Midterm #2 Vocabulary Flashcards
Glycolysis
Process that breaks glucose into 2 pyruvate molecules. Occurs in the cytosol.
Pyruvate Processing
Conversion of pyruvate to acetyl CoA (to be used as an electron carrier).
Occurs in mitochondrial matrix.
Citric Acid Cycle (AKA Krebs Cycle)
Process that completes the breakdown of glucose to CO2.
Occurs in mitochondrial matrix.
Electron Transport Chain
Uses the high energy electrons from the Krebs Cycle to convert ADP to ATP.
Occurs in inner membrane (cristae) of mitochondria.
Oxidation
Loss of electrons from the one substance
Reduction
Addition of electrons to another substance
Electron Donor
Compound that donates an electron to another, like in the electron transport chain.
Electron Acceptor
Compound that accepts an electron from a preceding one, like in the electron transport chain. In the electron transport chain, oxygen is the terminal (final) electron acceptor.
Mitochondrial Matrix
Location where pyruvate processing and the Krebs cycle takes place.
Acetyl CoA
Coenzyme that pyruvate in convereted into in the mitochondrion. Conversion is carrieed out by multienzyme complex that catalyzes 3 reactions.
Proton Gradient
The product of the electron transport chain. A higher concentration of protons outside the inner membrane of the mitochondria than inside the membrane is the driving force behind ATP synthesis.
NAD+/NADH
Nicotinamide adenine dinucleotide.
A coenzyme, electron carrier because it can cycle easily between oxidized (NAD+) and reduced (NADH) states. Functions as an oxidizing agent during respiration, and traps electrons using dehydrogenase enzymes.
ATP Synthase
Enzyme that makes ATP from ADP and inorganic phosphate
Oxidative Phosphorylation
Mode of ATP synthesis powered by redox reactions in the electron transport chain (energy stored in mitochondria). Accounts for ~90% of respiration’s ATP.
Substrate Level Phosphorylation
ATP synthesis by transferring a phosphate group from a substrate molecule to ATP
Fermentation
Catabolic process that partially degrades sugars or other organic fuels without the use of oxygen. Is essentially an extension of glycolysis that allows continuous generation of ATP by the substrate-level phosphorylation of glycolysis. Yields 2 molecules of ATP, therefore less effective than respiration.
Two types: alcohol fermentation (regenerates NAD+ and releases CO2) and lactic acid fermentation (regenerates NAD+, does not release CO2)
Autotroph
“Self feeder”
Sustains self without eating anything derived from other living beings. Produces organic molecules from CO2 and other inorganic raw materials. Also called “producers.”
Heterotroph
Lives on the compounds produced by other organisms. “Consumers.”
Thylakoid
Sacs that segregate the stroma form the thylakoid space. A column of thylakoid sacs is called a granum (plural grana).
Thylakoid Space
A membrane-bound compartment inside chloroplasts and cyanobacteria. They are the site of the light-dependent reactions of photosynthesis.
Stroma
Microscopic pore by which CO2 enters and O2 exists the chloroplast.
Pigment
Present in chloroplasts or photosynthetic bacteria and captures the light energy necessary for photosynthesis.
Chlorophyll
Green pigment in thylakoid membranes of the chloroplast. Absorbs light energy.
Carotenoids
Accessory pigments; hydrocarbons that are yellow and orange to absorb violet and blue-green light
Photosystems
Chlorophyll molecules organized with other small organic molecules and proteins in the thylakoid membrane.
There are two photosystems: I (best with 700 nm) and II (best with 680 nm)
Wavelength
Distance between the creasts of electromagnetic waves
Light Reactions
“photo” part of photosynthesis
The steps of photosynthesis that convert solar energy into chemical energy. Uses solar energy to reduce NADP+ to NADPH. Generates ATP using chemiosmosis to phosphorylate ADP. Produces NO sugar, occurs in thylakoids.
Calvin Cycle (AKA Dark Reaction)
Incorporates CO2 into organic molecules in chloroplast (carbon fixation). Uses NADPH and ATP form the light reaction to reduce the fixed carbon to carbohydrate.
Occurs in the stroma.
Carbon Fixation
The incorporation of CO2 into organic molecules in the chloroplast
DNA
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RNA
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Nucleotide
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Sugar
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Phosphate
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Base
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Ribose
The sugar making up RNA (as opposed to deoxyribose in DNA)
Deoxyribose
The sugar making up DNA (as opposed to ribose in RNA)
Adenine
Nitrogenous base, pairs with thymine in DNA and uracil in RNA
Thymine
Nitrogenous base, pairs with adenine
Guanine
Nitrogenous base, pairs with cytosine
Cytosine
Nitrogenous base, pairs with guanine
Uracil
Nitrogenous base in RNA that pairs with adenine
Strand
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Backbone
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Genes
The discrete unit of heredity. A distinct sequence of nucleotides forming part of a chromosome, the order of which determines the order of monomers in a polypeptide or nucleic acid molecule which a cell (or virus) may synthesize
Genetics
The study of heredity and the variation of inherited characteristics.
Inheritance
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Hereditary Information
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Base Pairing
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Complemenetary
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Antiparallel
Subunits run in opposite directions.
Double Helix
The form of native DNA, referring to its two adjacent antiparallel polynucleotide strands wound around an imaginary axis into a spiral
Replication
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Template
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Parental Strand
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Daughter Strand
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Chromatin
Complex of DNA and protein
Chromosome
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Histone
Protein responsible for the 1st level of DNA packing in chromatin.
Most common = H2A, H2B, H3, H4
Nucleosome
The basic unit of DNA packing. Consists of a segment of DNA would around a protein core composed of copies of each of the 4 histones
Messenger RNA (mRNA)
RNA, synthesized from a DNA template during transcription, that mediates the transfer of genetic information from the cell nucleus to ribosomes in the cytoplasm, where it serves as a template for protein synthesis
Transfer RNA (tRNA)
RNA that transfers amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome.
Ribosomal RNA (rRNA)
RNA molecules that, together with proteins, make up ribosomes.
Most abundant type of RNA.
5’ end
Refers to part of the DNA strand whose 5’ carbon has a phosphate group attached to it.
3’ end
Refers to part of the DNA strand whose 3’ carbon a hydroxyl group attached to it.
N terminus
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C terminus
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Transcription
The first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA) by the enzyme RNA polymerase
RNA Polymerase
An enzyme that produces primary transcript RNA, which is necessary for constructing RNA chains using DNA genes as templates, a process called transcription.
Transcription Factors
Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription
Promoter
DNA sequence where RNA polymerase attaches and initiates transcription
Template Strand
One of the two DNA strands that’s transcribed and provides the pattern for the sequence of nucleotides in an RNA transcript
- same strand always used in the particular gene
Non-template Strand
Opposite of a template strand, is not transcribed or provide pattern for the sequence of nucleotides in an RNA transcript.
RNA Processing
When enzymes in eukaryotic nuclei modify pre-mRNA before the genetic message is dispatched into the cytoplasm. Both ends of the primary transcript are altered.
5’ Cap
A modified form of guanine nucleotide added onto the 5’ end after transcription of the first 20-40 nucleotides
PolyA Tail
The addition of 50-250 more adenine nucleotides to the 3’ end after the polyadenylation sequence.
RNA Splicing
The removal of large portions of the RNA molecule that’s initially made
Exons
Segments of nucleic acids that will usually eventually be expressed and exit the nucleus (opposite of introns).
Introns
Noncoding segments of nucleic acids that lie between coding regions (opposite of exons).
Primary Transcript
The initial RNA transcript from any gene.
Mature mRNA
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Untranslated Regions (UTRs)
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Translation
The process in which cellular ribosomes create proteins. In translation, messenger RNA (mRNA)—produced by transcription from DNA—is decoded by a ribosome to produce a specific amino acid chain, or polypeptide.
Ribosome
Particle consisting of RNA and associated proteins, found in large numbers in the cytoplasm of living cells. They bind messenger RNA and transfer RNA to synthesize polypeptides and proteins.
Genetic Code
the nucleotide triplets of DNA and RNA molecules that carry genetic information in living cells.
Codon
A sequence of three nucleotides that together form a unit of genetic code in a DNA or RNA molecule.
Start Codon
The first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes- usually AUG.
Stop Codon
A nucleotide triplet within messenger RNA that signals a termination of translation
Reading Frame
Reading symbols in the correct groupings. With DNA, reading the nucleotide sequence in codons.
Mutation
Change to genetic information in a cell
Frame Shift Mutation
Alters the triplet grouping of nucleotides on the mRNAA read during translation
Occurs when insertion/deletion isn’t a multiple of 3
Differential Gene Expression
The expression of different genes by cells with the same genome
Enhancer
Distal control elements farther from the promoter
Control Elements
Segments of noncoding DNA that serve as binding sites for the proteins called transcription factors (which regulate transcription)
Transcription Activators
A protein that binds to DNA and stimulates transcription of a gene
Transcription Repressors
Protein that blocks attachment of RNA polymerase to the promoter, preventing gene transcription
DNA-binding Domain
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Activation Domain
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Differentiation
The process by which cells become specialized in structure and function, attaining its determined fate
Chromatin Structure/Modification
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MicroRNA
A cellular RNA fragment that prevents the production of a particular protein by binding to and destroying the messenger RNA that would have produced the protein.
Cell Cycle
The life of a cell from the time its first formed during division of a parent cell until its own division into two daughter cells
Mitosis
The division of genetic material in the nucleus
DNA Synthesis
The natural or artificial creation of DNA molecules.
DNA Replication
The process by which a double-stranded DNA molecule is copied to produce two identical DNA molecules
Chromatin
The entire complex of DNA and proteins that is the building material of chromosomes
Chromosome
Structure of packaged DNA molecules. Consists of a long DNA molecule associated with many proteins.
Sister Chromatids
Joined copies of the original chromosome, attached by cohesins.
G1 Phase
Part of interphase- the first gap
S Phase
Part of interphase- synthesis
G2 Phase
Part of interphase- the second gap
Mitotic (M) Phase
Phase including mitosis and cytokinesis
Prophase
Spindle formation
Chromosomes condense
Crossing over occurs
Prometaphase
Separates the duplicated genetic material of the nucleus
Nuclear envelope breaks down
Metaphase
Homologs line up at the metaphase plate
Anaphase
Each pair of homologs separate
Homologs move toward opposite poles
Telophase
2 haploid cells form
Each chromosome still has two sister chromatids
Cleavage furrow
Interphase
Period in cell cycle where the cell is not dividing. During this time, the cell grows to a larger size. Includes the G1, S, and G2 phase.
Cytokinesis
The division of the cytoplasm
Mitotic Spindle
Forms in prophase. Structure made of fibers from microtubules and associated proteins.
Centrosome
Subcellular region made of material that organizes microtubules
Centromere
Region of chromosomal DNA where the chromatid is attached most closely to its sister chromatid
Checkpoint
A control point in the cell cycle where stop and go-ahead signals can regulate the cycle. Important checkpoints exist in the G1, G2, and M phases.
Growth Factor
Protein released by certain cells that stimulates other cells to divide
Cancer
Uncontrolled growth of cells.
Metastasis
Spread of cancer cells to locations distant from their original site
Apoptosis
The death of cells that occurs as a normal and controlled part of an organism’s growth or development.
When apoptosis doesn’t occur like it should, cancer can occur
Deletion
Failure to copy one of the bases (a mutation) - a chromosome fragment is lost
DNA Polymerase
Enzyme that is responsible for forming new copies of DNA, in the form of nucleic acid molecules
Duplication
Product of a deleted fragment becoming attached as an extra segment to a sister chromatid
Germ-line Mutation
Changes in a cell used for reproduction
Helicase
Enzyme that untwists the double helix at the replication fork, separating the two parental strands, making them available as template strands.
Insertion
The addition of a new base or several bases as a mutation
Lagging Strand
DNA strand elongating away from the replication fork
Leading Strand
DNA strand made as DNA pol III adds nucleotides to the new complementary strand as the fork progresses
DNA Ligase
Enzyme that joins the sugar-phosphate backbones of all the Okazaki fragments into a continuous DNA strand
Missense Mutation
Substitutions that change one amino acid to another
Nonsense Mutation
Changes a codon for an amino acid into a stop codon, causing premature termination
Nuclease
An enzyme that cleaves the chains of nucleotides in nucleic acids into smaller units
Nucleotide Excision Repair
Removes damaged nucleotide sequences
Okazaki Fragments
Segments of the lagging strand that are synthesized discontinuously
Origins of Replication
Short stretches of DNA having a specific sequence of nucleotides. Where the replication of a chromosome begins.
Point Mutation
One base pair is changed (happens one in ever 10^10 base pairs)
Primase
enzyme involved in the replication of DNA. DNA primase is a type of RNA polymerase which creates an RNA primer
Primer
The initial nucleotide chain (RNA) that is produced by DNA synthesis
Proof Reading
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Replication Bubble
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Replication Fork
Y-shaped region where the parental strands of DNA are being unwound during replication.
Semi-conservative
Describes how each daughter molecule of DNA will have one strands of the “old” parental DNA and one “new” replicated strand
Silent Mutation
Mutation with no observable effect on phenotype
Single-Strand Binding Proteins
Bind to the unpaired DNA strands, keeping them from repairing
Somatic Mutation
A mutation that occurs in body cell that aren’t passed along to subsequent generations
Translocation
When a chromosome fragment joins a nonhomologous chromosome
Allele
Alternate version of a gene
Chiasmata
Visible points of crossing over
Chromatid
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Crossing Over
Process that breaks the physical connection between specific alleles on the same chromosome and the end points of 2 nonsister chromatids trade places
Dihybrid Cross
Cross between F1 (first fillial) generation dihybrids
Diploid
Having two sets of chromosomes
Dominant
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Gamete
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Haploid
Having a single set of chromosomes. ex: gametes
Heterozygous
Having two different alleles for a character. Not true breeding.
Homologous Chromosomes
2 chromosomes of a pair that have the same length, centromere position, and staining pattern.
Homozygous
Having a pair of identical alleles for a character.
Independent Assortment
2 or more genes assort independently- that is, each pair of alleles segregates independently of each other pair of alleles- during gamete formation
Linked Genes
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Locus
Specific location along the length of a chromosome where a gene is
Meiosis
Cell division to make haploid gametes
Monohybrid Cross
Cross between monohybrids (heterozygotes)
Parental Gametes
Gametes that share the same genotype as the parents. Results when crossing over does NOT occur.
Ploidy
The number of sets of chromosomes in a cell, or in the cells of an organism. ex: haploid, diploid
Punnett Square
Diagramatic device for predicting the allele composition of offspring from a cross between individuals of known genetic makeup
Recessive
Alleles that must be inherited together (homozygous) in order to be expressed. Usually represented in a Punnett Square with lower case letters (bb, for example).
Recombinant Gametes
Gametes that aren’t the same genotype as the parents. The result of crossing over.
Unlinked Genes
Genes that are found on different chromosomes and segregate independently into gametes.
Adaptation
Inherited characteristic of an organism that enhances their survival and reproduction in specific environments
Allele Frequency
The relative frequency of an allele (variant of a gene) at a particular locus in a population, expressed as a fraction or percentage. Specifically, it is the fraction of all chromosomes in the population that carry that allele.
Descent with Modification
Passing traits from parent to offspring, and this concept is one of the fundamental ideas behind Charles Darwin’s theory of evolution.
Differential Reproductive Success
The different amounts of success organisms have in a population of reproducing. As Dr. Decker says, “it just means that some are reproducing more than others.”
Evolution
Descent with modification - a change in the genetic composition from generation to generation
Gene Pool
The total genetic information in the gametes of all the individuals in a population.
Heritable Phenotypic Variation
Amount of phenotypic (observable) variation in a population that is attributable to individual genetic differences
Microevolution
The change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection (natural and artificial), gene flow, and genetic drift.
Natural Selection
Process in which individuals who have certain inherited traits tend to survive and reproduce at higher rates than other individuals BECAUSE of those traits.
Analogous Structure
Shared features between species because of convergent evolution.
Structures share similar function but NOT similar ancestry.
Artificial Selection
The process of modifying species over many generations by selecting and breeding individuals possessing desired traits
Binomial Nomenclature
a formal system of naming species of living things by giving each a name composed of two parts, both of which use Latin grammatical forms, although they can be based on words from other languages.
Biogeography
Scientific study of the geographic distributions of species
Comparative Anatomy
Study of similarities and differences in the anatomy of different species. Serves as evidence for evolution; it indicates that various organisms share a common ancestor.
Comparative Embrology
Branch of embryology that compares and contrasts embryos of different species. It is used to show how all animals are related. Many things are compared (such as whether or not the organism has a notochord or gill arches).
Convergent Evolution
The independent evolution of similar features in different lineages (flying squirrel vs. sugar glider)
Endosymbiosis
a type of symbiosis in which one organism lives inside the other, the two typically behaving as a single organism. It is believed to be the means by which such organelles as mitochondria and chloroplasts arose within eukaryotic cells
Fossil
Remain or trace of an organism from the past
Homologous Structure
Structure in different species that are similar because of common ancestry. ex: mammalian forelimbs
Radiometric Dating
A method of dating geological or archeological specimens by determining the relative proportions of particular radioactive isotopes present in a sample.
Strata
Layers of rock (singular stratum).
Can show fossil age (those on top would be younger than those on the bottom).
Systematics
The branch of biology that deals with classification and nomenclature; taxonomy.
Taxonomy
The classification of organisms.
Transitional Form
Fossils or organisms that show the intermediate states between an ancestral form and that of its descendants. These provide an abundance of evidence for change over time.
Vestigial Structure
Remnants of features that served a function in the organism’s ancestors (like leg bones inside of a whale).
What do the PolyA Tail and 5’ Cap do?
- Facilitate export of mature mRNA
- Help protect mRNA from degradation
- Help ribosomes attach to the 5’ end
