Condensed Information Flashcards
(106 cards)
1
Q
prokaryotes
A
bacteria, archaeons, lack a nucleus
2
Q
eukaryotes
A
store DNA in their nucleus
3
Q
nucleoid
A
where DNA is concentrated in prokaryotes
4
Q
plasmids
A
small molecules of DNA in prokaryotes
5
Q
pili
A
threadlike structures which transfer plasmids between bacteria
6
Q
location of mechanisms in eukaryotes
A
DNA is transcribed to RNA in the nucleus while translation occurs in the cytoplasm
7
Q
plasmodesmata
A
channels (in plant cells) that allow for the passage of large molecules such as mRNA and proteins between neighboring cells
8
Q
mitochondria
A
converts chemical energy to ATP
9
Q
protein kinase
A
enzyme that phosphorylates another molecule (ADDS a phosphate group), activates a protein
10
Q
phosphatease
A
enzyme that de-phosphorylates another molecule (REMOVES a phosphate group), de-activates a protein
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
12
Q
de-phosphorylation
A
(1) phosphatase removes a phosphate group from the target protein (2) releases de-phosphorylates protein
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
14
Q
Ras protein
A
GTP bound: activates and stimulates protein phosphorylation
15
Q
GAP (GTPase-activating protein)
A
inactivates Ras protein by hydrolyzing its bound GTP to GDP
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
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
18
Q
nuclear envelope
A
encloses nuclear DNA and separates the nucleus and the cytoplasm
19
Q
inner nuclear membrane
A
contains proteins that act as the binding site for chromosomes and the nuclear lamina
20
Q
nuclear lamina
A
finely woven meshwork of protein that provides the nuclear envelope with structural support
21
Q
outer nuclear membrane
A
continuous with the ER
22
Q
nuclear pore (complex)
A
gates on the nuclear envelope through which molecules can enter and exit the nucleus
23
Q
NLS (nuclear localization signal)
A
signal sequence which marks a protein for transport from the cytosol into the nucleus
24
Q
NIR (nuclear import receptors)
A
cytosolic proteins that recognize and transport proteins with a NLS
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NES (nuclear export signals)
proteins targeted for export from the nucleus by specific amino acid sequences
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exportin
receptors within the nucleus who recognize NES and direct protein transport into the cytoplasm
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Ran cycle
(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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nucleotides
DNA subunits made of a sugar, a base, and 1+ phosphate group
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deoxyribose
the sugar in DNA
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DNA complimentary bases
A (adenine) - T (thymine) form two H-bonds
G (guanine) - C (cytosine) form three H-bonds
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phosphodiester bond
DNA bonds that form when a phosphate group is covalently joined to another sugar unit
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DNA polarity
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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replication
(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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transcription
the synthesis of RNA from a DNA template molecule
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translation
the synthesis of a polypeptide chain from a mRNA template
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ribosomes
a complex structure of RNA and protein located in the cytoplasm
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ribose
the sugar in RNA
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RNA complimentary bases
A (adenine) - U (uracil) form two H-bonds
G (guanine) - C (cytosine) form three H-bonds
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RNA polarity
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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RNA polymerase
the enzyme that carries out the polymerization of the RNA transcript
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stages of transcription
(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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sigma factor
a protein in bacteria which facilitates RNA polymerase binding to promoters
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components required for transcription
(1) template DNA (2) supply of ribonucleoside triphosphates (3) RNA polymerase
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mRNA (messenger RNA)
RNA molecule which combines with ribosomes to direct protein synthesis
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prokaryotic transcription and translation
simplest form of transcription in which the primary transcript is the mRNA and can thus move directly into translation
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eukaryotic transcription and translation
requires RNA processing to convert the primary transcript into mRNA which can then be translated by the ribosome
47
RNA processing steps
(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
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exons
protein-coding region on transcripts
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introns
non-coding regions on transcripts
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rRNA (ribosomal RNA)
genetic information and transcripts are concentrated in the nucleolus
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tRNA (transfer RNA)
carries individual amino acids in a polypeptide chain for translational use
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snRNA (small nuclear RNA)
essential component of the spliceosome
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miRNA (microRNA) and siRNA (small interfering RNA)
small, regulatory RNA molecules that inhibit translation or cause the destruction of RNA transcripts
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structure of an amino acid
a central carbon atom bonded to (1) an amino group (2) a carboxyl group (3) an R group and (4) a hydrogen atom
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glycine
symmetric, small, non-polar R group which increases the flexibility of the polypeptide backbone
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proline
R group linked to amino group that creates kinks in the polypeptide chains and constrains protein folding
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cysteine
SH group that covalently joins R groups to form disulfide-bridges that connect different parts of the same protein together
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peptide bond
the bond formed between the carboxyl group of one amino acid and the amino group of another, the bonding releases H2O
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polypeptide (protein)
a polymer of amino acids connected by peptide bonds
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amino acid structure types
(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
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secondary structures of amino acids
(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
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denatured
the (unnatural) unfolding of proteins
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binding sites for tRNA
(1) A (aminoacyl) site, (2) P (peptidyl) site, and (3) E (exit) site
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codon
non-overlapping group of three adjacent nucleotides that codes for a single amino acid in the polypeptide chain according to a genetic code
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anticodon
the three nucleotides that undergo base pairing with their corresponding codon
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tRNA sequences
match amino acids to mRNA codons and have CCA at their 3' end
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aminoacyl tRNA synthetases
enzymes that attach a specific amino acid to a specific tRNA molecule
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initiation codon
the codon at which translation begins: AUG (specifies Met)
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stop codon
UAA, UAG, or UGA causes the polypeptide to be finished and released into the cytosol
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steps of translatoin
(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
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initiation factors
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
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elongation factors
a protein that breaks the high-energy bonds of GTP to provide energy for the elongation of a polypeptide chain
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release factor
a protein that causes a finished polypeptide chain to be freed from the ribosome
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operon
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)
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mutation and selection
sequences of amino acids can be altered by mutations which will affect their protein functions
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combining different folding domains
genes can gain new folding domains which provides additional functions
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vesicles
small, membrane-enclosed sacs that transport substances within a cell or from the interior to the exterior of the cell
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endomembrane system
system made up of the nuclear envelope, ER, golgi apparatus, lysomes, plasma membrane, and vesicles
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exocytosis
a vesicle fuses with the plasma membrane and empties its contents into the extracellular membrane OR delivers proteins to the plasma membrane
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endocytosis
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
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ER (endoplasmic reticulum)
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
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lumen
interior of the ER
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RER (rough endoplasmic reticulum)
the part of the ER studded with ribosomes, it synthesizes proteins
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SER (smooth endoplasmic reticulum)
the part of the ER that lacks ribosomes, it is the site of fatty acid and phospholipid biosynthesis
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golgi apparatus
(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
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lysomes
specialized vesicles (derived from the golgi apparatus) that degrade damaged or unneeded macromolecules
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glycoproteins
form a flexible and protective coat over the plasma membrane and is an important component of eukaryotic cell surfaces
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signal sequences
amino acid sequences that allow proteins to be recognized and sorted
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SRP (signal-recognition particle)
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)
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signal-anchor sequence
amino acid sequence in a polypeptide chain which marks it for embedding in the cell membrane
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organelles that import proteins from the cytosol
mitochondria, chloroplasts, peroxisomes, interior of the nucleus
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organelles that receive proteins indirectly from the ER
golgi apparatus, lysosomes, endosomes, inner nuclear membrane
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proteins moving from the cytosol to the nucleus
via nuclear pores
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proteins moving from the cytosol to the ER, mitochondria, or chloroplasts
via protein translocators through which proteins fold to snake across the membrane
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proteins moving from one compartment of the endomembrane system to another
via transport vesicles
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proteins translocated from the cytosol to the ER
(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
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coated vesicles
vesicles that bud from membranes and have a distinct protective coating on their cytosolic surface
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clathrin-coated vesicles
assemble into a basket-like network on the cytosolic surface of the membrane
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dynamin (GTPase)
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
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adaptins
secure clathrin coat to vesicle membranes to help select cargo molecules for transport
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Rab proteins (GTPase)
specific Rab proteins on the surface of vesicles are that are recognized by tethering proteins on the cytosolic surface of the target membrane
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SNARE transmembrane proteins
SNAREs on a vesicle (v-SNAREs) interact with complementary SNAREs on the target membrane (t-SNAREs) causing the vesicle to firmly doc in place
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pinocytosis
(cellular drinking) ingestion of fluid and molecules via small pinocytic vesicles
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phagocytosis
(cellular eating) ingestion of large particles via vesicles called phagosomes
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aytophagy
additional pathway that supplies materials to lysosomes that is used to degrade obsolete parts of cells (the cell eats itself)
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endosomal maturation
(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
