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UIC / Biological Sciences / BIOS 222 / What is the characteristics of living things?

What is the characteristics of living things?

What is the characteristics of living things?

Description

School: University of Illinois at Chicago
Department: Biological Sciences
Course: Cell Biology
Professor: Aixa alfonso
Term: Spring 2018
Tags: cellular biology
Cost: 50
Name: Cell Bio Exam 1 Study Guide
Description: 10 page study guide covering the learning targets for Exam 1
Uploaded: 02/07/2018
11 Pages 309 Views 6 Unlocks
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Exam 1 Study Guide


What is the characteristics of living things?



● Characteristics of living things: 

○ Highly organized structures, display homeostasis— maintaining a relatively constant internal environment, reproduce themselves, grow and develop, take energy and matter from the environment and transform it— metabolism, receive and respond to stimuli, fundamentally similar inside + extreme diversity ● Tenets of the Cell Theory: 

○ 1. All known living things are made up of cells

○ 2. Cell = structural and functional unit of all living things

○ 3. All cells come from pre-existing cells by division

○ 4. Cells contain hereditary information that is passed from cell to cell during division


Tenets of the cell theory refers to what?



○ 5. All cells are enclosed in a plasma membrane

○ 6. All cells are fundamentally the same in chemical composition and share functionally equal processes

○ 7. Life requires expenditure of energy

● How we visualize cells: Don't forget about the age old question of What are the ways to look at federalism?

○ Light microscope: magnifies up to 1000x; resolution as small as .2 micrometers; can be brightfield, phase contrast, and differential interference contrast ■ Brightfield— stained/unstained; passes light directly through specimen ■ Phase contrast— enhances contrast in unstained cells by amplifying variations in refractive index within specimen; useful for examining We also discuss several other topics like What does the ppf represent?

living, non pigmented cells


How we visualize cells?



■ Differential interference contrast— uses optical modifications to

exaggerate differences in refractive index

○ Fluorescence microscopy: filters light (2 filters) so that only certain wavelength reaches specimen/is detected; fluorescent dyes absorb light at 1 wavelength and emit it at another

○ Confocal microscopy: light rays from outside focal plane aren’t recorded; 3-D data sets can be recorded; scanning the object in x/y-direction as well as in z direction (along the optical axis) allows viewing the object from all sides; small dimension of illuminating light spot in focal plane = stray light and photo bleaching are minimized; many slices can be superimposed giving an extended 3D focus image; uses a laser to focus on single plane in specimen We also discuss several other topics like What is the representation of federalism?

○ Electron microscopy: beam of electrons; specimen not alive

■ Scanning: 3-D image

■ Transmission:

○ Using chemical composition:

■ Bases = eosin, acids = hematoxylin and methylene blue, and

carbohydrates = carmine

○ Using localization of targeted fluorescent molecules

○ Using presence of epitope/antigen immunohistochemistry

● Different size scales: 

○ Cells themselves are measured using micrometers usually

○ Anything inside the cell is measured using nanometers

● Classes of viruses/what makes viruses different from other cells 

○ DNA viruses:

■ Double-stranded— enveloped (encased in protein cover) or unenveloped ■ Single-stranded— unenveloped

○ RNA viruses:

■ + strand— directly replicated

■ - strand— needs a complementary strand to be replicated

○ Viruses need a host cell to reproduce, do not have a metabolism, do not have translation, and genome includes both DNA and RNA

● Immunohistochemistry: 

○ Using appropriately-labeled antibodies to bind specifically to target antigens in situ to image discrete components in tissues Don't forget about the age old question of What urinary system do?

○ Steps: tissue collection and perfusion(rinsing away blood), tissue fixation, tissue embedding (to maintain their natural shape and tissue architecture during long-term storage and to facilitate sectioning prior to IHC), sectioning and mounting, de-paraffinization and epitope (antigen) retrieval, quenching/blocking endogenous target activity, blocking non-specific sites; then counterstaining and immunodetection before sealing the sample We also discuss several other topics like When does the price fall?

○ Antigen— molecule that elicits an immune response

○ Epitope— part of antigen that stimulates immune response If you want to learn more check out What is the peripheral nervous system?

○ Antibody— protein with quaternary structure that specifically binds to unique epitopes

● Ways to categorize cells: 

○ Anatomy (example: nucleus or no nucleus?)

○ Staining— Dye binds to peptidoglycan, more abundant in gram + bacterial cell wall

○ Biochemical functions

■ Photoautotrophs— organisms that carry out photosynthesis CO2, H2O, sunlight to make sugars (plants)

■ Chemoautotrophs— organisms, typically bacteria, that derive energy from the oxidation of inorganic compounds

■ Heterotrophs— organisms that cannot fix carbon and use organic carbon for growth (humans)

○ rRNA sequence— ribosomal composition and structure

■ Isolate bacteria, extract DNA, amplify 16s rRNA gene, sequence portion of 16s rRNA gene, compare sequenced gene with GenBank for a match ■ Prokaryotes, eukaryotes, and archaea

● Intracellular organelles: 

○ Eukaryotes:

■ Cytoplasm— cytosol, ribosomes, membrane-bound organelles

● Cytosol— part of the cytoplasm that is not partitioned off within

intracellular membranes; where protein synthesis and degradation

as well as most of intermediary metabolism take place

■ Nucleus— nucleoplasm, nuclear envelope, nuclear matrix, nucleolus, ribosomes, chromatin, chromosomes; genetic info.

● Nuclear envelope— inner and outer membranes, pores

● Nucleoplasm— nucleotides, enzymes, and liquid

● Nuclear matrix— ribonucleoproteins, lamins, attached to nuclear

lamina

● Nucleolus— site of ribosome synthesis

● Ribosomes— RNA/protein molecules that translate

● Chromatin— DNA, RNA, and proteins

● Chromosomes— a chromatin molecule, condensed chromatin

■ Membranes— lipids and proteins

■ Cytoskeleton— microfilaments (actin), microtubules, intermediate filaments, and spectrin

■ Mitochondria— generate usable energy from food to power cell

● Matrix— enzymes

● Inner membrane— proteins that carry out oxidation reactions of

electron-transport chain and ATP synthase that makes ATP in

matrix

● Outer membrane— permeable to molecules because of porin

● Intermembrane space— enzymes that use ATP to phosphorylate

other nucleotides

■ Endomembrane system:

● Endoplasmic reticulum 

○ Smooth (lipid synthesis and chemical modification of

proteins) and rough (has ribosomes attached for protein

synthesis)

● Golgi apparatus— processes and packages proteins

● Endosomes— vesicles on their way somewhere or coming from

somewhere

● Lysosomes— intracellular digestion of cells

● Peroxisomes— protection of cells against hydrogen peroxide

■ Chloroplasts— capture energy from sunlight and use this energy to manufacture sugar molecules

■ Vacuoles— store water in plant cells

● Ways the human microbiome contributes to our well being and optimal function: ○ produce some vitamins that we do not have the genes to make

(metabolism)

○ break down food to extract nutrients we need to survive (essential nutrients) ○ teach our immune systems how to recognize dangerous invaders and even produce helpful anti-inflammatory compounds that fight off other disease-causing microbes

○ alterations in gut microbiota composition changes in the composition of our microbiomes correlate with numerous disease states

● How living systems obey the same physical and chemical laws as non living things: ○ Cells = “open” thermodynamic systems— exchange both energy and matter with their surroundings (energy and simple molecules go in; heat, waste, and complex molecules go out)

○ Laws of thermodynamics: 

■ 1. Energy cannot be created/destroyed; total amount of E in universe remains constant (in each conversion, some E is lost as heat)

■ 2. Energy conversions increase the disorder (entropy) of the universe ● E goes towards disorder spontaneously (think how easy it is for a

room to get messy and how much E it takes to bring that room

back to order)

○ Cellular respiration of glucose creates approximately 30 ATP (reactions require ATP hydrolysis)

● The chemistry of life: 

○ Cells are mostly water; have organic and inorganic (ions) compounds ○ Small molecules: monomers, vitamins, high E compounds, modified sugars & their derivatives, hormones, & neurotransmitters

○ Most soluble vitamins in the body function as coenzymes— help enzymes with their reactions

○ Enzyme— biological catalyst that promotes and speeds up a chemical reaction without itself being altered in the process; either cut (degradation), build (synthesis), or change (modification)

○ Predominantly carbon based; humans have mostly carbon, oxygen, nitrogen, and hydrogen

○ Element— substance that cannot be broken down/converted into other substances by chemical means

○ Atom— smallest unit of a chemical element that retains the distinctive chemical properties of that element

■ Made up of protons, electrons, & neutrons

○ Has an abundance of polymers (macromolecules made out of subunits or monomers)

■ Polypeptides, RNA, DNA, phospholipids and polysaccharides ■ Principles of the polymerization process: 

● Macromolecules are always synthesized by the stepwise

polymerization of structurally similar molecules (monomers)

● The addition of each monomer occurs with the removal of a water molecule (condensation reaction) 

● The monomeric units that are to be joined have to be activated before condensation

● Activation involves coupling to a carrier molecule to form an activated monomer; different kind of carrier is used for each kind of polymer

● E to activate the monomer is provided by ATP

■ Macromolecules can be:

● Informational molecules— order of monomers is non-random and highly significant to their function

● Storage or structural macromolecules consist of a single (or few) repeating monomers, as a result the order of monomers carries no information

○ Nonpolar covalent bond— bonding electrons shared equally between 2 atoms ○ Polar covalent bond— bonding electrons not shared equally between 2 atoms->partial charges on atoms

○ Ionic bond— complete transfer of 1/+ valence electrons->full charges on resulting ions

○ Covalent bonds have a characteristic bond length

○ Bond length and strength (amount of E required to break bond) are inversely correlated

○ Double covalent bonds restrict rotation of atoms

○ Water is the universal solvent in biological systems

■ Water molecules are polar (asymmetric charge distribution), cohesive (have an affinity for each other) and have high specific heat (can stabilize temperature)

■ Can form Hydrogen bonds, bonds with each other or other polar

molecules, or bond with charged ions

■ KNOW pH = -log[H+]

○ Acids donate protons and bases accept protons

● Weak non-covalent bonds specify the shape of macromolecules and allow macromolecules to bind other selected molecules: 

○ Electrostatic forces— attraction between opp. charges

○ Hydrogen Bonds— Hydrogen shared between 2 electronegative atoms (FON) ○ Van der Waals Forces— Fluctuation in electron clouds around molecules opp. Polarize neighboring atoms; temporary dipole

○ Hydrophobic forces— hydrophobic groups interact with each other to exclude water molecules

● Synthetic biology— design and construction of new biological entities such as enzymes, genetic circuits, and cells or the redesign of existing biological systems ○ Example = Synthia (Mycobacterium laboratorium)

● Polypeptides are put together and organized in three dimensions: 

○ Backbone model— ignores the structure of the individual amino acids and just shows where the backbone of the protein (where the amino acids are hooked together)

○ Ribbon model— parts of the protein’s structure are minimized so you can focus on the location of the one spiral (helix) and how the three parts of the sheet line up

○ Wire model— shows you where the important atoms are (balls) and how they connect to each other (sticks)

○ Space-filling model— best way to imagine what the actual 3-D shape of the protein is like; great amount of detail in a space filling model, but the image is so dense that it can make it difficult to tell what kind of structure the protein has (especially on the inside)

○ Peptide bonds— join together amino acids via amide linkage

○ 4 atoms in each peptide bond form a rigid planar unit

○ Proteins— long polymers of amino acids linked by peptide bonds ■ Peptides are shorter, usually fewer than 50 amino acids long

○ Different non-covalent bonds and forces help proteins fold into 3D ● Newly synthesized proteins must fold into a precise three-dimensional (3D) conformational to display biological activity: 

○ Primary structure— sequence of amino acids in the polypeptide chain

○ Secondary structure— alpha-helices (alpha-helixes) and beta-pleated sheets; held together with H bonds

○ Tertiary structure— single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains; interactions and bonds of side chains within a particular protein

○ Quaternary structure— number and arrangement of the protein subunits with respect to one another

○ Protein molecules are heterogeneous unbranched chains of amino acids; by coiling and folding into a specific three-dimensional shape, they are able to perform their biological function

● 3D structure and function of proteins is ultimately dictated by its primary structure and the techniques we can use to can determine it: 

○ We can determine structure using:

■ X-ray crystallography

■ Nuclear Magnetic Resonance Spectroscopy

■ Cryo electron-microscopy (cryo EM)

■ Electron tomography

■ Molecular dynamics simulations

● Role of chaperones in folding of polypeptides: 

○ help bind to partially folded chains and help them fold along the most energetically favorable

● Diseases caused by protein misfolding: 

○ Jakob Disease (CJD), Variant Creutzfeldt-Jakob Disease (vCJD),

Gerstmann-Straussler-Scheinker Syndrome (GSS), Fatal Familial Insomnia (FFI) ○ Alzheimer's (beta amyloid peptide, amyloid plaques)

○ Parkinson’s disease (alpha synuclein–Lewy body aggregates)

○ Huntington’s disease (polyglutamine expansion and aggregation)

● Why some organisms can make all 20 amino acids used in protein synthesis but humans cannot: 

○ Bacteria and plants can synthesize all amino acids, but humans can’t (essential and non essential amino acids)

■ Humans lack enzymes necessary

● Explain how protein function is regulated by post-translational modifications and what those modifications are: 

○ Presence or absence of transcript, whether mRNA is translated or not, directly at the protein level

○ Between DNA and RNA transcript— transcriptional control

○ Between RNA transcript and mRNA— RNA processing control

○ Between mRNA nucleus and mRNA cytosol— RNA transport and localization control

○ Between mRNA cytosol and inactive mRNA— mRNA degradation control ○ After mRNA — translation control

○ After protein— protein activity control (active/inactive)

○ Feedback inhibition or negative regulation— an enzyme is inhibited by a product in the reaction pathway

■ regulator binds at a site outside the active site of the enzyme, alters the rate not the reaction (triggers a conformational change— active to inactive enzyme)

○ Positive regulation— enzyme activity is stimulated by a regulatory molecule ○ Controlling protein function and diversity through enzymatic chemistry ○ Phosphorylation can control protein activity by triggering a conformational

change –addition of negative charges (can increase/decreases proteins activity) ○ GTP binding proteins are also regulated by the cyclical gain and loss of a phosphate group (molecular switch)

● How and why membrane lipid composition is diverse among different organisms, among different compartments within the same cells, and between the two leaflets of the same membrane 

○ Cell membranes=selective barriers: enclose, segregate, and compartmentalize ○ All cell membranes are composed up of proteins and lipids, but some membranes also have carbohydrates

○ Lipid bilayer is the fundamental structure of all cell membranes

○ Plasma membrane is composed up of lipid-rafts (flat/invaginated) and non lipid-rafts

■ Enriched in sphingolipids, saturated phospholipids, sterols (essential for eukaryotes; synthesized de novo or taken up from the environment; plant cells synthesize a complex array of sterol mixtures, unlike animal and fungal cells that have only 1; regulate membrane fluidity and

permeability) and certain lipid linked proteins

■ Why rafts are important:

● Modulate membrane geometry and lateral movement of molecules ● Provide an additional level of compartmentalization

● Serve as sorting platforms and hubs for signal transduction

○ Lumen of each compartment in the endomembrane system is spatially equivalent to the outside of the cell

○ All membranes are amphipathic (both polar and non-polar)

○ Animal cells have many phospholipid derivatives

○ Archaeal membranes differ in the chemical structure of their lipids, they are typically isoprenoidal alcohols that are ether-linked to glycerol

■ Monolayers— tend to be less permeable to ions than bacterial or

eukaryotic membranes

○ Membrane leaflets are asymmetric:

■ Growth in the ER is symmetric and distribution is random

■ Membrane asymmetry is established by the action of flippases

■ Phospholipids only move from one membrane leaflet to the other

membrane leaflet via the function of the enzymes that can flip them

● Compare and contrast how the identity and properties of membrane lipids affect membrane fluidity 

○ 3D shape of sphingolipids and cholesterol is likely to promote self-association and segregation into rafts

○ Water’s sphere shape is favorable

○ Fluidity:

■ Unsaturated=fluid

■ Saturated=Non-fluid

○ Width:

■ Unsaturated=thin

■ Sterol=thick

○ Packing defects:

■ Unsaturated=major packing defects

■ Saturated=minor packing defects

○ Surface charge:

■ Unsaturated=neutral charge

■ Anionic head group=negative charge

○ ER has low surface charge, major packing defects, and thin

○ PM has high surface charge, minor packing defects, and thick

● Enumerate how the functions of membranes are affected by alteration of lipid composition 

○ Transition temperature (Tm) or melting point is the temperature at which the membrane can go from solid-like (gel) to fluid-like (liquid crystal)

■ Higher Tm implies the membrane is “stiffer” (more kinks)

○ Fluidity of lipid bilayer depends on its composition: Hydrocarbon tail length and saturation (# double bonds)

■ Longer chains lead to higher Tm because they are able to form stronger van der Waals forces between molecules (less fluid)

■ Cholesterol has paradoxical effects on membrane fluidity

● Below Tm it increases fluidity

● Above Tm it decreases fluidity

● State where membrane lipid synthesis takes place and how lipid composition is regulated at distinct cellular sites 

○ Cell membranes arise from pre-existing membranes

○ Membrane assembly begins in the ER

○ As membrane components (lipids and proteins) move from the ER to other compartments they are modified by enzymes that reside in each of those compartments

■ Smooth ER (cytosolic side) and Golgi are the major sites of membrane lipid biosynthesis

● How and why the two sides of the lipid bilayer (cell membranes) are structurally and functionally dissimilar: 

○ When proteins and lipids are synthesized in the cell, they are inserted into the membrane in an asymmetric fashion

○ Asymmetry is retained for long periods of time because the proteins do not rotate from one side to the other (transverse diffusion) and because all membranes are created and elongated from pre-existing asymmetric membranes

○ Lipids such as phospholipids do rotate, the absolute asymmetry of the lipids is not retained (as the case is with proteins) but rather changes over time

○ Some lipids do not rotate (i.e. glycolipids) and those that do rotate do so very slowly, so lipid asymmetry contributes to the asymmetry of the membrane ○ Structure and function depend on the interactions (outside/inside)

● Functions of lipids besides those on the cellular membrane: 

○ Boundary & permeability

○ Organization & localization of mitochondria, ER, and Golgi Apparatus ○ Transport processes of nutrients and elements

○ Signaling

○ Cell-to-cell communication

● Function of integral membrane proteins: 

○ Transporters, linkers, channels, receptors, enzymes, structural

membrane-anchoring domains, proteins involved in accumulation and transduction of energy, and proteins responsible for cell adhesion

○ Interact with both inside and outside

● Advantages to compartmentalization: 

○ Efficiency of metabolism (substrates, reactants, enzymes)

○ Contained conditions (gradients, pH)

○ Isolation of damaging substances (hydrolases, ROS)

○ Number and location of organelles can be changed dependent on cell requirements

● Mechanisms and approaches used to restrict or measure protein mobility, respectively ○ Aggregate different enzymes required to catalyze a particular sequence of reactions into large multi-component complexes (prokaryotes and eukaryotes) ■ Ribosomes=translation; transcription and DNA replication; electron transport chain and synthesis of ATP

○ Confine different metabolic processes and the proteins required to perform them within different membrane enclosed intracellular compartments (eukaryotes)

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