Genetics
Table of Contents
Genetics.............................................................................................................................1
1. Core principles about molecules...............................................................................................2
Chapter 2......................................................................................................................................4
Chapter 3....................................................................................................................................10
Chapter 4....................................................................................................................................14
Chapter 5....................................................................................................................................16
Chapter 8....................................................................................................................................20
Chapter 10..................................................................................................................................29
Chapter 12..................................................................................................................................41
Chapter 14..................................................................................................................................47
Chapter 17..................................................................................................................................54
Chapter 18..................................................................................................................................59
Chapter 19..................................................................................................................................61
Extra information......................................................................................................................65
..................................................................................................................................................72
, 1. Core principles about molecules
Molecular biology is the study of how DNA, RNA and protein molecules store, transmit, and
exchange the information that determines the phenotypes of organism.
1. The ability of molecules to properly function in cells is regulated by molecular processes that
control their: synthesis, decay (destroying), interactions, localization, folding (three-dimensional
structure), modification (altering chemical structure).
2. Information is stored in nucleic acids
DNA sequences store coding information and noncoding information that regulates the production
of DNA, RNAs and proteins. Coding tells how to function and noncoding tells where to function.
3. Information is transferred between nucleic acids by base pairing
DNA base pairing to RNA = reverse transcription
RNA base pairing to DNA = transcription
tRNA base pairing to mRNA = translation
4. Structure determines function
Changes to higher-order structures affect function: Nucleic acids bind to other nucleic acids by
complementary base pairing, protein bind to nucleic acids through nucleic acid binding domains
(protein-DNA), and proteins bind to other proteins by covalent and non-covalent interactions (stable
protein-protein interactions and temporary).
Changes to primary structure affect function: some RNA undergo splicing, which precisely removes
large regions of nucleotides called introns and links together remaining nucleotide regions called
exons.
Structural cahnges due to chemical modification affect function: types of proteins involved in
chemical modifications are writers (add chemical modficiaiotns such as methyltransferase), erasers
(remove chemical modifications suc has demethylase enzyms and eraders that bind chemica
lmodifications, such as proteins that bind methyl groups.
Structural changes that result from nucleotide hydrolysis affect function
ATP --> ADP
5. Molecular outcomes are reversible
RNA synthesis = RNA polymerase
RNA decay = RNA nucleases
Core principles about molecular processes
1. Molecular processes are made up of distinct stages
Stages in a molecular process
Repression, keeping a process off
Activation/initiaion, starting a process
Maintenance, keepinga process going once it is started
Termination, stopping a process
Initation: involves defining where in a gene RNA polymerase will start transcription and synthesize a
short RNA molecule
Elongation, involves maintaining RNA synthesis through the whole gene
,Termination, involves defining where in a gene RNA synthesis stops and RNA polymerase dissociates
from DNA.
2. Signals regulate molecular processes
Despite the fact that cells in multi-celled organisms have the same information stored in their
genomic DNA sequence, they express different genes and have different phenotypes because they
receive different signals.
Environmental signal like nutrient level is sensed by a recepeter on the surface of the cell. The
receptor turns on a signaling pathway that activates the transcription of genes whose function is to
respons to the amount of nutrients.
3. Combinatorial control mechanisms determine the specificity and accuracy of molecular processes.
The enzymes that attach amino acids to tRNAs check in two different ways that the molecules are
correctly paired.
Core principles about molecular experiments
1. There are three basic types of molecular biology experiments that have different purposes.
Discovery/observation experiments: used to identify molecules that may be involved in a
molecular process or phenotype. Gives descriptive information.
Loss of function experiments: used to determine whether molecules are necessary for a
molecular process or phenotype to occur. What kind of gene is necessary for the molecular
mechanism.
Gain of function experiments: used to determine whether molecules are sufficient for a
molecular process or phenotype to occur. What kind of gene is sufficient to activate the
mechanism.
2. Molecular biology experiments are carried out using whole oragnism (in vivo) or isolated
molecules (in vitro)
Advantage of in vivo is tahat all molecules and molecular processes are intact and at physiological
levels, so the experimental findings are automatically biologically relevant. Disadvantage is that due
to the extraordinary complexity of molecules and molecuar procesess in whole organism, difficult to
determine detailed molecular mechanisms and wheter biological outcomes are due to direct or
indirect effects.
, Chapter 2
Wild type: most common form of any trait of an organism
Characters (traits): individual biological properties of a species.
Mutants: heritable variants observed in species that differ from wild type. Alternative forms of a
trait are called phenotypes.
Analyzing a trait through gene discovery
1. A mass mutants affecting the trait of interest
2. Cross (mate) mutant individuals to wild-type individuals to see if their descendants show ratios of
wild-type-to mutant phenotypes that are characteristic of single-gene inheritance
3. Deduce the functions of the gene at the molecular level
4. Deduce how the gene interacts with other genes to produce the trait in question.
Figure 2-1
Genetic analysis begins with mutants, because only then inheritance of genetic differences
between parents can be studied in crosses. In genetics, we infer the normal function of a
gene by studying the effects of mutations of the gene. Therefore, if you are interested in the
genes that are required for e.g. flowering in Arabidopsis, the first thing you need is flowering
mutants. These can be found as rare spontaneous mutants, but can also be induced
(mutagenic radiation or chemicals) and then selected for. The figure shows the wildtype as
well as a series of mutants with various phenotypic characteristics. Each mutant is given a
name mostly as acronym of the phenotype (e.g. lfy for leafy). In genetic dissection, the next
thing to do is to check each of these mutants for single-gene inheritance. This can be done
by crossing each mutant to the wildtype followed by selfing the F1 and phenotyping F1 and
progeny. If F1 shows mutant phenotype, the mutation is dominant and for single-gene
inheritance progeny should segregate 3:1 for mutant:wildtype. If F1 is wildtype, progeny
should segregate 3:1 wildtype:mutant. If the mutant phenotype is the result of mutations in
several genes, the ratio will be different (see next chapters).In order to find all genes
involved in flowering, you would have to isolate very many mutants, hoping that a mutant
of each gene involved is among these.
Genetic dissection: the use of recombination and mutation to piece together the various
components of a given biological function.
Forward genetics: strategy to understanding biological function starting with random single-
gene mutants and ending with their DNA sequence and biochemical function.
Reverse genetics: starts with genomic analysis at the DNA level to identify a set of genes as
candidates for encoding the biological trait of interest, then induces mutants trageted
specifically to those genes, and then examines the mutant phenotypes to see if they indeed
affect the trait under study
The genetic approach to understanding a biological trait is to discover the genes that control it.
One approach to gene discovery is to isolate mutants and chech each one for single-gene
inheritence patterns (specific ratios of wild-type and mutant expression of the trait in
descendants).
Table of Contents
Genetics.............................................................................................................................1
1. Core principles about molecules...............................................................................................2
Chapter 2......................................................................................................................................4
Chapter 3....................................................................................................................................10
Chapter 4....................................................................................................................................14
Chapter 5....................................................................................................................................16
Chapter 8....................................................................................................................................20
Chapter 10..................................................................................................................................29
Chapter 12..................................................................................................................................41
Chapter 14..................................................................................................................................47
Chapter 17..................................................................................................................................54
Chapter 18..................................................................................................................................59
Chapter 19..................................................................................................................................61
Extra information......................................................................................................................65
..................................................................................................................................................72
, 1. Core principles about molecules
Molecular biology is the study of how DNA, RNA and protein molecules store, transmit, and
exchange the information that determines the phenotypes of organism.
1. The ability of molecules to properly function in cells is regulated by molecular processes that
control their: synthesis, decay (destroying), interactions, localization, folding (three-dimensional
structure), modification (altering chemical structure).
2. Information is stored in nucleic acids
DNA sequences store coding information and noncoding information that regulates the production
of DNA, RNAs and proteins. Coding tells how to function and noncoding tells where to function.
3. Information is transferred between nucleic acids by base pairing
DNA base pairing to RNA = reverse transcription
RNA base pairing to DNA = transcription
tRNA base pairing to mRNA = translation
4. Structure determines function
Changes to higher-order structures affect function: Nucleic acids bind to other nucleic acids by
complementary base pairing, protein bind to nucleic acids through nucleic acid binding domains
(protein-DNA), and proteins bind to other proteins by covalent and non-covalent interactions (stable
protein-protein interactions and temporary).
Changes to primary structure affect function: some RNA undergo splicing, which precisely removes
large regions of nucleotides called introns and links together remaining nucleotide regions called
exons.
Structural cahnges due to chemical modification affect function: types of proteins involved in
chemical modifications are writers (add chemical modficiaiotns such as methyltransferase), erasers
(remove chemical modifications suc has demethylase enzyms and eraders that bind chemica
lmodifications, such as proteins that bind methyl groups.
Structural changes that result from nucleotide hydrolysis affect function
ATP --> ADP
5. Molecular outcomes are reversible
RNA synthesis = RNA polymerase
RNA decay = RNA nucleases
Core principles about molecular processes
1. Molecular processes are made up of distinct stages
Stages in a molecular process
Repression, keeping a process off
Activation/initiaion, starting a process
Maintenance, keepinga process going once it is started
Termination, stopping a process
Initation: involves defining where in a gene RNA polymerase will start transcription and synthesize a
short RNA molecule
Elongation, involves maintaining RNA synthesis through the whole gene
,Termination, involves defining where in a gene RNA synthesis stops and RNA polymerase dissociates
from DNA.
2. Signals regulate molecular processes
Despite the fact that cells in multi-celled organisms have the same information stored in their
genomic DNA sequence, they express different genes and have different phenotypes because they
receive different signals.
Environmental signal like nutrient level is sensed by a recepeter on the surface of the cell. The
receptor turns on a signaling pathway that activates the transcription of genes whose function is to
respons to the amount of nutrients.
3. Combinatorial control mechanisms determine the specificity and accuracy of molecular processes.
The enzymes that attach amino acids to tRNAs check in two different ways that the molecules are
correctly paired.
Core principles about molecular experiments
1. There are three basic types of molecular biology experiments that have different purposes.
Discovery/observation experiments: used to identify molecules that may be involved in a
molecular process or phenotype. Gives descriptive information.
Loss of function experiments: used to determine whether molecules are necessary for a
molecular process or phenotype to occur. What kind of gene is necessary for the molecular
mechanism.
Gain of function experiments: used to determine whether molecules are sufficient for a
molecular process or phenotype to occur. What kind of gene is sufficient to activate the
mechanism.
2. Molecular biology experiments are carried out using whole oragnism (in vivo) or isolated
molecules (in vitro)
Advantage of in vivo is tahat all molecules and molecular processes are intact and at physiological
levels, so the experimental findings are automatically biologically relevant. Disadvantage is that due
to the extraordinary complexity of molecules and molecuar procesess in whole organism, difficult to
determine detailed molecular mechanisms and wheter biological outcomes are due to direct or
indirect effects.
, Chapter 2
Wild type: most common form of any trait of an organism
Characters (traits): individual biological properties of a species.
Mutants: heritable variants observed in species that differ from wild type. Alternative forms of a
trait are called phenotypes.
Analyzing a trait through gene discovery
1. A mass mutants affecting the trait of interest
2. Cross (mate) mutant individuals to wild-type individuals to see if their descendants show ratios of
wild-type-to mutant phenotypes that are characteristic of single-gene inheritance
3. Deduce the functions of the gene at the molecular level
4. Deduce how the gene interacts with other genes to produce the trait in question.
Figure 2-1
Genetic analysis begins with mutants, because only then inheritance of genetic differences
between parents can be studied in crosses. In genetics, we infer the normal function of a
gene by studying the effects of mutations of the gene. Therefore, if you are interested in the
genes that are required for e.g. flowering in Arabidopsis, the first thing you need is flowering
mutants. These can be found as rare spontaneous mutants, but can also be induced
(mutagenic radiation or chemicals) and then selected for. The figure shows the wildtype as
well as a series of mutants with various phenotypic characteristics. Each mutant is given a
name mostly as acronym of the phenotype (e.g. lfy for leafy). In genetic dissection, the next
thing to do is to check each of these mutants for single-gene inheritance. This can be done
by crossing each mutant to the wildtype followed by selfing the F1 and phenotyping F1 and
progeny. If F1 shows mutant phenotype, the mutation is dominant and for single-gene
inheritance progeny should segregate 3:1 for mutant:wildtype. If F1 is wildtype, progeny
should segregate 3:1 wildtype:mutant. If the mutant phenotype is the result of mutations in
several genes, the ratio will be different (see next chapters).In order to find all genes
involved in flowering, you would have to isolate very many mutants, hoping that a mutant
of each gene involved is among these.
Genetic dissection: the use of recombination and mutation to piece together the various
components of a given biological function.
Forward genetics: strategy to understanding biological function starting with random single-
gene mutants and ending with their DNA sequence and biochemical function.
Reverse genetics: starts with genomic analysis at the DNA level to identify a set of genes as
candidates for encoding the biological trait of interest, then induces mutants trageted
specifically to those genes, and then examines the mutant phenotypes to see if they indeed
affect the trait under study
The genetic approach to understanding a biological trait is to discover the genes that control it.
One approach to gene discovery is to isolate mutants and chech each one for single-gene
inheritence patterns (specific ratios of wild-type and mutant expression of the trait in
descendants).
