Bio 302 FINAL (Cal Poly)

How does 6 feet of DNA fit into the tiny nucleus in each of our cells?

double helix shape and the multiple levels of extensively coiled DNA, which wraps twice around the histones and reduces it size

In what direction does DNA polymerase build DNA?

5' to 3' direction

Why is DNA synthesis considered to be semi-conservative?

Only one strand is conserved in each new molecule and one new strand is synthesized.

What biochemical property do histone proteins have that help them to bind DNA? What is their role in chromatin formation?

Histones contain a large proportion of positively charged amino acids, lysine and arginine in their structure. DNA is negatively charged due to the phosphate backbone. The histones form disc-like structures around which portions of the DNA wrap itself to form structural units, called nucleosomes, resembling beads along a string

Heterochromatin:

The chromatin can fold upon itself to compact the nucleosomes, forming a highly condensed structure. In the condensed heterochromatin structure, promoter regions are largely inaccessible to transcription factors; hence protein production is inhibited.

Eurchromatin:

This more relaxed chromatin structure whose structure exposes the promoter regions of particular genes that need to be transcribed at specific times and under specific conditions during the lifetime of a cell, allowing precisely regulated gene expression and resulting in protein production.

heterochromatin vs euchromatin

Which form would you expect to see during metaphase of mitosis? Why? Which form would you expect to see during interphase? Why?

During metaphase the Heterochromatin is tightly coiled to help protect itself/DNA during cell division.

During interphase the euchromatin are relaxing and replicating themselves.

Explain what is meant by the statement "Every gene has a control panel and a coding sequence." What does the control panel do? What does the coding sequence do?

Control panels contain instructions to tell the cell how to switch genes on and off (start or stop codons). Coding sequences have information for specific amino acids.

Compare and contrast DNA and RNA

three similarities

-Both are made up of monomers called nucleotides, and have Adenine, Cytosine, and Guanine in common (DNA has Thymine, and RNA has Uracil)

-Cytosine pairs with Guanine in both

-Both are necessary to make proteins

Compare and contrast DNA and RNA

three differences.

DNA

-Stores RNA and protein-encoding information, and translates information to daughter cells

-Double stranded

-Very Stable

RNA

-Carries protein-encoding information and helps to make proteins

-Single Stranded

-Not Stable

3. What are the three major classes of RNAs in the cell?

mRNA

tRNA

rRNA

mRNA

carries genetic information into the cytoplasm- which will be encoded into the sequence of amino acids

Two major information transfer processes involved in gene expression

Translation

Transcription

Describe the two major information transfer processes involved in gene expression and state where each occurs in the cell.

· Nucleus:

Transcription regulation determines which genes are transcribed and determines availability of mRNA to ribosomes

· Cytoplasm:

Translation regulation determines the rate at which proteins are made and the availability of the finished proteins

In what direction does RNA polymerase build RNA?

Builds the RNA in a 5' to 3' direction by moving 3' to 5' on the DNA sequence

How does RNA polymerase know where to start? How does it know where to stop?

Start: RNA binds to promoter

Stop:

When the RNA polymerase reaches the termination sequence (3' end),

What are the three modifications made to pre-mRNA molecules before they become mature mRNAs, and what is the function of each modification?

Removal of introns to generate a coding sequence that can make an amino acid chain

A nucleotide cap is added at the 5' end for ribosome binding

A poly-A tail is added at the 3' end for mRNA stability

8. How does the ribosome know where to start translation? How does it know where to stop?

Start codon, AUG is the only codon that tells the ribosome where to start translation. The stop codon (UAA, UAG, and UGA) terminate translation

How can a human cell (which contains only about 21,000 genes) create over 1 million different kinds of proteins? (hint: see Figures 9.5 and 9.14)

Splicing

Most of our DNA does not code for proteins. What does it do?

It turns out that many non-coding RNAs exist — that is, RNAs that don't code for proteins but play important roles in how genes are expressed

What are microRNAs, and how do they regulate gene expression?

short, non-coding RNA molecules that regulate gene expression at the post-transcriptional level by interfering with the translation of mRNA into proteins. Binds to specific mRNA sequences, either leading to mRNA degradation or preventing translation of the mRNA into a protein.

Describe what is meant by "alternative splicing" and give a specific example. How does alternative splicing affect protein structure?

exons can be retained or removed during splicing, allowing mature mRNAs to contain different combinations of exons (Figure 9.5). Alternative splicing allows one gene to encode information for several different forms of a protein.

Example: α-tropomyosin

Smooth-muscle mRNA or Striated-muscle mRNA

What is a histone? How does it interact with DNA? What epigenetic modifications happen to histones that can cause them to "loosen their grip" on DNA? How might this affect gene expression?

A histone is a protein that DNA wraps around to compact it.

Remodeling complexes (proteins) can loosen the binding between the histones and DNA, allowing for access to promoters. The process is called Chromatin remodeling.

Whether the promoter is exposed or not will determine if the gene is expressed.

Another way histones can loosen their grip is with lysine acetylation which increases gene expression.

What epigenetic modifications make histones hang on more tightly to DNA? How might this affect gene expression?

Histones hang on tightly to DNA because they are positively charged and DNA has a negative charge.

If the DNA is wrapped tightly, the promoter cannot be accessed and the gene can't be expressed.

Methylation (adding methyl group to cytosine bases) turns gene off, preventing expression as well.

How can a mutation in a region of DNA that does not code for protein result in too much, too little, or the wrong sized protein being made? (Hint: think about regulatory sequences and important non-coding regions of genes)

If the mutation is in a regulatory sequence, it can influence the amount of times that the region of DNA is read and copied, influencing the amount of the protein that is made.

If it's in a non-coding region of the gene then there is no influence/ change

Distinguish between a somatic and a germline mutation. Which one can be passed on to the next generation?

Somatic mutations

-occur in the cells of the body that do not form gametes (liver, muscle, kidney, etc).

-If a mutation occurs in a somatic cell it will be passed onto all daughter cells by mitosis, but cannot be transmitted to future generations.

Germline mutations

-occur in cells that produce gametes

-these mutations are passed onto future generations.

Explain the difference between a spontaneous mutation and an induced mutation? Which one happens normally in cells? Which one can be caused by the environment?

Spontaneous mutations can arise as the result of errors in DNA replication and transcription or as the result of structural (chromosomal rearrangements) shifts in nucleotide bases- occurs naturally in the cells

Induced mutations caused by the environment

7. list two types of mutations that can change the reading frame.

Mutations:

Insertion- An insertion changes the number of DNA bases in a gene by adding a piece of DNA. As a result, the protein made by the gene may not function properly.

Deletion- A deletion changes the number of DNA bases by removing a piece of DNA. Small deletions may remove one or a few base pairs within a gene, while larger deletions can remove an entire gene or several neighboring genes. The deleted DNA may alter the function of the resulting protein(s).

Duplication- A duplication consists of a piece of DNA that is abnormally copied one or more times. This type of mutation may alter the function of the resulting protein.

9. How do cells sense and fix mutations?

DNA polymerase corrects many errors that lead to mutations. If an incorrect nucleotide is inserted, the enzyme can detect the error and reverse direction, move backward and remove nucleotides until the incorrect nucleotide is eliminated

Somatic cell

- most human cells, carry 23 pairs or 46 chromosomes

Embryonic stem cell (ESC)

cells in the inner cell mass of early embryos that will form all the cells, tissues and organs of the adult.

Are somatic cells considered differentiated cells? Which would be undifferentiated?

The somatic cells would be considered differentiated cells and all of the others are different kinds of stem cells which are undifferentiated.

Adult Stem cell

stem cells recovered from bone marrow and other organs of adults

• Multipotent - can only form one or a few different cell types

- EX: blood stem cells, hair follicle stem cells, intestinal stem cells

Induced pluripotent stem cell (iPS)

Adult stem cells that can be reprogrammed by gene transfer to form cells with most of the developmental potential of embryonic stem cells, because of such development potential these stem cells are "pluripotent"

G1:

growth after initial division, makes the components of the cytoplasm like the various organelles, membranes, and ribosomes.

Mitosis:

takes less than an hour, when a complete set of chromosomes is distributed to each daughter cell

G2:

the cell is preparing to divide, by the end of this stage the cell is ready to divide, mitochondria divide, precursors of spindle fibers are synthesized

S phase:

a copy of each chromosome is made, DNA replication, formation of sister chromatids

G0:

this is the inactive state where the cell is not dividing, the cell's choices are to remain in the resting state or if it receives signals to replicate then it will rejoin the cell cycle

What is the purpose of mitosis?

The purpose of mitosis is to create genetically similar cells, which replace other existing cells.

What is the role of apoptosis in development?

Apoptosis is programmed cell death.

Describe two different ways of generating genetic variation in meiosis. For each, be able to explain whether it happens in meiosis I or meiosis II.

o Random assortment occurs in meiosis 1, puts random combination of chromosomes into gametes

o Crossing over occurs in meiosis 1, metaphase 1

What is gametogenesis?

the process of gamete production and maturation

Spermatogenesis

-produces 4 daughter cells

-it all begins at puberty and continues through life

-produce thousands/millions each meiotic event

-produce endless gametes through life

Oogenesis

produces 2 daughter cells and 2 polar bodies

-daughter cells are VERY large

-begins at birth and doesn't complete meiosis II until fertilization. lasts 12-50 years

-produce only 1 or maybe 2

-only produce the number born with

During what stage of embryonic development are cells taken to create embryonic stem cells? What kind of other cells can embryonic stem cells make?

Taken when the embryo is in the blastocyst stage. ESC are pluripotent and thus can form any fetal or adult cell.

What is Mendel's Law of Segregation? Which event in meiosis is responsible for this law? What is it that is doing the segregating?

Only one of the two genes is put into a gamete, at fertilization each offspring will receive one allele for each gene from each parent.

What is Mendel's Law of Independent assortment? Which event in meiosis is responsible for this law?

o Each allele pair segregates into gametes without being influenced by the manner of segregation of other allele pairs.

o The random alignment of chromosomal pairs in metaphase of meiosis accounts for this law

What is a "single-gene" trait? Give an example.

o This is when one gene controls the phenotype

o Ex. Widow's peak, attached or non attached ear lobes

Autosomal Recessive

• -two affected parents = affected offspring

• often skips generations

• -relatively rare

• -affected individuals have unaffected traits

Autosomal Dominant

• -every affected indiv has an affected parent

• -two affected could have unaffected

• -mostly hetero and homo recessive spouse

Incomplete Dominance:

Dominant allele does not completely mask the expression of the recessive allele. Ratio 1:2:1 example: Snap Dragons Red and White = Pink

Explain the reason why an autosomal dominant trait might skip a generation.

Most affected people are heterozygotes thus they can have an unaffected child.

Complementation

There may be different mutations in different genes that control the same thing, for example hearing.

What pattern of inheritance would you expect for a trait caused by a mutation in mitochondrial DNA? What would this look like in a pedigree?

The trait would be passed from mothers to all of their offspring. However, the males would not pass on this trait to their offspring since there is no mitochondria in the sperm that is passed to the offspring.

Multifactorial Trait

traits that result from environmental and genetic influence

Discontinuous Trait

variations are phenotypes that fall into 2 or more distinct, non-overlapping classes. The environment influences them very little.

Heritability

the proportion of the total phenotypic variation in a population that is due to genetic factors

Which has a greater heritability, eye color or height? State a reason for your answer.

eye color, because height is more influenced by environment (e.g. nutrition) whereas eye color is based off genetics

Explain how twin studies and adoption studies are used to determine whether there is a genetic component to a trait. Distinguish between monozygotic and dizygotic twins and discuss what can be learned from twins reared together vs. twins reared apart.

Twin studies look at cordenance between MZ (100% same DNA) and DZ (basically siblings born on same day) twins since their DNA is either the same or very similar. If MZ twins are reared apart, you can see the difference or similarities between the two that must be resulting from environmental influences since their genes are the same. DZ twins reared together you can look at any differences and can maybe determine more of an environmental impact since they each have more of the same experiences/environment than they share genetics

Describe how SNP analysis and genome wide association studies (GWAS) can be used to help identify genes involved in polygenic traits.

SNP's look at the single changes in the nucleotide sequence. GWAS sees all the individual differences in the sequence and tries to draw conclusions and sees relationships between where the changes are. Cant draw a lot of conclusions

What are some limitations to GWAS?

they'll see differences and similarities in single changes in genomes, but have no idea what those genes do

Explain how it is possible for a familial trait (one that is seen in many people in multiple generations of a family) to have a small genetic component.

o Shared environments, take on parents and family's habits, eat the same foods, live in the same SES.

o It is the emotional, economic, physical, and the entire environment that will enhance a small genetic trait or component in a family.

Describe the process of nondisjunction and explain when it takes place during cell division. What is the consequence if non-disjunction happens in mitosis? In Meiosis I? In Meiosis II?

o Nondisjunction:

when the chromosomes or sister chromatids don't separate correctly in meiosis. If it occurs, then there will be extra or too few sex chromosomes in the daughter cells.

o Meiosis 1= 2 n+1 and 2 n-1 daughter cells

o Meiosis 2= 1 n+1, 1 n-1 and 2 normal daughter cells

o Mitosis: 1 = 2n+1 or 1 = 2n-1 The new cell will either be trisomic or monosomic

Monosomy

a condition in which one member of a chromosome pair is missing; having one less than the dipolid number (2n-1)

o Trisomy -

a condition in which one chromosome is present in 3 copies, whereas all others are diploid (2n+1)

consequences usually include early death, but trisomy 21 (down syndrome) has people who live into their adulthood, just with cognitive delays

Explain what is meant by chromosomal, genetic, gonadal, and phenotypic sex. How are sex and the concept of gender related? How are these concepts different?

chromosomal- chromosomes are XX or XY or any of the above combinations

genetic- XX and XY

gonadal- if there is an SRY gene that will code for development of male or female (mutations)

phenotypic sex- the sex that is exhibited by the individual

-the phenotypic sex can change during puberty, pseudohermaphrodism

What is the SRY gene? On what chromosome is it usually found? How does it usually help to determine phenotypic sex in humans?

o The SRY gene is responsible for male sex determination in humans. It can only be found on the Y chromosome. It turns on the genes that promote male development and turns off the genes that promote female development.

X-inactivation

When either the maternal or paternal version of the x chromosome in a female is silenced in a random fashion, so it is a mosaic of expression of the male or female versions

tRNA

brings amino acids to the mRNA ribosome complex during translation. Each tRNA molecule has two attachment sites: 1st a nucleotide sequence of 3 nucleotides called anticodon which pairs with a complementary codon sequence in mRNA and 2nd a site for attachment of the amino acid specified by the mRNA codon

rRNA

the site of polypeptide synthesis- during translation the rRNA in the large subunits acts as an enzyme linking amino acids together to form a polypeptide

Nonsense mutation

Mutations that change an amino acid specifying a codon to one of the 3 stop codons POTENTIALLY NO EFFECT

Missense Mutation

Mutations that cause the substitution of one amino acid for another protein

Sense Mutation

Mutations that change a termination (stop) codon into one that codes for an amino acid. Such mutations produce elongated proteins

Silent Mutation

No change occurs

Frameshift Mutation

Mutational events in which a number of bases are added to or removed from DNA, causing a shift in the codon reading frame MOST DAMAGING

Codominance

in a heterozygote both alleles are fully expressed. example: A, B are the dominate, AB is the codominant and O is the recessive

Epistasis

an interaction of another gene that interferes with the expression of the genes you are looking at. 1 gene stops or masks another gene. Example: is Bombay phenotype.

Polygenic Traits

traits that result from 2 or more genes

Continuous Traits

distribution of phenotypic characters that is distributed from one extreme to another in an overlapping or continuous fashion. Very influenced by environment.

Trisomy

a condition in which one chromosome is present in 3 copies, whereas all others are diploid (2n+1)

consequences usually include early death, but trisomy 21 (down syndrome) has people who live into their adulthood, just with cognitive delays

What does a heritability value of .72 mean?

72% of phenotypic variability in the population is caused by genetic differences in the population

Aneuploidy

Chromosomal number that is not an exact multiple of the haploid set

Law of Independent Assortment

the alleles of two (or more) different genes get sorted into gametes independently of one another

Law of Segregation

during the formation of gametes, the two alleles for a particular trait separate from each other, so each gamete contains only one allele for that trait

Penetrance

whether or not a population shows its phenotype (either/or)

Incomplete Penetrance

individuals with the same genotype don’t express the phenotype or do

Expressivity

degree with which a trait is expressed

Narrow Expressivity

everyone with that genotype shows the phenotype in the exact same way or severity (rare)

Variable Expressivity

multiple degrees of severity/expression patterns for that trait

Heterogeneity

mutations in more than one gene can create the same phenotype

Dependent Assortment

when traits are inherited together, meaning they are likely to be found in the same offspring

Recombination and Linkage

the farther apart genes are a on a chromosome, the more likely crossing over will occur

X-Linked Recessive Trait Characteristics

males affected more frequently but the trait is never passed father to son. often skips generations

Rare X-Linked Inheritance Pattern

affected males produce only affected daughters and heterozygous affected mothers will transmit to half their kids

X-Linked Dominant Pedigree

males/females equally likely, affected sons always have affected mothers, ½ of offspring of affected mother are affected, and does not skip generations

Barr bodies

tightly wound X-chromosomes dependent on the # of X chromosomes present (cell remembers which is inactivated)

Sex-influenced traits

expressed in both sexes but expressed differently (eg variable expressivity and pattern baldness)

Sex-limited traits

inherited by both sexes but expressed only in one (eg incomplete penetrance)

What is genomic imprinting?

when one copy of a gene is inactivated depending on if it came from maternal or paternal (one copy inherited)

Promoter

TATA sequence that signals where to start transcription. Calls in transcription factors to regulate control panel