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UKCD Biochem Test II
definitions of terms for all chapters in Exam II
| Question | Answer |
|---|---|
| Hydrophilic | having a strong affinity for water, tend to have a charge |
| Hydrophobic | having little or no affinity for water, tend to be non polar |
| Amphipathic | having two different affinities, as a polar end (hydrophilic, charged) and non polar end (hydrophobic) |
| Common membrane lipids | glycolipids, phospholipids, cholesterol |
| Glycolipids | sugar containing lipid derived from sphinogosine |
| Cholesterol | steroid nucleus |
| Phospholipids | phosphoglycerides and sphingomyelin |
| Phosphoglycerides | glycerol backbone 3 types |
| Sphingomyelin | sphinogosine backbone |
| Micelles | circular group of lipids that form from soaps |
| Bi layers | spontaneous form of lipids due to steric hindrance |
| Naming Lipids/Fatty Acids | number of carbons/number of double bonds |
| Fatty Acids usually contain ____ number of carbons | Even |
| Fluid Mosaic Model | membranes are 2D solutions of orientated lipids and globular proteins (allows orientation) |
| Gram + | single membrane with cell wall ex streptococcus mutans involved in the production of caries, type of bacteria targeted by antibiotics |
| Gram - | two membranes, top layer has increased pores/channels, bottom layer has increased regulation ex. porphyromonas gingivalis involved in periodontal disease |
| Membrane Fluidity is controlled by | Fatty Acid composition and cholesterol content |
| Melting Temperature is controlled by | fatty acid chain length and degree of saturation |
| Role of Cholesterol | increase rigidity of membranes |
| Membranes are ____ structures | sheet like |
| Membranes are ___ molecules thick | 2 |
| Membrane thickness | 60-100 Angstroms |
| Membranes consist mainly of | lipids and proteins, contain some glycolipids and glycoprotein |
| Mass ratio of lipids to proteins ranges from | 1; 4 to 4; 1 |
| Glycolipids | carbohydrates covalently linked to lipids |
| Glycoprotein | carbohydrates covalent linked to proteins |
| Membrane proteins function as | pumps, channels, transporter enzymes and signal transducers (receptors) |
| Membranes are bound by | non covalent ionic and hydrophobic interactions |
| Membranes are asymmetric | two surfaces of cellular membranes are different |
| Lateral Diffusion | lipid molecules and proteins diffuse rapidly in the plane of the membrane |
| Transverse Diffusion | lipid molecules and proteins moving from one top/bottom does not readily occur and usually indicates death |
| Two types of protein/membrane association | integral/intrinsic and peripheral/extrinsic |
| Integral/intrinsic proteins | require a detergent to be soluble, penetrate hydrophobic core, includes trans membrane proteins |
| Trans membrane proteins | integral proteins that span the lipid bi layer |
| Peripheral/extrinsic proteins | proteins associated with membrane lipids/membrane proteins by electrostatic interactions (charged), requires 1 M KCl/NaCl to be soluble |
| Association of Peripheral proteins with membranes serves purpose of | 1. Bring specific signaling molecules together spatially 2. Bring proteins to substrates ex. Phospholipids, lipid kinases, and lipid phosphateases 3. Regulation of protein function b/c often reversible association |
| Hydropathy plots | number of trans membrane domains in protein can be predicated from sequence |
| Transport of molecules across of a membrane may be | active or passive |
| Passive transport | facilitated diffusion occurs when ion or polar molecules move down their concentration gradient, does not require energy, releases energy ex. channel |
| Lipophilic molecules pass by | simple diffusion |
| Active transport | movement of molecules against a concentration gradient and requires ATP hydrolysis, stores energy ex. pump |
| P-Type ATPases | pump ions against ion gradients by becoming transiently phosphorylated on aspartic acid |
| ATP binding cassettes (ABC domains) | use energy of ATP binding to drive conformational changes |
| Secondary transporters | use one concentration gradient to power the formation of another |
| Anti porters | flow of one to drive another ex Na/Ca exchanger |
| Sym porters | flow of one to drive another in the same direction ex. Na/glucose |
| Uni porters | gradient flow |
| Ion channels | facilitated by ion ion repulsion |
| Voltage gated channels | undergo confirmation changes caused by changes in membrane potential |
| Ligand gated channels | open after ligand binding |
| Gap Junctions | allow ion and small molecules to flow b/w communicating cells, composed of 12 molecules of connexin which associate to form two 6 member connexons or hemi-channels |
| Aquaporins | six membrane spanning alpha helices and a central channel lined with hydrophilic residues allow water molecules to pass in single file |
| Selectivity of ion channels | 1. Restricted entry-only allowing a certain size into initially pore ex anything but Na and K 2. Dehydration of ion by selectivity filters ex. Na being too small to interact 3. Transport rapidly by electrostatic repulsion |
| Each step of the signaling cascade is designed to ___ the signal | Amplify |
| Signal amplification comes from | enzyme activity and second messenger accumulation |
| Adaptors | regulated proteins that promote protein associations but do not inherently amplify by themselves, increases efficiency |
| Examples of cytosolic kinases that are inhibited by pseudosubstrate domains of regulatory domains | PKA and PKC |
| PKC | example step in signal transduction in which convergent signaling pathways are required for activation |
| Signal Transduction | purpose is to relay signals from outside of the cell to the inside of the cell to elicit a specific response |
| Signal cascades are composed of | first messengers, receptors, second messengers, signaling intermediates and effectors |
| Which signal cascades contribute significantly to amplification? | enzyme and second messengers |
| GPCR | 7-transmembrane helix spanning receptors that bind small extracellular legends i.e. epinephrine |
| Heterotrimer g-protein | activated by receptors to stimulate adenyl cyclases leading to cAMP second messenger and formation and activation of PKA |
| Protein Tyrosine Kinase receptors Ex. | insulin receptors, EGF receptors |
| Homology domains | protein modules that fold independently for specified purposes ex. SH2, SH3, EF hands |
| Pathways may ___ to alter output or improve efficiency of signaling | intersect |
| Transducers/Effectors (used to multiply) | second messengers, kinases (lipid, serine, threonine, tyrosine, add P), phosphatases (remove P), G proteins, GTP exchange factors, phosphilipases, scaffold proteins, transcription factors, co activators |
| Feed back | phosphodiesterases, phosphatases, ion pumps |
| Hormones that use cAMP as a second messenger | epinephrine, glucagon, folic-stimulating hormones, calcitonin, Parathyroid hormone |
| Mechanism of Signal Termination | dissociation (most effective/direct), signal termination (by phosphorylation and arrestin binding), GTPase mediate cleavage of GTP-GDP, dephosphorylation |
| Oncogenes | mutated copies of normal version of homolog (proto-oncogenes) and promote cancer progression |
| Tumor suppressors | block cancer progression and function normally as negative regulators of signal transduction, usually inactivated by mutations or silenced |
| Allele | copy of a gene that comes from one parent |
| Self Fertilization | allowing the plant to fertilize itself, with itself |
| Cross Fertilization | purposely fertilization plan with another plants pollen |
| Discrete trait | traits that can be easily analyzed by presence and absence |
| Continuous trait | traits that can vary over a wide range ex height |
| Reciprocal cross | crosses that control the gender of the one of the parents |
| Law of segregation | each allele in a pair segregates with equal probability to each of the gametes, and these merge together from each parent during the process of fertilization |
| Law of Independent assortment | during gamete formation, different pairs of alleles for different traits segregate independently of each other |
| Pure line | known to be exemplars of antagonistic trait pairs, homozygous |
| P | parental generation, exemplars of antagonistic trait pairs |
| F1 | First filial generation, offspring from cross fertilization of parental generation |
| F2 | offspring from self fertilization of F1 |
| Wild Type | non mutant |
| Mutant Alleles | allele that occurs with a frequency of <1% in the general population |
| Hybrids | offspring of a cross between two individuals that each display on discrete phenotype of an antagonistic trait pair |
| Monohybrid | cross involving a single trait |
| Di hybrid | cross of two traits |
| Product Rule | probability of two independent events occurring is equal to the product of their individual probabilities |
| Sum Rule | probability of at least one of a set of mutually exclusive events occurring is equal to the sum of their individual probabilities |
| Vertical Inheritance | common in dominant disease, affected individuals always have at least one affected parent, trait tends to show up in every generation of an extended family |
| Horizontal Inheritance | common in recessive disease, affected individuals show up all in on generation and then disappears |
| Un translated Regions (UTRs) | in typical eukaryotic mRNA two segments of mRNA that are not translated into protein on either end |
| 5’ UTR | directly controls how efficiently the message is translated into protein |
| 3’ UTR | contains information that determines the half life of mRNA, how rapidly it is degraded by the cell |
| Poly-A Tail | after splicing addition of ~ 200 adenosines added, through to be involved in mRNA export from nucleus and mRNA stability |
| 5’ Cap | unusual ribonucleosie added 7-methylguanosine, important for translation, contains linkage via 5’ to 5’ Triphosphate Bridge and an added methyl group to the guanine base at position 7 resulting in a net positive charge |
| Karyotype | depiction of the mitotic chromosomes arrayed from largest to smallest |
| AXIN2 | gene involved in both oligodontia and colon cancer, example of pleitropy |
| Haploinsufficiency | loss of one copy of gene causes a loss of function phenotype |
| Antagonistic Trait Pairs | constant, but mutually exclusive alternative traits |
| Genotype | underlying biological basis of the observable phenotype |
| Phenotype | observable traits |
| Dominant | gain of function |
| Recessive | loss of function, gain of toxic function |
| Homozygous | carrying identical copies of each factor of heredity, gees |
| Heterozygous | dominant trait override recessive so only the dominant phenotype is observed |
| Pedigree | form of a family tree that follows the transmission of a given trait from generation from generation, useful for determining how a trait is inherited |
| Expressivity | the degree or intensity that a particular genotype is expressed in a phenotype |
| Modifier Genes | genes which can have subtle secondary affect on the appearance of a phenotype, major influence on expressivity |
| Penetrance | describes how many members of a population with a particular genotype show the expected phenotype |
| Consanguineous Mating | mating between relatives, lead to reappearance of diseases in later generations |
| Carrier | heterozygous for the mutant allele |
| Intron | interrupting sequences, removed |
| Extron | expressed sequences |
| Pre-mRNA | primary RNA transcript where RNA polymerase begins |
| Pleitropy | gene that carries more than one trait or function |
| Autosomes | gene is not sex linked |
| Sex Chromosomes | X and Y |
| Cell Cycle | mitosis and interphase of diploid cells |
| G1 | gap portion of interphase that is the majority of life, cell perform normal function, grow in size and acquire nutrients and resources required for division |
| G0 | special state of G1 of cells in a multi cellular organism that don’t normally divide |
| S | synthesis portion of interphase, DNA is synthesized and sister chromatids are formed, length varies from cell type and species, once started always run to completion |
| G2 | second gap of interphase after S and before M during which the cell waits with a duplicate set of DNA for a final signal to enter M phase, usually much shorter than G1 |
| Mitosis (M) | when chromosomes, nucleus and cytoplasm of cell actively segregate into two separate identical daughter cells |
| Interphase | when the cell goes about whatever it does when it is not dividing, includes G1, S and G2 |
| Amelogenesis Imperfecta | genetic disorder affecting the normal development of enamel in the teeth, through changes in the critical protein enamilin |
| Osteogenesis Imperfecta | disorder that causes bone to fracture easily, wide range of skeletal deformities, and 50% of people with this have Dentinogenesis imperfecta |
| Dentinogenesis Imperfecta | discolored teeth prone to decay, |
| Incomplete dominance | F1 hybrid phenotype resembles neither parent actually resembles blending ex flower color |
| Co dominance | F1 hybrid phenotype includes aspects from both parents ex blood types |
| Epitasis | alleles of one gene mask those of another ex Bombay phenotype |
| Haploid | 1 n ex gametes |
| Diploid | 2 n |
| Homologous | matched chromosomes |
| Meiosis | process in germ cells that produces gametes, chromosomes replicate once and nuclei divide twice |
| Synapsis | process when matching chromomses become zipped together |
| Synatonemal Complex | elaborate protein structure of Synapsis molecular zipper |
| Chiasmata | point of crossing over that is visible |
| Cystic Fibrosis | recessive genetic disease, decreased water movement across cell membrane which builds up debris and bacteria that causes tissue damage, at high risk for dental caries |
| Haplotype | piece of a chromosome that you are following from generation to generation |
| Genome Wide Association study (GWAS) | used to map heritability of complex traits, examination of many common genetic variants in different individual to see if the variant is associated with a trait focus on associations between SNPs and traits like major disease |
| LOD score | logarithm of odds, base 10 compares likelihood of obtaining test data if two loci are indeed linked to the likelihood of observing the same data purely by change, >3-evidnece for linkage, <2 – evidence to exclude linkage |
| Centimorgans | roughly 1 million bases, measurement of the spots on a chromosome |
Created by:
wiechartm
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