Chapters 1-3 Flashcards
cells
- small, membrane-enclosed units filled with a concentrated aqueous solution of chemicals
- the fundamental units of life
Three domains of life
- Bacteria
- prokaryotic
- Archaea
- prokaryotic
- Eukaryotes
- contain protists, plants, animals, and fungi
- life is carbon-based(organic compounds)
- the building blocks of life are invariable
Prokaryotes
- most diverse and numerous cells on Earth
- Bacteria and Archaea
- No nucles; circular chromosome
- unicellular
- reproduce asexually
- Size: 0.2-10 micrometers (µm)
- may have cell wall made of peptidoglycan
- test positive for chemical Gram stain
Eukaryotes
- show increased complexity
- genetic material found in nucleus
- uni- or multicellular
- reproduce asexually and sexually
- some have cell walls
- Size: 10-100 µm
- membrane bound organelles
Plasma Membrane
- phospholipid bilayer
- regulates the flow of material into and out of the cell
Cytosol
- site of the metabolic
- cytoplasm without other organelles
nucleus
- contains genetic information(DNA)
- nuclear envelope
- two concentric membranes
Endoplasmic Reticulum
- Involved in protein and lipid synthesis
- Protein folding
- Rough
- studded with ribosomes
- Smooth
Golgi Apparatus
- Packages and folds proteins received from ER
Peroxisomes
- Hydrogen peroxide used to break down toxic materials
Lysosomes
- Site of intercellular digestion
- degrade old and worn organelles
- break down macromolecules
- part of exchanges between plasma membrane, Golgi, and ER
Mitochondria
- Enclosed in two membranes: inner and outer
- Site of ATP production, chemical fuel for cellular processes
- Have own DNA
Chloroplasts
- Enclosed in two membrans: inner and outer
- Capture energy from sunlight, site of photosynthesis
- not in animal or fungi cells
- have own DNA
- why: endosymbiotic theory: mitochondria and chloroplasts were formerly small prokaryotes that were engulfed by larger cells
- evidence
- have their own DNA (mtDNA and ctDNA)
- DNA is circular like bacteria
- If depleted, cell cannot remake
- membrane composition similar to bacteria(proteins and lipids)
- evidence
- why: endosymbiotic theory: mitochondria and chloroplasts were formerly small prokaryotes that were engulfed by larger cells
Animal vs. plant cell organelles
Viruses
- not cells
- cannot reproduce alone (need host)
- outer protein coat
- protected interior that contains genetic material(DNA or RNA) ~10 genes
- Size: 50nm(typically)
- 100 times smaller than bacteria
- Viruses are NOT alive
Pandoravirus(2013)
- Giant viruses
- larger than some bacteria
- First: Mimivius(2003)
- Pandoravirus genome: 2500 genes
- Many unclassifiable
- Some look like protein making…?
Elements that make up cells and are essential for health
- Cells are made of relatively few types of atoms
- mainly H,C,O,N
- “Trace elements” are essential for health but only in tiny quantities
- some are required to prevent disease
Element
pure subtance(a substance with constant composition that can’t be broken down by physical processes) that can’t be decomposed into other substances by ordinary means
Compound
- a pure substance that is composed of 2 or more elements linked together in fixed proportions that can be broken down to those elements by some chemical process
- elements combine to form compounds
atom
- the smallest particle of an element that cannot be chemically or mechanically divided into smaller particles
- smallest representative unit/particle of an element
Element Isotopes
- can be stable or radioactive
- same number of protons AND electrons
- atoms of an element containing different numbers of neutrons
- Z is the same, but diff #neutrons
- A = mass # = #protons + #neutrons
- Z = atomic number = #protons
- X = symbol
- Radioactive isotopes commonly used in medicine
- I131 used to treat thyroid cancer
- Diagnostics: alzheimer’s disease
valence shell electrons
- valence shell electrons determine atom properties
ionic bond
- Donating electrons!
- a chemical bond that results from the electrostatic attraction between a cation and an anion
- two atoms linked by a chemical bond tend to be lower in chemical energy than those two atoms w/o a bond
- aka bond = less chemical energy
- so, bonded atoms are more stable
covalent bond
- sharing one or more pairs of outer shell electrons
- nonpolar: equal sharing
- polar: unequal sharing due to electronegativity
- water is polar!
- EN increases as you go to the right and up on the periodic table
Hydrogen bonds
- form between hydrogen bound to an electronegative atom and an electronegative atom
- present in water molecules
- occurs btwn H atom bonded to a small, highly EN element (FON) and an O or N atom in another molecule.
- Molecules of HF also form hbonds
- play a huge role in DNA + allow protein folding
- also occurs in: water, proteins, and nucleic acids
Hydrophilic substances
- dissolve in water
- “water-loving”
- form hydrogen bonds or electrostatic interactions
- polar molecules
- ions are solvated
pH
- Acid: hydrogen ion donor/makes hydronium(H3O+) ions in solution
- Base: hydrogen ion accepter/makes hydroxide(OH-) ions in solution
Structure of Liquid Water
- water molecule reorients once/picosecond(10-12s)
- rapidly fluctuating, irregular, hydrogen-bonded network
Hydrogen bonds give water many life supporting properties
- Cohesion and surface tension
- moderates temperature
- ice is less dense than liquid water
- “universal” solvent
comparison of ionic, p and np covalent
Building Blocks of the Cell
Carbohydrates (sugars)
- From small sugar molecules (monomers) to large poly saccharides
- 1) monosaccharides: simple sugars, basic unit
- glucose
- 2) disaccharides: two monosaccharides covalently linked
- sucrose, lactose, and maltose
- 3) oligosaccharides: a 2-10 monosaccharides covalently linked
- glucose, fructose, galactose
- 4) polysaccharides: polymers consisting of chains of >10 monosaccharide or disaccharide units
- starch, glycogen, cellulose, chitlin
- 1) monosaccharides: simple sugars, basic unit
Fatty acids and other lipids
- lipids: water insoluble compounds, soluble in organic solvents
- includes: phospholipids, steroids, vitamins
- phospholipids are the main constituent of cell membranes
- includes: phospholipids, steroids, vitamins
- main biological functions:
- storing energy
- signaling
- structural component of cell membranes
- fatty acids are amphipathic and can be saturated or unsaturated
Hydrophobic effect
- tendency of water to minimize contact with hydrophobic molecules
- hydration of aggregated nonpolar molecules involves less water molecules
Micelles
- amphiphiles form micelles and bilayers due to hydrophobic effect
- amphipathic: hydrophilic and hydrophobic portion
- Ex: phospholipids
- key component of cell membranes
- Ex: phospholipids
Amino acids
- Building blocks of proteins(polypeptides)
- 20 amino acids
- R: acidic, basic, uncharged polar, and nonpolar
- have amino group, carboxyl group(COOH), and side chain(R)
nucleotide
- building blocks of nucleic acids
- sugar+phosphate+base
- can have several phosphates or additional chemical groups
nucleoside
- base+sugar = nucleoside
- when you add phosphate side becomes tide
- s comes before t
Bond strength
- strongest ~ weakest
- Covalent > noncovalent: ionic > noncovalent: H-bond
Weak noncovalent chemical bonds
- biologically important
- many weak noncovalent bonds can form a strong overall bond
- van der waals attractions
- electrostatic attractions
- hydrogen bonds
- many weak noncovalent bonds can form a strong overall bond
van der waals attractions
- weak attraction, due to proximity and fluctuating electrical forces
electrostatic attractions
- opposite charges/ionic bonds
- occurs in:
- two proteins
- enzyme and substrate
- charged ions/molecules
- occurs in:
catabolic pathway
A series of metabolic reactions leading to breakdown of a complex organic molecule to a simpler ones, with release of energy.
anabolic pathway/biosynthetic
The series of chemical reactions that constructs or synthesizes molecules from smaller units, usually requiring input of energy (ATP) in the process.
First Law of Thermodynamics
- Law 1: conservation of energy: energy can be converted from one form to another but it cannot be created or destroyed.
second law of thermodynamics
-
Law 2: systems will change spontaneously toward those arrangements/arrangement with the greatest probability
- OR the total entropy of an isolated system always increases over time
- entropy: measure of disorder
- biological order is made possible by the release of heat energy from cells
- entropy: measure of disorder
- OR the total entropy of an isolated system always increases over time
5*How cells extract energy
- key: transfer of electrons during chemical rxns
- redox rxns
- oxidation and reduction always happen together
- OIL: oxidation is loss of e-/CH bonds
- RIG: reduction is gain of e-/CH bonds
- COUNT C-H BONDS
- decrease = oxidation
- increase = reduction
- oxidation and reduction always happen together
- redox rxns
Free Energy (G)
- Energy that can be used to do work/drive reactions
- free energy = AVAILABLE energy
- total energy at top = potential energy (P)
- G reactants
- total energy at bottom = potential energy(p)
- G products
- deltaG= Gproducts–Greactants
- when deltaG<0 and downhill rxn = energetically favorable
- cellular respiration
- when deltaG>0 unfavorable rxn so order is created
- At chemical equilibrium, deltaG=0 b/c there’s no change in concentrations of reactants
- photosynthesis
- when deltaG<0 and downhill rxn = energetically favorable
- total energy at top = potential energy (P)
Comparing Energetics of Different rxns
- deltaGo
- depends only on reactants character
- always calculated in ideal conditions: concentrations of 1M, T=37oC
- directly proportional to equilibrium constant(K)
coupled reaction
- A reaction where the the free energy of a thermodynamically favorable transformation, such as the hydrolysis of ATP, and a thermodynamically unfavorable one, are mechanistically joined into a new reaction
- In a coupled reaction energy required by 1 process is supplied by another process.
- one rxn is endothermic and the other is exothermic
- deltaG=sum of two other deltaGs and can occur as long as it is negative overall
phosphoester bond
the linkage between the 5’ sugar hydroxyl and a phosphate group
phosphodiester bond
the linkage between two nucleotides
phosphoanhydride bond
linkages between phosphate groups
base
the nitrogen-containing aromatic ring
5*glycosidic bond
linkage between the sugar and the base
three main characteristics that support the rapid evolution of prokaryotic populations
large population, rapid growth, can exchange DNA
flow of genetic info/central dogma
replication, transcription, translation
recriplat
enzyme kinetics requires characterization of:
the rate of association with the substrate, the rate of catalysis, and the regulation of the enzyme activity
in the presence and absence of a competitive inhibitor(smthng similar in shape and size to the enzyme’s substrate) what remains the same?
Vmax
electrically charged basic aa’s
Histidine, Lysine, Arginine
CH2,NH….CHINS!
He-pentagon
Looks-straight
amazing-nah he’s got (NH2) on the right side
Polar side chains aa’s
Serine, Cysteine, Tyroseine (scirt)
CH2,OH,SH (CH2 oh shit-polarizing opinions)
Serine-OH
Cysteine-SH
Tyroseine-pentagon(mouth)
Electrically charged
Aspartic, Glutamic
acid is electric
CH2,COOH (OOH acid trip)
aspartic<glutamic>
</glutamic>
nonpolar side chain aa’s
Valine, Phenylalanine
CH,H3C,CH3 = Valine (CHiVes)
CH2, carbon hexagon = phenylalanine
lala=ring around the rosy
