The rest: Chapters 6, 7, 10, 11, 12, 13 Flashcards
Sickle cell anemia is caused by:
Recessive gene for malfunctioning hemoglobin
Mendel’s pea plant experiments:
1860s.
Studied 7 characters and traits (variations on characters)
Observed that many traits passed on to offspring unchanged and some were masked then reappeared in later generations
Heterozygote:
An individual with two different alleles of a gene
Test cross results:
If all offspring display dominant trait, unknown must be homozygous
If offspring are half dom half rec, unknown must be heterozygous
Dihybrid:
A zygote produced from a cross involving 2 characters
Dihybrid cross ratio:
9:3:3:1
Mendel’s second law: principle of independent assortment
Alleles of genes that govern different characters segregate independently during gamete formation
Mendel’s first law: law of segregation
Pairs of alleles that control a character segregate as gametes are formed. Half of the gametes carry one allele and the other half carry the other.
Sutton’s chromosome theory of inheritance:
Genes are their alleles are carried on chromosomes.
Parallels between chromosomes and genes:
Both occur in pairs
Both are separated and delivered singly to gametes
Independently assorted
Derived half from mother, half from father
Locus:
The site on a chromosome at which a gene is located
Incomplete dominance definition:
Effects of recessive alleles can be detested to some extent in heterozygotes.
Incomplete dominance notation:
Superscript to denote characters of incompletely dominant genes
Example of incomplete dominance in humans:
Sickle cell:
Heterozygotes will have sickle cell trait, a milder form of sickle cell anemia. Normal allele still produces normal hemoglobin.
Co-dominance:
Both alleles are expressed equally.
Multiple alleles:
Though an individual can only have two alleles, the gene may exist in many forms, caused by slight differences in DNA sequence.
ABO blood types: type, antibodies, accepted types
A - anti B - accepts A, O
B - anti A - accepts B, O
AB - none - accept A, B, AB, O
O - anti A, B - accepts O
Antigen:
Carbohydrate parts of glycoproteins on surface of red blood cells
Epistasis:
The interaction of genes with one or more alleles at one locus masking the effects of one or more others at a different locus.
If E is epistatic to B…
B is dependent on E.
Epistatic ratio:
9:3:4
Polygenic inheritance:
Several genes contribute to the same character
Continuous distribution:
More or less even gradation of character types. Ex: height.
What kind of plot does a quantitative trait give?
Bell curve. Quantitative traits are easily affected by environment. Ex: CHINESE GRANDMOTHERS
Pleiotropy:
A single gene affects more than one character. Ex: sickle cell
Linkage:
Genes are located on the same chromosome - no independent assortment.
Unit of linkage:
Map unit (mu) or centimorgan (cM) - relative unit
If 2 genes are 50 mu apart…
They will assort independently even though they are linked
Can 2 genes be more than 50 mu apart?
Yes, but test results max out at fifty. Distance can still be measured by adding the distances to a gene that lies between them.
Y chromosome has ___ so it can pair with X during meiosis.
A short region of homology
SRY gene:
Sex-determining region of Y.
Gene on Y that controls development toward maleness
After 6-8 weeks of embryonic development, SRY produces a protein that regulates expression of genes for testes. It also secretes hormones to degenerate female structures.
Hemizygous:
Having only one copy of a gene. Males are hemizygous for sex-linked genes.
Inactivation of one X-chromosome:
Since females have double the X but don’t need twice the products…
Expression of male X must be doubled
Expression of female X must be halved
Expression of 1 female X is “turned off”
Barr body:
Inactive, condensed X that is visible in nucleus as a dense mass of chromatin; forms during embryonic development
Who made the first structural model for DNA?
Watson and Crick, those thieving fuckers
DNA as hereditary molecules: Griffith
1928
Smooth S strain with capsule was virulent
Rough R strain without capsule was avirulent
Heat-killed S strain was avirulent
Heat-killed S strain plus live R strain is virulent
Conclusion: R can be converted to S with some factor from dead S cells
DNA as hereditary molecules: Avery
Heat-killed S treated with enzyme that breaks down RNA can still convert R to S
Heat-killed S treated with enzyme that breaks down DNA cannot make R virulent
Conclusion: DNA is the transforming principle
DNA as hereditary molecules: Hershey and Chase
Tagged proteins and DNA with radioactive label
Studied bacteriophages
DNA wins or something
Nitrogenous bases:
Adenine, guanine, thymine, cytosine
Purines:
A and G - carbon and nitrogen
Pyramidines:
T and C - carbon only
Chargaff’s rules:
A=T, G=C
Structures of AGTC
- diagram
At the 5’ end is a ___ group. At the 3’ end is a ___ group.
Phosphate, hydroxyl.
Sugar-phosphate backbone:
Polynucleotide chain of deoxyribose sugars and phosphate group
Each phosphate bridges the 5’ of one sugar to the 3’ of the next
Phosphodiester bond:
The linkage of 2 sugars and 1 phosphate group. Holds sugar-phosphate backbones together.
X-ray diffraction:
X-ray diffracts and exists a crystallized molecule as definite angles, which are visualized on a photographic film
Method of observing positions of atoms and Franklin:
She saw X-shaped diffraction pattern of DNA and deduced that it had a helical structure
Double-helix model of DNA:
2 backbones separated by a regular distance (0.34 nm), the perfect width for a purine and pyramidine to fit together
One full twist is 3.4 nm and contains 10 base pairs
Complementary base-pairing:
Chargaff’s rules.
A and T are stabilized by 2 hydrogen bonds; G and C are stabilized by 3
DNA can only be chemically stable if…
They are antiparallel, with the 5’ of one being complementary to the 3’ of the other
Replication model: semiconservative replication
Parental DNA unwinds and each strand serves as a template for the synthesis of a new molecule.
Results in 2 full helices with one new and one old strand each.
Replication model: conservative replication
2 original parental strands rewind together and the 2 newly created strands separate from template strands and wind up together.
Results in 2 helices, one old and one new.
Replication model: dispersive replication
Original helix splits into double-stranded segments, new double-stranded segments form on the originals, then everything matches up like puzzle pieces
Results in 2 helices with old and new DNA dispersed between.
Proof of semiconservative replication:
1958 Meselson and Stahl
Tagged parental DNA with N-15, a nonradioactive “heavy” isotope
Observed that DNA banding patterns matched only semiconservative model’s results
CsCl forms a density gradient when centrifuged and DNA moves to where it matches density
Kinds of DNA polymerases:
Deoxyribonucleoside triphosphates: substrates for polymerization reaction
Nucleoside triphosphate: nitrogenous base bound to sugar, which is bound to a chain of 3 phosphate groups
Deoxyribonucleoside triphosphate: uses deoxyribose sugar instead of ribose
DNA polymerase shape:
Several polypeptide subunits arranged to form different domains.
Shaped like a human hand: template DNA droops into the groove formed by fingers and thumb. Thumb and fingers close to facilitate binding of incoming nucleotide.
Compare DNA polymerase of bacteria/archaea/eukaryota:
Palm domain is evolutionarily related between; fingers are different for each of the three.
Sliding DNA clamp:
A protein that encircles DNA and binds to rear of DNA polymerase to tether it to the template strand.
Without clamp, polymerase would go away after tens of polymerizations. With it, it hangs on for tens of thousands.
Key molecular events of DNA replication:
Strands unwind.
DNA polymerase adds nucleotides to template chain in 5’ to 3’ direction, antiparallel to the template strand.
Nucleotides are added according to complementary base-pairing rules.
ORI:
A specific sequence on the chromosome where unwinding of DNA begins
DNA helicase:
Brought in by specific proteins bound to ORI to further unwind the strands.
Replication fork:
Y-shaped structure of unwinding DNA
Single-stranded binding proteins:
Proteins that coat the unwound segments to stabilize DNA the prevent them from rewinding
They are displaced when replication enzymes come in
Topoisomerase:
Prevents the yet-to-be-unwound DNA from becoming twisted by cutting, untwisting, and rejoining the double-strand ahead of the replication fork.
RNA primers:
Short chain of RNA nucleotides synthesized by enzyme primase, allowing DNA pmase to add onto the primer’s 3’ end to overcome the issue of DNA only being able to work from 5’ to 3’
Leading strand:
Synthesized continuously in the direction of unwinding
Lagging strand:
Discontinuously synthesized.
Okazaki fragments:
Short lengths of DNA that are later covalently bound into a single continuous chain.
Primase, DNA pmase 3, DNA pmase 1, ligase
Primase puts a buncha little primers on the lagging strand. DNA pmase 3 synthesizes backward as much as it can, then DNA pmase 1 comes in and replaces primer RNA with DNA. Ligase connects the fragments.
Replication bubble:
2 Y forks joined from ori extending in opposite directions.
Bacteria and archaea only have one ORI; eukaryotes can have hundreds so synthesis is much faster.
Replication problem with linear DNA:
DNA synthesis can’t reach the extreme ends of a molecule, so DNA gets shorter with every replication.
Telomere:
A region of very repetitive non-coding DNA at the ends of chromosomes that can afford to be lost
Telomerase:
A kind of DNA pmase that determines telomere length.
Contains its own template so it can add a telomere to the 3’ end of DNA without having to read a template
Usually only active in early embryos and germ cells
One gene-one enzyme hypothesis:
The direct relationship between genes and enzymes
Central dogma:
Flow of information from DNA to RNA to protein
mRNA:
RNA transcribed from a polypeptide-encoding gene
Differences in central dogma between pro/eu:
Eu have physically separate transcription/translation processes. Pro transcribe/translate simultaneously.
Codon:
A 3-letter section of the genetic code
Start codon:
AUG, initiator codon. Codes for AA methionine.
Stop codons:
UAA, UAG, UGA, termination/nonsense codon. Polypeptide synthesis stops here.
Transcription:
Info from DNA is made into a complementary RNA copy
Structure of a protein-coding gene:
Promoter - controls sequences, the site of RNA pmase binding
Transcription unit - section of gene that is transcribed
Steps of transcription:
Initiation - transcriptor molecules assemble at promoter
Elongation - RNA chain grows through action of RNA pmase
Termination - transcription ends and RNA mcule and RNA pmase are released from template
Differences in RNA pmase between eu/pro:
In prokaryotes, RNA pmase binds directly to DNA, directed to the promoter by a protein factor that goes away after transcription begins.
In eukaryotes, RNA pmase II, the enzyme that transcribes, can’t bind to DNA. It has to wait for transcription factors, proteins that recognize and bind to the TATA box then recruit RNA pmase II.
Differences in terminators between eu/pro:
In eukaryotes, there are no terminators.
In prokaryotes, 2 specific DNA sequences end transcription. They act after they are transcribed. The first terminator uses complementary base pairing with itself to form a hairpin; the second binds a protein to a specific terminator sequence.
Transcription of non-protein-coding genes in eu:
RNA pmase II transcribes protein-coding genes.
RNA pmase III transcribes tRNA genes and one rRNA.
RNA pmase I transcribes genes for other 3 rRNAs.
Guanine cap:
A reversed nucleotide at the 5’ end of pre-mRNA that protects the mRNA from degradation.
Added by a capping enzyme soon after transcription begins.
Termination of eu transcription:
No sequence - a polyadenylation signal binds protein and cleaves the RNA downstream of the transcription site.
Polyadenylation signal:
A DNA sequences transcribed into the pre-mRNA
Poly(A) polymerase:
Enzyme that adds 50-250 adenines to the 3’ end of the newly created pre-mRNA to protect it from getting eaten by digestive enzymes in the cytoplasm
Intron:
A non-protein-coding sequences in the RNA transcription unit of a protein-coding gene; removed by mRNA splicing from the pre-mRNA during processing in the nucleus
Exon:
The AA-coding sequences that are retained after introns are removed
mRNA splicing:
A process that removes introns from pre-mRNAs and joins exons together.
Spliceosome:
A complex of pre-mRNA and snurps
Snurp (small nucleoprotein particles):
Particles that bind to an intron in a particular order to form the active spliceosome
Alternative splicing:
Sometimes exons are removed, sometimes introns stay - it’s like evolution for mRNA
Resulting proteins have different but related functions
Translation:
mRNA-directed polypeptide synthesis; the assembly of AAs into polypeptides on ribosomes
tRNA:
Brings AAs to ribosome to add to a polypeptide chain
They can base pair with themselves to form 4 double-helical segments like a cloverleaf
tRNA anticodon:
Pairs with the mRNA’s codon
Opposite the anticodon is a free 3’ end that links to the corresponding AA
Wobble hypothesis:
All codons can be read by fewer anticodons/tRNAs because one tRNA can read a few different codons. I have literally no fucking clue what this damn hypothesis is.
Isonine or inosine or something
Aminocylation:
The process of adding an AA to a tRNA
Correct AAs must be available
Aminoacyl-tRNA:
A tRNA linked to the correct AA
Aminoacyl-tRNA synthetases:
Collection of enzymes that catalyze aminoacylation
Ribosome:
Ribonucleoprotein particles that carry out protein synthesis. Made of a small and large subunit.
Special ribosomal binding sites:
A site (aminoacyl): incoming aminoacyl-tRNA binds to mRNA P site (peptidyl): tRNA carrying growing polypeptide chain is bound E site (exit): exiting tRNA binds here as it leaves the ribosome
Stages of translation: initiation
Met-tRNA and its GTP friend bind to small unit to form a complex
Complex binds to 5’ cap of mRNA and scans until it reaches AUG start codon in P site
AUG base-pairs with anticodon in met-tRNA
Large ribosomal unit binds, GTP is hydrolyzed
Stages of translation: elongation
Initiator tRNA binds to P site and A site is empty. Aminoacyl-tRNA binds to A, facilitated by a protein elongation factor. When the ribosome translocates to the next codon, another EF is used. GTP hydrolysis powers the ribosome’s movement down the mRNA.
P site can only bind to…
Peptidyl-tRNA, a tRNA linked to a polypeptide chain with 2 or more AAs
Exception: recognizes met-tRNA even though it only has one AA
A site can only bind to…
Aminoacyl-tRNA
Peptidyl transferase:
A ribozyme that catalyzes the formation of a peptisde bond between the c-terminal of the growing polypeptide in the P site and the AA on the A site
Stages of translation: termination
When the stop codon arrives in the A site, a protein release factor binds to the A site and causes the ribosome to fall apart
Multiple ribosomes can translate a single mRNA simultaneously.
As soon as there’s room on the 5’ untranslated region, another ribosome can start translating
Polysome:
The beads-on-a-string structure of an mRNA molecule and multiple ribosomes attached to it
Sorting proteins to endomembrane system:
Proteins destined for endomembrane system produce a segment of AAs called a signal sequence near the N-terminal end. The sequence is recognized by a recognition particle that gets the protein into the lumen of the rough ER by a process called cotranslational import, called that because it occurs simultaneously with translation of mRNA. A recognition particle binds to its receptor in the ER membrane and tells signal peptidase
FUCK THIS
sorting proteins to nucleus, mitochondria, chloroplasts, microbodies:
fuck u
Mutations:
Base-pair substitutions (missense, nonsense, silent), frameshift
Cellular respiration definition:
The metabolic reactions within cells that break down food to produce ATP
Glucose and gasoline as sources of energy:
Both contain many C-H bonds, which are not very electronegative, so they readily lose electrons
In comparison, compounds containing oxygen hold their electrons closer because O is quite electronegative
Structure of gasoline and glucose:
- diagram
CR is an ___ reaction.
Exergonic - negative delta G
Dehydrogenases:
A group of enzymes that facilitate the transfer of electrons from food to carrier molecules
NAD+:
Nicotinamide adenine dinucleotide: the most common energy carrier. A coenzyme.
3 phases of CR:
Glycolysis, pyruvate oxidation and citric acid cycle, oxidative phosphorylation
CR phases: glycolysis
10 reactions that lead to the oxidation of glucose to produce 2 molecules of pyruvate. Occurs in the cytosol.
Glucose, 2ATP, 2NAD+, 4ADP -> oxidize -> 2NADH, 2ADP, 4ATP, 2 pyruvate
CR phases: pyruvate oxidation
Extracting free energy from the 2 pyruvates and trapping it in ATP and NADH. Occurs in mitochondrial matrix.
3-carbon pyruvate is oxidized into 2-carbon acetyl group and CO2.
How does pyruvate get into the mitochondrial matrix?
Diffuses across porous outer membrane
Crosses inner membrane by a pyruvate-specific membrane carrier
How does pyruvate become acetyl-CoA?
Decarboxylation reaction removes carboxyl group, which is lost as CO2. Oxidation reaction of other 2 carbons produces acetate.
2 electrons and 1 proton transfer from NADH to NAD+.
Acetyl group reacts with CoA to form acetyl-CoA.
CR phases: citric acid cycle
8 reactions (7 soluble in matrix, 1 bound to matrix side of inner membrane) Results in oxidation of acetyl groups to CO2 and synthesis of ATP, NADH, FAD.
FAD:
Flavin adenine dinucleotide
Per one cycle of citric acid cycle…
3 NADH, 1 FADH2, 1 ATP are synthesized and 2 CO2 are released.
Net equation of citric acid cycle:
1 acetyl-CoA + 3NAD+ + 1FAD + 1ADP + 1Pi + 2H2O -> 2CO2 + 3NADH + 1FADH2 + 1ATP + 3H+ + 1CoA
CR phases: oxidative phosphorylation, electron transport
Takes place on inner mitochondrial membrane
Facilitates transport of electrons from NADH and FADH2 to O
4 complexes of respiratory ETC:
I - NADH hydrogenase II - succinate dehydrogenase III - cytochrome complex IV - cytochrome oxidase Complex II is one protein, the rest are many
UQ:
Ubiquinone: Carries electron from NADH from complex I to complex II
Complex II’s role:
Puts electron from FADH2 directly into UQ, bypassing complex I
Cyt c
Cytochrome C: Carries 2 electrons in complex III to complex IV
How electrons move along the ETC:
Non-protein prosthetic groups bind to protein subunits of complexes to facilitate electron transfer by alternating between reduced and oxidized states.
Common prosthetic group: heme
Proton-motive force:
Energy stored by combination of concentration gradient and voltage difference across a membrane
- Free energy released during electron transfer is used to pump protons from matrix to intermembrane space
- UQ picks up protons as they accept electrons, then release their protons into the intermembrane space to retain neutral charge when they donate their electrons
What is the H+ concentration, pH, and charge of the intermembrane space?
High H+, low pH, positive charge
Chemiosmosis:
Using the proton-motive force to do work.
Energy can come from oxidation of food molecules or light energy
ATP synthase: what goes in, what comes out?
ADP and Pi go in, ATP comes out
ATP synthase: what is it?
A large, multiprotein complex that spans the inner mitochondrial membrane.
Basal unit: embedded in the membrane
Head piece: attached to basal unit by stalk
Stator: bridge across basal unit and headpiece.
ATP synthase: how does it work?
Protons move through a channel between the basal unit and the stator, causing the stalk and headpiece to spin
Uncoupling of electron transport and chemiosmosis:
Happens if the proton-motive force can’t establish itself
Ex: ionophores form channels across membranes that ions can pass through, allowing high rates of electron transport but preventing ATP synthesis.
Free energy from electron transport is lost as heat.
Using the uncoupling of electron transport and chemiosmosis:
Animals and others regulate body heat by altering expression of uncoupling proteins
Ideal ATP yield (pro/eu):
38 ATP for pro, 36 ATP for eu (due to energy cost of transport across mitochondrial membrane)
Actual ATP is lower because…
ETC and oxidative phosphorylation are rarely completely coupled
Inner mitochondrial membrane is “leaky” to protons
Proton-motive force is used for other functions
Actual ATP yield (%):
38
Other stuff can undergo glycolysis.
Carbs can be broken down into glucose/fructose and enter glycolysis in the early steps.
Fats break down into glycerol and fatty acids before entering oxidative reactions.
Proteins lose their NH2 amino group and break into AAs before oxidation.
Intermediates of glycolysis and citric acid cycle:
Used as starting substrates for synthesis of AAs, fats, bases for nucleic acids, and carbon backbones
CR is controlled by supply and demand.
Feedback inhibition:
Photofructokinase is an allosteric enzyme. When ATP is high, it inhibits pfkinase. When ATP is low, AMP builds up and acts as an activator for pfkinase.
Fermentation:
Pyruvate hangs out in cytosol and consumes NADH.
Lactate fermentation:
Pyruvate is converted to 3-carbon lactate, which temporarily stores electrons when O is not available.
Alcohol fermentation:
Pyruvate is oxidized to CO2 and ethyl alcohol
What does CR depend on?
NAD+ levels. ATP will continue to be synthesized.
Anaerobic respiration:
Many bacteria/archaea use molecules other than O2 as electron acceptors. Anything with high electron affinity works.
Why is O2 the best terminal electron acceptor?
It’s the most electronegative, it’s the most effective.
Different kinds of aerobes/anaerobes:
Strict aerobe - most eu, many pro; need oxygen to survive
Facultative aerobe - muscle cells, some bacteria; switch between
Strict anaerobe - some bacteria; die in oxygen
Toxicity of oxygen:
If O2 does not receive 4 electrons, it becomes a reactive oxygen species (ROS), which steals everyone’s electrons and rips shit up.
Antioxidant system:
Superoxide dismutase converts ROS into hydrogen peroxide, which catalase reduces to water.
Vitamin C and E also act as reducing agents.
Cytochrome oxidase and why it’s the coolest:
The last complex in electron transfer.
Has four chambers that each hold one electron, then it transfers all four electrons to O2 at once to produce 2 molecules of water and no ROS!
Definition of photosynthesis:
Conversion of CO2 into organic molecules using light energy.
Overall balanced equation for photosynthesis:
6 CO2 + 12 H2O -> C6H12O6 + 6H2O
Stuff in the thylakoid membrane:
Proteins, pigments, etcarriers, and ATP synthase
Stuff in the stromae:
Enzymes that catalyze Calvin reactions
Visible light:
Ranges from 400-700 (blue-red) nm
Blue has highest energy
A couple of things can happen when a pigment absorbs a photon
But i don’t care about them
Difference between chlorophyll A and B:
A has CH3, B has CHO
Engelmann:
did stuff with bacteria and a prism (rainbow)
Photosystem: parts and definition
Complexes of proteins and pigments inside thylakoid membrane
Composed of an antennae complex that funnels energy to the core reaction centre
Photosystem I:
Has P700 chlorophyll A
Photosystem II:
Has P680 chlorophyll A
Linear electron transport:
PSII to cytochrome (plastoquinone)
Cytochrome to PSI (plastocyanin proteins)
PSI to ferredoxin (ferredoxin is an iron-sulfur protein)
Ferredoxin to NADP+ reductase enzyme
Enzyme reduces NADP+ to NADPH using 2 electrons from electron transport and a proton from water.
No oxidation gradient between PSII and PSI:
Must be powered by light absorption
In photosynthetic ETC, proton gradient comes from:
Plastoquinone doing the same thing UQ does
Oxidation of water on lumen side of PSII adds 2 protons
A proton is taken from the stroma during NADPH synthesis
Photosynthetic proton-motive force is used to…
Synthesize ATP by chemiosmosis using chloroplast ATP synthase
Stoich of linear electron transport:
8 photons (4 per system) must be absorbed to produce 1 molecule of O2
Cyclic electron transport:
PSI functions independently from PSII.
Recycles electron instead of donating it to NADP+ reductase
NADPH is not formed.
ATP is formed by proton pumping.
Why is the cyclic electron transport chain necessary?
Calvin cycle requires more ATP than NADPH; other parts of the cell need ATP.
Calvin cycle:
11 reactions that reduce unusable CO2 into sugar using NADPH
Calvin cycle is overall ___.
Endergonic (requires ATP)
Phases of Calvin cycle: list
Fixation, reduction, regeneration
Phases of Calvin cycle: Fixation
Carbon from CO2 is incorporated into 5-carbon RuBP to produce two 3-carbon 3-phosphoglycerates.
Phases of Calvin cycle: Reduction
Each 3-pglycerate gets another P group from ATP breakdown to produce two 1,3-bipglycerates.
Each 1,3-bpglycerate is reduced by NADPH electrons to produce G3P
Phases of Calvin cycle: Regeneration
5 of 6 carbons in the two G3Ps are rearranged to form one RuBP for the next round
3 turns of the Calvin cycle generates:
One surplus molecule of G3P. Requires 9ATP and 6NADPH.
Rubisco: SUPER IMPORTANT
Ribulose-1,5-bisphosphate carboxylase oxygenase
Enzyme that catalyzes fixation
Provides organic carbon for everybody - is carbon Oprah
Cube-shaped with 8 large and 8 small subunits. Large subunit contains active site to bind CO2 and RuBP
Rubisco synthesis:
Large subunit is encoded by a gene in the chloroplast genome.
Small subunit is encoded by a gene in the nucleus’ genome.
Small subunit is synthesized in cytosol then imported to chloroplast
