Comprehensive Review (plus Unit #4 terms) Flashcards
Cleavage
Cell division without growth (in animals)
Blastula
In vertebrates, an early embryonic stage consisting of a hollow, fluid-filled ball of cells one layer thick; a vertebrate embryo after cleavage and before gastrulation.
Gastrula
In vertebrates, the embryonic stage in which the blastula with its single layer of cells turns into a three-layered embryo mads up of ectoderm, endoderm, and mesoderm.
Zygote
A diploid cell
Morula
Solid ball of cells in the early stage of an organism.
Endoderm
One of three embryonic germ layers of early vertebrate embryos, that later line internal structures such as digestive and respiratory tracts.
Ectoderm
One of three embryonic germ layers of early vertebrate embryos, gives rise to outer layers of body (skin, hair, nails), and nerve tissue.
Mesoderm
One of three embryonic germ layers of early vertebrate embryos, gives rise to inner tissues like muscles, blood, bone, etc.
Blastomere
One of the cells of the blastula
Nurse cells
Help an egg grow before fertilization (like insect) by moving some of their own maternally encoded mRNA into the cytoplasm of the oocyte (maturing egg).
Syncytium
A single cytoplasm with ~4000 nuclei in embryonic development of insects like Drosophila.
Imaginal disks
One of about a dozen groups of cells set aside in the abdomen of a larval insect and committed to forming key parts of the insect’s body
Instars
A larval development of insects
Pupae
Developmental stage of some insects in which the organism is nonfeeding, immobile, and sometimes encapsulated in a cocoon. Between larval and adult stages.
Meristem
Undifferentiated plant tissue from which new cells arise.
Cotyledon
A seed leaf that generally stores food, providing nourishment during seed germination.
Pluripotent
Cells that are capable of becoming many things (but are limited in scope)
Induction
- Binding of an inducer to a repressor allows transcription of an operon.
- In embryonic development, when development of a cell is influenced by interaction with an adjacent cell.
Totipotent
A cell that can become anything else in an organism (blastomeres).
Homeotic
Series of “master switch” genes that determine the form of segments developing in the embryo.
Segmentation mutant
Give segmentation problems (like 2-legs per section which became millipedes).
Homeobox
A sequence of 180 nucleotides located in homeotic genes that produces a 60-amino-acid peptide sequence active in transcription factors.
Apoptosis
A process of programmed cell death, in which dying cells shrivel and shrink; used in animal cell development to produce planned and orderly elimination of cells not intended for the final tissue.
C. elegans
A nematode worm with 959 somatic cells. One of most completely described models of development.
Blastocyst
Mammal egg initial division results in a lingle layer of cells surrounding a fluid-filled center.
Inner cell mass
Inside the blastula. Becomes the embryo with endoderm, mesoderm, and ectoderm.
Trophoblast
In vertebrate embryos, the outer ectodermal layer of the blastodermic vesicle. Becomes the placenta.
Oncogene
A mutant form of a growth-regulating gene that is inappropriately “on”, causing unrestrained cell growth and division.
Protein
Polymers of amino acids. (shape and specific order of amino acid monomers determines the structure and function)
Functions:
* enzyme catalysts
* defense (anti-bodies)
* transport (iron in living things, bind O)
* support (can be structural, connective tissue, ligaments)
* motion (muscles contracting)
* regulation (turn on/off other processes)
* storage (of amino acids)
RNA
- Ribonucleic acid, single-stranded.
- Nitrogenous bases consist of adenine, guanine, uracil, and cytosine.
- Mostly for info retrieval (broken down). Reads DNA for protein construction (directs their synthesis) and genetic information.
DNA
- Deoxyribonucleic acid
- double-stranded in a double helix, connected by H bonds.
- Nitrogenous bases consist of adenine, guanine, thymine, and cytosine.
- Mostly for information storage (built up). Read to build proteins. Also, genetic information stored in the sequence of nucleotides.
Lipid
- Fats (triglycerides) and phospholipids
- Hydrophobic (caused by high proportion of C-H bonds)
- symmetrical
Glycogen
A polymer of glucose monosaccharides for energy storage in animals. Stored in a branching structure (like a bush) to quickly store or release sugar molecules.
Amino Acid
- Monomer that composes the polymers that are proteins.
- There are 20 different kinds.
- Joined by peptide bonds (covalent)
- Structure: a central C bonded to one amino group, one carboxyl group, one H, and an R group (which determines the unique character of the 20 different amino acids).
Fatty acid
Long hydrocarbon chains that can be saturated, unsaturated, or polyunsaturated.
Nucleotide
A single unit of nucleic acid, composed of a phosphate, a five-carbon sugar (ribose or deoxyribose), and a purine or a pyrimidine.
Nucleus
- In atoms, the center of an atom, with protons and neutrons
- In eukaryotic cells, the organelle that houses the DNA
- Site of gene transcription.
Mitochondrion
- The “power house” of the cell - generates ATP.
- Contains its own DNA.
- -surrounded by 2 membranes:
- smooth outer membrane
- folded inner membrane with layers (called cristae)
Lysosome
- The “trash can” of the cell.
- membrane bound vesicles containing digestive enzymes to break down macromolecules
- destroy cells or foreign matter that the cell has engulfed (by phagocytosis)
Golgi Apparatus
- The “shipping and receiving” department of the cell.
- flattened stacks of interconnected membranes
- packaging and distribution of materials to different parts of the cell
- synthesis of cell wall components
Endoplasmic Reticulum
- Functions: Synthesize proteins and fats, detoxify foreign substances, store calcium
- Composition: phospholipid bilayer embedded with proteins
Glycolysis (definition/description)
- The break-down of glucose in a cell for metabolism
- E- of C-H bonds are stripped off in a series of reactions
- Occurs in the cytoplasm
- Results in net gain of 2 ATP
Krebs cycle (definition)
- 9-step process to reduce the acetyl group from Pyruvate Oxidation
- Occurs in the matrix of the mitochondria
- Otherwise known as the citric acid cycle or TCA cycle
- When the cell’s ATP concentration is high, the process shuts down and acetyl-CoA is channeled into fat synthesis.
Electron Transport Chain
- Series of e- carriers to store energy from oxidation reactions
- Located in the inner membrane of the mitochondrion.
- Electrons from NADH and FADH2 are transferred from complex to complex, with some e- energy lost at each transfer, used to pump H+ out of matrix to inter-membrane space.
Lactic Acid Fermentation
- rids body of pyruvate
Muscle cells convert pyruvate into lactic acid (lactate is ionized form). An excess of production contributes to muscle fatigue.
Alcoholic Fermentation
Glycolysis produces pyruvate which CO2 is stripped from (a by-product) and converted to acetaldehyde which becomes ethanol.
Chemiosmosis
see ATP synthase
ATP Synthase
- An enzyme that facilitates the synthesis of ATP through oxidative phosphorylation (a second method to substrate-level - energy to transfer the phosphate comes from a proton gradient).
- A membrane-bound enzyme that uses the energy of the proton gradient to synthesize ATP from ADP + Pi
- 1 proton results in 1 ATP
- process is called chemiosmosis
Proton Pump
see ATP synthase
NADH dehydrogenase
- the first membrane-embedded enzyme to receive e- in the e- transport chain
- oxidizes NADH to NAD+ and releases a proton (H+) to the intermembrane space
Cytochrome b-c complex
- bc complex is the second enzyme in the e- transport chain which uses energy from e- to pump a proton to the intermembrane space
- cytochrome oxidase complex does the same thing, pumping another proton
Calvin Cycle
- also called light-independent reactions (of photosynthesis) and carbon fixation reactions
- If O2 is available, uses ATP and NADPH to synthesize organic molecules from CO2
- If O2 is not available, side reactions store (?) as oxyloacetate when plant stomata are closed (C4 plants)
G3P
Intermediate product of glycolysis and end product of the Calvin Cycle
Acetyl-CoA
- The end product of Pyruvate Oxidation
- consists of 2 carbons from pyruvate attached to coenzyme A
- Reacts with oxyloacetate to start the Krebs Cycle
- When the cell’s ATP concentration is high, the process
shuts down and acetyl-CoA is channeled into fat
Oxaloacetic Acid
- “Feeder” molecule (4-carbon) that reacts with acetyl-CoA to start the Krebs Cycle
- Also the Step 9 product of the Krebs Cycle
Citric Acid
- Step 1 product of the Krebs Cycle, a 6-carbon molecule
Alpha-ketoglutarate
Step 4 product of the Krebs Cycle, a 5-carbon molecule
Succinyl-CoA
Step 5 product of the Krebs Cycle, a 4-carbon molecule
Dominant
the form of each trait expressed in the F1 generation (offspring resulting from a cross of true-breeding parents)
Recessive
the form of the trait not seen in the F1 generation (offspring resulting from a cross of true-breeding parents)
Genotype
total set of alleles of an individual
PP = homozygous dominant
Pp = heterozygous
pp = homozygous recessive
Phenotype
outward appearance of an individual
Dihybrid cross
- examination of 2 separate traits in a single cross
- The F1 generation of a dihybrid cross (RrYy) shows only the dominant phenotypes for each trait
- results in a 9:3:3:1 dominant:recessive ration
DNA primase
An RNA polymerase enzyme that synthesizes short stretches of RNA on a DNA strand to function as primers for the DNA polymerase.
DNA polymerase
Enzyme responsible for matching the existing DNA bases on the template strand with complementary nucleotides and then linking the nucleotides together to make a new strand.
DNA ligase
Enzyme that forms the last phosphodiester bond between Okazaki fragments in DNA strand replication.
DNA gyrase
Enzyme that acts to relieve the torsional strain (resulting in supercoiling) caused by unwinding DNA.
Hydrogen bond
- Weak attractions between the partially negative oxygen of one water molecule and the partially positive hydrogen of a different water molecule.
(Most important property of water.) - Also binds DNA strands together
Peptide bond
Links amino acids together in proteins through dehydration synthesis (covalent).
Phosphodiester bond
A pair of ester bonds that use the phosphate group of nucleotides to link them together.
Metastasis
The process by cancer cells move from their point of origin to other locations in the body.
Ribosome
The key organelle in translation, using mRNA and tRNA.
A site
Binding site on a bacterial ribosome
* Binds to the tRNA carrying the next amino acid to be added.
P site
Binding site on a bacterial ribosome
* Binds to the tRNA attached to the growing peptide chain.
E site
Binding site on a bacterial ribosome
* Binds the tRNA that carried the previous amino acid added.
Central dogma
DNA -> RNA -> proteins
Transcription
Produces a complementary copy of the DNA template strand (except T (thymine) is substituted with U (uracil)).
Prokaryotes:
Performed by the enzyme RNA polymerase simultaneously with translation.
Eukaryotes:
Performed by the enzyme RNA polymerase II in the nucleus.
Translation
One of the most complex and energy-intensive functions that cells perform.
Replication
Occurs during Interphase (S phase) – synthesis of DNA (DNA replication)
- 2 sister chromatids are produced
Continuous
In DNA replication, each parent strand is duplicated from the 3’ end to the 5’ end, but the strands are assembled antiparallel (opposing ends). So when the DNA molecule is split into two strands to be duplicated, the strand that starts with the 3’ end (leading strand) can be replicated continuously.
Discontinuous
In DNA replication, each parent strand is duplicated from the 3’ end to the 5’ end, but the strands are assembled antiparallel (opposing ends). So when the DNA molecule is split into two strands to be duplicated, the strand that starts with the 5’ end (lagging strand) must be replicated in sections, starting from where the strands still meet, to where the last section started.
Leading strand
The strand of DNA starting with the 3’ end which can be replicated continuously (building the 5’ to 3’ sister strand).
Lagging strand
The strand of DNA starting with the 3’ end which can be replicated continuously (building the 5’ to 3’ sister strand).
Palindrome
reads the same forwards and backwards
Restriction endonuclease
An enzyme that cleaves a DNA duplex molecule at a particular base sequence, usually within or near a palindromic sequence; also called a restriction enzyme.
Vector
A plasmid, phage or artificial chromosome that allows propagation of recombinant DNA in a host cell into which it is introduced.
PCR
Polymerase Chain Reaction
DNA replication in a test tube through heating and cooling with DNA, DNA (Taq) polymerase, deoxynucleotides, and DNA primers.
Lac-Z
Gene in the lac operon for beta galactosidase production (which metabolizes lactose)
Lac operon
In E. Coli, the operon containing genes that encode the enzymes to metabolize lactose.
Ti Plasmid
A plasmid from plant bacterium Agrobacterium tumefaciens used extensively to introduce recombinant DNA into broadleaf plants and some cereal grains.
Transposon
DNA sequence capable of transposition.
DNA fingerprinting
An identification technique that makes use of a variety of molecular techniques to identify differences in the DNA of individuals.
Intron
“Interventng sequences”
* noncoding DNA that interrupts the sequence of the gene.
Exon
The coding sequences that are expressed.
Pseudogene
A copy of a gene that is not transcribed.
Shotgun sequencing
The method of DNA sequencing in which the DNA is randomly cut into small fragments and the fragments cloned and sequenced. A computer is then used to assemble a final sequence.
Operator
Regulatory sites on DNA to control gene expression. Act as a roadblock to prevent the polymerase from initiating effectively.
Promotor
- A short sequence found upstream of the start site and is therefore not transcribed by the polymerase.
- Forms a recognition and binding site for the RNA polymerase.
- In bacteria, two 6-base sequences are common: one at position -35 upstream and the other at -10. (Provides the site of initiation as well as the direction of transcription.)
Repressor
Proteins that mediate negative control of gene expression.
- Bind to regulatory sites on DNA (operators).
- Respond to specific effector molecules.
Isomer
One of a group of molecules identical in atomic composition but differing in structural arrangement; for example, glucose and fructose.
Isotope
Atoms of the same elements that have different atomic masses due to differing numbers of neutrons.
Atomic number
Count of protons in an atom
Atomic mass
Sum of protons and neutrons in an atom.
Ion
Charged atoms, that have gained or lost one or more electrons.
(Cations - positively charged, lost electron(s)
Anions - negatively charged, gained electron(s))
Biology
The study of living things; the science of life.
Hypothesis
a possible explanation for an observation
(-must be tested to determine its validity
-is often tested in many different ways
-allows for predictions to be made)
Theory
- is a body of interconnected concepts
- is supported by much experimental evidence and scientific reasoning
- expresses ideas of which we are most certain
Darwin
- Charles Darwin - naturalist
- Sailed on the HMS Beagle about 180 years ago as ship’s naturalist.
- 5-year journey that led to development of the theory of evolution by natural selection (core of the science of biology).
- Wrote “On the Origin of Species”
natural selection
individuals with superior physical or behavioral characteristics are more likely to survive and reproduce than those without such characteristics
(proposed by Darwin)
Controlled experiment
- tests the hypothesis
- must be carefully designed to test only one variable at a time
- consists of a test experiment and a control experiment
pH
A scale used to measure acidity and basicity. The negative log of H+ concentration, from 0 to 14, with 7 neutral.
NADH
- Reduced form of NAD+, that has accepted 2 e- and one proton
- Reaction is reversible: can release 2 e- and 1 proton to become NAD+ again
- Used in the mitochondrion in the e- transport chain
FADH2
- Reduced e- carrier (FAD that has accepted 2 e-)
- Bound to its enzyme in the inner mitochondrial membrane, so only releases e- to the electron transport chain.
- Worth 2 ATP
Fumarate
Step 7 product of the Krebs Cycle, a 4-carbon molecule
Malate
Step 8 product of the Krebs Cycle, a 4-carbon molecule
Succinate
Step 6 product of the Krebs Cycle, a 4-carbon molecule
Citrate
Step 1 product of Krebs Cycle
Isocitrate
in isomer of citrate where on OH group is repositioned
Glucose-6-Phosphate
- Step 1 product of glycolysis
glucose has gained a phosphate from ATP
Fructose-6-Phosphate
- Step 2 product of glycolysis
glucose 6-phosphate has been reorganized
Fructose-1,6-Biphosphate
- Step 3 product of glycolysis
Thylakoid
- In the chloroplast
- internal membrane arranged in flattened sacs
- contains chlorophyll and other pigments
Grana
- stacks of thylakoid membranes
* includes a thylakoid space
Cristae
The folds of the inner membrane layer of the mitochondrion, creating many layers to pack lots of e- transfer enzymes
primary structure
Amino acid sequence in proteins. Backbone is always N-C-C repeating.
secondary structure
Protein structure when you add H bonding to a primary structure (alpha helix or beta pleated sheet).
tertiary structure
Final 3D shape of a protein with regions of different secondary structures. Shape determines its activity (proteins need a tertiary structure in order to function)
quaternary structure
The final structure of a protein, when multiple polypeptides are involved in tertiary structure.
beta pleated sheet
Bend-and-folded shape of a protein in secondary structure, bonded in shape by H bonds.
Darwin’s evidence - Population growth vs. availability of resources
- population growth is geometric
- increase in food supply is arithmetic
- Darwin realized that not all members of a population survive and reproduce.
- Darwin based these ideas on the writings of Thomas Malthus.
Darwin’s evidence - Similarity of related species
Darwin noticed variations in related species living in different locations. (specifically finches from the Galapagos Islands)
Rough endoplasmic reticulum (why “rough”, function)
- “Rough” due to embedded ribosomes in the membranes.
* Function: synthesis of proteins to be secreted, sent to lysosomes or plasma membrane.
Smooth endoplasmic reticulum (why “smooth”, function)
- “Smooth” due to few embedded ribosomes in the membranes.
- Functions:
- synthesis of membrane lipids
- calcium storage
- detoxification of foreign substances
Krebs Cycle (process)
- Step 1: (Condensation) Oxaloacetate reacts with acetyl-CoA to produce citrate.
- Steps 2/3: (Isomerization) 2-step process to rearrange citrate into an isomer isocitrate.
- Step 4: (1st Oxidation) Isocitrate is oxidized, producing alpha-ketoglutarate, one CO2, and one NADH.
- Step 5: (2nd Oxidation) alpha-ketoglutarate is oxidized, producing succinyl-CoA, one CO2, and one NADH.
- Step 6: (Substrate-level Phosphorylation) Succinyl-CoA is cleaved into two molecules and the energy released bonds a phosphate to GDP, which releases it to ADP, producing succinate and one ATP.
- Step 7 (3rd Oxidation) Succinate is oxidized, producing fumarate and one FADH2.
- Step 8/9 (Regeneration of Oxaloacetate) Fumarate accepts a water molecule, turning into malate, which is then oxidized, producing oxaloacetate one NADH.
Krebs Cycle output
- 2 CO2
- 1 ATP
- 3 NADH (3 pairs of e-)
- 1 FADH2 (1 pair of e-)
Glycolysis (process)
- Step 1: Phosphate group added to glucose by ATP (to ADP). Produces Glucose 6-phosphate
- Step 2: Rearrange Glucose 6-phosphate into Fructose 6-phosphate. Produces Fructose 6-phosphate
- Step 3: Phosphate group added to Fructose 6-phosphate by ATP (to ADP). Produces Fructose 1,6-biphosphate
- Step 4/5: Fructose 1,6-biphosphate is split into two 3-carbon molecules. Produces one G3P and one that is converted into G3P in a second reaction.
- Step 6: Two G3P molecules are each oxidized by NAD+ and a P-group added. Produces 2 NADH and 2 BPG.
- Step 7: One phosphate group removed from each BPG by ADP. Produces two ATP and two 3PG.
- Step 8: Two 3PG molecules rearranged into two 2PG.
- Step 9: Dehydration reaction on two molecules of 2PG. Produces 2 molecules of water and two PEP.
- Step 10: One phosphate group removed from each of two molecules of PEP by ADP. Produces two ATP and two Pyruvate.
Calvin Cycle (process)
- Phase I - carbon fixation
- Phase 2 - reduction
- Phase 3 - regeneration of RuBP
Neurula
Final frog embryo stage of development before it develops into a tadpole, forming a nerve tube with brain, spinal cord, etc.
