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Scientists believe that all living cells today evolved from an ancestral cell that existed more than three _____ years ago.
billion
By definition, prokaryotic cells do no possess ______.
a nucleus
The _____ of an atom specifies the rules of chemistry by which atoms combine to form molecules.
electrons
When an electron jumps from one atom to another, two ions of opposite charge are generated. The ions can be held together by a mutual attraction known as
ionic bond
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Table indicates the electrons in the first 4 atomic electron shells for selected elements. Which element will form ions with a net charge of +1 in solution?
sodium, potassium
Water molecules tend to stick to each other via
hydrogen bonding
Enthalpy can be defined as
the heat content of a substance (H)
The ultimate source of energy for most living organisms is
the sun
Antibody molecules (H & L chains) and spectrin molecules (a and B subunits) are examples of multiple peptide chains. The interactions that hold the polypeptide chains together are examples of
quaternary structure
The α-helix and β-pleated sheet are examples of protein structures that are based on the formation of what type of bonds
hydrogen bonds
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The R groups found in the amino acids shown below are examples of
basic sidechains
Two or three α helices can sometimes wrap around each other to form coiled-coils. The stable wrapping of one helix around another is typically driven by _____ interactions.
hydrophobic
A lipid is considered to be an amphipathic molecule because it
interacts equally well with water and non-aqueous environments
The rate of lipid diffusion in a biological membrane is
similar to the rate of diffusion of small polar molecules in the cytoplasm
The lipid component of biological membranes that has a relatively large hydrophobic region but a very small polar head consisting only of a hydroxyl group (-OH) is
cholesterol
Lipid flip-flop refers to
the movement of lipid from one leaflet of a membrane to the other
What causes yeast demise
inability to import sugar into the cell
Placing red blood cells in a hypotonic solution, where the salt concentration is much lower than normal, leads to
cell bursting and loss of hemoglobin to create a cell ghost
Each sodium channel in a cell's membrane can conduct 1 million sodium ions across the lipid bilary, making it very important to precisely regulate when it opens and closes. Opening of the sodium channel is triggered by:
a change in membrane potential, binding of a chemical ligand to the extracellular domain of the ion channel & mechanical stress affecting the shape of the lipid bilayer
(T/F) archae are more closely related to bacteria that eukaryotes.
false
Cell theory
all living things are produced by replication of other cells
Major disadvantages of electron microscopy
samples must be dead, expensive equipment, requires great expertise
All eukaryotic cells have
a nucleus
Subatomic particle that determines the atomic number and therefore the element identity?
proton
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According to the chart, which elements are chemically inert?
helium, neon
How do protein, nucleic acid and polysaccharides molecules polymerize?
dehydration synthesis
What is the weakest type of bond?
van der Waals
Enzymes
catalysts that lower the activation energy for a given reaction
What is the ΔG for a reaction at chemical equilibium?
0
Chemical reactions that break down polymers into monomers
catabolic
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What does the Km value roughly indicate with respect to enzyme substrate interactions?
the enzyme-substrate binding affinity
_____ is often used in anabolic reactions white _____ is used mainly for catabolic reactions.
NADPH, NAD+
Protein can be unfolded by a process called
denaturation
How does an allosteric inhibitor affect the active site of an enzyme?
It binds to a second site, causing a conformation change in the enzyme that makes the active site less accommodating to the substrate.
Large-scale study of proteins
proteomics
Why are a helices and B sheets common folding patterns in polypeptides?
amino acid side chains are not involved in forming the hydrogen bonds, allowing different sequences to adopt those folding patterns.
The α-helix and β-pleated sheets are examples of protein ____ structure.
secondary
The nonpolar amino acids leucine, isoleucine and valine are conserved in the binding pocket of a particular class of proteins. What types of interactions might these residues be involved in?
hydrophobic bonding (van der Waals)
In a DNA double helix,
the 2 DNA strands run antiparallel
DNA helix 5'-GCAAGGCAGCAA-3' complentary strand?
5'-TTCGCTGCCTTGC-3'
prokaryotic
simple structural org, complexity lies in molecular organization
eukaryotic
complex structural org.
size range of a prokaryote
0.1-10 µm
size range of a eukaryote their organelle size
10-100 µm 2 µm
mitochondria & chloroplasts examples of?
endosymbiotic events
what century was microscope invented
17th
Robert Hooke discovered ___, how?
cells, in slice of cork, coined "cells" from medival monastery architectural term
Antony van Leeuwenhoek
discoveries in descriptions of protozoa, bacteria & many plants & animal cells, oral microbiology w/teeth crud sample
18th century
enlightenment, cells and microscopes were insignificant, quality of microscopes were poor
Homunculus
18th c microscope interpretation of human sperm cell
Early 19th century
advances in optical theory, construction of achromatic lense
achromatic lens
lens that is designed to limit the effects of chromatic and spherical aberration. Achromatic lenses are corrected to bring two wavelengths (typically red and blue) into focus in the same plane.
Cell theory first formulation (2 things), by who?
all organisms made of cells -cell is fundamental unit of life Mattias Schleiden & Theodor Scwann
Cell theory refinement, by who?
modern cells arise only by division of preexisting cells Rudolf Virchow
Late 19th century
link cell biology to other biological processes
apochromatic optics
resolution/visualization at the theoretical limits of visible light optics
ultracentrifuge
allowed development of protocols of cell fractionation (separates parts of cell)
Zernike
phase contrast optics, high contrast images of LIVING cells w/o staining
E.B. Wilson
wrote The Cell in Development and Heredity, combining cells with genetics & embryogenesis
After WWII (3 major developments)
radioactive isotope labels (follow), electron microscope (see), electrophoresis (separate)
1970s-Present
molecular/genetics techniques, gene chips (expression of 1000s genes at once), genomics (study of gene sequence), proteomics (study of proteins)
eukarya "crown group" kingdoms
plantae, animalia, fungi
why are/aren't viruses alive?
has nucleic acid DNA OR RNA not both & proteins, doesn't metabolize
why are/aren't viroids (plant parasites) alive?
small pieces of naked RNA, no proteins
why are/aren't prions alive
strictly proteins
central dogma sequence
DNA synthesis/replication > RNA synthesis (transcription) > protein synthesis (translation)
ionic bonds
complete transfer of e-
covalent bonds, strength?
sharing of pairs of e-, strong: 80-100 kcal/mol E
polar bond
unequal sharing of pair
non-polar bond
equal sharing of electron pair
polar covalent bonds display
partial charges
hydrogen bonds
weak interactions, 2-5 kcal/mol E, collectively are strong
hydrophilic molecules
polar & ionic, readily dissolve in water
hydrophobic molecules
non-polar, usually insoluble in water
hydrophobic interactions (van der Waals)
interactions between molecules with non-polar covalent bonds, weak: 0.1-0.3 kcal/mol E
4 macromolecules
carbohydrates, lipids, proteins, nucleic acids
monomers of polysaccharides, lipids, proteins and nucleic acids
sugars, fatty acids, amino acids, nucleotides
dehydration synthesis
removal of 1 H2O to join monomers into polymer
carbohydrates function
energy storage (starch, glycogen), structural (cellulose, chitin, peptidoglycan, cell surface/signaling markers)
hydrolysis
adding H2O to break down polymer into monomer
disaccharides
maltose (glucose + glucose) lactose (galactose + glucose) sucrose (glucose + fructose)
difference between α and β glucose
H and OH on carbon 1 are flipped
difference between cellulose and starch
carbon 5 is CH2OH on the top and OH the number 2 carbon on the bottom of all glucose monomers in starch, in cellulose it is alternating with CH2OH and OH on top and bottom of the carbon 5 and 2
glycogen
made by animals in liver, energy storage polymer
cellulose
structural polymer, hard to break down
protozoan-termite relationship
protozoan live inside termite, breaks down wood, anaerobic, put termites in pure O2 to kill them
monomer of chitin
N-acetyl glocosamine
oligosaccharides
non-repetitive sugar sequence
lipids
non-polar, hydrophobic compounds
function of lipids
energy storage (fats, triglycerides), structural (phospholipid membrane)
fatty acid
long, (mostly) ubranched hydrocarbon chains with single carboxyl group on the end, 14-20 carbons
amphipathic
hydrophilic end (carboxyl) and hydrophobic end (hydrocarbon)
triglycerol
glycerol + 3 fatty acids
saturated fat
no double bond in hydrocarbon chain
unsaturated fat
double bond in hydrocarbon chain
What links glycerol and fatty acids by dehydration synthesis?
ester linkage
phospholipid
glycerol + 2 fatty acids + phosphate group (+polar group), highly amphipathic (phosphate, polar group and glycerol are hydrophilic, fatty acid is hydrophobic), self-sealing
triaglycerols
form large spherical fat droplets in cell cytoplasm
micelle
lipid molecules that arrange themselves in a spherical form in aqueous solutions, 1 layer of hydrophilic head and tail
Phospholipid bilayer
A double layer of phospholipid molecules that is the primary component of all cellular membranes
how does soap clean
Traps the bacteria in a soap micelle, then the water washes it away. The thing about this is that we don't need to kill the bacteria on our skin, because they get trapped in the micelle and slide of in the water
cholesterol
membrane component, 4 rung structure, mostly hydrophobic w/hydroxyl or ketone group at one end
function of cholesterol, in eukaryotes or prokaryotes?
membrane components of ONLY eukaryotes to stabalize fluidity, regulate animal hormones
proteins
macromolecules, high degree of specificity in functions, 10,000 different types
protein monomer
amino acid
amino acid
amphoteric - amino groupd (base) + carboxy group (acid) + side group (polar or non-polar)
what is the polarity of an amino acid based on?
its side chain
folding of hydrophobic amino acids
folded into core of protein
folding of hydrophilic amino acids
folded out to surface of protein
what links amino acids? between which compounds?
peptide bond, amino + carboxyl groups
general structure of protein
peptide backbone + amino end (N-terminus) + carboxyl end (C-terminus) + side chains all linked by peptide bonds
primary (1°) protein structure
amino acid sequence, covalent peptide bond
secondary (2°) protein structure
- α-helix and β sheets - NO side groups involved - amino acids linked by hydrogen bonds
tertiary (3°) protein structure
3D conformation of R-group interactions including hydrophobic interactions (van der Waals), disulfide bridge, ionic bond still ONE protein
tertiary (4°) protein structure
R-group association of SEPERATE and multiple proteins
collagen
protein that makes up hair, nails etc in animals, stretchy
what structures (°) in proteins have strong bonds? weak?
strong - 1° weak - 2°, 3°, 4°
what denatures proteins?
increase in temp, increase [urea]
chaperonin protein
molecule that steers proteins along productive folding pathways, helping them fold correctly and preventing them from forming aggregates inside the cell
conditions inside chaperonin
limited hydrophilic environment--not much H2O or ions
nucleic acid components
1 - pentose sure (ribose/deoxyribose) 2 - phosphate group 3 - nitrogenous base
nucleic acid function? monomer?
storage and transmission of genetic info, nucleotide
2 types of nitrogenous bases
1. Purine adenine guanine 2. Pyrimidine thymine cytosine uracil (only in RNA)
is deoxyribose and ribose in which DNA or RNA?
deoxyribose - DNA ribose - RNA
what bond links nucleotides? at which carbons?
- phosphodiester bonds - 5'-3'
what is backbone of nucleic acid?
sugar-phosphate, the bases change
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1 - deoxyribose 2 - ribose 3 - A, T, G, C 4 - A, U, G, C 5 - double 6 - single 7 - genetic info storage 8 - genetic info expression
kinetic vs potential E
kinetic - motion potential - position
bioenergetics
energy transformation in living organisms
1st law of thermodynamics
conservation of energy - energy cannot be created or destroyed
breaking bonds = releasing or gaining ____?
releasing kinetic energy
2nd law of thermodynamics
events in universe have direction, E tend to proceed downhill from high E to low E states, in energy transformation there is a decreasing amount of energy available to do work
entropy
energy not available to do work "disorder"
Spontaneous reaction
Reaction that occurs without a constant input of energy
Gibbs Free Energy Equation
∆G = ∆H + (-T ∆S) G = Free Energy ∆H = Enthalpy ∆S = Entropy T = Absolute Temperature (Kelvins)
ΔG<0? ΔG>0? which one is favorable?
- exergonic "spontaneous" - endergonic "non-spontaneous" needs energy of activation ΔG<0
is EA in gibbs free energy budget?
no
energy of activation
energy needed to start a reaction
catalyst, example?
reduces energy of activation, interacts with components but comes out unchanged ex. enzymes: promote specific rxns
enzymes are ___ for reaction & substrate
highly specific
what happens in enzyme reaction
substrate binds to active site which changes shape of substrate and releases it
current model of active site function
induced fit
active site
center of catalytic function
substrate
reactants for a specific enzyme
2 types of enzyme inhibitors
competitive and non-competitive
non-competitive inhibitor
binds to opposite side of enzyme and changes shape of protein
Competitive Inhibitor
the binding of a ligand to an enzyme's active site to inhibit its function, do not produce product
Vmax
saturated substrate
what does Vmax/2 help determine
[substrate]
allosteric regulation
using kind of non-competitive inhibitor to regulate [ ] of molecules in a cell Z controls amt of [X], if too high it turns off enzyme
anabolic
builds complex molecules from simpler ones, endergonic
catabolic
breaks down complex molecules into simpler ones, either for components or as energy release, exergonic
ATP used for what type or rxns?
energy currency of cell, energetic
NAD+/NADH which is oxidized/reduced?
electron carrier, redox cofactor oxidized: NAD+ reduced: NADH
oxidation
loss of a pair of electrons
reduction
gain of a pair of electrons
coupled reactions
when an exergonic and endergonic reaction are coupled together so that the energetically favorable and the unfavorable reactions happen at the same time, in the same place
functions of membrane
compartmentalize, selectively permeable, signal detection, cellular interactions, surface for some reactions, energy capture/transduction
membranes allow
different environment inside than outside the cell
Langmuir Trough
creates 1 molecule thick membrane layer
what percent of a membrane mass is protein
50%
who created Fluid Mosaic Model of membrane structure? what is it?
Singer-Nicholson, bimolecular layer of lipids with proteins in globular form "floating in a sea of lipids"
Davson-Danielli Model of membrane structure
bimolecular layer of lipids coated with extended proteins
are lipids amphipathic?
yes, has hydrophobic and hydrophilic regions
what makes up a membrane
phospholipid bilayer + proteins + carbohydrates + cholesterol + glycolipids
sphingolipids, function?
amino alcohol, fatty acid carboxy group, critical component of brain cells, assemble/localize certain types of proteins
membrane carbohydrates percentage? components (types)? how are they bound? function?
- 10% - lipids (glycolipids) + proteins (glycoproteins) - covalenty - cell-cell recognition and cell interaction w/environment
what side of cell are membrane carbohydrates located?
exterior face
membrane proteins percentage? types?
- 50% - integral, peripheral & lipid-anchored
integral proteins, aka?
embedded in lipid layer, have hydrophobic region, aka transmembran
peripheral proteins
located on membrane surface, NO hydrophobic domains
lipid-anchored proteins
attached covalently to lipids, hydrophobic
3 membrane protein functions
transport, enzymatic activity, signal transduction
liquid crystal concept of membrane
lipids are aligned with one another in gel-like arrays, NOT rigid, components can slide past one another
_____ serves as buffer to prevent abrupt transition from gel to crystal states?
cholesterol
asymmetry of membrane
molecular composition of each half of lipid bilayer are different (in an out of cell)
types of protein mobility
freely mobile, anchored, pulled in specific direction, drift within boundaries
FRAP
fluorescence recovery after photobleaching method of measuring the membrane diffusion rate
Apical plasma membrane
regulation of nutrient and water intake regulated secretion protection
lateral plasma membrane
cell contact & adhesion cell communication
basal membrane
cell-substratum contact generation of ion gradients
passive diffusion ex?
go down concentration gradient osmosis/diffusion facilitated transport
active transport
goes against concentration gradient requires ATP, ion pumps

what types of molecules get through passive diffusion? ex?
small hydrophobic molecules O2, CO2, N2, benzene
 small uncharged polar molecules H2. O, glycerol, ethanol

what types of molecules do active diffusion? ex?
large uncharged polar molecules amino acids, glucose, nucleosides

 ions H+, Na+, K+, Ca2+, Cl-, Mg2+
plant in hypotonic, isotonic & hypertonic solutions
turgid - water enters cell

 flaccid - water enters + leaves cell

 plasmolyzed - water leaves cell


animal cell in hypotonic, isotonic & hypertonic solutions
lysed - cell bursts
 normal
 shriveled - water leaves cell


phagocytosis
eating food
pinocytosis
drinking liquid
receptor-mediated endocytosis
specific molecules are ingested, vesicle coated in pili
central catabolic pathway for most cells, ΔG=?, pathways?
glucose + O 2 > CO 2 + H 2 O
 -686 kcal/mol
 glycolysis, krebs, ETC/oxidative phosphorylation
types of work for ATP phosphorylation
transport work phosphorylates transport proteins, mechanical work phosphorylates motor proteins, chemical work phosphorylates key reactants
glycolysis: where? budget? output?
cytosol
 1 glucose, 2 ATP
 2 pyruvate, 4 APT (net 2 ATP), 2 NADH


2 pathways after production of pyruvic acid
aerobic, anaerobic (fermentation)
anaerobic pathway after glycolysis; types?
alcohol - produces 2 ethanol + CO 2 
 lactic acid - 2 lactate (in muscles)

3 obligate aerobic organs
brain, kidney, heart
aerobic pathway after glycolysis
Krebs cycle
Krebs cycle, where?
mitochondrial matrix, CO2 produced
mitochondria structures size?
outer membrane, intermembrane space, inner membrane, matrix 0.2 - 1 μm diameter by 1 - 4 μm long
mitochondria inner membrane
cristae (highly folded)
 UNIQUE lipid & protein content 


mitochondrial matrix contains ___ and ___
mitochondrial DNA & ribosomes
mitochondria protein vs lipid percentages
2/3-3/4 protein to 1/3-1/4 lipid (mostly protein)
pleiomorphic organelle ex?
changes shape, divides, fuse ex. mitochondra
pyruvate shuttle
uses a fatty acid derivative (coenzyme A) as a carrier molecule to get across BOTH mito membranes
(1) pyruvate pathway to krebs
3 C => 1 > CO2 2 > enzyme > acetyl coA NAD+ reduced to NADH + H+
one turn of krebs cycle (per 1 acetyl coA)
1 ATP 3 NADH 1 FADH2 2 CO2
krebs cycle leads to
electron transport/oxidative phosphorylation
electron transport/oxidative phosphorylation, where?
release of E from e collected, oxidation of reduced NADH and FADH2 electrons passed to O2 thru series of redox proteins (cytochromes) in ETC, coupled to ATP synthesis

 inner mitochondrial membrane


glycogen
glucose polymer (storage), stored in liver
respiration per glucose molecule yields
2 ATP = 4 ATP (krebs) - 2 ATP (NADH mito shuttle doesn't apply to prokaryotes) 30 ATP = from 10 NADH 4 ATP = from 2 FADH2 6 H2O, 6 CO2 ===> 36 (or 38) ATP total under ideal conditions, reality is 30 ATP
who does photosynthesis
plants, protistans (algae), cyanobacteria
process of photosynthesis? ΔG? 2 major linked pathways?
CO 2 + H 2 O > glucose + O 2 ΔG= +709 kcal/mol endergonic hill reaction, calvin cycle

Planck's equation, meaning of variables?
E = hc/λ energy = planck's constant X speed of light / wavelength
energy of 1 mol photon
~42 kcal
Engelmann experiments
action/absorption spectrum
shorter wavelength=? longer wavelength=?
stronger energy weaker energy
chlorophylls have greatest absorbance at which wavelength
blue and red light (500 and 700)
chloroplast structures
outer envelope membrane inner envelope membrane thylakoids stroma
thylakoids
stacks into grana, space inside sac is called lumen
stroma
chloroplast DNA, ribosomes, etc.
Hill reaction what does it do? require? where?
"Z scheme" / "light reactions"; capture of light E converted to e- (bond) E requires intact photosystems I and II with absorptive pigment in thylakoid membranes (hydrophobic environment)
what does Hill reaction produce? from what?
ATP from ETC, electrons stripped from oxidation of H2O to produce O2 & e- used to reduce NADP+
calvin cycle, where? uses what enzyme?
fixes CO2 into sugar, requires ATP and reducing power stroma of chloroplast RUBISCO
inputs & outputs of calvin cycle
ATP + NADPH => ADP+P + NADP+ + CH2O (sugar)
inputs & outputs of light reactions
H2O + light => O2 + NADPH + ATP
3 phases of the calvin cycle
1. carbon fixation 2. reduction 3. regeneration of the CO2 acceptor (RuBP)
budget of photosynthesis per molecule of glucose
48 photons 18 ATP 36 ATP (12 NADPH) 6 O2 produced => costs 54 ATP to make a glucose
both mitochondria and choroplast ___
make ATP by same basic mechanism: ETC active transport of H+ across a membrane making pH gradient release of pH gradient coupled to ATP synthesis in special enzyme arrays
chemiosmosis [H+] in mitochondria and chloroplast? what are gradients released thru?
mito - [H+] in intermembrane space is 104 higher than in matrix chloro - [H+] in thylakoid lumen is 104 higher than in lumen - released thru ATP synthase
ATP synthase
Spans the membrane and and allows H+ ions to pass through it
what is used to make ATP in plants
proton gradient and membrane potential
what causes plant to do photorespiration
severe (dry) environments, too much O2 accumulates in leaf space
Which of the following are products of the light reactions of photosynthesis that are utilized in the Calvin cycle?
ATP and NADPH
Where does the Calvin cycle take place?
stroma of the chloroplast
When oxygen is released as a result of photosynthesis, it is a direct by-product of
splitting water molecules
A plant has a unique photosynthetic pigment. The leaves of this plant appear to be reddish yellow. What wavelengths of visible light are being absorbed by this pigment?
blue and violet
Which statement describes the functioning of photosystem II?
The electron vacancies in P680⁺ are filled by electrons derived from water.
Which of the following are directly associated with photosystem I?
receiving electrons from the thylakoid membrane electron transport chain
Some photosynthetic organisms contain chloroplasts that lack photosystem II, yet are able to survive. The best way to detect the lack of photosystem II in these organisms would be
to test for liberation of O₂ in the light.
In a plant cell, where are the ATP synthase complexes located?
thylakoid membrane and inner mitochondrial membrane
In mitochondria, chemiosmosis translocates protons from the matrix into the intermembrane space, whereas in chloroplasts, chemiosmosis translocates protons from
the stroma to the thylakoid space
Where are the molecules of the electron transport chain found in plant cells?
thylakoid membranes of chloroplasts
In photosynthetic cells, synthesis of ATP by the chemiosmotic mechanism occurs during
both photosynthesis and respiration.
What is the primary function of the Calvin cycle?
synthesize simple sugars from carbon dioxide
In a plant leaf, the reactions that produce NADH occur in
neither the light reactions nor the Calvin cycle
The NADPH required for the Calvin cycle comes from
reactions initiated in photosystem I.
Reactions that require CO₂ take place in
the Calvin cycle alone.
Photorespiration lowers the efficiency of photosynthesis by
3-phosphoglycerate molecules
Very low concentrations of detergent make membranes leaky to small molecules and ions without damaging proteins. In isolated mitochondria exposed to detergent, the molecules of the electron transport chain and of ATP synthase remain intact. Do you expect ATP synthesis to continue in the p…
No, because with a leaky membrane, H+ gradient cannot be maintained.
The pH in the stroma of the chloroplast should be ____________ compared to the thylakoids due to the ____________.
higher; higher concentration of hydrogen ions in the thylakoid
If oxygen is unavailable, predict what happens to the citric acid cycle.
it stops because the supplies of NAD+and FAD become depleted.
Photorespiration in chloroplasts differs from cellular respiration in mitochondria in that ____________.
ATP is required for photorespiration but is a product of mitochondrial respiration

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