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BIOS Exam 2 > Condensed Information > Flashcards

Condensed Information Flashcards

1
Q

prokaryotes

A

bacteria, archaeons, lack a nucleus

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2
Q

eukaryotes

A

store DNA in their nucleus

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3
Q

nucleoid

A

where DNA is concentrated in prokaryotes

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4
Q

plasmids

A

small molecules of DNA in prokaryotes

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5
Q

pili

A

threadlike structures which transfer plasmids between bacteria

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6
Q

location of mechanisms in eukaryotes

A

DNA is transcribed to RNA in the nucleus while translation occurs in the cytoplasm

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7
Q

plasmodesmata

A

channels (in plant cells) that allow for the passage of large molecules such as mRNA and proteins between neighboring cells

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8
Q

mitochondria

A

converts chemical energy to ATP

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9
Q

protein kinase

A

enzyme that phosphorylates another molecule (ADDS a phosphate group), activates a protein

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10
Q

phosphatease

A

enzyme that de-phosphorylates another molecule (REMOVES a phosphate group), de-activates a protein

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11
Q

phosphorylation

A

(1) protein kinase binds ATP and target protein (2) transfers a phosphate group to the target protein (3) releases phosphorylates protein and ADP

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12
Q

de-phosphorylation

A

(1) phosphatase removes a phosphate group from the target protein (2) releases de-phosphorylates protein

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13
Q

GTPase (GTP-binding proteins)

A

enzymes that bind to GTP and hydrolyze it to GDP, activated proteins are bound to GTP and inactivated proteins are bound to GDP

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14
Q

Ras protein

A

GTP bound: activates and stimulates protein phosphorylation

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15
Q

GAP (GTPase-activating protein)

A

inactivates Ras protein by hydrolyzing its bound GTP to GDP

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16
Q

GEF (guanine nucleotide exchange factor)

A

indirectly activates Ras protein by binding to GDP-Ras and causing it to release its GDP which then allows the empty Ras to pick up a new GTP molecule

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17
Q

GTPase switch cycle

A

(1) on its own GTPase slowly hydrolyzes GTP to GDP (2) GDP slowly dissociates from the GTPase (3) once GDP comes off the GTPase, GTP quickly takes its place

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18
Q

nuclear envelope

A

encloses nuclear DNA and separates the nucleus and the cytoplasm

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19
Q

inner nuclear membrane

A

contains proteins that act as the binding site for chromosomes and the nuclear lamina

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20
Q

nuclear lamina

A

finely woven meshwork of protein that provides the nuclear envelope with structural support

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21
Q

outer nuclear membrane

A

continuous with the ER

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22
Q

nuclear pore (complex)

A

gates on the nuclear envelope through which molecules can enter and exit the nucleus

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23
Q

NLS (nuclear localization signal)

A

signal sequence which marks a protein for transport from the cytosol into the nucleus

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24
Q

NIR (nuclear import receptors)

A

cytosolic proteins that recognize and transport proteins with a NLS

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25
Q

NES (nuclear export signals)

A

proteins targeted for export from the nucleus by specific amino acid sequences

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26
Q

exportin

A

receptors within the nucleus who recognize NES and direct protein transport into the cytoplasm

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27
Q

Ran cycle

A

(1) Ran-GTP binds to importin (2) moves through the nuclear pore to the nucleus (3) changes conformation and releases the cargo protein to the nucleus (3) importin-Ran is exported to the cytoplasm (4) importin-Ran is hydrolyzed by Ran-GAP to Ran-GDP (5) Ran-GDP releases the importin to the cytoplasm (6) Ran-GDP is bound to NTF2 and transported to the nucleus (7) Ran-GDP is stimulated by Ran-GEF to release its GDP (8) empty Ran picks up new GTP (9) Ran-GTP binds to exportin (10) moves through the nuclear pore to the cytoplasm (11) Ran-GTP is hydrolyzed to Ran-GDP (12) the cargo protein is released into the cytoplasm

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28
Q

nucleotides

A

DNA subunits made of a sugar, a base, and 1+ phosphate group

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29
Q

deoxyribose

A

the sugar in DNA

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30
Q

DNA complimentary bases

A

A (adenine) - T (thymine) form two H-bonds
G (guanine) - C (cytosine) form three H-bonds

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31
Q

phosphodiester bond

A

DNA bonds that form when a phosphate group is covalently joined to another sugar unit

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32
Q

DNA polarity

A

the top of a DNA strand has a 5’ phosphate group and the bottom has a 3’ hydroxyl group, because of this two strands run antiparallel to each other

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33
Q

replication

A

(1) parental DNA strands unwind (2) each individual strand serves as a template for the synthesis of a complementary daughter strand (3) the process completes with two molecules, each with one parent and one daughter strand

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34
Q

transcription

A

the synthesis of RNA from a DNA template molecule

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35
Q

translation

A

the synthesis of a polypeptide chain from a mRNA template

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36
Q

ribosomes

A

a complex structure of RNA and protein located in the cytoplasm

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37
Q

ribose

A

the sugar in RNA

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38
Q

RNA complimentary bases

A

A (adenine) - U (uracil) form two H-bonds
G (guanine) - C (cytosine) form three H-bonds

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39
Q

RNA polarity

A

the top of a RNA strand has a 3’ hydroxyl group and the bottom has a 5’ phosphate group, the RNA builds by adding to the 3’ top of the sequence

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40
Q

RNA polymerase

A

the enzyme that carries out the polymerization of the RNA transcript

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41
Q

stages of transcription

A

(1) initiation: RNA polymerase and other proteins are attracted to DNA
(2) elongation: successive nucleotides are added to the 3’ end as the RNA polymerase proceeds along the template strand
(3) termination: the RNA polymerase encounters a stop codon and releases the RNA transcript
transcription always starts at a promoter and ends at a terminator

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42
Q

sigma factor

A

a protein in bacteria which facilitates RNA polymerase binding to promoters

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43
Q

components required for transcription

A

(1) template DNA (2) supply of ribonucleoside triphosphates (3) RNA polymerase

44
Q

mRNA (messenger RNA)

A

RNA molecule which combines with ribosomes to direct protein synthesis

45
Q

prokaryotic transcription and translation

A

simplest form of transcription in which the primary transcript is the mRNA and can thus move directly into translation

46
Q

eukaryotic transcription and translation

A

requires RNA processing to convert the primary transcript into mRNA which can then be translated by the ribosome

47
Q

RNA processing steps

A

(1) a 5’ cap is added to the 5’ end of the primary transcript which allows for ribosomes to recognize the mRNA (2) the transcript goes through polyadenylation in which 250 A-bearing ribonucleoptides are added to the 3’ end forming poly(A) tail (3) the transcript finally goes through RNA splicing (catalyzed by a spliceosome) where noncoding introns are removed

48
Q

exons

A

protein-coding region on transcripts

49
Q

introns

A

non-coding regions on transcripts

50
Q

rRNA (ribosomal RNA)

A

genetic information and transcripts are concentrated in the nucleolus

51
Q

tRNA (transfer RNA)

A

carries individual amino acids in a polypeptide chain for translational use

52
Q

snRNA (small nuclear RNA)

A

essential component of the spliceosome

53
Q

miRNA (microRNA) and siRNA (small interfering RNA)

A

small, regulatory RNA molecules that inhibit translation or cause the destruction of RNA transcripts

54
Q

structure of an amino acid

A

a central carbon atom bonded to (1) an amino group (2) a carboxyl group (3) an R group and (4) a hydrogen atom

55
Q

glycine

A

symmetric, small, non-polar R group which increases the flexibility of the polypeptide backbone

56
Q

proline

A

R group linked to amino group that creates kinks in the polypeptide chains and constrains protein folding

57
Q

cysteine

A

SH group that covalently joins R groups to form disulfide-bridges that connect different parts of the same protein together

58
Q

peptide bond

A

the bond formed between the carboxyl group of one amino acid and the amino group of another, the bonding releases H2O

59
Q

polypeptide (protein)

A

a polymer of amino acids connected by peptide bonds

60
Q

amino acid structure types

A

(1) primary structure: the sequence of amino acids in a protein which determines how a protein folds
(2) secondary structure: formed by interactions between stretches of amino acids in a protein
(3) tertiary structure: the overall three-dimensional shape of the polypeptide which is supported by the long-range interactions between secondary structures
(4) quaternary structure: a protein made up of multiple interacting polypeptides

61
Q

secondary structures of amino acids

A

(1) alpha helix: right handed coil which is stabilized by H-bonds
(2) beta helix: pleated back-and-forth sheet that is stabilized by H-bonds

62
Q

denatured

A

the (unnatural) unfolding of proteins

63
Q

binding sites for tRNA

A

(1) A (aminoacyl) site, (2) P (peptidyl) site, and (3) E (exit) site

64
Q

codon

A

non-overlapping group of three adjacent nucleotides that codes for a single amino acid in the polypeptide chain according to a genetic code

65
Q

anticodon

A

the three nucleotides that undergo base pairing with their corresponding codon

66
Q

tRNA sequences

A

match amino acids to mRNA codons and have CCA at their 3’ end

67
Q

aminoacyl tRNA synthetases

A

enzymes that attach a specific amino acid to a specific tRNA molecule

68
Q

initiation codon

A

the codon at which translation begins: AUG (specifies Met)

69
Q

stop codon

A

UAA, UAG, or UGA causes the polypeptide to be finished and released into the cytosol

70
Q

steps of translatoin

A

(1) initiation: the initiator AUG codon is recognized and Met is established as the first amino acid in the polypeptide chain (2) elongation: successive amino acids are added to the growing chain (3) termination: the addition of amino acids stops and the polypeptide chain is released

71
Q

initiation factors

A

a protein that binds to mRNA to initiate translation, these factors recruit a small subunit of the ribosome and the other initiation factors bring up a tRNA charged with Met, this complex moves along the mRNA unit it encounters the first AUG triplet which then establishes the translational reading frame

72
Q

elongation factors

A

a protein that breaks the high-energy bonds of GTP to provide energy for the elongation of a polypeptide chain

73
Q

release factor

A

a protein that causes a finished polypeptide chain to be freed from the ribosome

74
Q

operon

A

a group of functionally related genes located in tandem along the DNA and transcribed as a single unit from one promoter (very common in prokaryotes)

75
Q

mutation and selection

A

sequences of amino acids can be altered by mutations which will affect their protein functions

76
Q

combining different folding domains

A

genes can gain new folding domains which provides additional functions

77
Q

vesicles

A

small, membrane-enclosed sacs that transport substances within a cell or from the interior to the exterior of the cell

78
Q

endomembrane system

A

system made up of the nuclear envelope, ER, golgi apparatus, lysomes, plasma membrane, and vesicles

79
Q

exocytosis

A

a vesicle fuses with the plasma membrane and empties its contents into the extracellular membrane OR delivers proteins to the plasma membrane

80
Q

endocytosis

A

a vesicle buds off from the plasma membrane and brings material from outside the cell into the vesicle that can then fuse with other membranes

81
Q

ER (endoplasmic reticulum)

A

an organelle which is involved in the production and transportation of many proteins and lipids used both inside and outside the cell, it is physically continuous with the nuclear envelope

82
Q

lumen

A

interior of the ER

83
Q

RER (rough endoplasmic reticulum)

A

the part of the ER studded with ribosomes, it synthesizes proteins

84
Q

SER (smooth endoplasmic reticulum)

A

the part of the ER that lacks ribosomes, it is the site of fatty acid and phospholipid biosynthesis

85
Q

golgi apparatus

A

(1) further modifies proteins and lipids produced by the ER, (2) it acts as a sorting station as these proteins and lipids move to their final destination, and (3) it is the site of synthesis of most of the cell’s carbohydrates

86
Q

lysomes

A

specialized vesicles (derived from the golgi apparatus) that degrade damaged or unneeded macromolecules

87
Q

glycoproteins

A

form a flexible and protective coat over the plasma membrane and is an important component of eukaryotic cell surfaces

88
Q

signal sequences

A

amino acid sequences that allow proteins to be recognized and sorted

89
Q

SRP (signal-recognition particle)

A

RNA-protein complex that binds with a part of a polypeptide chain and marks the molecule for incorporation into the ER (eukaryotes) or the plasma membrane (prokaryotes)

90
Q

signal-anchor sequence

A

amino acid sequence in a polypeptide chain which marks it for embedding in the cell membrane

91
Q

organelles that import proteins from the cytosol

A

mitochondria, chloroplasts, peroxisomes, interior of the nucleus

92
Q

organelles that receive proteins indirectly from the ER

A

golgi apparatus, lysosomes, endosomes, inner nuclear membrane

93
Q

proteins moving from the cytosol to the nucleus

A

via nuclear pores

94
Q

proteins moving from the cytosol to the ER, mitochondria, or chloroplasts

A

via protein translocators through which proteins fold to snake across the membrane

95
Q

proteins moving from one compartment of the endomembrane system to another

A

via transport vesicles

96
Q

proteins translocated from the cytosol to the ER

A

(1) water-soluble proteins: translocated across the ER membrane into the ER lumen
(2) prospective transmembrane proteins: partially translocated across the ER membrane to become embedded in it

97
Q

coated vesicles

A

vesicles that bud from membranes and have a distinct protective coating on their cytosolic surface

98
Q

clathrin-coated vesicles

A

assemble into a basket-like network on the cytosolic surface of the membrane

99
Q

dynamin (GTPase)

A

assembles as a ring around the neck of each deeply invaginated coated pit and causes ring to constrict, pinching off vesicles from parent membranes allowing them to be moved by ATP-driven motor proteins

100
Q

adaptins

A

secure clathrin coat to vesicle membranes to help select cargo molecules for transport

101
Q

Rab proteins (GTPase)

A

specific Rab proteins on the surface of vesicles are that are recognized by tethering proteins on the cytosolic surface of the target membrane

102
Q

SNARE transmembrane proteins

A

SNAREs on a vesicle (v-SNAREs) interact with complementary SNAREs on the target membrane (t-SNAREs) causing the vesicle to firmly doc in place

103
Q

pinocytosis

A

(cellular drinking) ingestion of fluid and molecules via small pinocytic vesicles

104
Q

phagocytosis

A

(cellular eating) ingestion of large particles via vesicles called phagosomes

105
Q

aytophagy

A

additional pathway that supplies materials to lysosomes that is used to degrade obsolete parts of cells (the cell eats itself)

106
Q

endosomal maturation

A

(1) formation of multi-vesicular bodies (2) glycosylation: luminal side of endosome is protected by attaching carbohydrates to proteins in the endosome membrane (3) acidification: throughout endosome maturation the pH is steadily decreasing meaning that late endosomes are very acidic, the late endosomes are now prepared to fuse with lysomes

BIOS Exam 2 (7 decks)

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