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Bio Test III
| Question | Answer |
|---|---|
| oxidative phosphorylation | two stages: electron transport chain and chemiosmosis |
| electron transport chain | use energy from electrons to make H gradient, pump H against gradient |
| chemiosmosis | flow back with gradient through ATP synthase, uses E to phosphorylate ADP to ATP |
| electron transport chain 1: | electrons from NADH flow through Cl to electron shuttle Q |
| electron transport chain 2: | CI pumps 4 H out against gradient |
| electron transport chain 3: | electron from FADH2 enter through CII to Q CII does not pump H |
| electron transport chain 4: | Q carries electron from CI or CII to CIII |
| electron transport chain 5: | CIII passes electron to cytochrome C (electron shuttle) CIII pumps 2H per electron |
| electron transport chain 6: | Cyto C carries electron to C4 C4 passes electron to oxygen to water |
| electron transport chain 7: | C4 pumps 4H out |
| Per NADH | 10 H pumped |
| Per FADH2 | 6 H pumped |
| oxygen is the... | final electron acceptor, need oxygen for this process |
| chemiosmosis | H flow with gradient through ATP synthase use energy to add Pi to ADP- ATP |
| ATP made by oxidative phosphorylation | 1 NADH- 2.5 ATP 1 FADH2- 1.5 ATP |
| glycolysis results in | 7 ATP |
| pyruvate oxidation | 5 ATP |
| citric acid cycle | 20 ATP |
| fermentation | oxygen absent |
| Process can do without oxygen | glycolysis, which could cause a buildup of NADH |
| fermentation convert NADH- NAD | allows glycolysis to continue |
| 2 types of fermentation | yeast and mammals |
| yeast | ethanol |
| mammals | lactic acid |
| pyruvate- no oxygen | fermentation |
| pyruvate- oxygen | pyruvate oxidation, citric acid cycle, and oxidative phosphorylation |
| catabolism for ATP production 1 | carbohydrates |
| catabolism for ATP production 2 | fatty acids by betaoxidation- CAC |
| catabolism for ATP production 3 | proteins- amino acids- glycolysis and CAC |
| regulation of catabolism | key enzyme: phosphofructokinase AMP, ATP, Citrate |
| phosphofructokinase | in glycolysis, allosteric enzyme |
| AMP | low energy, activates it |
| ATP | high energy, inhibits it |
| Citrate | CAC intermediate, inhibits it |
| yeast mating | 2 mating types- a and alpha |
| yeast mating | factors bing receptors on opposite cell type, response of mating/cell fusing, new cell a/ alpha |
| local signalling types | direct contact, release ligand |
| direct contact | gap junctions, plasmodesmata, recognition molecules |
| release ligand | autocrine, paracrine, synaptic endocrine |
| gap junctions | cytoplasmic communication |
| plasmodesmata | plant cell communication |
| recognition molecules | cell surface- ligand and receptor on outside of cells |
| autocrine | ligand acts on cell secreting it |
| paracrine | ligand secreted locally and act on nearby cells |
| synaptic | neurotransmitter (specific type of ligand) is released into a synapse |
| endocrine | long distance signalling- ligand travels through the blood |
| receptors | highly specific for a ligand changes shape when ligand binds |
| GPCR | g-protein coupled receptors |
| bound to GTP | active |
| bound to GDP | inactive |
| GPCR activation step 1: | inactive G protein is bound to GDP |
| GPCR activation step 2: | ligand bings GPCR, activates G protein by removing GDP and replacing it with GTP |
| GPCR activation step 3: | G protein activates target molecule- initiates a cellular response |
| GPCR activation step 4: | G protein converts GTP to GDP to become inactive (hydrolyzes) |
| RTK activation step 1: | RTK exists as monomers on cell surface |
| RTK activation step 2: | Ligand bind and RTK dimerize |
| RTK activation step 3: | RTK transphosphorylate tyrosine on the receptor |
| RTK activation step 4: | PTyr- allows target molecules (proteins) to bind and activate- cell response |
| Ion Gated Channels | allow ions to flow through with concentration gradient, ligand controls open/closing of channel |
| Ion Gated Channel step 1: | no ligand- gate is closed ions cannot move through |
| Ion Gated Channel step 2: | ligand binds channel- opening it ions move through- cell response |
| Ion Gated Channel step 3: | ligand leaves- closes the channel |
| intracellular receptors | nucleus/cytoplasm small/hydrophobic ligands- enter cell via diffusion |
| ligand | hormone |
| signal transduction | multiple step pathways, amplify signals, regulation |
| kinase cascade | kinase a phosphorylates kinase b phosphorylates kinase c |
| phosphatase | dephosphorylate proteins-removes P used to shut off signalling pathway |
| second messengers | small nonprotein water soluble molecules or ions spread out in cell by diffusion |
| examples of second messengers | cyclic AMP cAMP, Calcium, IP3, DAG |
| GPCR- PKA Pathway Step 1: | steps of GPCR activation (write out) |
| GPCR- PKA Pathway Step 2: | GTP bound G protein activate adenylyl cyclase (target enzyme) |
| GPCR- PKA Pathway Step 3: | AC convert ATP- cAMP |
| GPCR- PKA Pathway Step 4: | cAMP binds and activates PKA- P targets and trigger cell response |
| Calcium as second messengers | High Concentration of Ca- in ER, mitochondria, outside cell Low Concentration of Ca- in cytoplasm, ligand gated ion channel- opening results in high Ca solutions in cytoplasm |
| GPCR to Calcium Pathway Step 1: | ligand bind GPCR |
| GPCR to Calcium Pathway Step 2: | GPCR activates G protein by removing GDP- GTP |
| GPCR to Calcium Pathway Step 3: | G protein activates phospholipase C |
| GPCR to Calcium Pathway Step 4: | phospholipase C cleaves the phospholipid PIP2 into DAG and IP3 |
| GPCR to Calcium Pathway Step 5: | IP3 bind to an IP3 gated calcium channel in ER membrane |
| GPCR to Calcium Pathway Step 6: | Calcium channel opens and calcium flows out with gradient |
| GPCR to Calcium Pathway Step 7: | Calcium binds to proteins to activate them cellular response |
| Regulation of Cell Response- 4 aspects of control | amplification, specificity, scaffolding for effiency, termination |
| amplification | each step increases number of molecules activated |
| specificity | each cell type- different proteins present- different response to one ligand |
| scaffolding for effiency | scaffold proteins- bind molecules in a signalling pathway together- increases speed of signal |
| termination | shut off signal |
| phosphotases | counteract kinases |
| CAD | trigger protein to hydrolyze the GTP- GDP |
| apoptosis | programmed cell death |
| apoptosis 1: | chop up DNA and proteins in cell |
| apoptosis 2: | package contents |
| apoptosis 3: | immune cells eat the packages |
| C elegans apoptosis: | capases- enzyme that cleave and activate proteins for apoptosis normal condition- no death ced 9 active- inhibits ced 4- pathway shut off |
| proteases | chop up protein |
| nucleases | chop up DNA |
| Regulation of Gene Expression | DNA transcribed into RNA which is translated into protein |
| Regulation 1: | DNA packaging/ chromatin structure |
| Regulation 2: | Transcription |
| Regulation 3: | RNA processing |
| Regulation 4: | RNA transport out of nucleus |
| Regulation 5: | Translation |
| Regulation 6: | Degrade the mRNA |
| Regulation 7: | Protein Processing |
| Regulation 8: | Transport protein to cell location/activate |
| Regulation 9: | Degrade protein |
| Chromatin Structure | packaging of DNA |
| Heterochromatin | tightly packaged, transcription is inhibited, deacetylation of histone and methylation |
| Euchromatin | loosely packaged, transcription is more active, acetylation of histone and demethylation |
| packaging is regulated by _______ in nucleosome | histones |
| histones | have tails that can be modified |
| Acetylation of histones | euchromatin add an acetyl group |
| Deacetylation of histones | heterochromatin remove acetyl group |
| Methylation | heterochromatin add methyl |
| Demethylation | euchromatin remove methyl |
| Epigenetics | inherit histone/DNA modification- gene expression patterns can be passed down |
| Transcription | initiation components of a gene- codes for a protein all sequences of DNA |
| promoter | site of where general transcription factors and RNA polymerase bind |
| transcription start site | RNA polymerase starts making mRNA |
| exons | expressed regions code for protein |
| introns | noncoding removed during RNA processing |
| poly A seq | codes for translation |
| termination region | codes for stop of transcription |
| enhancers | location where transcription activates proteins |
| control elements | sequence bound by transcriptional regulators |
| Transcription is controlled by: | general transcription factor and RNA polymerase bound to promoters combination of activators/ repressors binding control elements |
| Nuclear Localization of gene: | gene is near nuclear envelope (outside)- transcription is inhibit gene is near middle of nucleus- transcriptionally active |
| mRNA processing step 1: | add a 5 inch methyl Gcap |
| mRNA processing step 2: | removal of introns by splicing |
| mRNA processing step 3: | add poly A tail to the 3 inch end |
| Alternative Splicing | make different proteins from one gene by changing exons included |
| Transport to Cytoplasm | only processed mRNA can leave- look for 5' cap, exons, and poly A tail- leaves through a nuclear pore |
| Translation | use mRNA to make protein |
| mRNA degradution | determined by 3' UTR- untranslated region controls half-life |
| half-life | time it takes to break down half of the mRNA |
| Protein Processing | protein cleavage, covalent modification |
| Protein Cleavage | activate zymogens- inactive form of enzyme that gets cleaved to be activated digestive enzymes |
| Covalent Modification | add functional group to protein |
| Transport to all Location | transport protein to correct cellular compartment signal sequence in the protein aa that tells it where to go |
| Protein Degraduation | add ubiquitin tag- send protein to proteosome |
| proteosome | cylinder that breaks down proteins in amino acids |
| micro-RNA | small, single stranded RNA molecules that can complementary bind mRNA |
| if perfect base pair match.... | degrade the RNA |
| If partial base pair match..... | blocks the translation |
| Cancer | uncontrolled growth of cells invade other tissue spaces |
| Metastasis | breaks free from original tissue and travels to new tissue |
| oncogenes | cancer causing |
| protoncogenes | normal genes that control cell growth - can be mutated into oncogenes |
| epigenetic | change chromatin packaging to express more |
| translocate | to a new active promoter |
| gene amplification | more copies of the gene- more expression |
| point mutation | changes one nucleotide in the DNA |
| in a control element... | stimulates more transcription |
| in a coding sequence.... | protein constitutively active always on |
| Ras | g protein that signals to cell division- in 30 percent |
| Tumor Suppressor Genes | prevent uncontrolled growth |
| p53 | loss of function |
| pathogens | microbes that cause disease |
| microbes | bacteria, viruses, fungi, protozoans, prions |
| innate | present at birth, no prior exposure, fast (sec to hrs), broad (nonspecific), barriers prevent entry, internal, present in all animals |
| adaptive | develop after exposure, slow (days to week) the first time, second time is fast, specific- every pathogen is a diff response, consists of humeral and cellular, and only found in invertebraes |
| humeral | antibodies |
| cellular | cytotoxic cells |
| barrier defenses for invertebraes | exoskeleton made of chitin, line stomach with chitin, presence of lysozyme |
| lysozyme | enzyme that breaks down bacterial cell walls |
| internal defenses for invertebraes | eliminate pathogens that got through barriers |
| hemocytes (phagocytes) | phagocytose (eat) bacteria/other foreign substances |
| Process of Phagocytosis 1: | pseudopodia surrounds pathogen |
| Process of Phagocytosis 2: | pathogens fully surrounded by membrane and engulfed by endocytosis |
| Process of Phagocytosis 3: | vacoule forms- compartment |
| Process of Phagocytosis 4: | fuse vacuole with the lysosome |
| Process of Phagocytosis 5: | destroy pathogen |
| Process of Phagocytosis 6: | debris released |
| antimicrobial proteins | kill bacteria and fungi |
| innate immunity- barriers | skin, mucus membranes- mucus, ciliated epithelial cell, saliva and tears |
| mucus membranes | any internal surfaces open to environment |
| mucus | trap the pathogen |
| ciliated epithelial cells | push mucus out |
| saliva, tears | has lysozome |
| cell based defenses | innate cells use Toll like receptors to recognize pathogens |
| key examples of Toll like receptors | TLR4, TLR5, TLR3, TLR9 |
| TLR4 | bacterial LPS- cell surface- bacteria are extracellular |
| TLR5 | bacterial flagellan- cell surface- bacteria are extracellular |
| TLR3 | diRNA- virus- vesicles- viruses intracellular |
| TLR9 | unmethylated DNA- vesicles- virus intracellular |
| Innate Phagocytes | neutrophils, macrophage, dendritic cells, eosinophils |
| neutrophils | circulate in blood and first cells to respond |
| macrophages | main phagocytic cells- found in tissues |
| dendritic cells | present fragments of pathogens to T cells (adaptive) |
| eosinphilis | attack large parasitic pathogens |
| Inflammation | mast cells recognize damage and release histamine and cytokines |
| histamine | vasodilation- (open/widen), blood vessels- increase blood flow- bring in innate cells |
| Cytokines | activate innate cells |
| neutrophils arrive first.... | macrophages clean up damage and tissue heals |
| Fever | increase body temp to prevent pathogens from growing |
| Hypothalamus | controls temperature |
| Septic Shock | too extreme inflammation throughout the body |
| vasodilation everywhere.... | decrease blood pressure... leads to organ failure |
| Adaptive Immunity | made of lymphocytes, recognize antigens |
| Lymphocytes | B cells- produce antibodies T cells- cellular immunity |
| antigens | small, specific pieces of a pathogen |
| Antigen receptors | BCR- B cell receptor secreted as an antibody |
| v- variable | different for each BCR/ antibody |
| c- constant | same for everyone |
| disulflide bond | hold together |
| TCR | can't directly bind antigen requires antigen presentation MHC binds antigen TCR recognizes MHC antigen complex |
| 4 Major Characteristics | immense diversity of BCR and TCR, self tolerance, clonal expansion, and memory |
| immense diversity of BCR and TCR | achieved by gene rearrangement |
| self-tolerance | eliminate cells that recognize self |
| clonal expansion | cell proliferate/divide when activated |
| memory | respond faster and stronger with repeated exposure |
Created by:
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