Biology 202 Lesson 2: How Genetic Information is organized in the genome

diploid

2 sets of chromosomes

If you could build a protein with 10 amino acids, and any amino acid could be at each position, how many variations are possible?

20^10

Together LINES and SINES make up what percent of the DNA of the human genome?

34%

homologous chromosomes

Pair of chromosomes that are the same size, same appearance and same genes.

Thinking back to what you've already read about telomeres, how are telomeres an example of repetitive DNA?

They are repetitive sets of DNA sequences that read as TTAGGG and AATCCC

Nucleosome

a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones.

When a gene from the bacterium is inserted into the corn DNA, it is called:

a transgenic organism

coding region

contains the information for the structure of the expressed protein

As we age the length of our telomeres _____________

decreases

What is meant by the outcomes in the model?

develop new tech, address social issues, build knowledge, inform policy, satisfy curiosity, etc

After chromosome separation and cell division, cells enter the interphase stage of the cell cycle, during which the components of the chromosomes uncoil and are present in the form referred to as.....

chromatin

Do mitochondria and chloroplasts occur in both prokaryotes and eukaryotes?

no just eukaryotes

Do prokaryotes have introns?

no just exons, shown in the fact that the length of prokaryotic mRNA is the same to the length of its DNA

Was Mendel's immediately accepted in the scientific community?

no, his work was not known until it was duplicated by other scientists

Can we predict relative genome size based on the complexity of the organism?

nope! e.g. an onion has a larger genome than humans, yet we are more complex organisms

Are the number of genes proportional to genome size?

nope! e.g. yeast and humans

mitosis

part of eukaryotic cell division during which the cell nucleus divides

Histones

protein molecules around which DNA is tightly coiled in chromatin. positively charged molecules primarily composed of the amino acids lysine and arginine and are electrostatically bonded to the negatively charged phosphate groups of DNA.

Why is mRNA so much shorter in eukaryotes relative to their long DNA lengths?

removal of introns

SINEs

short interspersed nuclear elements

STRs

short tandem repeasts (2-6 bp in length)

what does it mean that the scientific process is not pre-determined?

step not clear always

Proteomics

study of the structure and function of proteins in the human body

Genomics

study of whole genomes, including genes and their functions

Tandem vs. interspersed

tandem=bp sequences occur in repetition by another (aka as microsatellites) interspersed= random throughout the genome

Which of these parts of the non-linear model central to the process of science?

testing ideas

what does it mean that the scientific process is iterative?

that it circles back on itself

Chromosomes in mitochondria and chloroplasts

(found in eukaryotes), circular, packaged loosely

VNTR

(variable number of tandem repeats) tandem (next to each other) repeats of a short DNA sequence (10 to 60 base pairs) with varying numbers of repeats among individuals

haploid

An organism or cell having only one complete set of chromosomes.

Phenotype

An organism's physical appearance, or visible traits.

Social benefits/outcomes of the Lifestyle may lengthen telomeres, a measure of Cell aging" study?

-aging cancer or other diseases

Heterochromatin...

-has relatively few genes -remains relatively condensed (tightly coiled) during the cell cycle -is found in the telomeres and the centromere

What is wrong with the simplified linear model for the process of science?

-implies science is linear -individual -little room for creativity -concludes

What are the main differences between genes in eukaryotic organisms vs. prokaryotic organisms?

-simple eukaryotes ARE similar to prokaryotes (e.g. yeast) -In complex eukaryotes, genes are farther apart with non-coding DNA in between genes. (Genes are larger and with more exons too)

Community analysis and feedback weaknesses of the Lifestyle may lengthen telomeres, a measure of Cell aging" study?

-small sample size -only men with prostate cancer- will this apply broadly? -randomized assignments to control or experimental group?

What were the results of the Lifestyle may lengthen telomeres, a measure of Cell aging" study?

10% increase in the experimental group, 3% decrease in the control group

TTQ: You are asked to find the location of a DNA sequence resulting in a protein that is being overexpressed in a disease state? This sequence most likely resides within: 1) heterochromatin 2) a LINE 3) a STR 4) likely to be any of these 5) not likely to be any of these

5) not likely to be any of these Explanation: LINEs (repetitive transposable DNA sequences) and STR's (nucleotide repeats dispersed throughout the genome) are not associated with gene expression and Heterochromatin is DNA that is really tightly packed around histones (protein) so that the "transcription machinery" aka RNA polymerase can not reach the DNA, therefore no gene expression occurs

The human genome has about 20,000 functional genes. These DNA sequences account for what percent of the entire human genome?

<2%

chromosome theory of inheritance

A basic principle in biology stating that genes are located on chromosomes and that the behavior of chromosomes during meiosis accounts for inheritance patterns.

Nucleoid

A dense region of DNA in a prokaryotic cell.

What does the cell theory state?

All living things are made up of cells, cells are the basic units of structure and function in living things, new cells are produced from existing cells

What bacterial/prokaryotic DNA compacted tightly around?

Hu and H-NS proteins NOT histones as seen in eukaryotic DNA

Physicians being able to order diagnostics tests for genetic syndrome falls under what part of the model.?

Benefits and outcomes

What makes an erythrocyte different from a myocyte?

Both cells have the same DNA, but different mRNA and proteins because different genes are expressed.

Meiosis

Cell division that produces reproductive cells in sexually reproducing organisms

In eukaryotes, DNA and its associated proteins is called what?

Chromatin

What is the first order of chromatin packing?

Coiling around nucleosomes The first order of chromatin packing occurs when DNA coils around nucleosomes, whereby DNA is reduced to about one‑third its original length

Central Dogma

DNA -> RNA -> Protein

genes

DNA segments that serve as the key functional units in hereditary transmission.

_______ stores the genetic information and serves as the template for its own reproduction ________ and for the production of ______ copies of ____________________ These copies carry the genetic information to be used for the synthesis of ________________ ____________________

DNA, replication, RNA, transcription, proteins, translation

Outline the steps from DNA to protein:

DNA->trranscription->mRNA->translation->Ribosome + tRNA + amino acid

alleles

Different forms of a gene

What was the experimental group in the Lifestyle may lengthen telomeres, a measure of Cell aging" study?

Four lifestyle factor changes: plant-based diet, sleep, stress reduction, and moderate exercise (n=15)

How is the genetic information encoded in a DNA molecule?

Genetic information is encoded in DNA by the sequence of bases (nucleotides)

What is telomerase and what cells express this protein?

In germline cells (egg and sperm), an enzyme called telomerase is responsible for adding more repeat sequences to the end of the DNA, thus making them "immortal," however in somatic cells it functions at lower levels making these cells normal

DNA

Long ladder-like macromolecule that twists to form a double helix. Each linear strand of the helix is made up of subunits called nucleotides. (A=T and C=G)

What was the control group in the "Lifestyle may lengthen telomeres, a measure of Cell aging" study?

No change in lifestyle (n=25)

What does figure 1-1 tell us about how scientists once incorrectly thought about reproduction?

Prior to the cell theory; the theory of preformationism stated that the fertilized egg contains a complete minature adult called a homunculus

Eukaryotic gene

Promoter - UTR - Exons - Introns - Exon - Intron - UTR- PolyA signal

Prokaryotic gene

Promoter -UTR -Gene 1 - Gene 2 -UTR -termination signal

Telomeres

Repeated DNA sequences at the ends of eukaryotic chromosomes.

Why is the linear model of science too simple?

Science is repetitive and scientists work in groups and get feedback from the scientific community

how do new versions of genes (alleles) arise in a population?

mutation

What is the DNA sequence of the telomere?

TTAGGG

What was the dependent variable in the Lifestyle may lengthen telomeres, a measure of Cell aging" study?

Telomere length of white blood cells (immune cells)n 5 years later

What happens to the structure of hemoglobin when the B-globin gene has a mutation that changes a codon from GAG to GUG?

The hemoglobin molecule polymerizes; phenotype = sickle-cell anemia

The majority of repetitive DNA serves.....

no function

Write a few sentences outlining the central dogma:

Transcription utilizes DNA in the nucleus to create a strand of complementary mRNA which is then moved to the cytoplasm and binds to a ribosome where translation occurs and tRNA carries the appropriate amino acid corresponding the codons in the mRNA sequence.

What makes up the protein component of the nucleosome core?

Two tetramers of histone proteins

Mutations

a random error in gene replication that leads to a change

Higher-level eukaryotes generally have what?

more exons per gene, larger genes and introns are removed

bioinformatics

application of mathematics and computer science to store, retrieve, and analyze biological data

mtDNA and cpDNA contain rRNA and tRNA genes of their own for their organelle‑specific functions and are similar to what?

bacterial cells (prokaryotes) suggests that perhaps a prokaryote was once engulfed by eukaryotic cell (evolution)

Why was Darwin's theory of natural selection controversial when he published it?

because it lacked the basic understanding of the genetic basis of variation and inheritance, a gap that left his theory open to reasonable criticism

Chromatin structure influences the expression of gene without doing what?

changing the actual DNA sequence

euchromatin vs heterochromatin

euchromatin: uncoiled genetic material (lighter stained) where mRNA is transcribed heterochromatin: coiled genetic material that is transcriptionally inactive

Differences in eukaryotic cells and prokaryotic cells

eukaryotes have nuclei and membranous organelles, divide by mitosis and meiosis Prokaryotes lack these things

what group of living organisms is defined by the presence of a nucleus?

eukaryotic organisms

The second order of chromatin packing occurs when nucleosomes coil together to form a fiber that is 300nm in diameter?

false- the second order of chromatin packing occurs when nucleosomes coil together to form a solenoid fiber that in 30 nm in diameter

What kinds of things are done in community analysis and feedback?

feedback and peer review, replication and discussion etc

STRs and VNTRs are used in what?

fingerprinting

What things are done during testing ideas?

gathering and interpreting data

Genotype

genetic makeup of an organism

the totality of all the genetic material in a given organism is called what?

genome

Chromosomes in prokaryotes (bacteria)

in cytoplasm, circular, packaged loosely

Regulatory Region

information on where and when a gene will be transcribed during development; usually upstream of the coding region (tells polymerase where to start making mRNA)

Transcription Termination Region

is the "stop" signal for where transcription should end; "downstream" of the coding region

LINEs

long interspersed nuclear elements

What things are apart of exploration and discovery?

making observations, asking questions, sharing data and ideas, finding inspo

Where would we be more likely to find a gene that is actively expressed in this cell? why?

the dark regions are heterochromatin and densely packed. Recall that heterochromatin is tightly wound around histones therefore RNA polymerase can not transcribe it. The lighter regions are euchromatin and can be transcribed so the light regions would be transcribed here.

What is the centromere and what does the DNA sequence look like at the centromere?

the part of the chromosome that connects 2 sister chromatids. The DNA sequence is largely repetitive (composed of heterochromatin)

Chromosomes

threadlike structures made of DNA molecules that contain the genes

Where are the telomeres located on the chromosome?

tips of chromosomes; there are 4

One tetramer is composed of what?

two units of each histone H2A and H2B, and the other is composed of two units each of histones H3 and H4

What would the result if the telomeres stopped shortening?

would potentially prevent the cell's eventual susceptibility to death after a certain number of cell cycles