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257 Cards in this Set

  • Front
  • Back
Cellular Level
Atoms, Molecules, Organelle, Cell
Organismal Level
tissue, organ, organ system, organism
Population
species, community, ecosystem, biosphere
Hypothesis
Possible explanation for an observation that is tested in many ways to allow predictions
Theory
Interconnected concepts supported by experimental evidence to express ideas to which we are almost certain about
Reductionism
break into simpler parts
systems biology
Focus on larger parts that can't be understood by simpler parts
Deductive reasoning
uses general principles to make specific predictions "V"
Inductive reasoning
specific to general conclusions "^"
Founder Effect
alleles lost or changed drastically
Bottleneck Effect
Population size reduced results in loss of genetic variation
Natural Selection
change occurs. Population adapts and favors phenotype with greater fitness
Artificial Selection
Favors phenotype traits
5 agents of evolutionary change
mutation, gene flow, non-random mating, small pop. size, selection.
components of fitness
survival, # of offspring, sexual selection, traits favored for one component may be disadvantage for others
7 objections of evolution
Evolution not demonstrated, no fossil intermediates, intelligent design, violates thermodynamics, proteins too improbable, doesn't imply evolution, irreducible complexity
Counter to objections
not enough evidence, some proposed have been found, natural selection not random, not closed system, can't argue backwards, artificial selection, evolution from simple changes
elements found in living organisms
Carbon, Hydrogen, Oxygen, Nitrogen
Hydrogen bond properties of water
High specific heat, high heat of vaporization, solid water less dense than liquid water, good solvent, organizes nonpolar, forms ions, pH=7
Covalent bond
Atoms share 2 or more valence electrons. No net charge
Ionic bond
oppositely charged ions
Hydrogen bond
Polarity of water allows it to attract to one another
Polar
unequal sharing of electrons
Non-polar
equal sharing of electrons
Reduction
gain of electron
Oxidation
loss of electron
Hydrophilic
water-loving
Hydrophobic
water-fearing
Acid
dissociates in water to increase [H+] and lower pH
Base
combines with H+ in water to lower [H+] and increase pH
Buffer
keeps [H+] relatively constant. Absorbs H+ ions when acid is added and releases them when base is added
Carbohydrate
(1:2:1) (CH2O)n
monomer of a Carbohydrate
sugar monomers-> glucose, fructose, galactose
4 types of polysaccharides
starches, glycogen, cellulose, chitin
starches
O bonds, alpha linkage
glycogen
animal energy forms
cellulose
Beta-linkage. Forms tough fibers
Chitin
anthropods, polymer of glucose and proteins
Protein functions
enzymes, defense, transport, support, motion, regulation, storage
Amino Acid Structure
central carbon atom attached to an Amino Group, Carboxyl group, a single hydrogen, and an "R" group. Monomer of proteins
"R" group in an amino acid
determines function and structure of proteins
Four levels of protein structure
Primary:sequence of amino acids
Secondary: group in peptide bonds
tertiary: final folded shape of protein
Quaeternary: multimetric folding
Peptide bond formation
covalent bond that holds amino acids together formed in ribosomes through dehydration synthesis. OH is removed from carboxyl, H from amino, and covalent bond forms between the two giving off water as excess
Chaperone proteins
helps proteins fold correctly (heat shocked proteins)
Structure of a nucleotide
in DNA: sugar (deoxyribose), a Base (ATCG) and a phosphate
DNA
deoxyribose. Double helix connected by H-bonds, ATCG, with a sugar phosphate backbone
RNA
Ribonucleic acid. U instead of T. Single polynucleotide strand used from DNA to specify sequence
Cell theory
all organisms are made from cells, cells are the smallest living things and arise from existing cells only
Prokaryotic Cells
Cell wall, plasma membrane, nucleoid, flagella, capsule, pili. Lack membrane
Eukaryotic Cells
membrane, cytoskeleton bound organelles and endomembrane system
Animal Cell:
endomembrane system, vesicles, chromosomes, cytoskeleton, nucleus, nucleolus, nuclear envelope, nuclear pores, chromatin, ribosome, RER, SER, golgi apparatus, mitochondrion
Plant Cell:
cell wall, cell membrane, endoplasmic reticulum, vesicles, ribosomes, microtubules, golgi apparatus, nucleus, mitochondria, chloroplast, chromosomes, lysosomes
Cytoskeleton
Contains actin filaments, microtubules, intermediate filaments
Actin filaments
protein chains that have + and - ends that designate growth of filaments. Responsible for cellular movements such as pinching and crawling during division
Microtubules
alpha and beta tubulin. Tube Shaped. Organize cytoplasm and move material within cell itself
Intermediate filaments
Fibrous protein that gives mechanical strength
Cell membrane components
phospholipid bilay, transmembrane proteins, interior protein network, cell surface markers
Phospholipid bilayer
flexible matrix barrier to permeability
transmembrane proteins
transport and communicate across membrane
Interior protein network
reinforce membrane shape
cell surface marker
identity markers
Phospholipid structure
hydrophobic tail (non-polar) with a hydrophilic head
Membrane transport
small molecules (water) move eaily across but large molecules must use vesicles
Osmosis
Net diffusion of water across membrane toward higher solute. Force needed to stop & creates pressure. Reach equilibrium inside and out.
Passive Transport : Diffusion
high to low [ ] no energy required
Passive transport: Facilitated
requires channel protein to move through channel when open OR carrier protein that attaches then changes shape
Hypertonic
higher solute [ ] than water. Causes cells to shrivel
Hypotonic
lower solute [ ] than water. Causes cells to burst.
Isotonic
same osmotic [ ]
Active Transport proteins
Uniporters, symporters, antiporters
Uniporters
one molecule moved at a time
Symporters
two molecules in same direction
Antiporters
two molecules in opposite directions
Coupled transport
Na+ uses diffusion of Na+ to move glucose against [ ] gradient. Molecules move in same direction
Active Transport steps
1. uses ATP directly. antiporter moves 3Na+ out and 2K+ in against gradient. changes shape of carrier protein and binds, ATP,"", shape change, Release 3Na+ to pick up 2K+ and releases shape change.
Exocytosis
movement of substances out of a cell
phagocytosis
cell takes in solid matter
Pinocytosis
cell takes in fluid matter
Receptor-mediated endocytosis
specific molecules are taken in after binding to receptor
Energy
Capacity to do work
Entropy "S"
measure of a system's disorder
Forms of energy
mechanical, light, radioactive, heat, sound, and electric are all types
Enthalpy "H"
internal energy of a system plus the product of pressure and volume (H=E+PV). The amount of energy released or used in a system at constant pressure
Role of ATP in cell
"currency" all cells use. Drives endergonic reactions
Exergonic
- delta G (cellular respiration)
Endergonic
+ delta G (photosynthesis)
Free energy
energy that can be taken in or extracted at standard conditions.
+ delta G
products > reactants. Non spontaneous, endergonic
- delta G
products < reactants. spontaneous, exergonic
Delta G
change in free energy
ATP and structure
Adenosine Triphosphate: ribose, adenine, 3 phosphates
Protein enzymes
enzyme to substrate and convert to product at active site. forms enzyme to substrate complex and applies stress to distort a bond and lower the activation energy
Coupling
sharing of intermediates to drive an equation
metabolism
total of all chemical reactions carried out by an organism
catabolism
harvest energy by breaking down molecules
Anabolism
expand energy to build up molecules
Feedback inhibition
end product of pathway binds to an alleosteric site on enzyme that catalyzes first rxn in pathway
Structure of Chloroplast
Thylakoid membrane, Grana, Stroma lamella, Stroma
Thylakoid Membrane
chlorophyll and pigments clustered into photosystems
Grana
Stacks of thylakoid membrane sacs
Stroma lamella
surround grana
Stroma
semiliquid around thylakoid membranes
Pigments involved in photosynthesis
1. chlorophylls 2. carotenoids. Capture visible light ~400-740 nm
Photosynthesis Equation
6CO2 + 12H2O --> C6H12O6 + 6H2O + 6O2
Light independent reaction
Catalyze RuBP to PGA (RuBP + CO2 --> PGA)
PGA to G3P (reduction)
PGA regenerates RuBP
3 turns for carbon to produce 1 G3P
6 turns for 1 Glucose
Light dependent reaction
energy from sunlight to make ATP and reduce NADP+ to NADPH.
1. Photon is captured by pigment
2. charge separation- energy is transfered to rxn center and an excited e- is transported to acceptor
3. e- transport. e- move through carriers to reduce NADP+
4. Chemiosmosis- produces ATP
Chemiosmosis in photosynthesis
Electrochemical gradient to synthesize ATP.
Move down gradient to allow ADP + Pi to make ATP
Choroplast has ATP synthase enzymes in Thylakoid membrane to allow protons in stroma.
Stroma has enzymes that catalyze rxn of carbon-fixation/calvin cycle rxns
Carbon Fixation / Calvin Cycle
1. Attaches CO2 to RuBP to get PGA. Uses enzymes called RUBISCO
2. RuBP + CO2 --> PGA
3. PGA reduce to G3P
4. Regeneration PGA to RuBP

3 turns of carbon for 1 G3P
6 turns of carbon for 1 Glucose
Heterotroph
live on organic compounds produced by others
Rubisco
most prodominant enzyme in animal kingdom
- lowers activation energy of reactions
Autotroph
produce their own organic molecules through photosynthesis
Fermentation
After glyolysis
Pyruvate + NADH + H to lactic acid and/ or ethanol + NAD+
Cellular Respiration Equation
C6H12O6 + 6O2 --> 6H2O + 6CO2
Aerobic respiration
final e- receptor is O2
Anaerobic respiration
final e- receptor is an inorganic molecule (not O2)
ATP in the cell
ADP + Pi = ATP; substrate- level phosphorylation and oxidative phosphorylation
Substrate level phosphorylation
transfer phosphate directly to ATP during glycolysis
Oxidative phosphorylation
ATP synthesis uses energy from a proton gradient
Stages for complete oxidation of glucose
1. glycolysis
2. pyruvate oxidation
3. krebs cycle
4. electron transport chain
glycolysis
occurs in cytoplasm
1. priming: phosphates from 2 ATP break down glucose
2. Clevage: glucose to 2 pyruvate
3. oxidation: produces ATP; 3 carbon release phosphate to make ATP
Products of glycolysis
1. 4 ATP (2 net)
2. 2 NADH
Pyruvate oxidation
in mitochondria. Plama membrane of Pro,
1. pyruvate oxidized to acetyl-CoA to enter Kreb's cycle (aerobic)
2. Pyruvate reduced to oxidize NADH back to NAD+ for fermentation (anaerobic
Pyruvate oxidation + Glycolysis Products
(per glucose)
1. 4 ATP
2. 2 CO2
3. 2 NADH
4. 2 Acetyl- CoA
Kreb's Cycle
in matrix of mitochondria. Oxidizes acetyl group from pyruvate
1. Acetyl-CoA + oxaloacetate --> citrate
2. citrate rearrangement and decarboxylation
3. Regeneration of oxaloacetate
4. e- to carriers (NADH and FADH2) citrate to oxaloacetate
Krebs cycle Products
(per glucose)
4 CO2
2 FADH
2 ATP
6 NADH
Krebs + Pyruvate + Glycolysis Products
(per glucose)
6 CO2
4 ATP
10 NADH
2 FADH2
Electron Transport chain
1. e- from NADH and FADH2 to complexes of ETC
2. create proton motive force
3. powers synthase: pump produces gradient for chemiosmosis)
4. produces high amounts of ATP
- occurs in innermembrane mitochondria
Theoretical yield
~36 ATP
Actual Yield
~30 ATP
Reason for difference in ATP yields
leaky membrane
use of proton gradient for other purposes
Binary Fission
colonal cyle.
single chromosome is replicated (circular)
origin to termination
Septation
separate cell components. begins formation of ring of FtsZ protein. Pinch cell into 2 cells
Chromosomes
specific to species. Humans have 46 or 23 pairs
made of chromatin,
chromatid
half of a chromosome
Chromatin
complex of DNA and protein
homologus
maternal + paternal chromosome
Heterochromatin
Not expressed
Euchromatin
expressed
Solenoid
nucleosome coiled further
histones
+ charged proteins attracted to phosphate groups of DNA
nucleosome
DNA + Histones that guide coiling
centromere
hold sister chromatids together
kinetochore
attach to microtubules. Connected to chromosomes
Haploid
one set of chromosomes
Diploid
total number of chromosomes in a cell (2x haploid) or (2n)
cell cycle
1. G1
2. S
3. G2
4. Mitosis
5. Cytokinesis
Interphase
includes G1, S, and G2
G1
cell growth
S
DNA replicates
G2
chromosomes coil tightly using motor proteins; centrioles replicate tubulin synthesis
Checkpoints
G1/S
G2/M
Late Metaphase
G1/S Checkpoint
cell decides to divide
-primary point for external influence
Checks DNA
G2/M
makes commitment to mitosis
assesses success of DNA replication
Late metaphase
Checks to make sure all chromosomes are attached to spindle
M phase in mitosis
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
Prophase
chromosomes condense, held together at centromere, spindle forms, envelope breaks down
Prometaphase
chromosomes attach to microtubules, each X connected at different poles, and move to center
Metaphase
X aligned, attach to opposite poles and under tension
Anaphase
centromeres split, cohesion proteins removed. sisters pulled to opposite poles. X to outside poles to outside
telophase
spindle disassembles, nuclear envelope forms around X's, X's uncoil, nucleolus appears
Cytokinesis
clevage of the cell into 2. Animals : constriction of actin filaments
Cell regulation
1. cell cycle has 2 reversible points
-replication of genetic material
-separation of sister chromatids
2. can be put on hold at specific points
-checked for accuracy and halted
-respond to signals
Cyclin-dependent Kinases (Cdks)
enzymes that phosphorylate proteins. levels go up when in a phase and down when not
primary mechanism for cell controll
Tumor-suppressor genes
prevent development of mutated cells. Key role in G2 checkpoint that monitors integrity of DNA
Proto-oncogenes
Encode receptors for growth factors. If damaged, result in uncontrollable cell division
Apoptosis
self-destruction of a cell
sexual life cycle
made of meiosis and fertilization
diploid cells are
somatic cells of adults 2 sets of X's
haploid cells are
gametes 1 set of X's (germ cell)
sexual life cycle is an alternation of...
haploid and diploid stages
humans: diploid dominates
mitosis to diploid meiosis to haploid
Nondisjunction
failure of x's to move to opposite poles during either division
meiosis vs mitosis: 4 features
synapsis and crossing over
sister chromatids remain joined at centromeres throughout meiosis 1
dna replication suppressed b/w meiosis 1 and 2
Meiosis
includes meiosis 1 and 2.
Each has PMAT
Crossing over
swapping of genetic materials b/w non-sister chromatids
Meiosis Prophase 1
x coil tightly become visible envelope disappears, spindle forms. Synapsis and crossing over
Meiosis Metaphase 1
chiasmata holds x's together. microtubules from opp poles align x
Meiosis Anaphase 1
microtubules shorten; chiasmata break, pairs separate. each pole has haploid set x. Independent assortment of maternal and paternal x
Meiosis Telophase 1
envelope reforms; sisters no longer same
2 cells into meiosis 2
meiosis 2 prophase 2
new spindle, envelope break down (like mitosis)
meiosis 2 metaphase 2
x align, microtubules attach to kinetochores (like mitosis)
meiosis 2 anaphase 2
microtubules shorten. sister chromatids to opposite side (mitosis)
meiosis 2 telophase 2
membrane forms, cytokinesis into 4 haploid cells with none alike
DNA primase
RNA polymerase that makes RNA primer
Primer
made by primase.
DNA ligase
seals backbone and fragments
DNA polymerase 3
proofreads in the 3'-5' direction
3 Models of DNA replication
conservative
semi-conservative (correct)
dispersive
DNA replication steps
1. initiation
2. Elongation
3. Termination
requires parent DNA
DNA replication
1. initiation
replication begins
DNA replication
2. Elongation
new DNA strands formed by DNA polymerase
DNA replication
3. Termination
replication is terminated of DNA
Helicases
use energy from ATP to unwind DNA
Single-stranded-binding proteins
coat strands of DNA to keep apart
Topoisomerase
prevent tangling of DNA during DNA replication
DNA gyrase
relax super- coils of DNA
Semidiscontinuous
DNA synthesize 1 way (5'-3')
leading strand
3'-5' strand. continuous from primer
lagging
requires multiple primers 5'-3' strand
okazaki fragment
multiple fragments for lagging strand
DNA polymerase
matches existing bases with complimentary nucleotides then links them
Prokaryotic DNA replication
single circle dna begins at origin to both directions around x
DNA polymerase 1
remove primers and replace with dna on lagging strand
DNA polymerase 2
DNA repair polymerase
DNA polymerase 3
replication enzyme that also has proofreading capability for DNA
Replisome components
1. enzyme involved in DNA replication form a macromolecular assembly
Primosome in the Replisome
Primase, helicase, proteins
complex of 2 DNA pol 3
Telomeres
protect end of x's and are turned off as we age
mutagens
any agent that increases the # of mutations
photorepair: non-specific
that uses single mechanism to repair multiple lesions of DNA
photorepair: specific
one mechanism for one lesion of dna
Early ideas about genes came from....
studying drosophilia and human diseases
one gene/one-enzyme hypothesis
each gene codes for the production of a specific polypeptide
Central dogma
information flows from DNA->RNA->Protein
________ violate the order of the central dogma using reverse transcriptase to convert _____ genome into _____
Retroviruses, RNA, DNA
Transcription is...
DNA to RNA
Translation is....
RNA to Protein
Genetic code
order of nucleotides in DNA encoded amino acid order
codon
block of 3 DNA nucleotides that correspond to an amino acid
degenerate coding
some amino acids are specified by more than one codon
Prokaryotic Transcription
doesn't require a primer. does require promoter, start site, termination site
Prokaryotic transcription promoter
forms recognition and binding site for RNA polymerase. is upstream of start site and not transcribed
Prokaryotic transcription elongation
5'-3' direction. forms bubble: RNA polymerase, DNA template and growing RNA transcript. After it passes DNA is rewound as it the leaves the bubble
Prokaryotic transcription termination
sequence signals stop to polymerase.
causes formation of phosphodiester bonds to stop
RNA-DNA hybrid within transcription bubble dissociates RNA polymerase releases DNA and it rewinds
Prokaryotic translation
coupled to transcription. mRNA begins to translate before transcription is finished
Eukaryotic Transcription
RNA polymerases
polymerase 2 transcribes mRNA and each recognizes its own promoter
Modified Primary Transport in Eukaryotic Transcription
adds 3' poly-A tail created by poly-A polymerase for protection
adds 5' cap to protect and for initiation
splicing
in eukaryotic transcription to cut out introns
Introns
non-coding regions
exons
coding regions
splicesome
remove introns specifically
Transportation for Eukaryotic Transcription
mature mRNA are taken to cytoplasm for translation
Binding Site
multiple sites for tRNA translation
P-site
binds tRNA attached to growing peptide chain
A-site
binds tRNA carrying the next amino acid
E-site
Binds tRNA that carried the last amino acid
Ribosome functions in transcription/translation
decode mRNA and forms peptide bonds
peptidyl transferase
forms peptide bonds b/w amino acids
Eukaryotic Translation
initiation
complex forms on mRNA with large and small ribosomal units. initiator tRNA with first amino acid on p-site (a-site empty)
Eukaryotic Translation
Elongation
adds amino acids. 2nd charged tRNA can bind to a-site. Peptide bond forms. Addition of successive amino acid occurs as a cycle
Euk. Translation
tRNA & codons
fewer tRNA's than codons
wobble pairing allows less stringent pairing b/w 3' base of codon & 5' base of anticodon
Allows fewer tRNA to accomodate all codons
Euk. Translation
Termination
elongation continues until ribosome encounters a "stop" codon that is recognized by release factors that release the polypeptide from the ribosome
Prokaryotic regulation
Activators
control of transcription initiation. + control increases frequency of initiation of transcription
positive control effectors
enhance binding of RNA polymerase to promoter
positive control repressors
can enhance or decrease
Negative control
decrease frequency
negative control effectors
bind to operators in DNA, allosteric
Negative control repressors
respond to effector molecule and enhance or abolish binding to DNA
Eukaryotic vs. Prokaryotic regulation
control of transcription, more complex.
Eu. have DNA into chromatin
protein-DNA interaction can alter transcription
eu. occurs in nucleus
amount of DNA differs
regulatory proteins
control gene expression by binding to specific DNA sequences
motifs
gain access to bases of DNA at major groove and sit there
Zinc-Finger
pattern of secondary structure that possess DNA-binding motifs. Every protein that binds to DNA has one
Induction
enzymes for a certain pathway that are produced in response to a substrate
+ control. Nothing blocked
Repression
capable of making an enzyme but doesn't. Environment doesn't need it to
lac operon
group of genes that code for proteins that work together in a pathway. Use of lactose as energy source gene for lacl is linked to rest of it.
lacZ
B-galactosidase
lacY
permease
lacA
transacetylase