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246 terms

AP Biology Semester 1 Review

STUDY
PLAY
matter
any substance in the universe that has mass and occupies space
atoms
small particles that make up all matter
electrons
negatively charged subatomic particles that are transferred and shared between atoms
ion
a charged particle
acid
any substance that dissociates in water to increase the concentration of H+ ions; pH values of acids are from 1-7
base
any substance that combines with H+ ions when dissolved in water; pH values from 7-14
oxidation
the loss of an electron
reduction
the gain of an electron
molecules
groups of atoms held together by energy in a stable association
chemical bond
joins atoms in a molecule
ionic bond
attraction between ions of opposite charge in an ionic compound
covalent bond
a stable chemical bond formed when two atoms share one or more pairs of electrons
pH
indicates concentration of hydrogen ions in a solution (the more H+ ions a solution produces, the lower its pH; pH scale- less than 7 is acidic, 7 is neutral, above 7 is basic)
chemical reactions
formation and breaking of chemical bonds
hydrogen bonds
the weak bond bridging hydrogen atoms and atoms of the opposite charge
adhesion
attraction of water molecules to other molecules
cohesion
attraction of water molecules to water molecules
reactants
original molecules before the reaction starts
products
molecules resulting from the chemical reaction
hydrophobic
when nonpolar molecules do not form hydrogen bonds with water ("fearing water")
hydrophilic
when polar molecules readily form hydrogen bonds with water ("water-loving")
hydrocarbons
biological molecules consisting only of carbon and hydrogen
functional groups
specific groups of atoms with definite chemical properties that they retain no matter where they occur
dehydration synthesis
condensation reaction in which the -OH and H groups are removed during the synthesis of a new molecule- water is removed
hydrolysis
process in which a hydrogen atom is attached to one subunit and a hydroxyl group to the other- water is added
denaturation
process in which a protein's shape is changed due to a change in its environment- pH change, temperature, or ionic concentration of surrounding solution affect it
Enzyme
Biological catalyst made of amino acids.
Substrate
Reactant an enzyme catalyzes
Active Site
structure on the enzyme
Reactants
The molecules needed for a chemical reaction to occur
Products
Molecules that are made when a chemical reaction is over
Activation Energy
The amount of energy needed for a reaction to occur.
Heat of Reaction
The difference in energy between the reactants and products of a chemical reaction
Exothermic
a reaction that has a "-" heat of reaction b/c it releases more energy that it stores
Endothermic
a reaction that has a "+" heat of reaction and stores more energy than it releases.
Catalyst
Speeds up a chemical reaction
Variables that effect enzyme reaction rate
Temperature, pH, enzyme concentration, substrate concentration
denature
enzyme becomes "inactive" due to changes in the active site structure
enzyme specificity
enzyme only bonds to one substrate due to shape of active site
cell membrane
regulates movement of materials in and out of cells, maintains cell shape and allows cells to communicate with each other
smooth endoplasmic reticulum
makes or synthesizes lipids, detoxification of drugs/medicines
rough endoplasmic reticulum
has ribosomes associated with it and transports proteins
ribosomes
makes proteins
Golgi
modifies, sorts and packages substances made by the cell and sends them to vacuoles, other organelles or out of the cell
lysosomes
cell organelle filled with enzymes needed to break down certain materials in the cell
vacuoles
store food and water
mitochondria
Powerhouse of the cell, organelle that is the site of ATP (energy) production
chloroplast
organelle in plant cells that converts the energy in sunlight into sugars
centrioles
Located near the nucleus and help to organize cell division
nucleus
the control center of the cell
nucleolus
makes ribosomes
chromosomes
threadlike structures made of DNA molecules that contain the genes
cytoplasm
a jellylike fluid inside the cell in which the organelles are suspended
nuclear membrane
double membrane surrounding the nucleus that controls what enters and leaves the nucleus
Organelle
a tiny cell structure that carries out a specific function within the cell
Cell theory
idea that all living things are composed of cells, cells are the basic units of structure and function in living things, and new cells are produced from existing cells
phospholipid
A type of lipid that makes up the cell membrane.
cytoskeleton
network of protein filaments within some cells that helps the cell maintain its shape and is involved in many forms of cell movement
Prokaryote
A unicellular organism that lacks a nucleus and membrane bound organelles
Eukaryote
A cell that contains a nucleus and membrane bound organelles
Cell Wall
strong layer around the cell membrane in plants, algae, and some bacteria
phospholipid
a lipid made of a phosphate head and two fatty acid tails
lipid bilayer
cell membranes composed of two layers of phospholipids, with the tails pointed inwards towards each other, and the heads facing outward
cell surface markers
a membrane protein that identifies the cell type
receptor proteins
a membrane protein that binds to signals outside the cell
transport proteins
transports substances unable to diffuse across a cell membrane
active transport
energy is required to move a substance across a cell membrane
passive transport
no energy is required to transport substances across cell membranes
equilibrium
when randomly moving molecules fill up a space evenly
concentration
the amount of a particular substance in a given volume
concentration gradient
a difference in the concentration of a substance across a distance
diffusion
substances moving down the concentration gradient (from high to low concentration)
simple diffusion
small, nonpolar molecules passing directly through the lipid bilayer
facilitated diffusion
transport proteins helping ions and polar molecules to diffuse through the bilayer
channel proteins (pores)
tunnels that open for ions and polar molecules to pass through the cell membrane
carrier proteins
a protein that transports substances across a cell membrane by changing shape
osmosis
the process of water diffusing across a selectively permeable membrane
water channels
channel proteins that aid in osmosis, and only allow water molecules to pass through
hypertonic solution
the solute has high concentration, the water has low, water moves out of the cell
hypotonic solution
the solute has low concentration, the water has high, water moves into the cell
isotonic solution
the solute and water have an equal concentration to the cell's cytoplasm, water moves into and out of the cell at equal rates
contractile vacuoles
colllect excess water in unicellular eukaryotes and force the water out of the cell
sodium-potassium pump
a carrier protein that uses ATP to actively transport 3 sodium ions out of a cell, and 2 potassium ions into a cell
endocytosis
the process of a large substance moving into a cell using a vesicle
exocytosis
the process of a large substance moving out of a cell by means of a vesicle
signaling cell
a cell that produces a signal that is detected by a target cell
signal
anything that serves to direct, guide or warn
target cell
a cell that responds to a signal sent by a signaling cell
receptor proteins
a protein that binds to specific signal molecules, causing the cell to respond
binding site
the outer folds of a receptor protein, where the signal binds
permeability change
transport proteins opening or closing in response to a signal
second messenger
a signal molecule inside a cell, generated when a substance attaches to the outside of the cell membrane, causes changes in the cytoplasm and nucleus
Mitosis
in eukaryotic cells, a process of cell division that forms two new nuclei, each of which has the same number of chromosomes
Meiosis
(genetics) cell division that produces reproductive cells in sexually reproducing organisms
Cytokinesis
organic process consisting of the division of the cytoplasm of a cell following karyokinesis bringing about the separation into two daughter cells
Chromatin
The complex of DNA and proteins that makes up a eukaryotic chromosome. When the cell is not dividing, it exists as a mass of very long, thin fibers that are not visible with a light microscope.
Sister Chromatids
Replicated forms of a chromosome joined together by the centromere and eventually separated during mitosis or meiosis II.
Centromere
a specialized condensed region of each chromosome that appears during mitosis where the chromatids are held together to form an X shape
Cell Cycle
series of events that cells go through as they grow and divide
Interphase
the period of the cell cycle during which the nucleus is not undergoing division, typically occurring between mitotic or meiotic divisions
Centrioles
Located near the nucleus and help to organize cell division
Nucleoli
dense masses of RNA and protein that manufacture ribosomes, several of these are located in the nucleus.
Prophase
first and longest phase of mitosis, during which the chromosomes become visible and the centrioles separate and take up positions on the opposite sides of the nucleus
Metaphase
second phase of mitosis, during which the chromosomes line up across the center of the cell
Anaphase
the third phase of mitosis, during which the chromosome pairs separate and move toward opposite poles
Telophase
the final stage of meiosis or mitosis, in which the separated chromosomes reach the opposite poles of the dividing cell and the nuclei of the daughter cells form around the two sets of chromosomes
Cell Plate
A double membrane across the midline of a dividing plant cell, between which the new cell wall forms during cytokinesis.
Cleavage Furrow
pinching of the cell ("drawstring"): develops in animal cells only
Meiosis II
the second phase of meiosis consisting of chromatids separating, along with the two diploid cells splitting in two
Prophase I
The first phase of meiosis I. the replicated chromosomes condense, homologous chromsomes pair up, crossing over occurs between homologous chromosomes, the spindle is formed, and the nuclear envelope breaks apart into vesicles. the longest phase of meiosis.
Anaphase I
The third phase of meiosis I. the replicated homologous chromosomes are separated (the tetrad is split) and pulled to opposite sides of the cell.
Metaphase I
The second phase of meiosis I. the paired homologous chromsomes (tetrads) align at the center of the cell (the metaphase plate).
Telophase I
The fourth of meiosis I. the number of chromosoms is now reduced by half. After this phase the cell is considered to be haploid. Note however, that the chromosomes are still replicated, and the sister chromatids must still be separated during meiosis II.
Prophase II
The first phase of meiosis II. identical to the mitotic step, except that the number of chromosomes was reduced by half during meiosis I.
Metaphase II
The second phase of meiosis II. identical to the mitotic step, except that the number of chromosomes was reduced by half during meiosis I.
Anaphase II
The third phase of meiosis II. the sister chromatids are finally spearated at their centromeres and puled to opposite sides of teh cell. is identical to mitotic anaphase, excep the number of chromosmes was reduced by half during meiosis I.
Telophase II
The fourth and final phase of meiosis II. the number of chromosomes was reduced by half during meiosis. I.
Haploid
term used to refer to a cell that contains only a single set of chromosomes and therefore only a single set of genes
Diploid
(genetics) an organism or cell having two sets of chromosomes or twice the haploid number
Synapsis
the side by side pairing of homologous maternal and paternal chromosomes at the start of meiosis
Tetrads
the paired chromosomes consisting of four chromatids
Crossing Over
the interchange of sections between pairing homologous chromosomes during the prophase of meiosis
Somatic Cells
any cell other than a gamete, has 46 chromosomes, body cells
Gametes
sex cells
Zygote
a fertilized egg
g1 Checkpoint
checks to see if cell size is adequate; chromosomes replication is successfully completed and checks for DNA errors
g0 Checkpoint
if condidtions are not apporpiate for the cell to divide or if it is not programmed to divide they are in this phase
g2 Checkpoint
asses if DNA replication has occured, go ahead signal triggers mitosis
Cyclin Dependent Kinases
cdk enzymes activate proteins to regulate the cell
Growth Factors
factors that stimulate the cell to divide
Density Dependent Inhibition
The phenomenon observed in normal animal cells that causes them to stop dividing when they come into contact with one another.
Anchorage Dependence
the requirement that to divide, a cell must be attached to a solid surface.
allele
one of two alternate forms of a gene that can have the same locus on homologous chromosomes and are responsible for alternative traits
Law of Segregation
Mendel's law that states that the pairs of homologous chromosomes separate in meiosis so that only one chromosome from each pair is present in each gamete
Law of Independent Assortment
states that allele pairs separate independently during the formation of gametes
Monohybrid Cross
hybridization using a single trait with two alleles (as in Mendel's experiments with garden peas)
Dihybrid Cross
hybridization using two traits with two alleles each
Incomplete Dominance
creates a blended phenotype; one allele is not completely dominant over the other
Codominance
a condition in which both alleles for a gene are fully expressed
Multiple Alleles
three or more forms of a gene that code for a single trait (such as blood types)
Epistasis
A type of gene interaction in which one gene alters the phenotypic effects of another gene that is independently inherited., One gene masks the expression of a different gene for a different trait
Pleiotropy
A single gene having multiple effects on an individuals phenotype (more than one phenotypic expression)
Linked Genes
genes located on the same chromosome that tend to be inherited together in genetic crosses
Sex Linked Inheritance
Traits located on the sex cells. EX: Colorblindness, hemophilia.
X Inactivation
During development, females inactivate half of their X gene elles in order to prevent producing double the amount of the protein.
Nondisjunction
error in meiosis in which homologous chromosomes don't separate; gametes end up with wrong number of chromosomes
Polyploidy
condition in which an organism has extra sets of chromosomes
Point Mutations
changes in a DNA sequence caused by substitution of one nucleotide for another
Aneuploidy
an abnormality involving a chromosome number that is not an exact multiple of the haploid number (one chromosome set is incomplete)(causes down sydrome and turners syndrome)
karyotype
the appearance of the chromosomal makeup of a somatic cell in an individual or species (including the number and arrangement and size and structure of the chromosomes)
homologous chromosomes
chromosomes that have the same sequence of genes, that have the same structured, and that pair during meisosis
Autosomes
non-sex chromosomes
Down Syndrome
a congenital disorder caused by having an extra 21st chromosome
5' cap
The end of a pre-mRNA molecule modified by the addition of a cap
A site
One of a ribosome's three binding sites for tRNA during translation. Holds the tRNA carrying the next amino acid to be added to the polypeptide chain.
anticodon
A specialized base triplet at one end of a tRNA molecule that recognizes a particular complementary codon on an mRNA molecule.
base-pair substitution
A type of point mutation; the replacement of one nucleotide and its partner in the complementary DNA strand by another pair of nucleotides.
codon
A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.
deletion
1) A deficiency in a chromosome resulting from the loss of a fragment through breakage. (2) A mutational loss of one or more nucleotide pairs from a gene.
E site
One of a ribosome's three binding sites for tRNA during translation. The place where discharged tRNAs leave the ribosome.
exon
A coding region of a eukaryotic gene or expressed region
frameshift mutation
A mutation occurring when the number of nucleotides inserted or deleted is not a multiple of three, resulting in the improper grouping of the following nucleotides into codons.
insertion
A mutation involving the addition of one or more nucleotide pairs to a gene.
intron
A noncoding, intervening sequence within a eukaryotic gene.
messenger RNA (mRNA)
A type of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.
missense mutation
The most common type of mutation, a base-pair substitution in which the new codon makes sense in that it still codes for an amino acid.
mutagen
A chemical or physical agent that interacts with DNA and causes a mutation.
mutation
A rare change in the DNA of a gene, ultimately creating genetic diversity.
nonsense mutation
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein
one gene-one polypeptide hypothesis
The premise that a gene is a segment of DNA that codes for one polypeptide.
P site
One of a ribosome's three binding sites for tRNA during translation. Holds the tRNA carrying the growing polypeptide chain. (P stands for peptidyl tRNA
point mutation
A change in a gene at a single nucleotide pair
poly-A tail
The modified end of the 3' end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides.
primary transcript
An initial RNA transcript; also called pre-mRNA when transcribed from a protein-coding gene
promoter
A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA
ribosome
A cell organelle constructed in the nucleolus and functioning as the site of protein synthesis in the cytoplasm; consists of rRNA and protein molecules, which make up two subunits.
ribozyme
An enzymatic RNA molecule that catalyzes reactions during RNA splicing.
RNA polymerase
An enzyme that links together the growing chain of ribonucleotides during transcription.
RNA processing
Modification of RNA before it leaves the nucleus, a process unique to eukaryotes.
RNA splicing
The removal of noncoding portions (introns) of the RNA molecule after initial synthesis.
signal-recognition particle (SRP)
A protein-RNA complex that recognizes a signal peptide as it emerges from the ribosome.
spliceosome
A complex assembly that interacts with the ends of an RNA intron in splicing RNA, releasing the intron and joining the two adjacent exons.
TATA box
A promoter DNA sequence crucial in forming the transcription initiation complex.
template strand
The DNA strand that provides the template for ordering the sequence of nucleotides in an RNA transcript.
terminator
In prokaryotes, a special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene.
transcription
The synthesis of RNA on a DNA template.
transcription unit
A region of a DNA molecule that is transcribed into an RNA molecule.
transfer RNA (tRNA)
An RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA.
translation
The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of languagefrom nucleotides to amino acids
recombinant DNA
DNA molecules formed when segments of DNA from two different sources are combined in vitro
biotechnology
manipulation of organisms or their components to make useful products
genetic engineering
direct manipulation of genes for practical purposes
plasmids
small circular DNA molecules that replicate separately from the bacterial chromosome
gene cloning
production of multiple copies of a single gene
restriction enzymes
enzymes naturally occurring in bacteria, cut DNA molecules at a limited number of specific locations
restriction site
sequence of DNA 4-8 nucleotides long, symmetrical where the restriction enzyme cuts
restriction fragments
created when a specific restriction enzymes cuts a piece of DNA many times
sticky ends
single-stranded ends formed when restriction enzyme cuts DNA
DNA ligase
enzyme that bonds sticky ends with other DNA molecules cut with the same enzyme
cloning vector
DNA molecules that can carry foreign DNA into a host cell and replicate there
ampR
gene on plasmid; if bacterium has this plasmid, will be able to grow on agar with ampicillin. If does not have plasmid, will not grow on agar with amp.
lacZ
gene part of the lac operon. If gene is intact, produces a product that can break down lactose and Xgal, colony will be blue. If not intact, will not break down Xgal, colony will be white.
Step 1 bacterial transformation
isolate plasmid and DNA sample
Step 2 bacterial transformation
cut both plasmid and dna with same restriction enzyme
Step 3 bacterial transformation
plasmid may take up DNA
Step 4 bacterial transformation
seal DNA with DNA ligase
Step 5 bacterial transformation
put the plasmids into bacteria with no functioning lacZ gene. Use heat or high Ca2+ to stimulate transformation
Step 6 bacterial transformation
grow bacteria on agar with ampicillin and xgal
genomic library
complete set of plasmid-containing cell clones, each carrying copies of a particular segment from the original genome
phage library
clones in bacteriophages
reverse transcriptase
enzyme that makes single-stranded DNA transcripts from mRNA molecules
Step 1 gel electrophoresis
cut DNA with restriction enzyme, put sample in well of chamber, let fragments "run," add dye so you can see DNA, observe with UV light
In gel electrophoresis, smaller fragments move
faster towards the postive end
DNA - function and structure
contains hereditary information (genes) of the cell; double helix
mRNA - function and structure
provides the instructions for assembling amino acids into a polypeptide chain; linear; nucleotides are codons
tRNA - function and structure
short RNA molecule; transports amino acids to their proper place; "clover-leaf" shaped; nucleotides are anticodons
rRNA -function and structure
building blocks of ribosomes; DNA is transcribed into rRNA in the nucleolus; globular
DNA Replication
Process in which unzipped DNA strands serve as templates for complementary strands. Occurs during interphase of the cell cycle.
semiconservative replication
DNA replication; each double-stranded molecule of DNA consists of a single strand of old DNA and a single strand of new, replicated DNA.
helicase
enzyme that unwinds the DNA helix during DNA replication
replication fork
Y-shaped structure that arises when helicase unwinds a DNA helix
single strand binding protein
protein that attaches to each strand of uncoiled DNA during DNA replication to keep the strands separate
DNA polymerase
enzyme that assembles the new DNA strand in DNA replication. Moves in 3' to 5' direction.
antiparallel
5' to 3'; direction in which complement strand grows
Okasaki segments
Short segments of complementary DNA formed when DNA polymerase assembles DNA on the 5' to 3' strand; caused b/c polymerase must return to replication fork after each segment. Connected by DNA ligase.
DNA ligase
Connects Okazaki segments formed during DNA replication on the 5' to 3' template strand.
lagging strand
The 5' to 3' template strand of DNA replication. Takes longer to assemble, and so "lags" behind the 3' to 5' strand.
primase
enzyme that initiates DNA replication with a short segment of RNA nucleotides (RNA primer)
RNA primer
A short segment of RNA nucleotides that begins, in DNA replication, the leading strand as well as every Okazaki segment on the lagging strand. Enables DNA polymerase to attach DNA nucleotides to the primer.
telomerase
enzyme which attaches itself to the end of the template strand in DNA replication to extend the strand by adding a short sequence of DNA nucleotides over and over again. Prevents loss of preceding coding DNA.
one-gene-one-polypeptide hypothesis
the gene is a DNA segment that codes for a particular polypeptide.
one-gene-one-enzyme hypothesis
the gene is a DNA segment that codes for a particular enzyme. Proven false and replaced with one-gene-one-polypeptide hypothesis.
protein synthesis
the process that describes how enzymes and other proteins are made from DNA
3 steps of protein synthesis
transcription, RNA processing, translation
transcription
a step of protein synthesis in which RNA molecules are created by using DNA molecules as a template
RNA processing
RNA molecules are modified with deletions and additions
translation
processed RNA molecules are used to assemble amino acids into a polypeptide.
codon
three adjacent nucleotides on mRNA that code for a specific amino acid
anticodon
three adjacent nucleotides on tRNA which base pair with the codon of the mRNA during translation.
wobble
Allows anticodons of some tRNAs to base-pair with more than one type of codon, because exact base pairing between the third nucleotide of the anticodon and codon are usually not required.
3 phases of transcription
initiation, elongation, termination
initiation (transcription)
RNA polymerase attaches to the promoter region on the DNA and begins to unzip the DNA into two strands.
TATA box
the nucleotide sequence T-A-T-A; often occurs in the promoter region during mRNA transcriptions.
elongation (transcription)
RNA polymerase unzips the DNA and assembles RNA nucleotides using one strand of DNA as a template.
termination (transcription)
RNA polymerase reaches a special sequence of nucleotides that serves as a termination point. In eukaryotes, the termination region contains the DNA sequence AAAAAA.
promoter region
region of DNA that RNA polymerase attaches to to begin transcription.