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