Biology

Cell Resp

Extract energy from food and transfer to ATP

Anaerboic Cell Resp

Glycolysis followed by Lactic or Alcohol Fermentation

Aerobic Cell Resp

Glycolysis followed by Krebs Cycle, ETC, Oxidative Phosphorylation

ATP release energy by

Converting to ADP, change from less stable to more stable releases energy.

Glycolysis

10 step process. Breaks down 1 molecule of glucose into 2 3 carbon molecules of pyruvate or pyruvic acid and release 4 molecules of ATP. Energy of activation is 2. 2 ATP + 1 Glucose yields 1 Pyruvate and 4 ATP. Net gain of 2 ATP. Occurs in Cytoplasm without oxygen. Pyruvate used for Krebs Cycle. ATP is produced by substrate level phosphorylation by enzymatic transfer of phosphate to ADP.

Phosphofructokinase

Allosteric, inhibits glycolysis when cell has enough ATP and does not need anymore.

Facultative Anaerobes

Tolerate presence of Oxygen

Obligate Anaerobes

Cannot live in environment containing oxygen

Fermentation generate ATP using supply of

NAD to accept electrons.

Alcohol Fermentation

Convert pyruvate from glycolysis into ethyl alcohol and carbon dioxide

Lactic Acid Fermentation

Pyruvate from glycolysis reduced to form lactic acid or lactate. NADH oxidized back to NAD+.

Krebs Cycle

Aerobic. Citric acid cycle; occurs in matrix of mitochondria, requires pyruvate from glycolysis.

• Acetyl CoA combines with oxaloacetic acid to produce citric acid. Each glucose turned to 2 pyruvate, for each glucose KC happens twice.

• Pyruvate combines with Coenzyme A to form acetyle coA. Conversion of pyruvate to acetyl coA produces 2 NADPH. ! NADPH for each pyruvate

• Each turn of Kreb Cycle releases 3 NADH, 1 ATP, 1 FADH

• ATP produced by substrate level phosphorylation

NAD and FAD

Coenzymes that carry protons or electrons from glycolysis and KC to ETC.

• NAD and FAD dehydrogenase facilitates transfer of hydrogen atom from substrate to NAD+

• With NAD+ both process fail and cell dies.

• Both are vitamin derivative

• NADH carries 1 proton and 2 electrons

ETC

Proton pump, uses energy from exergonic flow of e- to pump proton from matrix to outer compartment. Establishes proton gradient. ETC makes no ATP directly but allows chemiosmosis to produce ATP. Collection of molecules embedded in cristae membrane of mitochondria.

• Carries electrons from NAD and FAD from glycolysis and KC to oxygen (final electron acceptor) through a series of redox rxns.

• NAD delivers electrons to high energy level in chain than does FAD

• NAD produces 3 ATP and Fad 2

• ETC consists mostly of Cytochromes

Oxidative Phosphorylation

Phosphorylation of ADP into ATP by oxidation of carrier molecules NADH and FADH2.

• Powered by redox rxns of ETC

• Proton gradient created between outer and inner compartments

• Protons can’t diffuse through cristae membrane, flow only down the gradient into the matrix through ATP synthase channels. As protons flow through the ATP synthase channels, generate energy to phosphorylate ADP into ATP; this is called chemiosmosis.

• Oxygen is the final hydrogen acceptor, combine ½ oxygen with 2 electrons and 2 protons forming water.

Photosynthesia

Light energy to chemical bond energy.

6CO2 + 12 H2O yields C6H12O6 + 6H2O + 6O2

Light rxns

Use light directly toproduce ATP

Light independent rxns

Calvin cycle, produces sugar. CC uses ATP from light rxns, both rxns occurs only when light present.

Photosynthetic Pigments

• Chlorophyll a and b are green and absorb red, blue and violet range

• Carotenoids are yellow, orange and red. Absorb blue, green and violet range.

• Xanthophyll are carotenoids with diff chem variation

• Phycobilins are reddish and absorb light in blue and green range

• Chlorophyll b, caroteinoids and the phycobilins are antenna pigments, capture light in wavelengths other than those captured by chlorophyll a

• Chlorophyll a participates in light rxn directly. Large molecule with single magnesium atom in head surrounded by alternating double and single bonds

• Head of chlorophyll a is called porphyrin ring, attached to long hydrocarbon tail.

• Double bonds play role in light rxns. Source of electrons that flow through the ETC.

Chloroplast

• Chloroplast contain grana, where light rxns occur, and strom, where light-independent rxns occur.

• Grana consists of layers of thylakoids, site of photosystem 1 and 2.

Photosystems

Light harvestic complexes. 2 types: PS 1 and PS2. PS2 operated first. PS1 absorbs 700 nm range, PS2 absorbs 680 nm range.

Light rxns

Light is absorbed by photosystems in thylakoid membrane and electrons flow through ETC. 2 routes: Noncyclic and Cyclic Phosphorylation.

Noncyclic Photophosphorylation

Electrons enter 2 electron transport chains, and ATP and NADPH are formed.

• Energy absorbed by P2. Electrons from double bond in head of CA becomes energized and move to higher energy level, captured by primary electron acceptor (Pheophytin).

• Photolysis: Water splits. Give electrons to those lost from CA in P2.

• Electrons from P2 pass along ETC consisting of Plastoquinone, 2 cytochromes and other protein, and ultimately ends up in P1. Flow of energy is exergonic and gives energy to form ATP by chemiosmosis, this process called photophosphorylation.

• ATP formed from light rxns, protons that were released from water during photolysis and pumped by thylakoid membrane from stroma into thylakoid space. ATP formed, diffuse down gradient through ATP synthase channels, and into the stroma. ATP here provides energy for Calvin Cycle

• NADP reduced, picks up 2 protons released from water in P2. NADPH carries hydrogen to Calvin Cycle to form sugar.

• Energy absorbed by P1. Electrons from head of chlorophyll a become energized and captured by primary electron receptor. Similar to P2 but electron that escape from CA are replaced with electrons from P2 instead of water. Also ETC in P1 contains ferrodoxin and ends with production of NADPH not ATP.

Cyclic Photophosphorylation

Produce ATP, No NADPH produced. When CC occurs large amounts of ATP used so CP used to replenish ATP levels. Electrons travel from P2 ETC to P1, to primary electron accepter and then back to cytochrome complex in P2 ETC.

Calvin Cycle

Produces 3 carbon sugar PGAL (phosphoglyceraldehyde). Carbon enters stomates of leaf in form of CO2 and gets fixed into PGAL.

• Carbon fixation

• Reduction rxn, Carbon gains hydrogen

• CO2 enters, attaches to 5 carbon sugar, ribulose biphosphate, forming 6 carbon molecules. 6 carbon unstable, breaks doring into two 3 carbon molecules or 3 phosphoglycerate. Rubisco catalyzes this step.

Photorespiration

Plants where CO2 is fixed into 3PGA are called C3 plants. First step not efficient because rubisco binds with O2 as well as with CO2, when rubisco binds with O2 instead of CO2, this process diverts process of photosynthesis where no ATP is produced or no sugar formed. Instead peroxisomes break down the products of photorespiration.

C4 Photosynthesis

Dry environment. Modified anatomy. Thrive in hot and sunny environment. Ex. Corn, Sugar cane and Crabgrass.

• CO2 enters mesophyll cell, combines with 3 carbon molecules, Phosphoenolpyruvate (PEP), to form 4 carbon molecule oxaloacetate.

• PEP carboxylase doesn’t bind with oxygen and can fix CO2 more efficiently than rubisco.

• Oxaloacetate produces malic acid or malate, pumps through plasmodesmata into bundle sheath cells. Once malate is in bundle sheath cell, releases CO2, gets incorporated into PGAL by CC. Bundle sheath cell is deep within leaf and little oxygen present, rubsico can fix CO2 efficiently. This pathway is called the Hatch Slack Pathway. Remove CO2 from air space near the stomate.

• Steep CO2 gradient between airspace in mesophyll of leaf near stomates and the atmosphere around leaf

• Kranz anatomy: Structure of C4 leaves that differ from C3 leaves, in C4 leaves the bundle sheath cells under mesophyll. Light rxns occur in mesophyll and dark rxns in bundle sheath cells. C3 leaves all photosynthetic cells have direct access to oxygen.

CAM

Crassulacean acid metabolism, dry conditions. Keep stomates closed during day and open at night; reverse of how most plants behave. Mesophyll cells store CO2 in organic compounds they synthesize at night. During day, light rxns supply energy for CC, CO2 is released from organic acids made night before to become incorporated into sugar.

Cell Division

Growth, repair and reproduction. Mitosis produces 2 genetically identical daughter cells and conserves chromosome number (2n), Meiosis occurs in sexually reproducing organisms and results in cells with half chromsomes of parent cell (n).

Cell Cycle

Ratio of Cell volume to SA (area increases square volumes increases cube) and Capacity of Nucleus limit cell size and promote cell division.

Interphase

G1: Intense growth and biochemical activity, S: Synthesis or replication of DNA, G2 is when cell continues to grow and complete prep for cell division. 90 percent of life in here. Chromatin threadlike. In animal cells, centrosome in cytoplasm can be seen. Plants lack centrosomes so they have MTOCs.

Mitosis

Dividing of nucleuse. Prophase metaphase anaphase telophase

Prophase

Nuclear membrane disintegrates, nucleolus disappears, mitotic spindle begins to form, longest phase of mitosis.

Metaphase

Chromosomes line up in single file are equator, Centrosome are at opposite poles of the cell.

Anaphase

Centrosomes of each chromosome separate. Shortest phase of mitosis.

Telophase

Chromosome cluster at opposite ends of cell, nuclear membrane reforms. Super coiled chromosomes began unraveling and return to normal, pre-cell division condition. 2 individual nucleoli form, mitosis is complete.

Cytokinesis

Dividing of cytoplasm. In animal cells, a cleavage furrow forms down middle of cell as actin and myosin microfilaments pinch in the cytoplasm. In plants, cell plate forms during telophase as vesicle from Golgi coalesce in middle. Sticky middle lamella cements adjacent cells together in daughter plant cells.

Cancer

Reaction to overcrowding called contact inhibition where cells stop dividing and enter G zero. Anchorage dependence is another characteristic of normal cell. Cancer cells require non these allowing them to grow and metastisize.

Meiosis

Produces gametes with haploid chromosome number. 2 stages: Meiosis 1 and 2. In M1 homologous chromosomes separate. M2 is like mitosis. In M1, each chromosomes pair up with homologue into a synaptonemal complex by process called synapsis and form structure called tetrad or bivalent. Synapsis ensure each daughter cell receive one homologue, makes crossing over possible. In M2, sister chromatids seperate. At beginning of meiosis cells have diploid, at end have haploid.

M1

Prophase 1: Synapsis, Crossing Over (produces recombinant chromosomes that combines genes from both parents), Chiasmata (visible manifestation of cross over event), Longest.

Metaphase 1: Homologous chromosomes line up double file, Spindle fibers from poles of cell attached to centrosome of each homologues.

Anaphase 1: Homologous chromosomes separate.

Telophase 1: Homologous pairs continue to separate until reach ends of poles, each pole has haploid number of chromosomes.

Cytokinesis 1: Occurs simultaneously with Telophase 1. Interphase occurs between M1 and M2.

Cell CYcle Control System

Timing of cell division controlled by Cyclins and CDKs. First CDK discovered called MPF (M-phase promoting factor).

Law of Dominance

When 2 organisms each homozygous for 2 opposing traits are crossed, offspring will be hybrid, but only exhibit dominant trait while hidden is recessive.

Law of Segregation

During formation of gametes, 2 traits carried by each parent separate. Cross is called monohybrid.

Testcross/Backcross

Way to determine genotype of individual plant or anime showing the dominant trait.

Law of Independent Assortment

Cross between 2 individuals hybrid for 2 or more traits that are not on the same chromosome. Dihybrid cross.

Dihybrid Cross

Cross between 2 F1 plants is called dihybrid cross.

Incomplete Dominance

Blending.

Codominance

Both traits show (MN blood groups)

Multiple Alleles

There are more than 2 allelic forms of a gene. 4 different blood types: A, B, AB, O. A and B are codominant, O is recessive.

Pleiotropy

One single gene to affect organism in several or many ways. Ex) Marfan Syndrome where one single defective gene results in abnormalities of eyes, skeleton and blood vessels.

Epistasis

2 separate genes control one trait, but one gene masks expression of other gene. Gene that masks other gene known as epistatic.

Polygenic Inheritance

Blending of several separate genes that vary along a continuum. These traits are polygenic.

Sex linked

If sex linked trait is due to recessive mutation, female express phenotype only if she carries 2 mutated genes. If she carries one, she is carrier. If dominant, female express phenotype with only one mutated gene. Males inherit only one x linked gene, if male inherits mutated x linked gene, he will express the gene. Recessive occur more often than Dominant. Ex of recessive) Color blindness, hemophilia, Duchenne muscular dystrophy.

Barr Body

In development of embryo of female, one of the x chromosomes are inactivated in each somatic cell. Results in genetic mosaic, some cells have one X inactivate, some have other X inactivated. Not all cells of female mammals are identical. Inactivated chromosomes condenses into dark spot of chromatin called Barr body. Proof seen in Calico cats. Another is X linked recessive mutation preventing development of sweat glands.

Phenylketonuria

Autosomal recessive

Cystic Fibrosis

Autosomal recessive

Tay-Sachs Disease

Autosomal recessive

Huntington’s disease

Autosomal dominant

Hemophilia

Sex linked recessive

Color blindness

Sex linked recessive

Duchenne muscular dystrophy

Sex linked recessive

Sickle cell disease

Autusomal recessive

Down Syndrome

47 chromosomes due to trisomy 21

Turner’s syndrome

XO 45 chromosomes due to a missing sex chromosomes

Klinefelter’s Syndrome

XXY 47 chromosomes due to extra x chromosome.

Deletion

Fragment lacking centromere is lost during cell division

Inversion

Reattaches to original chromosome but in reverse orientation.

Translocation

Fragment of a chromosome becomes attached to a nonhomologous chromosome

Polyploidy

Cell has extra set of chromosome

Nondisjunction

Meiosis, homologous chromosomes fail to seperate as they should. One gamete receive 2 of the same type of chromosome and another gamete receives no copy. Any abnormal number of chromosomes is known as aneuploidy.

Extranuclear inheritance

Defects in mitochondrial DNA reduce amount of ATP cell can make. Because mitochondria passed to zygote all comes from cytoplasm of egg, these diseases are always inherited from the mother.

Xray Crystallography

Determine 3 dimensional structure of a molecule. Purified sample of DNA crystalized and bombarded with X rays.

DNA

2 strands running in opposite directions. One runes form 5’ to 3’, other 3’ to 5’. Polymer of repeating nucleotides. 5 carbon dugar, a phosphate and nitrogen base. 4 nitrogenous bases: Adenine, thymine, cytosine, guanine. Adenine double bond to thymine, Cytosine triple bond to guanine.

Purines

Adenine and Guanine

Pyrimidines

Thymine and Cytosine

Replication

Begins at origins of replication, 2 new strands of DNA separate to form replication bubbles. Replication bubble expands as replication proceeds in opposite direction, end of bubble is replication fork. DNA polymerase catalyzes elongation of new DNA strands, buils 5’ to 3’. Rate of elongation is 50 nucleotides per second. Cannot initiate synthesis, can only add nucleotide to 3’ end of preexisting chain. Preexisting chain consists of RNA primer. Primase joins RNA nucleotides to make primer. DNA polymerase replicates 2 original strands of DNA differently. One strand formed toward the replication fork in an unbroken linear fashion. Called leading strand. other strand forms in direction away from the replication fork in segments called Okazaki fragments. Called lagging strand. Okazaki fragment (100-200 nucleotides) joined by DNA ligase. Helicase is enzyme that untwists double helix at replication fork. Single Stranded Binding proteins act as scaffolds, holding 2 DNA strands apart. Topoisomerases make cuts in DNA lessening tension on tightly wound helix. Eukaryotes has special nonsense nucleotide sequences at end of chromosomes that repeat thousands of times, called telomers, maintained by telomerase.

Transciption

DNA makes RNA. mRNA carries messages directly from DNA to cytoplasm, tRNA is shaped like cloverleaf and carries amino acids to mRNA at ribosome, rRNA is structural, making up ribosome, which is formed in nucleolus.

Initiation

RNA polymerase recognizes and binds to DNA at promoter region. Collection of proteins called transcription factors recognize area in promoter called TATA box, mediating binding of RNA polymerase to the DNA. Creates transcription initiation complex. Elonqation of strain continues as RNA polymerase adds nucleotides to 3’ to end of growing chain. Stretch of DNA that is transcribed into an mRNA molecule is called a transcription unit (unit with codons). Termination when RNA polymerase transcribes termination sequence.

5’ cap

Modified guanine nucleotides is added to 5’ end.

poly (A) tail

Consists of string of adenine, added to 3’ end. Protects RNA from degradation by hydrolytic enzymes.

Introns

Noncoding region of mRNA, removed by snRNPs and spliceosomes. Removal allows exons to leave nucleus. mRNA that leaves nucleus is great deal shorter than original transcription unit.

Translation

Codons of mRNA changed into an amino acid sequence. One end of tRNA bears amino acid, other end bears nucleotide triple called anticodon. tRNA can be used repeatedly, energy for process by GTP. Each amino acid is joined to correct tRNA by enzyme called aminoacyl-tRNA synthetase (20 different kinds). AUG codes for methionine and also start codon. UAA, UGA, UAG. Relaxation of base pairing rules called wobble. Initiation when mRNA attaches to ribosome. First codon always AUG. Elongation when tRNA bring amino acid. Termination when release factor breaks bonds.

Point Mutation

Base pair subst. Chem change in just one base pair in a single gene. Sickle cell anemia is PM. Can result in no change due to wobble.

Insertion or Deletion

Deletion loss of one codon and insertion is adding one. Both cause frameshift.

Missense mutation

PM or FS change codon within gene into stop codon, translation will be altered into missense mutation.

Bacteriphage

In lytic cycle, phase enters host cell, takes control of cell machinery, replication and causes cell to burst. In lysogenic, viruses replicate without destroying host cell. Phage virus incorporated into specific cite in host’s DNA. Remains dormant within genome and called prophase. Trigger causes prophage to switch to lytic phase. Temperate viruses do both.

Retroviruses

Contain RNA instead of DNA and replicate in unusual way. RNA serves as template for synthesis of cDNA because it is complementary to DNA it copied from. Retroviruses reverse usual flow of information from DNA to RNA. Reverse transcription occurs under direction of enzyme called reverse transcriptase. Transduction where phage viruses acquire bit of bacterial DNA as they infect on another.

Bacteria

Replicate DNA in both direction by process called theta replication. Bacteria have many plasmids and will express genes carried by plasmids. First plasmid found called F plasmid standing for fertility. F plasmid contains genes for production of pili, cytoplasmic bridges that connect to adjacent cell and that allow DNA to move from one cell to another in a form of sexual reproduction called conjugation. R plasmid is resistant to specific antibiotics.

Operon

Set of genes and switches that control expression of those genes. Lac operon is switched off until is it induced to turn on. Tryptophan operon is always in on position until it is needed and becomes represent or switched off.

Lac Operon

Lactose not available in bacteria to fo E coli to use lactose, 3 structural genes must be transcribed to produce enzyme to break down lactose. 3 Enzymes: b-galactosidase, permease and transacetylase are coded for by 3 structural genes in Lac Operon. For transcription to occur, RNA polymerase must bind to DNA at promoter. If repressor binds to operator, RNA polymerase is prevented from binding to the promoter and transcription of the structural genes is blocked or repressed. Noncompetitive Inhibition. If allolactose is present is is inducer or allosteric effector. Repressor cannot bind to operator and RNA polymerase is free to bind to promoter.

Tryptophan Operon

Repressible by corepressor. 5 structural genes that code for enzyme for tryptophan. Repressor is initially active. RNA polymerase free to bind to promoter leading to production of tryptophan. When inactive repressor combines with specific corepressor molecule (tryptophan), changes its conformation and binds to operator, preventing RNA polymerase from binding to promoter and thus blocking transcription of structural genes. Tryptophan is an allosteric effector.

Prions

Misfolded version of protein found in brain. Infectious and cause brain diseases like Scrapie, Mad cow disease and Creutzfold-Jakob disease.

Transposons

Jumping genes, Barbara McClintock. Cut and paste fashion, 2 classes of jumping genes, insertion sequences and complex transposons. Insertion sequences is with one gene, codes for transposase. Can cause mutation. Complex transposons are longer than insertion sequences and include extra genes, like gene for antibiotic resistance or for seed color.

Human Genome

97 percent of DNA does not code for protein product and called junk. Regulator sequences that control gene expression, some are introns that interrupt genes and most are repetitive sequences. Huntington’s is caused by abnormally long stretches of tandem repeats. The tandems make up telomeres.

Recombinaant DNA

Taking DNA from 2 sources and combining them into one molecule.

Cloning Genes

To produce protein product or replace nonfunctioning gene. Prepare multiple copies of gene for analysis or engineer bacteria.

Restriction Enzymes

Extracted from bacteria, cut at specific recognition sequences or sites. Leaving single stranded sticky ends to form temporary union with other sticky ends. Fragments made are called restriction fragments.

Gel Electrophoresis

Separates large molecules of DNA on basis of rate of movement through agarose gel. Smaller the molecules, faster it runs. DNA flows from cathode to anode. DNA is going to run through a gel, first cut up by restriction enzymes in to pieces small enough to migrate through gel. DNA probe can identify location of specific sequence within DNA.

PCR

DNA piece that is to be amplified into test tube with Taq polymerase with supply of nucleotides and primers necessary for DNA synthesis.

Restriction fragment

Segment of DNA results when DNA is treated with restriction enzymes. Each person RFLPs are unique, except identical twins and inherited in mendelian fashion.