuclear membranes (inner and outer), and underlying nuclear lamina, and nuclear pore complexes

354
Q

How does the internal composition of the nucleus get established?

A

the selective traffic of proteins and RNA’s through the nuclear pore complexes

355
Q

What is the relationship between the outer nuclear membrane and the rough ER membranes?

A

outer nucleus membrane is continuous with the membranes of the rough ER

356
Q

What is the critical function of the nuclear membranes?

A

act as a barrier that separates the contents of the nucleus from the cytoplasm

357
Q

Where is the inner and outer nuclear membranes joined at?

A

nuclear pore complex

358
Q

What does the nuclear lamina underly?

A

the inner nuclear membrane and is a fibrous meshwork that provides structural support to the nucleus

359
Q

Where do lamins extend through?

A

in a loose meshwork throughout the interior of the nucleus

360
Q

What are lamins?

A

60-80 kDa fibrous proteins that make up the nuclear lamina

361
Q

What do lamins associate with?

A

each other to form higher-order structures like other intermediate filament proteins

362
Q

What do lamins bind to?

A

specific inner nuclear membrane proteins such as emerin and the lamin B receptor and bind to chromatin through histones as well as other chromatin proteins

363
Q

What are the lamins connected to?

A

the cytoskeleton by LINC complexes that span the inner and outer membranes

364
Q

What is a nuclear membrane?

A

a phospholipid bilayer permeable only to small nonpolar molecules

365
Q

What are nuclear pore complexes?

A

are the only channels through which most polar molecules, ions, and macromolecules (proteins, RNA) can travel between the nucleus and the cytoplasm

366
Q

What are the two different mechanisms molecules can travel through the nuclear pore complex?

A

passive diffusion or selective transport

367
Q

What does a nuclear pore complex consist of?

A

a structure with eightfold symmetry organized around a large central channel, which is the route that the proteins and mRNAs cross through

368
Q

What does the nuclear pore complex consist of from a 3D view?

A

eight spokes attached to rings on the cytoplasmic and nuclear sides surrounding the central channel

369
Q

Where are the spoke-ring complexes anchored?

A

at the sites of fusion between the inner and outer membrane

370
Q

What structures form the nuclear basket-like structure on the nuclear side?

A

protein filaments extend from both cytoplasmic and nuclear rings

371
Q

What regulates transport through the central channel of the nuclear pore complex?

A

proteins lining the central channel

372
Q

What proteins are imported from the cytoplasm to the nucleus?

A

histones, DNA & RNA polymerases, transcription factors, and splicing factors

373
Q

How are these proteins tagged for import into the nucleus?

A

tagged with NLS- specific amino acid sequences recognized by transport receptors that direct their transport through the nuclear pore complex

374
Q

Who mapped the first NLS and when?

A

Alan Smith in 1984- with simian virus antigen which is localized to the nucleus of infected cells

375
Q

What happens if there is a mutation in the NLS?

A

mutation of a single Lys residue in the NLS prevents nuclear import

376
Q

What are the nuclear localization signals generally composed of?

A

short stretches of basic amino acid residues, such as lysine and arginine

377
Q

What is the T antigen nuclear localization signal?

A

a single stretch of amino acids

378
Q

What does the nuclear localization signal of nucleoplasmin consist of?

A

Lys-Arg sequence followed by Lys-Lys-Lys-Lys sequence ten amino acids downstream (called bipartite)

379
Q

What are nuclear transport receptors?

A

proteins that recognize nuclear localization signals and mediate transport across the nuclear envelope

380
Q

What are karyopherin proteins?

A

nuclear transport receptors- can be exportins or importins

381
Q

What are importins?

A

transport macromolecules to the nucleus from the cytoplasm

382
Q

What are exportins?

A

transport macromolecules from the nucleus to the cytoplasm

383
Q

What proteins regulates the movement of macromolecules through the nuclear pore?

A

Ran regulates the movement of macromolecules through the nuclear pore

384
Q

What type of protein in Ran?

A

one of several small GTP-binding proteins

385
Q

How is the activity of Ran regulated?

A

by GTP binding and hydrolysis

386
Q

What does RanGAP do?

A

RanGAP- Ran GTPase activating protein, exchanges Ran GTP for Ran GDP and localizes it to the cytoplasm

387
Q

What does RanGEF do?

A

RanGEF, Ran guanine nucleotide exchange factors, exchanges Ran GDP for Ran GTP and localizes it to the nucleus

388
Q

Where is there a high concentration of Ran GTP and Ran GDP?

A

Ran GTP- in the nucleus
Ran GDP- in the cytoplasm

389
Q

What are NLS recognized by?

A

importins

390
Q

What happens to the complex after importins recognize the NLS?

A

the complex is translocated through the nuclear pore complex

391
Q

What occurs when Ran?GTP binds to importin in the nucleus?

A

binding of Ran/GTP to importin in the nucleus changes importin conformation

392
Q

What happens after the conformation of importin changes?

A

the cargo (protein) is released

393
Q

What occurs to the importin/Ran/GTP complex after cargo release?

A

the importin/Ran/GTP complex is re-exported through the NPC, where Ran GAP hydrolyzes the GTP to GDP

394
Q

What are nuclear export signals?

A

specific amino acid sequences that target proteins for export from the nucleus

395
Q

What happens to cargo proteins in the nucleus in association with Ran/GTP?

A

in the nucleus, exportins form a stable complex with cargo proteins in association with Ran/GTP

396
Q

Where does the complex with cargo proteins go through?

A

the complex is translocated to the cytoplasmic side through the nuclear pore complex where Ran GTP hydrolyzes the GTP to GDP

397
Q

What occurs after the GTP is hydrolyzed?

A

release of Ran/GDP followed by dissociation of the cargo

398
Q

What happens to exportin after cargo release?

A

exportin is then translocated back to the nucleus

399
Q

What are the two ways transcription factor import into the nucleus are managed?

A

transcription factors associate with cytoplasmic proteins that mask their nuclear localization signals- transcription factors are maintained in the cytoplasm by phosphorylation at the NLS

400
Q

Rather than randomly winding around one another, each chromosome occupies what?

A

a discrete region of the nucleus

401
Q

What does the nuclei of mammalian cells contain?

A

clustered sites of DNA replication within which the replication of multiple DNA molecules takes place

402
Q

Components of the mRNA splicing machinery are concentrated in what?

A

discrete nuclear bodies termed nuclear speckles

403
Q

What does the Nuclei contain?

A

several other types of distinct structures, such as PML bodies-sites of accumulation of different transcription factors

404
Q

What does each nucleolar organizing region contain?

A

a cluster of tandemly repeated rRNA genes separated from each other by non-transcribed spacer DNA

405
Q

What is the primary transcript of the rRNA genes?

A

large 45S pre-rRNA, which contains the 18S, 5.8S, and 28S rRNAs

406
Q

What does the formation of ribosomes involve?

A

the assembly of the ribosomal precursor RNA with both ribosomal proteins and 5S rRNA

407
Q

When does the association of ribosomal rRNA begin?

A

while the pre-rRNA is still being synthesized

408
Q

What combines with ribosomal proteins in the nucleolus to form pre-40S and pre-60S ribosomal subunits?

A

rRNA molecules and the 5S rRNA combine with the ribosomal proteins in the nucleolus to form pre 40S and pre 60S ribosomal subunits

409
Q

What is in oocytes?

A

the rRNA genes are amplified to support the synthesis of the large numbers of ribosomes required for early embryonic development

410
Q

What are the three distinguishable regions of the nucleoli?

A

fibrillar center, dender fibrillar component, and a granular component

411
Q

What do these regions (regions of the nucleoli) thought to represent?

A

are thought to represent the sites of progressive stages of rRNA transcription, processing, and ribosome assembly

412
Q

How are eukaryotic cells distinguished from prokaryotic cells?

A

by the presence of membrane-enclosed organelles within their cytoplasm

413
Q

What is the endoplasmic reticulum?

A

a network of membrane-enclosed tubules and sacs that extends from the nuclear membrane throughout the cytoplasm

414
Q

What is the rough ER covered by?

A

ribosomes on its outer surface and is involved in protein metabolism

415
Q

What is the transitional ER involved in?

A

protein processing and is where vesicles exit to the golgi apparatus

416
Q

What is the smooth ER involved in?

A

lipid metabolism and is not associated with ribosomes

417
Q

What is the secretory pathway?

A

a cellular process where proteins are synthesized, processed, and transported to their final destination outside the cell

418
Q

What happens during the chase phase in the secretory pathway?

A

cells are incubated in media containing nonradioactive amino acids, allowing labeled proteins to be detected in the golgi

419
Q

Where do proteins travel after the golgi during a longer chase?

A

proteins travel from the golgi to the cell surface in secretory vesicles, which then fuse with the plasma membrane to release their contents outside of the cells

420
Q

What happens after a short pulse of radioactive amino acids in the secretory pathway?

A

newly synthesized proteins are localized to the rough ER

421
Q

What is the pathway for proteins in the secretory pathway?

A

rough ER —> Golgi —> secretory vesicles —> cell exterior

422
Q

How are proteins destined to remain in the cytosol or other organelles synthesized?

A

proteins destined to remain in the cytosol or to be incorporated into the nucleus, mitochondria, chloroplasts, or peroxisomes are synthesized on free ribosomes and released into the cytosol

423
Q

What does the entrance of proteins into the ER represent?

A

a major branch point for the traffic of proteins within eukaryotic cells

424
Q

Where are most proteins translocated in mammals?

A

into ER while their translation is still in progress

425
Q

What are proteins targeted to?

A

to the ER based on localization sequences that eventually get cleaved

426
Q

What is the first step in targeting proteins to the ER?

A

the association of ribosomes with ER

427
Q

David Sabatini and Gunter Blobel first proposed what in 1971?

A

that the signal for ribosome attachment to the ER might be an amino acid sequence near the amino terminus of the growing polypeptide chain

428
Q

What are microsomes?

A

small vesicles formed from the endoplasmic reticulum when cells are disrupted, so can be used in experiments instead of ER

429
Q

What happened when the secretory protein mRNA was translated on free ribosomes?

A

the proteins produced were slightly larger than the normally secreted protein

430
Q

What occurred when microsomes were added during translation?

A

the growing polypeptide chains were incorporated into the microsomes

431
Q

How were the signal sequences removed?

A

by proteolytic cleavage

432
Q

What does an amino terminal leader sequence target?

A

the polypeptide chain to the microsomes and is then cleaved by a microsomal protease

433
Q

What is the mechanism by which secretory proteins are targeted to the ER during translation?

A

the mechanism involves signal sequences that span about 20 amino acids, including a stretch of hydrophobic residues

434
Q

What happens as proteins emerge from the ribosome?

A

signal sequences are recognized and bound by signal recognition particles

435
Q

SRP consisted of SRP proteins are associated with what?

A

small cytoplasmic RNA

436
Q

What are SRP receptors?

A

are proteins on the membrane of the ER that bind the signal recognition particle

437
Q

What is a translocon?

A

is a membrane proteinous channel through which polypeptide chains are transported into the ER

438
Q

What do signal peptidase cleave?

A

the signal sequence and releases it into the lumen of the ER

439
Q

What happens to proteins destined for secretion from the cell or residence within the lumen of certain organelles?

A

these proteins are translocated across the ER membrane and released into the lumen of the ER

440
Q

Where are integral membrane proteins embedded?

A

in the ER membrane by hydrophobic sequences that span the phospholipid bilayer

441
Q

How is the lumen of the ER related to the exterior of the cell?

A

is topologically equivalent to the exterior of the cell

442
Q

What does this topological equivalence imply for plasma membrane proteins?

A

implies the domains of plasma membrane proteins that are exposed on the cell surface corresponds to the regions of polypeptide chains that are translocated into the ER lumen

443
Q

How are most transmembrane proteins destined for other compartments in the secretory pathway delivered?

A

in transport vesicles

444
Q

What is preserved regarding the orientation of these proteins during delivery?

A

the orientation of the proteins is preserved

445
Q

What needs to happen for polypeptides to be useful?

A

polypeptides must fold into distinct 3D conformations- in many cases, multiple polypeptide chains must be assembled into a functional complex

446
Q

Where do many protein folding and processing events occur for proteins in the secretory pathway?

A

occur either during translocation across the ER membrane or within the ER lumin

447
Q

What processes occur in the rough ER?

A

protein folding, assembly of multisubunit proteins, disulfide bond formation, the initial stage of glycosylation, and the addition of glycolipid anchors to some plasma membrane proteins occur

448
Q

What is glycosylation?

A

a process in which many proteins, particularly in eukaryotic cells, are modified by the addition of carbohydrates

449
Q

What are glycoproteins classified as?

A

either N-linked (on asparagine) or O-linked (on serine or threonine) depending on the site of attachment of the carbohydrate side chain

450
Q

What are most glycoproteins in eukaryotic cells destined for?

A

secretion or incorporation to plasma membrane which are transferred into ER where N-linked glycosilation is initiated

451
Q

What is the first step of N-glycosylation?

A

the transfer of a common oligosaccharide consisting of 14 sugar residues to an asparagine residue within the sequence (Asn-X-Ser or Asn-X-Thr) of a growing amino chain

452
Q

Where is the oligosaccharide assembled before being transferred in N-glycosylation?

A

within the ER on a lipid carrier called dolichol

453
Q

What happens after the oligosaccharide is transferred in N-glycosylation?

A

after transfer, 3 glucose residues are removed, with more modification occurring in the golgi

454
Q

How does O-linked glycosylation differ from N-glycosylation?

A

O-linked- sugars are added one residue at a time usually in the Golgi
N-linked- a oligosachride consisting of 14 sugar residues is added to asparagine residue in ER, removal of some residues in ER, removal of some residues and addition of other sugars in Golgi

455
Q

How are some proteins attached to the plasma membrane?

A

by glycolipids, specifically glycosylphosphatidylinositol (GPI) anchors

456
Q

Where are GPI anchors made?

A

in the ER membrane

457
Q

When are GPI anchors added to the protein?

A

to the c-terminus of the protein in the ER immediately after the completion of protein synthesis

458
Q

How are proteins attached to glycolipids transported to the cell surface?

A

like transmembrane proteins, proteins attached to glycolipids are transported to the cell surface via the secretory pathway

459
Q

How are proteins oriented in the plasma membrane when attached to glycolipids?

A

oriented in the plasma membrane with the protein exposed outside of the cells (inside the ER lumen equals outside of the cell)

460
Q

Why are many proteins synthesized in the ER rapidly degraded?

A

because protein folding in the ER is not efficient, leading to misfolded proteins

461
Q

What happens to misfolded proteins in the ER?

A

misfolded proteins are recognized and sent back out to the cytosol to be degraded by the proteasome through a pathway called ER-associated degradation

462
Q

What occurs to properly folded proteins in the ER?

A

exit the ER to the Golgi and beyond, continuing along the secretory pathway

463
Q

What is the unfolded protein response?

A

a cellular stress response in which an excess of unfolded proteins in the ER leads to general inhibition of protein synthesis, increased expression of chaperones, and increased proteasome activity

464
Q

Where are membrane lipids primarily synthesized?

A

in the ER

465
Q

Why are membrane lipids synthesized in association with existing cellular membranes?

A

Membrane lipids are synthesized in association with existing cellular membranes because they are extremely hydrophobic and cannot be synthesized in the aqueous environment of the cytosol.

466
Q

How are phospholipids synthesized on the cytosolic side of the ER membrane?

A

Phospholipids are synthesized on the cytosolic side of the ER membrane, allowing the hydrophobic fatty acid chains to remain buried in the membrane while membrane-bound enzymes catalyze their reactions with water-soluble precursors in the cytosol

467
Q

What are glycerol phospholipids synthesized from in the ER membrane?

A

Glycerol phospholipids are synthesized in the ER membrane from two fatty acids (linked to coenzyme A) and glycerol-3-phosphate, yielding phosphatidic acid, which is then inserted into the membrane. Phosphatidic acid is converted to diacylglycerol (DAG), and different polar headgroups are attached to DAG to yield different phospholipids.

468
Q

What are the three main types of lipids composing the membranes of eukaryotic cells?

A

phospholipids, glycolipids, and cholesterol.

469
Q

Why are the phospholipids added only to the cytosolic half of the ER membrane?

A

so they are added only to the cytosolic half of the bilayer

470
Q

How are phospholipids translocated across the ER membrane to ensure even growth of both halves of the bilayer?

A

by flippases, membrane proteins that catalyze the rapid translocation of phospholipids, resulting in even growth of both halves of the bilayer

471
Q

What are the two other membrane lipids synthesized in the endoplasmic reticulum (ER)?

A

Cholesterol and ceramide are synthesized in the ER.

472
Q

What is the role of the Smooth ER besides lipid synthesis?

A

The Smooth ER is involved in the production of steroid hormones and detoxification of organic chemicals.

473
Q

Where is Smooth ER abundant, and why?

A

Smooth ER is abundant in cell types that are particularly active in lipid metabolism because it plays a large role in lipid metabolism and detoxification.

474
Q

What is one of the main functions of smooth ER in liver cells?

A

One of the main functions of smooth ER in liver cells is detoxification.

475
Q

How does smooth ER adapt to detoxification needs?

A

Smooth ER can double its surface area within a few days to assist with detoxification, returning to its normal size when the assault has subsided.

Cell Bio Midterm (2 decks)

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