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BS 161: FINAL EXAM
Covalent Bond |
Bond between two atoms involving the sharing of a pair of valence electrons.
Strongest bond.
|
Polar |
One atom is more electronegative than the other.
Valence electrons are not shared equally.
|
Order of electronegativity |
H=C<N<O
|
Non-covalent bond |
Attraction between atoms that does not involve sharing of valence electrons.
|
Ionic Bond |
Bond between positive and negative charged ions
|
Hydrogen bond |
Bond between an H atom
Weak bond
|
Hydrophilic |
Has an affinity for water
|
Hydrophobic |
Does not have an affinity for water.
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Carboxyl |
CHO2 |
Carbonyl |
CO |
Amino |
NH2 |
Hydroxyl |
OH |
Sulfhydryl |
SH |
Phosphate |
Phosphate |
Methyl |
CH3 |
Polysaccharides |
Polymers of sugars formed by polymerization/dehydration
|
Starch |
A plant polysaccharide
|
Glycogen |
An animal polysaccharide
|
Cellulose |
A polymer of glucose, major component of plant cell walls, most abundant organic compound on earth
|
Nucleic Acids |
Store and transmit hereditary information
Two types: DNA-double strandedRNA-single stranded
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Nucleotides |
Monomer of building blocks of nucleic acids
|
Purines |
Two rings. Larger bases, smaller term
|
DNA |
Sugar phosphate background
|
Proteins |
Encoded by genes
Composed of amino acids
Nucleotide sequence of gene specifies amino acid sequence of protein
Most structurally complex macromolecule
Composed of more than one polypeptide
|
Polypeptide |
A single chain (polymer) of amino acid. The monomer building blocks of polypeptides are amino acids.
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Primary Structure
|
Unique sequence of amino acids in a polypeptide (order and length)
Specified directly by the nucleotide
Determines other levels of structure
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Secondary Structure
|
Regular repeated pattern of coils or folds created by predictable patterns of H bending between atoms along the polypeptide backbone
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Tertiary Structure
|
Overall 3D shape of polypeptide
Results from interactions between sidechains
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Quarternary Structure
|
Overall protein structure resulting from interactions between side chains
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Motif |
Small regions in different proteins with common structural features
|
Domain |
Discrete functional unit of protein
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Denaturation |
Unraveling of a protein, loss of tertiary structure
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Saturated Fats |
Solid at room temperature because fatty acid tails are packed tightly
|
Unsaturated Fats |
Liquid at room temperature because fatty acid tails are kinked
Also called oils
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Steroids |
Lipids having a carbon skeleton consisting of four fused rings, a component of cell membranes
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Cytoplasm |
A semifluid matrix that fills the interior of every cell
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Cytosol |
The fluid in which organelles are suspended
|
Mitochondrion |
Organelle in which energy is extracted from food during oxidative metabolism
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Lysosome |
Vesicle that breaks down macromolecules and digests worn out cell components
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Golgi Complex |
Collects, packages, and distributes molecules
|
Peroxisome |
Vesicle that contains enzymes that carry out particular reactions such as detoxifying potential harmful molecules
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Ribosomes |
Small complexes of RNA and protein that are the sites of protein synthesis
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Nucleolus |
Site where ribosomes are produced
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Smoother Endoplasmic Reticulum |
System of internal membranes that aids in the manufacturing of carbohydrates and lipids
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RER |
Internal membranes studded with ribosomes that carry out protein synthesis
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Chloroplasts |
Organelle containing thylakoids, the sites of photosynthesis
|
Difference between plant and animal cells |
Plants have a cell wall, vacuole, and chloroplasts. Animal cells have lysosomes.
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Difference between prokaryotic and eukaryotic cells |
Prokaryotic cells have no nucleus
Eukaryotic cells have genetic material enclosed in the nucleus and many membrane bound compartments called organelles |
Common to all cells
|
Plasma membrane
DNA
Ribosomes
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Mitochondria |
Produce most of the ATP needed for cellular activities via respiration. They function in programmed cell death, normal development, destruction of damaged cells
|
Nucleus |
Sit of DNA synthesis
Site of ribosome subunit assembly
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Phagocytosis |
Uptake and lysosome-mediated digestion of food particles, bacteria, viruses, and other foreign particles
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3 main types of protein fibers that make up the cytoskeleton
|
Actin filament
Microtubules
Intermediate filament
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Endosymbiosis |
Evolution of mitochondrion and chloroplasts
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Facilitated Diffusion |
Process of diffusion mediated by a membrane protein
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Channel Proteins |
Have a hydrophilic interior that provides an aqueous channel through which polar molecules can pass when the channel is open
|
Carrier Proteins |
Bind specifically to the molecule they assist
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Osmosis |
The movement of water across membranes. Both water and solutes tend to diffuse from regions of high concentration to ones of low concentration, that is, they diffuse down their concentration gradients.
|
Passive Transport |
Involves diffusion, which requires a concentration gradient
|
Facilitated Diffusion |
Through a channel of carrier proteins
|
Passive Processes |
Does not require energy
Diffusion
Facilitated diffusion
Osmosis
|
Active Processes |
Requires energy
Protein carrier
Coupled transaport
|
Valences to know |
Hydrogen valence=1
Oxygen valence=2Nitrogen valence=3Carbon valence=4
|
Ionic, Hydrogen, and Hydrophobic bonds are all |
Non-covalent bonds
|
Hydrogen bonds to what in hydrogen bonds |
Nitrogen, Oxygen, or Fluorine
|
3-Carbon Sugar |
Chains |
5-Carbon Sugar |
No OH on inside of ring
|
6-Carbon Sugar |
Have an OH on the inside of the ring
|
Subunits of Phospholipids
|
Glycerol
Fatty acids
A phosphate group
|
Solubilities |
nonpolar=hydrophobic=not water soluble
polar=hydrophilic=soluble
|
Amphipathic |
Part hydrophilic, part hydrophobic
|
Synthesis involves dehydration reactions applies to |
All macromolecules
|
The breakdown of nucleic acids to nucleotides occurs by |
Hydrolysis |
a-helix formation in proteins involves the |
formation of hydrogen bonds
|
Flow of genetic information in a eukaryote |
Transcription in nucleus -> transport of mRNA to cytosol -> translation on ribosomes
|
If a mutation occurs that prevents two polypeptides from associating, |
the enzyme will no longer catalyze hydrolysis
|
Route for transport of a secreted protein |
RER -> Golgi -> Vesicles that fuse with plasma membrane
|
Key components of flagella in sperm cells |
Microtubules |
Separate chromosomes of eukaryotic cells |
Microtubules |
Plasmodesmata in plant cells are most similar to |
gap junctions in animal cells
|
The movement of protons from outside to inside the cell occurs by |
Facilitated diffusion
|
The most direct source of energy for transport is |
Protons |
Metabolism |
Sum total of biochemical reactions required forl ife
|
Catabolic Pathways
|
Break down complex molecules into simpler compounds
Release energy
ex. Respiration
|
Anabolic Pathways
|
Build complicated molecules from simpler ones
Consume energy
ex. Protein synthesis
|
Energy |
Capacity to do work
|
1st Law of Thermodynamics |
Energy can be transferred or transformed but neither created nor destroyed
|
2nd Law of Thermodynamics |
Whenever energy is converted from one form to another, only some of that energy can be used to do work
|
Entropy |
disorder of surroundings
|
Spontaneous |
Moves toward equilibrium
negative delta GRelease energyExergonicCatabolicDisorder happens spontaneously (messy room)
|
Nonspontaneous |
Moves away from equilibrium
positive delta GRequires energyEndergonicAnabolicOrganization requires energy (clean room)
|
Coupled processes must be overall |
Exergonic
Negative delta G
|
Do enzymes affect change in energy? |
No, instead they accelerate reactions that would occur eventually
|
What is the "goal" of respiration? |
Release energy tied up in the chemical bonds of organic molecules and convert is to chemical bonds in ATP
|
Exergonic breakdown of glucose is coupled to |
endergonic synthesis of ATP
|
Redox reactions |
Transfer of electrons from on reactant to another
The electron donor is being oxidizedThe electron acceptor is being reduced (because electrons are negatively charged)
|
Oxidation-reduction cycle
|
Enzymes that use NAD+ as a cofactor for oxidation reactions bind NAD+ and the substrate (energy rich molecule)
Two electrons and a proton are transferred to NAD+ creating NADH
NADH diffuses away and can then donate electrons to other molecules (reduction)
|
Autotrophs |
Organisms that harvest energy from sunlight and convert the radiant energy into chemical enrgy
|
Cellular Respiration |
The oxidation of organic compounds to extract energy from chemical bonds.
|
2 mechanisms by which cells make ATP
|
In substrate level phosphorylation, ATP is formed by transferring phosphate groups directly to ADP from a phosphate bearing intermediate. During glycolysis, the initial breakdown of glucose, the chemical bonds of glucose are broken providing the energy required to form ATP.
In oxidative phosphorylation, ATP is synthesized by the enzyme ATP synthase, using energy from a proton gradient. This gradient is formed by high energy electrons harvest by the oxidation of glucose. These electrons are then donated to oxygen. ADP+Pi ->ATP
|
Glycolysis |
Occurs in the cytoplasm and converts glucose into two 3-carbon molecules of pyruvates. For each molecule of glucose that passes through this transformation, the cell nets two ATP molecules and two NADH.
|
Process of Photosynthesis |
6CO2+12H20+Sunlight -> C6H12O6+6H2O+6O2
Carbon dioxide+water -> glucose+water+oxygen
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Net equation of the Calvin Cycle |
6CO2+18ATP+12NADPH+water -> 2 glyceraldehyde 3-phosphate +16Pi+18ADP+12NADP+
|
Phases of the Calvin Cycle
|
Carbon fixation
Reduction
Regeneration of RuBP
|
Hydrolysis of ATP by a motor protein is |
exergonic |
Photosynthesis is |
an anabolic process
|
ATP hydrolysis reactions
|
Often coupled to the formation of a phosphorylated intermediate
Has a negative delta G
Often coupled to a reaction that requires energy
Typically catalyzed by an enzyme
Exergonic
|
Route for delivery of the hydrolytic enzymes to the lysosomes? |
RER -> Golgi -> vesicles that fuse with lysosomes
|
Which curve represents the most likely profile for most lysosomal enzymes? |
The curve with the lower pH
|
The import of protons to the lysosomes from the cytosol |
is endergonic
|
A chemical reaction A+B->C+D is proceeding spontaneously towards the formation of A+B |
This implies that:
The formation of A+B (reverse reaction) moves the reaction towards its equilibrium
The forward reaction has a positive delta G
The reverse reaction has a negative delta G
The forward reaction requires energy
The reverse reaction is exergonic
|
A+B->C+D, delta G=0 |
This implies that:
The formation of more C+D would move the reaction away from equilibrium
The reaction is proceeding nonspontaneously towards the formation of more C+D
The formation of more A+B would more the reaction away from equilibrium
The formation of more A+B would require energy
The formation of more C+D would require energy
|
How might sever fever affect enzymes in your body if the fever is not controlled? |
The tertiary structure of your enzymes may be disrupted
|
During respiration, the carbon atoms in glucose ultimately wind up in |
CO2 |
Photosynthesis results in |
The transfer of electrons from water to sugar
|
Both respiration and photosynthesis |
generate ATP by chemiosmosis
|
The breakdown of glucose to CO2 and water during respiration |
Is catabolic
Releases energy, some of which is recaptured in ATP
It occurs in many small steps, decreasing the amount of energy lost as heat and increasing the amount of energy available for ATP synthesis
Does NOT result in a transfer of electron from more electronegative atoms in glucose to less electronegative oxygen
|
Site of glycolysis in plants |
Cytosol |
Accumulation of protons in this location powers photophosphorylation of ADP |
Thylakoid space
|
The pH of this compartment increases in the light |
Stroma |
Hexokinase catalyzes the first step in glycolysis |
The most likely site of hexokinase synthesis is ribosomes in the cytosol because glycolysis takes place in the cytosol
|
In the reverse reaction of photosynthesis |
C6H12O6 would be oxidized and O2 reduced
|
Produces most of the ATP during respiration |
Oxidative phosphorylation
|
Stage of respiration that releases most of the CO2 |
Krebs cycle
|
Flow of electrons during respiration |
glucose -> NADH -> electron transport chain -> O2
|
What can continue in the absence of O2? |
Glycolysis |
What is the primary function of the Calvin Cycle? |
to synthesize sugar from CO2
|
The relationship between light reactions of photosynthesis and the Calvin Cycle |
The light reactions provide ATP and NADPH to the Calvin cycle, and the Calvin cycle returns ADP, Pi, and NADP+ to the light reactions.
|
6CO2+6H20+Energy->glucose+ oxygen |
The maximum number of glucose molecules that could be produced from the fixation of 6 molecules of CO2 during photosynthesis is 1
|
In mitochondria, chemiosmosis results in |
the passive transport of protons from the matrix into the intermembrane space
|
In chloroplasts, chemiosmosis results in |
the passive transport of protons from the thylakoid space to the stroma
|
ATP is synthesized by an ATP synthase |
Occurs in both oxidative phosphorylation and photophosphorylation
|
Rubisco |
The enzyme that catalyzes the first step in the Calvin Cycle. One of its substrates is CO2, it catalyzes a carboxylation reaction.
|
Green light is least effective for driving photosynthesis because |
Photons in the green part of the visible spectrum are absorbed least effectively by chlorophyll.
|
Calvin Cycle
|
Synthesis of a 3-carbon sugar phosphate
fixation of CO2
Hydrolysis of ATP
Oxidation of NADPH
|
Increases in mass come primarily from |
CO2 |
Cycling of O2 through the ecosystem |
O2 in the atmosphere is produced by photosynthesis and consumed by respiration
|
Polygenic Inheritance |
Occurs when multiple genes are involved in controlling the phenotype of a trait
|
Pleitropy |
Refers to an allele which has more than one effect on the phenotype
|
Incomplete Dominance |
Heterozygotes is an intermediate phenotype between the two homozygotes. ex. Red x white=pink flowers
|
Codominance |
Heterozygote shows some aspect of the phenotypes of both homozygotes. ex. AB blood type
|
Interphase |
G1: First gap pahse, involves growth and preparation for DNA synthesis
S: a copy of the genome is synthesizedG2: 2nd gap phase, prepares cell for mitosis
|
M phase |
Mitosis: Replicated chromosomes are divided
Cytokinesis: divides the cell into 2 cells with identical genomes
|
Five stages of Mitosis
|
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
|
Metaphase |
All chromosomes are aligned at the metaphase plate. Chromosomes are attached to opposite poles and are under tension.
|
Anaphase |
Proteins holding centromeres of sister chromatids are degraded, freeing individual chromosomes. Chromosomes are pulled to opposite poles. Spindle poles move apart.
|
Telophase |
Chromosomes are clustered at opposite poles and decondense. Nuclear envelope re-forms around chromosomes. Golgi complex and ER re-form
|
Zygote |
Egg and sperm
|
Meiosis |
Reduces the number of chromosomes. Occurs during gamete formation, producing haploid cells
|
Somatic-line cells |
Form all of the cells of the adult body
|
Germ-line cells |
Cells that will eventually undergo meiosis to produce gametes
|
Meiosis I |
Metaphase I: Crossovers and sister chromatid cohesion lock homologues together. Microtubules connect to the kinetochores of sister chromatids so that homologues are pulled toward opposite poles
Anaphase I: Microtubules pull the homologue chromosomes apart, but sister chromatids are held together at the centromere
|
Mitosis |
Metaphase: Homologues do not pair; kinetochores of sister chromatids remain separate; microtubules attach to both kinetochores on opposite sides of the centromere.
Anaphase: Microtubules pull sister chromatids apart
|
3 models of DNA replication
|
Conservative
Semiconservative
Dispersive
|
3 common features of DNA polymerase
|
They all add new bases to the 3' end of the existing strands
They synthesize in the 5' to 3' direction
They all require a primer to begin synthesis
|
Helicases |
Enzymes that use energy from ATP to unwind the DNA template
|
Telomeres |
Structures found on the ends of all eukaryotic chromosomes. They protect the ends from nucleases and maintain integrity of the linear chromosomes
|
Chargaff's Rules
|
The proportion of A always equals that of T, and the proportion of G always equals that of C.
|
Walter Fleming |
Discovered that chromatin formed threadlike bodies during cell division
|
Centromere |
The point of constriction on chromosomes that contains repeated DNA sequences that bind specific proteins
|
Histones |
Proteins that double stranded DNA molecules wrap around in eukaryotes
|
Sister chromatids |
After replication, the resulting two parts of each chromosome are held together by cohesion at the centromere.
|
# of sister chromatids |
=1/4 # of haploid number
=2* # of chromosomes
|
Alleles |
Alternate forms of the same gene
|
Phages |
Viruses that attack bacteria
|
Translation |
Synthesizes insulin
|
Subunits of Insulin |
Amino acids
|
The mutation responsible for Sickle-cell anemia is |
missense mutation
|
Transcription of the operon, synthesis of the polypeptides, and Trp synthesis all |
Occur in the cytoplasm
|
Transcription
|
DNA directed synthesis of RNA
Only one strand of DNA is used
U in DNA is replaced by T in RNA
mRNA used to direct synthesis of polypeptides
|
Translation
|
Synthesis of polypeptides
Takes place at ribosome
Requires several kinds of RNA
|
Codons |
Consist of 3 nucleotides specify all the amino acids
|