Biology 115 Exam 2 Study Guide

Chapter 10: Photosynthesis

Photosynthesis: the process by which light energy is converted into the stored
chemical energy of organic molecules.
Overall Reaction of Photosynthesis: 6 CO2 + 12 H2O C6H12O6 + 6 O2 + 6 H2O.
Oxygen produced by photosynthesis comes directly from H2O.
The synthesis of ATP during photosynthesis occurs as a result of phosphorylation
of ADP.
Photosynthesis involves:
o Light Reactions
Energized electrons reduce NADP+ to NADPH.
Energized electrons pass down the electron transport chain using
mechanism of chemiosmosis to generate ATP in a process called
photophosphorylation.
o Calvin Cycle
CO2 is fixed with RuBP then three-carbon compound
phosphorylated and reduced (using NADPH and ATP) to form
G3P, which is made into glucose and other carbohydrates.
Autotrophs sustain themselves without eating anything derived from other living
beings.
Photoautotrophs are organisms that use light as a source of energy to synthesize
organic substances.
Heterotrophs obtain organic food molecules by eating other organisms or
substances derived from them.
Chloroplasts are organelles found in plants and photosynthetic protists that absorb
sunlight and use it to drive the synthesis of organic compounds from carbon
dioxide and water.
o Chloroplasts are found mainly in the cells of the mesophyll, the tissue in
the interior of the leaf.
Stomata are microscopic pores that allow gas exchange between the environment
and the interior of the plant.
Stroma: the dense fluid within the chloroplast surrounding the thylakoid
membrane and containing ribosomes and DNA; involved in the synthesis of
organic molecules from carbon dioxide and water.
Thylakoids: flattened, membranous sacs inside the chloroplast.
Chlorophyll: green pigment that gives leaves their color.
Light behaves as waves and also as particles called photons.
Pigments are substances that absorb visible light.
Chlorophyll a: the key light-capturing pigment that participates directly in the
light reactions.
o The spectrum of chlorophyll a suggests that violet-blue and red light work
best for photosynthesis.
Chlorophyll b: an accessory pigment that transfers energy to chlorophyll a.
Photosystem: composed of a reaction-center complex surrounded by several lightharvesting complexes.

o Each light-harvesting complex consists of various pigment molecules

bound to proteins.
o Two types: Photosystem II (PS II) and Photosystem I (PS I)
Primary electron acceptor: a specialized molecule that shares the reaction-center
complex with a pair of chlorophyll a molecules and that accepts an electron from
them.
Linear electron flow: a route of electron flow during the light reactions of
photosynthesis that involves both photosystems and produces ATP, NADPH, and
O2.
Cyclic electron flow: a route of electron flow during the light reactions of
photosynthesis that involves only one photosystem and that produces ATP.
The Calvin Cycle uses the chemical energy of ATP and NADPH to reduce CO2 to
sugar.
o It takes 3 turns of the Calvin Cycle to fix 3 molecules of CO2 and produce
1 molecule of G3P.
o Cycle can be divided into 3 stages: Carbon Fixation, Reduction,
Regeneration of CO2 acceptor (RuBP).

Chapter 12: Cell Cycle

Cell Division is essential for the perpetuation of life.

o It provides for development, growth, and repair of multicellular
organisms.
o It provides for reproduction of unicellular organisms.
Cell Division creates genetically equivalent daughter cells.
o In eukaryotes by mitosis.
o In Prokaryotes by binary fission.
The Cell Cycle extends from the formation of a new cell by the division of its
parent cell to its own division into two daughter cells.
Genome: a cells complete complement of DNA.
o This is organized into chromosomes.
Each Eukaryotic chromosome is a very long DNA molecule with associated
proteins that help structure the chromosome and control the activity of genes, the
units of inheritance.
Chromatin: the entire complex of DNA and protein.
Every diploid eukaryotic species has a characteristic number of chromosomes in
each somatic cell; reproductive cells, gametes (sperm & egg), have half that
number of chromosomes.
Prior to cell division, a cell replicates its DNA. Duplicated chromosomes consist
of two identical sister chromatids, attached along cohesions.
o Each sister chromatid has a centromere, a region where proteins bind to
specific centromeric DNA sequences and hold the chromatids closely
together.
o Two sister chromatids separate during mitosis, and then the cytoplasm
divides during cytokinesis.
Phases of the Cell Cycle:
o Mitotic (M) phase and Interphase. Interphase includes the G1 Phase, S
Phase, and G2 Phase.
Mitosis has 5 stages: Prophase, Prometaphase, Metaphase, Anaphase, and

Telophase.
Mitotic spindle: an assemblage of microtubules and associated proteins that is
involved in the movement of chromosomes during mitosis.
Mitosis: During prophase, the nucleoli disappear and the chromatin fibers coil and
fold into visible chromosomes. During prometaphase, some of the spindle
microtubules attach to each chromatids kinetochore. At metaphase, the
centromeres of all the chromosomes are aligned at the metaphase plate. At
anaphase, chromosomes are separated and move toward the poles. In telophase,
equivalent sets of chromosomes are at the two poles of the cell. Nuclear envelopes
form, nucleoli reappear, cytokinesis begins.
Cleavage: the process that separates the two daughter cells.
Cell plate: forms the fusion of membrane vesicles.
Single-celled eukaryotes reproduce by process of binary fission.

Chapter 13: Meiosis

Genetics if the scientific study of the transmission of traits from parents to

offspring and the variation between and within generations.
Sexual Life Cycle:
o Involves meiosis, which produces spores produced by plants by
sporophyte generation. This alternates with gametophyte generation,
which produces gametes, which join in fertilization forming a diploid
zygote, which divides by mitosis to form life.
o Meiosis includes Meiosis I and Meiosis II.
Meiosis I: includes synapsis, crossing over, and independent
assortment, all of which result in genetic variation.
Meiosis II: sister chromatids separate and 4 haploid cells are
produced.
Offspring acquire genes from parents by inheriting chromosomes.
When gametes fuse in fertilization, genes from both parents are transmitted to
offspring.
The DNA in eukaryotes is packaged into a species-specific number of
chromosomes present in all somatic cells.
A genes locus is its location on a chromosome.
Asexual reproduction: single parent passes copies of all its genes to its offspring.
Sexual reproduction: an individual receives a unique combination of genes
inherited from 2 parents.
Life cycle: the sequence of stages from conception to production in an organism.
Two chromosomes of each type, homologs, are present in each somatic cell.
Karyotype is an ordered display of an individuals condensed chromosomes.
Sex chromosomes: determine the sex of a person: females XX, males XY.
Autosomes: chromosomes other than sex chromosomes.
Diploid (2n) / Haploid (n)
Fertilization, or fusion of sperm and egg, produces a zygote containing both a
paternal and maternal set of chromosomes.
Meiosis: special type of cell division that halves the chromosome number and
provides a haploid set of chromosomes to each gamete.
Plants have life cycle called alternation of generations.

Stages of Meiosis:
o Interphase: each duplicated chromosome consists of two genetically
identical sister chromatids that remain attached at the centromere and
along their length by sister chromatid cohesion.
o Prophase I: homologous chromosomes pair up and genetic material is
exchanged by crossing over between non-sister chromatids.
o Metaphase I: homologous pairs line up at the metaphase plate.
o Anaphase I: each pair separates with one homolog moving toward each
pole.
o Telophase I: a haploid set of chromosomes reaches each pole.
o Meiosis II: looks like regular mitotic division, in which chromosomes line
up individually on the metaphase plate.

Chapter 14: Mendel and the Gene Idea

Mendel used the scientific approach to identify two laws of inheritance.
Mendel studied seven characters that occurred in alternative forms called traits.

He used true-breeding varieties of pea plants.

Mendel performed hybridizations in which he mated contrasting true-breeding
varieties, and then allowed the next generation to self-pollinate.
o P generation: true-breeding parental plants
o F1 generation: offspring of the first cross
o F2 generation: offspring of the self- or cross-pollinated F1 generation
The Law of Segregation: states that two alleles in a pair segregate (separate) into
different gametes during gamete formation.
The Law of Independent Assortment: states that each pair of alleles segregates, or
assorts, independently of each other pair during gamete formation; applies to
genes for two characters located on different pairs of homologous chromosomes
or when they are far enough apart on the same chromosome to behave as though
they are on different chromosomes.
Homozygous versus Heterozygous
Genotype versus Phenotype
Dominant allele versus Recessive allele
Monohybrid Cross
Dihybrid Cross
Probability laws govern Mendelian inheritance
o Multiplication rule: states that the probability that a certain combination of
independent events will occur together is equal to the product of the
separate possibilities of the independent events.
o Addition rule: states the probability is equal to the sum of the separate
probabilities of the different, mutually exclusive ways it can occur.
Complete Dominance: the phenotype of the heterozygote is indistinguishable
from that of the dominant homozygote.
Incomplete dominance: intermediate phenotypes are characteristic of alleles
showing this.
Codominance: each allele will affect the phenotype in separate, distinguishable
ways.

Chapter 15: Chromosomes

Chromosome theory of inheritance: genes occupy specific positions (loci) on

chromosomes, and it is the random alignment of pairs of homologous
chromosomes that result in the independent assortment and segregation of alleles
in gamete formation.
ORGANIZER:

Chapter 16: DNA

DNA is precisely copied in the process of DNA replication.

Chargaff determined the number of adenines and thymines are approximately
equal, and the number of guanines and cytosines was also equal.
o A=T and G=C
Double Helix: shape of DNA, two strands.
Watson and Crick constructed model of double helix that had the paired
nitrogenous bases on the inside of the helix and two sugar-phosphate chains
running in opposite directions on the outside.
Semiconservative Model of DNA: predicts that the two daughter DNA molecules
each have 1 parental strand and 1 newly formed strand.
Meselson & Stahl tested models of DNA using E.coli.
DNA Replication:
o Replication of most bacterial chromosomes begins at a single origin of
replication, where proteins that initiate replication bind to a specific
sequence of nucleotides and separate the two strands to form a replication
bubble. Replication proceeds in both directions in the two replication
forks. Eukaryotic chromosomes have many origins of replication.
o Enzyme called helicase unwinds the helix and separates the parental
strands at each replication fork.
o Single-stranded binding proteins keep the separated strands apart while
they serve as templates.
o Topoisomerase helps relieve the strain from the tighter twisting of DNA
strands in front of helicase.

o Primase joins RNA nucleotides based-paired to the parental strand to form

the primer needed to start the new DNA strand.
o DNA polymerases connect nucleotides to the growing end of a new DNA
strand. DNA polymerase III and I are involved in replication.
o DNA ligase joins the sugar-phosphate backbones of the fragments.
o Okazaki Fragments.
Multiple repetitions of a short nucleotide sequence at the ends of chromosomes,
called telomeres, protect an organisms genes from being eroded during
successive DNA replication.

Chapter 17: Gene Expression

Gene Expression: the DNA-directed synthesis of proteins.

Genes specify proteins via transcription and translation.
Beadle and Tatums one gene- one enzyme hypothesis
Transcription: the transfer of information from DNA to mRNA.
Translation: transfers information from mRNA to a polypeptide, changing from
the language of nucleotides to that of amino acids.
o Ribosomes are the sites of translation
In prokaryotes, transcription and translation can occur simultaneously.
In eukaryotes, mRNA is processed before it exits the nucleus and enters the
cytoplasm, where translation occurs.
The initial RNA transcript of any gene is called the primary transcript.
The translation of nucleotides into amino acids uses a triplet code to specify each
amino acid.
The nucleotide base triplets along the template strand of a gene are transcribed
into complementary mRNA codons.
During translation, the sequence of codons, read in the 53 direction,
determines the sequence of amino acids in the polypeptide.
The nucleotide sequence on mRNA is read in the correct reading frame, starting at
the start codon and reading each triplet sequentially.
The promoter is the DNA sequence where RNA polymerase attaches and initiates
transcription.
In bacteria, the terminator is the sequence that signals the end of transcription.
The specific binding of RNA polymerase to the promoter determines where
transcription starts and which DNA strand is used as the template.
The promoter includes the transcription start point and recognition sequences,
such as the TATA box.
In eukaryotes, transcription factors must first recognize and bind to the promoter
before RNA polymerase can attach, at which point the assembly is called the
transcription initiation complex.
Eukaryotic cells modify RNA after transcription.
o A modified guanine nucleotide is attached to the 5 end of a pre-mRNA,
and a string of adenine nucleotides, called a poly-A tail, is added to the 3
end.
RNA splicing: the process after a primary transcript is made of a gene, introns are
removed and exons joined together after the mRNA leaves the nucleus.
Ribozymes: RNA molecules that act as enzymes.
Alternative RNA splicing: allows different polypeptides to be produced from a

single gene.
Transfer RNA (tRNA) molecules carry amino acids to ribosomes, where they are
added to a growing polypeptide.
o Each tRNA carries a specific amino acid and has an anticodon that basepairs with a complementary codon on mRNA.
o Each amino acid has a specific aminoacyl-tRNA synthetase that attaches it
to its appropriate tRNA molecules to create an aminoacyl tRNA.
A phenomenon known as wobble enables the third nucleotide of some tRNA
anticodons to pair with more than one kind of nucleotide in the codon.
Ribosomes consist of a large and a small subunit, each composed of proteins and
a form of RNA called ribosomal RNA (rRNA).
Ribosomes have three tRNA binding sites:
o P site: hold the tRNA carrying the polypeptide chain
o A site: hold the tRNA carrying the amino acid
o E site: exit site

Chapter 18: Gene Regulation

Bacteria often respond to environmental change by regulating transcription

In bacteria, genes for different enzymes of a single metabolic pathway may be
grouped together into one transcription unit or served by a single promoter.
An operator is a segment of DNA within the promoter that controls the access of
RNA polymerase to the genes.
An operon is the DNA segment that includes the clustered genes, the promoter,
and the operator.
A repressor is a protein that binds to a specific operator, blocking attachment of
RNA polymerase.
Regulatory genes code for repressor proteins.
The activity of the repressor protein may be determined by the presense or
absence of a corepressor.
In the trp operon, the repressor is synthesized in its inactive form. Trytophan is
the corepressor that binds to the trp repressor, changing it into its active shape,
which has a high affinity for the trp operator and switches the trp operon off.
The transcription of a repressible operon, such as the trp operon is inhibited when
a specific small molecule binds to and activates a repressor.
The transcription of an inducible operon is stimulated when a specific small
molecule binds to and inactivates a repressor.
The lac operon is an inducible operon.
The regulation of the lac operon includes both negative control by the repressor
protein that is inactivated by the presence of lactose, and positive control by CAP
(catabolite activator protein) when complexed with cAMP.
Differences between cells with the same genome are the result of differential gene
expression.
Gene Expression:
o Regulation of Chromatin Structure
o Regulation of Transcription Initiation
o Post-Transcriptional Regulation
Embryonic Development:
o Cell Division

o Cell Differentiation
o Morphogenesis

Chapter 20: Biotechnology

DNA sequencing and DNA cloning are valuable tools for genetic engineering and
biological inquiry.
Biotechnology involves techniques and tools such as:
o DNA sequencing, recombinant DNA, gene cloning, polymerase chain
reaction (PCR), hybridization with nucleic acid probes, gel
electrophoresis, restriction enzymes, DNA microarray, and
complementary DNA.
Automated sequencing machines enable DNA sequencing, determining a genes
complete nucleotide sequence.
DNA cloning: making multiple copies of a specific DNA segment.
o One approach makes use of plasmids.
Recombinant DNA may be made by inserting foreign DNA into plasmids.
Gene cloning provides multiple copies of the gene and may also be used to
produce protein coded for by the foreign DNA.
Cloning vectors: DNA molecules that can move foreign DNA into a cell and
replicate there.
Restriction enzymes protect bacteria from phages or other organisms.
o Most restriction enzymes recognize restriction sites.
o The most useful restriction enzymes cut the backbone in a staggered way,
leaving sticky ends of short single-stranded sequences on both sides of the
resulting restriction fragment.
Polymerase Chain Reaction (PCR): can produce billions of copies of a secretion
of DNA in only a few hours.
Expression vector: a cloning vector that has an active promoter just upstream
from the gene insertion site.
Electroporation: process in which an electric pulse briefly opens holes in the
plasma membrane through which DNA can enter.
Using a nucleic acid probe allows researchers to determine in which cells a
particular gene is being expressed.
The technique of in situ hybridization uses labeled probes to detect the locations
of mRNAs within an intact organism.
Reverse transcriptase-polymerase chain reaction (RT-PCR) allows scientists to
study sample sets of mRNA.
Using DNA microarray assays, scientists can test all the genes expressed in a
tissue for hybridization.
Cloned organisms are useful for basic research and other applications.
Practical applications of DNA-based biotechnology include:
o Medical applications
o Forensic Evidence
o Agricultural Applications