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146 Cards in this Set

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Things to Know
[x] = concentration of substance 'x'
--> = yields
I capitalize things I deem important to know (i.e. distinction between mitosis and meiosis)
I heartily suggest youtube to watch all of the following:
mitosis, meisos, Krebs Cycle, active and inactive transport, DNA synthesis, protein synthesis...etc. Youtube is the visual wikipedia - you can find ANYTHING on there.
I also advise using the website for your bio textbook, whatever that may be. Mine is Pearson's.
Enzyme Structure and Function I (ESF begins)
Enzymes are highly selective catalysts for biochemical reactions; remain unchanged.
How do enzymes affect rate and equilibrium?
Alter rate of reaction, not position of equilibrium
How do enzymes work?
Enzyme's active site specifically binds substrate.
Enzyme-Substrate complex changes shape
What is the rate of reaction dependent on?
Dependent on [enzyme] and [substrate].
-->rate-limiting factor is amount of enzyme
--> unlimited substrate+correct pH+temp = rate of reaction is proportional to [enzyme]
Define 'inhibitor'.
things that decrease/stop catalytic activity by disrupting enzyme's active site.
What are competitive inhibitor?
...they compete WITH substrate for enzyme's active site.
...addition of more substrate speeds up reaction
...do NOT alter site
Typical rxn -
(ES ends)
E + S <-- --> ES --> EP <-- --> E + P
What are noncompetitive inhibitor?
...alter the enzyme site by binding to another portion of it (NOT active site)
...substrate can 'no longer fit'
...addition of more substrate WILL NOT speed reaction
What reactions help organisms harvest energy?
catabolic and anabolic reactions
Define and give an example of 'catabolic' rxn.
'Break down' substrates.
Glycolosis
Define and give an example of 'anabolic' rxns.
'Build up'
Amino acid synthesis
What is glycolosis?
Literally means 'glucose breaking'!
...the first stage of aerobic (and anaerobic) respiration.
...takes place in the cytoplasm of the cell.
Express the chemical forumal for glycolosis.
C6H12O6 + 2ATP + 2NAD+2 YIELDS pyruvate + 4ATP + 2NADH
What is the net yield of ATP?
2ATP.
...cell invests 2ATP but gets out 4ATP which gives us above net yield answer.
Where does the 2NADH go?
Mitochondria.
...energy in them will be converted to ATP.
Recap Glycolosis (1)
...part of both aerobic and anaerobic respiration.
...process that splits glucose, a six-carbon compound, into two pyruvate molecules, each of which has three carbons.
...a 2 ATP investment results in a 4 ATP payoff.
Recap Glycolosis (2)
...the rest of aerobic respiration takes place in the mitochondria BUT glycolysis takes place in the cytoplasm of the cell.
...does NOT require oxygen
What is the Krebs Cycle?
...Helps in chemical conversion of carbs, fats, and proteins into CO2 and H2O to make energy!
...part two of the energy harvest!
What happens while pyruvate is transported to mitochondria?
...hree-carbon pyruvate is converted into the two-carbon molecule called acetate
...coenzyme A is added on to create one of the reactants of this cycle!
Is ATP used in glycolosis?
Yes.
...ATP is used to split glucose molecules into a three-carbon compound called pyruvate.
What is the citric acid cycle?
The Krebs Cycle!
...don't be fooled or misled. they refer to the same thing and are used interchangeably.
...it's because The Krebs cycle begins when acetyl-CoA and oxaloacetate interact to form the six-carbon compound citric acid.
Krebs Cycle (2)
Occurs in mitochondrial matrix...
2Pyruvate (glycolysis) decarboxylated in mitochondria -> 2acetyl CoA + 2NADH + 2 CO2
Krebs Cycle (3)
Two turns of cycle produces -
2 ATP, 6 NADH, 2 FADH2, 4CO2
Krebs Cycle - Visual!
Make sure you know what the end products are.
Krebs Cycle Recap (2)
...does not directly require oxygen, it can only take place when oxygen is present because it relies on by-products from the electron transport chain, which requires oxygen.
..is therefore an aerobic process.
Krebs Cycle Recap (1)
...results in 2 ATP molecules for each glucose molecule run through glycolysis.
...sends energy-laden NADH and FADH2 molecules on to the next step in respiration, the electron transport chain.
Electron Transport Chain (ETS begins)
What does it do?
Couples e- donor (i.e. NADH, FADH2) and e- acceptor (O2).
How does ETS work?
H+ ions are transferred across the inner mitochondrial membrane into the inetermembrane space.
...creates pH gradient
How does ETS work?
...ATP synthase helps H+ flow back into matrix, producing ATP
Nucleotide Structure & Function - What are the three components of nucleotides? (NSF)
1)Pentose (5 carbon ring) sugar. {DNA or RNA}
2)Nitrogenous bases on the 1' carbon of pentose (C,U,T, A, G)
3)One to three phosphate groups attached to 5' carbon
What types of nitrogenous bases?
Pyrimidines (small 6 membered rings)
- cytosine, uracil (replaces thymine in RNA), thymine
Purines (6 membered ring fused to 5 membered ring)
- adenine, guanine
How do nucleotides polymerize?
3' to 5' direction
How to nucleotides polymerize in 3' to 5' direction?
...3' carbon attached to a -OH group
...5' carbon attached to phosphate
The following images compares RNA & DNA -
Draw them out for practice.
The next slide shows everything together.
Examine a full nucleotide.
Name the two types of bases - and relegate the five nitrogenous bases to each type.
...Purine - A, G, U
...Pyrimidine - C T
How do they match up? (complimentary bases)
C&G, A&T
Specific name for double-helix structure of DNA molecule? Describe, for brownie points.
Watson-Crick Model.
...5' end of one strand lies to 3' end of another.
...the first nucleotide will have the phosphate on it, and the last will have a free OH
...hydrogen bonding!
What is the diff between RNA and DNA?
RNA has -OH at 2' AND 3'.
How many types of RNA are there?
Three.
...mRNA - messenger. DNA is transcribed to mRNA in nucleus {template for protein!}
...rRNA - ribosomal.
...tRNA - transfer - brings specific amino acids (AA) to ribosome for protein synthesis.
True or false:
one animo acid can be associated with multiple tRNAs.
False.
...specific tRNAs for each AA
Name the four key regions of tRNA.
...aminoacyl attachment site (where AAs are joined to tRNA)
...anticodon that binds complementary mRNA
...T loop
...D loop
DNA Synthesis/Replication
Know ALL chemicals involved - DNA polymerase I and III, topoisomerase, RNA primer etc...
DNA Replication Step-by-Step
A set of questions and fill in the blanks to be followed.
____ nicks double helix of DNA and releases coiling.
Topoisomerase
What makes RNA primer?
Primase
What does primase make RNA primer for?
DNA Polymerase III
The ____ strand features continuous complimentary strand.
leading
The lagging strand must be completed in short segments called ____.
Okazaki fragments.
What unifies all the Okazaki fragments?
DNA ligase
What proofreads each added nucleotide?
Exonuclease
_____ removes the RNA primer laid down by DNA polymerase III
DNA polymerase I
Sources of damage to DNA can come from ______
...gamma rays, X rays, UV light, chemicals, free radicals
____ is the removal and replacement of damaged bases.
Base excision.
...note that DNA glycosylase identifies damaged bases and DNA polymerase beta replaces them.
___ is the removal and replacement of numerous adjacent nucleotides.
Nucleotide excision.
...think of it as multi-base excision.
What corrects incorrect pairing of normal bases?
Mismatch repair.
Define recombinant DNA.
Artificially created or altered DNA.
...restriction enzyme used to cut DNA at a specific point - sticky ends will hybridize with another DNA.
In vitro gene cloning -
PCR (polymerase chain reaction) is used for DNA replication for analysis.
In vivo gene cloning -
Plasmids! They carry circular DNA, enter bacteria, replicate
...cultured cells transformed with a human gene manufa
DNA Synthesis!
Brownie points - what's the central dogma?
DNA --> RNA --> protein
How do we accomplish the central dogma?
...Transcription (DNA --> mRNA) in nucleus
...Translation (mRNA --> protein) in ribosomes of cytoplasm or ER
...in prokaryotes EVERYTHING is done in the cytoplasm, translation occurs before transcription is finished, and the operon controls series genes.
Transcription (1)
...start with promoter regions which are "conserved sequences".
Transcription (2)
...double helix opens so one DNA strand (determined by promoter) can be template for RNA polymerase
What is the direction?
5' to 3'
...until terminator sequence is reached.
Where are transcripts 'processed'?
Nucleus.
...introns are spliced out while exons are kept
...poly-A sequence at 3' end and 5''cap added for stability so it''s recognized as mature/ready for translation
Translation (1)
Begins at 5' cap of mRNA where initiator tRNA is loaded into P-site of small ribosomal subunit.
...initiation factors to start!
Ribosome in translation
Ribosomes are >50 proteins and rRNA. Two units -
...small subunit is in charge of joining correct tRNA to mRNA
...large subunit catalyzes peptide bond
How many binding sites does a ribosome have?
Four.
...one for the mRNA codon
...three for the tRNAs: the A site (where tRNA binds), P site(break AA-tRNA bond and make AA-AA bond), the E site (easy to remember as EXIT site for tRNA)
Translation (2)
mRNA binds at start codon (AUG methionine). tRNA with complimentary anticodon (UAC) loads into A-site.
START.
Translation (3)
(UAC) moves to P-site where it is broken away from tRNA to start polypeptide chain.
Next complimentary tRNA loads into A-site.
Process continues until one of three stop codons is reached.
Transcription visuals - take note that this in nucleus.
Be able to name ALL sites involved.
Translation - take note, this is in cytoplasmic or ER ribosomes.
Again, be able to name and distinguish between P, A, E site etc.
What is the Wobble hypothesis?
...that the first two basses bind tRNA
How many different AAs? and codons?
20 different AA
64 different codons
...start - AUG
...stop - UAA, UAG, UGA
Name 2 differences in PROKARYOTIC from eukaryotic protein synthesis.
...mRNA is not spliced b/c no introns. polycistronic.
...because no 5' cap, ribosome binds at ribosome-binding sequence (upstream to AUG)
Name a differences in EUKARYOTIC from prokaryotic protein synthesis.
...1 mRNA makes 1 protein
Structure of Eukaryotic Chromosomes
Questions and fill in the blanks about lots different types of chromatin.
What is double-stranded DNA packaged with protein called?
(this is a DUH easy question)
Chromatin.
And highly coiled chromatin is called ____.
Chromosomes.
True or false - Circular DNA is found only in prokaryotes.
True.
H2A, H2B, H3, and H4 are examples of _____, which package DNA into ______.
Histones.
...note that each histone is an octamer b/c 2 of each histone protein does the pacaging.
Nucleosomes.
...these are the first level of chromosome packing.
True or false -
In DNA packaging, coiling is not dynamic.
False.
What are euchromatin?
Areas of chromosome-expressing genes; LESS tightly packed during interphase.
What are heterochromatin?
HIGHLY coiled, not expressed areas.
Now let's talk about chromosomes and cancer.
Define a centromere.
...Region of mitotic chromosome holding sister chromosomes together.
...Also is site of kinetochore formation & mitotic spindle binds
What are telomeres?
It's what we call the chromosome end of the DNA sequence
...i.e. TATATATATATATATA - a bit of repetitive nonsense
What does telomerase do?
...adds telomeres.
...it's so the LAGGING strand doesn't lose its end bits which are essential
True or false -
Cancer is caused by the failure of normal cellular control.
True.
...oh-so-true. failure of normal cellular control --> immortal cell --> clumps of immortal cell --> tumor.
The normal cell control path is:
disruption of growth factors, receptors, signaling pathways (RAS)...dna repair/damage response through the p53 pathway.
All of this should induce apoptosis if the cell feels it can't save itself.
Usually this holds true but a single mutation in an oncogene or tumor suppressor gene can spell cancer for an individual.
...damaged proto-oncogene; 1 mutation --> malignancy
...tumor suppressor NORMALLY prevents cancer; 2 mutations --> cells grow wildly --> malignancy
Mendelian Genetics (1)
Studied pea plants and derived two laws.
a) segregation of characteristics - one allele expressed per gamete
b) independent assortment - genes for characteristics are independently inherited
Mendelian Genetics (2)
Phenotype - external look
Genotype - internal genetic maeup
Gene - region of DNA that controls hereditary characteristic
Mendelian Genetics (3)
Alleles - alternative forms of gene.
Pay attention...
diploid cells have 2 alleles each occupying SAME LOCUS of homolgous chromosomes.
...homozygous - identical alleles for given gene (ss/SS)
...heterozygous - different (Ss)
Inheritance (1)
Wild type - typical form of an organism in natural conditions
Recessive trait - produced by homozygous recessive allele (ss)
Complete dominance - this allele will always be expresses (S!)
Penetrance - proportion of individuals expressing a certain phenotype
What is linkage?
If 2 genes lie close on a chromosome, chances are they'll be inherited together.
...far apart genes participate in recombination
...linkage is useful for gene mapping
Inheritance follow-up:
What is the Hardy-Weinberg principle?
"punnet square for a population"
...based on genetic equilibrium concept
How can you calculate allele frequency based on the frequency of an autosomal recessive (AR) disease?
p^2 + 2pq + q^2 = 1
...p - frequency of dominant allele
...q - frequency of recessive allele
Inheritance (2)
Incomplete/partial dominance - heterozygous genotype expressed halfway
...RR is red
...rr is white
...but Rr is pink
Codominance - heterozygous individual expresses BOTH phenotypes (blood typing! i.e. ABO)
____ is the breeding of a PP with a pp individual.
Test cross
What happens to a gene to cause Down's Syndrome?
Trisomy 21...the homologs didn't separate on chromosome 21.
Easy brownie points question:
The ___ is the first generation bred from two closely related species.
F1
Y chromosome characteristics are -
Y chromosome, whose presence always produces testes development.
Y linked disorders - color blindness, hemophilia...
And the F2 generation is ____.
The kids/progeny of F1
X chromosome characteristics are -
Normal females contain 2...one is active and the other is a barr body.
A ____ is the breeding of the F1 and another pp.
Back cross
Cell Reproduction Showdown -
Mitosis vs. Meiosis
1) DNA packaged into chromosomes must replicate.
2) Copies of the chromosomes and organelles must migrate to opposite ends of the cell.
3) The cell must physically split into two separate cells.
True or false - Crossover occurs during Meoisis II.
False.
...occurs in Meosis I before anaphase I
Meiosis -
Meiosis I results in two independent cells. One cell contains the maternal homologous pair, with a small segment of the paternal chromosome from crossover. The other cell contains the paternal homologous pair, likewise with a small segment of the maternal chromosome.
[i suggest youtube to watch this]
Meiosis -
The two cells that move from meiosis I into meiosis II are haploid—each have 23 replicated chromosomes.
Separation of sister chromatids YIELDS 4 haploid cells.
Mitosis vs. Meiosis
Mitosis --> identical daughter cells. In somatic.
Meiosis --> genetically diverse gametes. In ovaries & testes.
Meiosis General Recap
Errors in meiosis leads to aneuploid.
Remember it includes IPMAT [I played Manny's atrocious trumpet.)
interphase, anaphase, prophase, metaphase then telophase. same as mitosis.
Meiosis
2 stages - MI and MII - and end product of 4 haploid (23N) cells.
...in males, creates 4 sperm
...in females, creates 1 ovum & 3 polar bodies
Remember, XX is girl and XY is boy.
Meiosis visual for those who want it! Remember youtube is actually a really good source of animated videos for this, mitosis, the krebs cycle etc...
Be able to explain why two sets of IPMAT are needed.
Mitosis Rumble
Note that this is ONLY in somatic cells. Results in 2 identical daughters.
Nuclear division + cytokinesis
[I played Manny's atrocious trumpet.]
Interphase - cell growth, DNA synthesis, chromosome replication, G1, S, and G2
Mitosis Rumble
Prophase - chromosomes tighten, nucleoli disappears, centrioles move to opp. ends and mitotic spindle forms.
Mitosis Rumble cont'd
Metaphase - nuclear membrane dissolves, microtubules attach to kinetochores and spindle fibers align chromosomes along metaphase plate
Mitosis Rumble
Anaphase - pull apart! chromatids polarize and spindle fibers become indistinct
Telophase - the chromatids are on opposite ends, nuclear membrane forms, spindle fibers disappear
Remember cytokinesis! {separation of cytoplasm, completes division}
Mitosis Recap!
...DNA packaged into chromosomes must replicate.
...copies of the chromosomes and organelles must migrate to opposite ends of the cell.
...the cell must physically split into two separate cells.
...note some say mitosis starts at the prophase.
Mitosis visual
What are mutations? Where do they occur? Why do they occur?
...heritable changes in DNA. They can be advantageous or deleterious.
...in both germ and somatic cells.
...either induced by mutagens or spontaneous.
Point mutations are as follows -
Base pair substitutions -
...transversions: purine --> pyrmidines so that
a. no new a.a. (silent mutation)
b. new a.a. (missense) may or may not lead to dif.
in final protein function
c. premature stop (nonsense)
Point mutations are as follows cont'd -
Frameshift mutations.
...insertion/deletion of nucleotide which changes ENTIRE reading frame. definite mutation.
...usually leads to a useless or nonfunctioning protein.
Chromosomal mutations are serious.
Could be brought about by deletion, insertion, duplication OR translocation.
...human disorders:
a. cri du chat
b. CML leukemia
c. Down syndrome
Give the five total examples of spontaneous mutations -
1. unstable nucleotide bases
2. chemical reactions change bases
3. uncorrected errors by DNA polymerase
4. mistakes in meiosis
5. transposons
Talk about Fungi!
one of the 5 kingdom of organisms.
NO photosynthesis. CHITIN in cell walls.
Fungi structure
...differ in level of cellular organism (1 nucleus vs. 1000 nuclei, multicell-vs-unicell)
...asexual reproduction, some can choose sexual in addition
...generally haploid for most of life cycle
True or false -
Fission is an example of sexual reproduction in fungi.
False.
...asexual reproduction includes fission, spores, fragmentation, budding
Talking about Viruses!
...little moochers!
...they contain either DNA or RNA to encode genetic information.
...their genome can either be circular or linear, double or single stranded.
What's an extremely famous and detrimental virus that doubles as an STD?
HIV.
What do some viruses require to copy themselves?
Reverse transcriptase! (HIV requires this)
The outer protein ___ surrounds nucleic acid in virus.
capsid
How do eukaryotic infecting viruses get past cell membranes?
They are further encased by lipid bilayers with special viral proteins that they stole from host.
Virus (1)
Outside of a living cell, a virus is dormant, but once inside, it takes over the resources of the host cell and begins the production of more virus particles. Viruses are more similar to mechanized bits of information, or robots, than to animal life.
Virus Structure
Made up of head and tail!
...head has capsid and nuclei acid core
...tail has the sheath (bacteriophages), plug and tail fibers.
Virus structure - revisiting the REGULAR animal virus
Please note that I only described ingredients for bacteriophage prior to this.
Normal animal viruses just need a capsid, some sort of glycoprotein envelope around the capsid, and nucleic acid on the inside. The flu is a great example of a normal animal virus.
Virus visual - bacteriophage
Viruses - bacteriophages in depth
Lytic (virus replicates madly so that bacterial cell wall bursts)
Lysogenic (incorporates itself into host genome so that it is replicated with host DNA)
HIV and retroviruses
HIV is retroviral.
maintain their genetic information in the form of ribonucleic acid (RNA). Through the use of an enzyme known as reverse transcriptase, HIV and other retroviruses are capable of producing deoxyribonucleic acid (DNA) from RNA, whereas most cells carry out the opposite process, transcribing the genetic material of DNA into RNA. The activity of the enzyme enables the genetic information of HIV to become integrated permanently into the genome (chromosomes) of a host cell.
Retroviruses
ssRNA...transduction is the act of transfering the viral DNA.
HIV Virus Structure
Investigate structures on your own. MCAT doesn't go in deeply.
Prokaryote (1)
It's unicellular but can form colonies and act like a multicellular organism if need be.
Prokaryote (2)
...no nuclear envelope
...complexed with proteins but not histones
...plasmids and episomes can be present
...cell wall, ribosomes, plasma membrane can be present
More on the Plasma membrane
NO glycolipids or cholesterol
Prokaryote Cell wall complex
Gram (+) = thick peptidoglycans
Gram (-) = not as much peptid. and ion passage is way regulated
Flagella, pili, slime layer might be present
Prokaryote (3)
...rod - bacilli, spiral - spirilli, round - cocci
...can be aerobic or anaerobic
...usually in symbiotic relationship w/something else
...reproduction = binary fission