Biology I Exam I Terms

Hypothesis

A tentative statement about the natural world leading to predictions that can be tested.

Fact

an observation that has been repeatedly confirmed, and for all practical purposes, is accepted as "true".

Theory

a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences, and tested hypotheses.

Interphase

cell grows and DNA is replicated.

Mitotic Phase

The replicated DNA and cytoplasmic contents are separated, and the cell cytoplasm is typically partitioned by a third process of the cell cycle called cytokinesis.

G1 Phase

Accumulating resources (energy, DNA, building blocks, associated proteins) to complete the task of replicating all of its DNA.

S Phase

DNA replication can proceed through the mechanisms that result in the formation of identical pairs of DNA molecules -- sister chromatids -- that are firmly attached to each other at the centromere (chromosomes are replicated).

G2 Phase

The cell replenishes its energy stores and synthesizes proteins necessary for chromosome manipulation and movement that will take place in the M phase. Some cell organelles are duplicated and cytoskeleton is dismantled to provide resources for the mitotic phase (proteins for movement, organelle duplication).

G0 Phase

Inactive stage that occurs when cells exit the cell cycle.

G1 = 9 hours

S = 10 hours

G2 = 4.5 hours

M = 1.5 hours

Cell cycle time (mammalian cells)

G1 Checkpoint

Cell checks if there are adequate reserves of energy and resources, the cell size is appropriate, and there is no DNA damage.

G2 Checkpoint

Bars entry into the mitotic phase if certain conditions are not met. Ensures that all the chromosomes have been replicated and that replicated DNA is not damaged.

M Checkpoint

determines whether all the sister chromatids are prepared to migrate appropriately.

Cyclins

positive regulator. proteins that regulate the cell cycle only when bonded to Cdks.

cyclin-dependent kinases (Cdks)

Positive regulator. protein kinases that is active only when attached to a particular cyclin.

Kinase

enzymes that phosphorylate other proteins.

relatively stable.

level of Cdks

fluctuate and determine when Cdks/cyclin complexes form.

level of cyclins

CDK inhibitors

Molecules that prevent the full activation of Cdks, and monitor a particular cell-cycle event and will not be removed until that specific event is completed.

Retinoblastoma proteins (Rb)

group of tumor-suppressor proteins common in many cells.

p53

multifunctional protein that acts when there is damaged DNA in cells that are going under the preparation process in G1. If damaged DNA is detected, halts cell cycle and recruits specific enzymes to repair DNA. If it cannot repair, cell suicide is performed.

p21

enforces the halt in the cycle dictated by p53 by binding to and inhibiting the activity of the Cdk/cyclin complexes.

Rb

largely monitors cell size, will exert its regulatory influence on other positive regulator proteins. in the active dephosphorylated state. binds to E2F.

transcription factors (E2F)

"turn on" specific genes, allowing the production of proteins encoded by that gene. when Rb is bound to E2F, production of proteins necessary for the G1/S transition is blocked.

Proto-oncogenes

genes that code for the positive cell cycle regulators.

Oncogenes

Cancer-causing genes that are formed due to mutations. causes a gain-of-function. Dominant, thus only need one copy to increase cell proliferation.

Tumor suppressor genes

genes that code for the negative regulator proteins. Mutation allows cell cycle to continue even if there is DNA damage. Causes loss-of-function. Recessive, thus two are needed to lose ability to suppress cell cycle.

Mitosis

the sequence of events that splits eukaryotic cells into two daughter cells that are genetically equivalent cells.

Genome

A cells DNA, packaged as a double-stranded DNA molecule.

prokaryotes = single, double-stranded DNA molecule in the form of a loop, stored in nucleoid.

eukaryotes = several, double-stranded linear DNA molecules and must be condensed, stored in nucleus.

Chromosomes

Condensed DNA. Humans have 2 copies of each chromosome. Humans have 23 chromosomes that code for unique sets of genes, and two copies of each making it 46.

homologous chromosomes

chromosomes that code for the same sets of genes.

Ploidy

number of copies of each type of chromosome.

1st level of compaction

short stretches of the DNA double helix wrap around a core of 8 histone proteins at regular intervals along the entire length of the chromosome.

Chromatin

DNA histone complex.

Nucleosome

beadlike, histone DNA complex.

Linker DNA

DNA connecting nucleosomes.

2nd level of compaction

occurs as the nucleosomes and the linker DNA between them coil into 30 nm chromatin fiber.

3rd level of compaction

a variety of fibrous proteins are used to "pack the chromatin". Also ensures that each chromosome in a non-dividing cell occupies a particular area of the nucleus that does not overlap with any other chromosome.

DNA condenses -> Nuclear envelope dissolves -> Chromosomes line up at midline -> Sister chromatids move apart to opposite sides -> cytokinesis

Stages of mitosis (simple)

Prophase

(1st Phase) DNA coils to form condensed chromosomes

Prometaphase

(2nd Phase) nuclear envelope dissolves and each sister chromatid develops a kinetochore protein structure in the center. Proteins of kinetochore attract and bind to the mitotic spindle microtubules on the ends getting attached on both sides.

polar microtubules

spindle microtubules that do not engage the chromosomes. they overlap each other midway between the two poles and contribute to cell elongation.

Metaphase

(3rd phase) All chromosomes are aligned in a plane called the metaphase plane, midway between both poles. Maximally condensed.

Anaphase

(4th phase) Cohesion proteins degrade, and the sister chromatids separate at the centromere. each chromatid is pulled rapidly toward the centrosome.

Telophase

(5th phase) Chromosomes reach opposite poles and begin to decondense. the mitotic spindles are depolymerized into tubulin monomers that will be used to assemble cytoskeletal components for each daughter cell. nuclear envelopes form around chromosomes, and nucleosomes appear within the nuclear area.

Cytokinesis (animal cells)

begins during late anaphase. contractile ring of actin filaments forms just inside the plasma membrane at the former metaphase plate. filaments pull the equator of the cell inward, forming a fissure called the cleavage furrow.

Cytokinesis (plant cells)

Golgi apparatus accumulates enzymes, structural proteins, and glucose molecules before breaking into vesicles and dispersing throughout dividing cell. During telophase, these Golgi vesicles are transported on microtubules to form a phragmoplast at the metaphase plate. these vesicles fuse and coalesce from the center toward the cell walls; called a cell plate. cell wall forms.

Microtubule organizing center (MTOC)

A special protein complex from which microtubules are organized.

Motor proteins

Proteins that can generate force and transport cellular components.

Aneuploidy

Occurs when mitosis produces daughter cells with incorrect numbers of chromosomes. (mutation)

Spindle Assembly Checkpoint (SAC)

safeguard against aneuploidy. properly working cell will not enter anaphase until all chromosomes are connected to microtubules. enforced by signaling proteins that can determine which criteria are met.

monomers

building blocks of polymers

polymers

large compound formed from combinations of many monomers

phosphate group, pentose sugar, nitrogenous base

Nucleotide components

Nitrogenous base

organic base that contains carbon and nitrogen, are bases because they contain an amino group that has the potential of binding an extra hydrogen.

Adenine (A), Thymine (T in DNA), Uracil (U in RNA), Guanine (G), Cytosine (C)

nitrogenous base pairs

Adenine and Guanine, two carbon-nitrogen rings

Purines

cytosine, thymine, uracil, Single carbon-nitrogen ring

Pyrimidines

the presence of the hydroxyl group on the ribose's second carbon and the hydrogen on the deoxyribose's second carbon.

difference between sugars of DNA and RNA

5' - 3' Phosphodiester linkage

phosphate residue attaches to the hydroxyl group of the 5' carbon of one sugar and the hydroxyl group of the 3' carbon of the sugar of the next nucleotide.

A-T

G-C

DNA bonds

made up of the sugar and phosphate of the nucleotides, nitrogenous bases stacked inside.

DNA structure

2 hydrogen bonds

A-T bond

3 hydrogen bonds

G-C bond

DNA (deoxyribonucleic acid)

molecule that contains an organisms genetic material, and is present in all living cells. specifies how and when to bind proteins and other cellular products.

Protein

A biochemical molecule made of one or more amino acid polymers. essential to cells, facilitating virtually every process within them.

Transcription

The information in a section of DNA is "transcribed" into a similar molecule of RNA.

Translation

cell "translates" the information in RNA, using it to assemble a sequence of amino acids together to make the protein.

5' to 3'

Direction DNA is made

3' to 5'

Direction DNA is read

Deoxyribonucleotide triphosphate (dNTP)

molecules used by DNA polymerases as the raw materials for synthesizing DNA. Each of these consist of a deoxyribose sugar, three phosphate groups, and a nitrogenous base. when it is incorporated into a DNA strand, two phosphate groups are removed , creating a nucleotide in the growing stand.

Polymerase

enzymes that catalyze the assembly of polymers, such as nucleic acids. polymerases that synthesize DNA and RNA create phosphodiester bonds that link nucleotides together.

Histone

proteins found in the nuclei of eukaryotic cells.

pre-replication complex

Recognizes and binds to the origin of replication before (or pre) replication begins.

Helicase

Unwinds the DNA double helix, resulting in the formation of the replication bubble.

Single-stranded binding proteins

Binds single-stranded DNA within the replication bubble, ensuring the strands stay separated.

Topoisomerase

Acts on the topology (geometry) of DNA to ensure the helix outside of the replication bubble isn't twisted too tightly.

Primase

Synthesizes RNA primers, which DNA polymerases then build upon.

DNA polymerases

Forms bonds between nucleotide monomers, creating DNA polymers during replication.

Ligase

Ligates (joins) nicks between adjacent nucleotides by forming phosphodiester bonds.

Initiation

(1st step) proteins bind to the origins of replication to form the pre-replication complex and begin unzipping the DNA, pulling the strands apart and proteins called helicase continue this process using ATP.

Replication forks

ends of the replication bubble.

Making primers

(2nd step) after DNA is unzipped, primase begins to assemble a new strand by building a complementary RNA strand from dNTPs present in the cell. Nucleic acids are always synthesized by adding to the 3' end, and the newly synthesized strand has the opposite orientation as the template strand. Primase makes a short stretch of RNA called a primer before it detaches, meanwhile, a second molecule of primase is attaches to the other strand of DNA and synthesizes a primer there. Synthesized in the 5' to 3' direction.

Extension

(3rd step) DNA polymerase III binds to the 3' end of the RNA primer and then assembles a complementary DNA strand from dNTPs. base pairing dictates which nucleotide is added to the 3' end. moves in the 5' to 3' direction.

Leading strand

a region of a replication bubble where newly synthesized DNA is produced in a continuous manner.

Lagging strand

a region of a replication bubble where newly synthesized DNA is produced in a discontinuous manner. characterized by having several separate pieces of newly synthesized DNA called Okazaki fragments. construction requires several primase and polymerase proteins. RNA primers always on the 5' end of Okazaki fragments.

Connecting DNA fragments

(4th Step) DNA polymerase I adds DNA to the 3' end of DNA using dNTPs present in the cell. DNA polymerase I removes bases from the RNA primer ahead of it, effectively replacing the primer with DNA which creates a nick in the backbone of the DNA strand. Ligase uses energy from ATP to create the phosphodiester bond to make the backbone continuous.

semiconservative replication

after replication, the original DNA is divided between the two daughter DNA molecules, one new and one original.

Proofreading

DNA polymerase III removes the incorrect nucleotide and tries again. If a kink is detected, the polymerase backs up, removes the mismatched nucleotide and inserts the correct one. fixes 99% of its internal errors.

Mutations

Random errors in gene replication that lead to a change in the sequence of nucleotides.

DNA replication in Eukaryotic cells

unwinds DNA. RNA primers form by primase. DNA pol a adds a short DNA fragment to the RNA primer on both ends before handing it off to a second polymerase. while leading strand is continuously synthesized by DNA pol s, the lagging strand is synthesized by DNA pol e. PCNA holds the DNA pol in place so it does not slide off the DNA. As DNA pol s runs into the primer RNA on the lagging strand, it displaces it from the DNA template. The displaced primer RNA is then removed by RNase H and replaced with DNA nucleotides. gaps sealed by ligase.

Telomere replication

ends are unreplicated. telomeres are added to the ends of chromosomes by telomerase. it attaches to the end of the chromosome and DNA nucleotides complementary to the RNA template are added to the 3' end of the DNA strand. once it is sufficiently elongated, DNA polymerase can add the nucleotides complementary to the ends of the cromosomes.

Mismatch repair

specific repair enzymes recognize the mismatched nucleotide and excise part of the strand that contains it. it is then resynthesized. may lead to more permanent damage if not repaired.

Nucleotide Excision Repair (NER)

used to remove damaged bases rather than mismatched ones. repair enzymes replace abnormal bases by making a cut on both the 3' and 5' ends of damaged base. the segment is removed and replaced with correctly paired nucleotides via DNA polymerases. once filled, gap is filled with ligase. often employed when UV exposure causes formation of pyrimidine dimmers.

Base Excision Repair (BER)

repairs chemically altered bases due to oxidation, deamination, and alkylation. Deamination converts a cytosine base into uracil. the uracil is detected and removed , leaving a baseless nucleotide. the baseless nucleotide is removed, leaving a small hole in the DNA backbone. hole is filled with right base by a DNA polymerase and gap sealed by ligase.

Induced mutations

result from an exposure to chemicals, UV rays, x-rays, or some other environmental agent

Spontaneous mutations

occur without any exposure to any environmental agent; they are a result of natural reactions taking place within the body.

Point mutations

mutations that affect a single base pair

Subsitutions

when once base is replaced by another

Transition Subsitution

refers to a purine or pyrimidine being replaced by a base of the same kind; for example, adenine may be replaced by guanine.