cell cycle Flashcards
made of lipids and proteins, phospholipid bilayer, fluid mosaic model (constant movement of different types of molecules in a pattern making it impossible to form a fully impenetrable barrier), semi-permeable
plasma membrane
contains primary genome of the cell. transcription of RNA, controlled import and export of both RNA and proteins
nucleus
3 types: actin (forms filaments that provide cells with mechanical support and driving forces for movement), microtubules (the components of cell skeleton that determine the shape of the cell), intermediate filaments (structural function bear tension to maintain the shape of the cell and anchor nucleus and other organelles)
cytoskeleton
nuclear envelope, rough ER, smooth ER, golgi apparatus,
endomembrane system
lipid membrane that separates nucleus from the cytoplasm
nuclear envelope
protein biosynthesis, vesicles where synthesized proteins are packaged; lipid biosynthesis; primary store of the important secondary messenger Ca2+ in animal cells
rough ER, smooth ER
double membrane, a major site of primary metabolism, oxidative phosphorylation (harnesses the reduction of oxygen to generate ATP), fatty acid catabolism (body accessing energy stored as triglycerides), has a circular genome, evolved from symbiotic relationship with prokaryote
mitochondria
breaks down larger molecules back to useful building blocks, degradation of materials taken into the cell via endocytosis, degredation of misfolded proteins, plants have lytic vacuole instead
lysosome
double membrane, photon antenna complex, site of carbon capture, site of fatty acid biosynthesis, has a circular genome, evolved from symbiotic relationship with prokaryote
chloroplast
beta-oxidation of VLCFAs (process of breaking down very long chain fatty acids), metabolism of ROS (reactive oxygen species=byproducts of aerobic metabolism, oxidative bursts (rapid production of ROS); ROS detoxification
peroxisome
often takes up the majority of plant cell, regulates turgor in cell/plant, primary store of the important secondary messenger Ca2+, stores water and nutrients, stores cytotoxic compounds
vacuole
the process in which cells make proteins through transcription and translation
protein synthesis
DNA is a double helix with the bases on the inside and the sugar-phosphate backbones on the outside of the molecule; bases on the opposite strands are paired by hydrogen bonds between adenine (A) and thymine (T), and between guanine (G) and cytosine (C), the two DNA strands run in opposite directions defined by the 5’ and 3’ groups of deoxyribose
nucleic acid base pairing
takes place on ribosome where mRNA is read and translated into the string of amino acid chains that make up synthesized proteins
translation
recognizes and binds to its corresponding codon in the ribosome, transfers the appropriate amino acid to the end of the growing amino acid chain, then continues (with ribosome) to decode the mRNA molecule until the entire sequence is translated into a protein; aminoacyl AMP creates a charged tRNA using aminoacyl tRNA synthetase
tRNA
initiation=ribosome binds mRNA at start codon, elongation=polypeptide chain elongates by successively adding amino acids, termination=when a stop codon is encountered polypeptide is released and ribosome dissociates
translation
made up of large ribosomal subunit (60S) and small ribosomal subunit (40S); A site=aminoacyl tRNA site, P site=peptidyl tRNA site, E site=exit site
ribosome
initiation tRNA binds eukaryotic initiation factor (elF2), small ribosomal subunit (40S) binds initiator tRNA and multiple other elFs, initiator tRNA and elF2 complex binds the 40S complex, mRNA and associated elFs bind the small ribosomal subunit and elF4E binds the 5’ mRNA cap and polyA binding protein (PABP) binds the polyA 3’ tail of the mRNA, initiator tRNA/small ribosomal subunit bind the mRNA complex and scans the mRNA for first start codon-ribosome scanning requires energy provided by ATP hydrolysis, once the start codon is located, GTP hydrolysis occurs, releasing the elFs and allowing the large ribosomal subunit (60S) to bind to complete the ribosome
initiation of translation
following initiation, the first methionine tRNA is within the P site of the ribosome, the next tRNA binds to the A site along with eEF (elongation factor) if the correct base pairing is achieved between the mRNA codon (proofreading) and the tRNA anti-codon then GTP is hydrolyzed and eEF is released, the tRNA catalyzes the formation of a peptide bond between the amino acids in the P and A sites and the methionine is released from the initiator tRNA, the ribosome translocates down the mRNA molecule three nucleotides so that the E and P sites are now occupied by tRNA’s, tRNA in the E site exits ribosome
elongation of translation
stop codon aligns in the amino-acyl (A) position of the ribosome, release factor (a protein) binds to stop codon in A site, release factor allows growing peptide to be released from the final tRNA and the ribosome, once peptide released the ribosome complex disassembles
termination of translation
an enzyme that is responsible for copying a DNA sequence into an RNA sequence during transcription
RNA polymerase
recognize (via accessory proteins where to start transcription, unwind and separate DNA strands (via a DNA helicase), catalyze the addition of ribonucleotide bases to form a growing RNA strand, re-wind and reform the base pairs of the transcribed DNA
transcription
a sequence at 5’ (carbon number on sugar) end of the gene where relevant proteins (like RNA polymerase and transcription factors) bind to initiate transcription of the gene
DNA promoters
subunit of RNA polymerase II that helps initiate transcription; when this protein binds to its sequence in DNA, it causes the DNA helix to bend
TATA-binding protein (TBP)
RNA polymerase binds to the promoter region of DNA using transcription factors; TFIID, TFIIB, and TFIIF interact with the TBP to bind RNA polymerase II, TFIIE and TFIIH are necessary for promoter clearance and TFIIH unwinds DNA; mediator protein complex binds, phosphorylation of C-terminal domain (CTD)-multiple phosphorylation of the CTD of RNA polymerase II leads to the dissociation of most transcription factors and the actual synthesis of RNA
initiation of transcription
must undergo processing: addition of a 5’ guanine cap-assists in nuclear export, protects against exonucleases; addition of a 3’ poly A tail-protects against exonucleases; introns removed in a process called splicing by spliceosome; alternative splicing leads to transcript diversity
pre-mRNA to mature mRNA
RNA polymerase adds a complementary nucleotide along the template strand in the 3’ to 5’ direction
elongation of transcription
the minimum amount of energy required to activate molecules so that they can undergo a chemical reaction; transition states have the maximum amount of free energy and are very unstable, if lower there is a higher chance of the reactant (substrates) being able to achieve transition state; major determinant of reaction velocity
activation energy
lower the activation energy of a reaction; almost always a protein; speed up the rate of reactions (reaction velocity); not used up; do not change the substrate or product’s free energy, do not make reactions occur that would not normally occur
enzyme
general structure: amine group, alpha-carbon (center), carboxylic acid, R-group; differ from one another based on R-groups; building blocks of proteins
amino acids
formed when the amine group of one amino acid forms a bond with the carbonyl carbon of another (water is lost, condensation reaction); a specific type of amide bond that is used to reference proteins
peptide bond
inhibitor that binds in place of a substrate
competitive inhibition
inhibitor attaches to allosteric site and changes the shape of the active site so the substrate can’t bind to it
allosteric regulation/inhibition
double-stranded RNA is recognized and cleaved into siRNAs (20-25bp), siRNAs loaded into RNA-induced silencing complex (RISC), RISC breaks siRNA into ssRNA complexed to RISC and binds complementary mRNA, mRNA is not translated and cleaved; argonaute in RISC carries out cleavage
how dsRNA leads to silencing of mRNA signal
endogenous miRNA encoding sequences transcribed which forms secondary structure which is processed by Drosha and Dicer to form mature miRNA duplex (22-24bp), RISC/miRNA binds to target mRNA and blocks translation and degrades mRNA
miRNAs and PTGs (post-transcriptional gene silencing)
splicing differences, post-transitional modifications/functional modifications (e.g. phosphorylation), expression levels (e.g. red blood cells have lots of hemoglobin other cells don’t)
how do the proteins in different cells differ
play a major role in regulating protein expression levels; binds to a DNA sequence specific to the activator, increases gene transcription by interacting with other molecules
activator proteins
play a major role in regulating protein expression levels; prevent activator from binding DNA/transcriptional protein complex, prevent elongation of RNA by binding RNA polymerase complex
repressor proteins
primary structure: the order of amino acids end terminus to C terminus; secondary structure: alpha helix and beta pleated sheets, looking at how the amino acids are interacting with each other; tertiary structure: overall three-dimensional arrangement of its polypeptide chain, how the secondary structure elements interact with each other; quaternary structure: association of several protein chains/subunits into a closely packed arrangement, interaction of different tertiary structures
levels of folding
hydrophobic effect (proteins in a solution surrounded by water nonpolar R groups fold into itself because they want to be away from water), ionic bonds, hydrogen bonds, van der waals forces (weak electrostatic forces between different types of matter), covalent bonds (only between two cysteine residues)
forces that cause protein folding
enzyme that catalyzes the formation and breakage of disulfide bonds between cysteine residues in proteins when they fold
protein disulfide isomerase
a chemical modification of an amino acid R-group (with an exception) after translation (covalent)
post-translational modification
speed up protein folding utilizing ATP, assist folding of polypeptides during translation, prevent protein aggregation in the crowded cellular environment, also known as heat shock proteins (hsps) because of their response to stress
chaperone proteins aid correct protein folding
if the R groups of the amino acid are on the outside of the protein more than they should be, exposed hydrophobic surfaces
the chaperone machinery recognizes misfolded proteins
binds protein cell membrane via phospholipid, linked through C-terminus, synthesized in ER
glycosylphosphatidylinositol (GPI) anchor
occurs in ER and golgi apparatus, modification of newly synthesized proteins; increases protein solubility, decreases protein aggregation, signaling and receptor binding, mutation in glycosylases often embryo lethal; adding chains of sugars to the backbone of a protein through an enzymatic reaction
protein glycosylation by golgi complex
oligosaccharide is transferred from a dolichol lipid carrier to peptide chains during their translocation across the ER membrane, three glucose residues are removed; modifies proteins at one or more asparagine residues with a unique carbohydrate structure that is used as a signaling molecule in their folding pathway; post-translational modification
ER protein glycosylation
undergo cycles of glucose addition and glucose trimming
incompletely folded ER proteins
chaperone proteins help other polypeptides fold properly which go through the golgi and are sent where they need to go, if they’re misfolded they will be shuttled to ubiquitin complex where the protein is marked and proteasome (protein-degrading complex) breaks it down for recycling
ER-Associated Degradation (ERAD) pathway
in the golgi, proteins destined for the lysosome are tagged with mannose-6-phosphate
targeting of lysosomal enzymes
