Lecture 2 Notes

All living things have genetic material, what is this genetic material for some viruses and most living things?

Some viruses (HIV and Sars-Cov-2) use RNA

All other living things use DNA

Define chromosomes

Arrays of genes organized into longer DNA molecules

• transmitted from one generation to the next very precisely

• this precise process is how organisms maintain genetic continuity

What do gene products direct?

Gene products direct the metabolic activities of a cell

Pre 1940s, knowledge was limited for cell structures, what was being made during this time to understand the finer details of the cell?

The transmission electron microscope was being developed which allowed for finer details of the cell to be seen.

What does the plasma membrane do?

Do all cells have it?

The plasma membrane keeps the cell in tact and all cells have it.

• It is made with phospholipid bilayer

What do plants use instead of the cytoplasm?

Cells have a cell wall which is made of cellulos

Define glycocalyx (cell coat)

An outer layer made of glycoproteins and polysaccharides that many animal cells have

• provides biochemical identity to cells and the components that give this identity are genetically controlled

• ex: AB antigens on red blood cells

Where are receptor proteins located and what do they do?

Receptor proteins are located on the surface of the cell membrane. These sites transfer chemical signals across the cell membrane.

Define cytoplasm

Everything outside of the nucleus

• contains organelles and cytosol

What is the relationship between cytosol and the cytoskeleton?

Cytosol contains many tubules and filaments that give the cell its shape, the cytoskeleton

Define microtubules

Part of the cytoskeleton and are made of the protein tubulin

Define microfilaments

Located in the cytoskeleton and are made of the protein actin

What is the rough ER

Ribosomes are present, site of synthesis (translation) of membrane proteins and proteins destined for export from the cell

What is the smooth ER

No ribosomes present, sit of fatty and phospholipid synthesis

What are free ribisomes?

Ribosomes in the cytoplasm that translate proteins not meant to be in membrane organelles or exported out of the cell

What is the role of the mitochondria

The site of the TCA cycle, the ETC, and the production of ATP

What is the role of the chloroplast

The site of photosynthesis

Where does the mitochondria and chloroplast evolve from

The organelles are ancient products of endosymbiosis of bacteria

• A prokaryote started living inside of an archean, they developed a mutualistic symbiotic relationship. The prokaryote provided a fast way of producing ATP and the archean provided a safe place to live.

Define Eukaryotes

Organisms that have a nucleus and membrane-bound organelles

• fungi, plants, animals, etc.

Define prokaryotes

Lack nucleus, membrane-bound organelle, mitochondria and chloroplasts

• Bacteria and Archaea

What is the role of the nucleus in a eukaryotic cell?

They are membrane-bound structures that houses genetic material

Define nuclear envelope (nuclear membrane)

membrane around the nucleus and has 2 lipid bilayers

Define nucleolus

Located in nucleus where rRNA is made and the first steps of ribosome assembly occur

Define nuclear pore

Where the molecules enter and exit the nucleus

Define chromatin

Diffuse network of DNA and associated proteins within the nucleus in non-condensed form

• loosely packed DNA in the nucleus

Do both eukaryotes and prokaryotes have ribisomes?

YES. The cell makes a copy of a gene (mRNA), the mRNA travels to a ribosome. The ribosome reads the instructions on the mRNA and then builds the protein based on those instructions

How do Prokaryotes differ from Eukaryotes?

• Lack nucleus

• Usually contain singular circular chromosome, some exceptions

• Chromosome is not membrane bound but exists in the nucleoid region

• Doesn’t have a distinct nucleolus but contains rRNA genes

• Chromosome is compared into the nucleoid region and sometimes anchored to the cell membrane

  • never compared in the same way as eukaryotes

• DNA isn’t nearly as extensively associated with proteins

True or false: Are chromosomes easily visualized during cell division

True

True or false: Chromosomes contain a constricted region called the centromere

True

Define centromere

Specialized DNA sequences that serves as the site of kinetochore attachment

True or false: All somatic cells (germ like cells: egg/sperm) of a species contain the same number of chromosomes?

True

Where is the metacentric of a centromere?

Middle

Where is the submetacentric of a centromere?

Between middle and end

Where is the acrocentric of a centromere?

Close to the end

Where is the telocentric of a centromere?

The end

True or false: Most eukaryotes are diploid?

True

True or false: Most prokaryotes are haploid and dont have homologous pairs

True

What are sister chromatids?

Products of a chromosome that has replicated, meaning they have identical sequences

Define homologous chromosomes

Contain the same genes but derived from different parents

True or false: chromosomes vary across species

True

True or false: within species chromosome number does not normally vary

True

True or false: chromosome number doesn’t correlate well with genome size or complexity?

True

Define Karyokinesis

Separating the genetic material from mitosis evenly. This precedes separation of the cytoplasm, also known as cytokinesis

True or false: Mitosis is not the basis for asexual reproduction in some organisms

False. Mitosis is the basis for asexual reproduction in some organisms

• Ex: budding yeast

How is mitosis the basis for sexual reproduction

Mitosis is the basis for complex multicellular organisms to go from a single celled zygote to fully developed adults

What happens when cells lose control of mitosis?

When cells lose control of mitosis, tumors begin to form

What part of the cell cycle doesn’t include mitosis?

What does it have?

Interphase does not include mitosis.

This phase has G1, S, and G2

What happens during the subphase of interphase?

• After cells divide, they are half the size of the mother cell and need to grow

• Generally a newly formed nucleus is not smaller than the nucleus of the mother cell

• Growth and high levels of metabolic activity are occuring during G1, S, and G2

Explain what happens during the G1, S, and G2 phases in the subphases of the interphase stage.

• Growth and high levels of metabolic activity are all occurring during G1, S, and G2

• G1 can either lead into G0 (nondividing but metabolically active state) or lead into cell division

  • Some cells can be stimulated to exit G0 and divide again

• During S phase the DNA is replicated

  • Entering the S phase is when a cell is committed to dividing and there is no going back

• G2 has more growth and preparation for mitosis

  • By the end of G2, cell volume has roughly doubled so now cells can divide into 2 daughter cells

Are chromosomes visible during interphase?

No, chromosomes are not visible during interphase

What happens during prophase in mitosis?

• Centrioles move to the opposite sides of the cell (area called the centrosome)

• Nuclear envelope breaks down and nucleolus is no longer visible

• Chromosomes condense into visible structures t form sister chromatids which are joined at the centromere and are genetically identical

  • sister chromatids are held together along their length by cohesion (protein)

What are centrioles?

What organisms are they found?

• Centrioles are organelles found in both plant/animal cells made mostly of tubulin (protein) that organize the microtubules of the cell into spindle fibers

• Most plants and fungi lack centrioles so they’re not universally responsible for organization of spindle fibers

What happens during prometaphase in mitosis?

• Centrioles reach opposite poles

• Spindle fibers form

  • Not all spindle fibers are used for the same thing. Some are used for chromosomal movement, others stabilize the cell as it divides, and some facilitate cell elongation before cytokinesis

• Kinetochore binds the centromere

• Spindle fibers attach to kinetochore

• Cohesin is degraded by separase (enzyme)

  • occurs everywhere except the centromere region where shugoshin (protein) protects cohesin from being degraded

• The number of kinetochore that attaches per chromosome varies across organisms

What happens during metaphase in mitosis?

• All chromosomes are aligned on the metaphase plate

• Centromeres are aligned

• Order of chromosomes are random and the arms (p and q) are extended outward

What happens during anaphase in mitosis?

• Disjunction occurs

  • Shugo Skin needs to unwind at the centromere to allow the breakdown of the remaining cohesin by separase

• Separated chromosomes are now called daughter chromosomes

• Chromosomes separation is accomplished by molecular motors that shorten spindle fibers in an ATP dependant fashion

Define disjunction

Where does it occur?

Process where sister chromatids are held together only at the centromere disjoin

• occurs during anaphase in mitosis

What happens during telophase in mitosis?

• Complete sets of chromosomes are on opposite sides of the cell

• Cytokinesis occurs whereby one cell physically separates into 2

  • animal cells use cell furrow

  • plant cells cant divide this way so they use a cell plate

• During later stages

  • Nuclear envelope start to reform

  • Chromosomes start to decondense

  • nucleolus gradually becomes more visible

Explain the cell cycle regulation and its checkpoints

• Cell cycle is heavily regulated

• When problems occur, the cell will either die for become rapidly uncontrolled growth leading to cancer

• Cyclins, which are proteins are expressed in different point sin the cell cycle that bind cyclin dependant kinases, activating and allowing them to phosphorylate

• There are 3 checkpoints

  • G1/S checkpoint: needed because when a cell pases, it is committed to dividing

  • G2/M checkpoint: Checks that DNA is fully replicated and that there is no damage before entering mitosis

  • M checkpoint: ALl chromosomes are present in metaphase plate and are connected to the spindle fibers (also called the spindle fiber assembly)

Explain which cells can reproduce sexually and asexually

• Bacteria and Archaea generally reproduce sexually

  • Accomplished through binary fussion

• Single-celled Eukaryotes like yeast can reproduce asexually or sexually

• With a few exceptions, all multicellular eukaryotes rely on sexual reproduction which requires meiosis

What is Meiosis?

• Process by which gametes (egg, sperm, spores) are produced

• Reduces ploidy from diploid to haploid

  • Prevents genetic information from doubling to the next generation

• Major source of genetic variation because many different gametes can be made by each parent

• There are 2 divisions that have their own prophase, metaphase, anaphase, and telophase

  • Prophase 1: homolog pairs (already duplicated)

What is the differences between mitosis and meiosis?

What is the similarities between them?

Similarity:

• In both, the chromosomes are first replicated and condensed

Differences:

• In mitosis, sister chromatids align on the metaphase plant, homologs DO NOT pair to form tetrads

• In meiosis 1, homologous pairs (synapse) form bivalents, and then eventually form tetrads, and then crossing over between homologs occurs

• In anaphase of mitosis, sister chromatids are pulled apart

  • no reduction in ploidy

• In anaphase 1 of meiosis, homologous pairs are pulled apart

  • reduction in ploidy, ½-ing the number of centromeres

What occurs during prophase 1 in meiosis?

• Leptonema

• Zygonema

• Pachynema

• Diplonema

• Diakinesis

What occurs during, Leptonema, in prophase 1 in meiosis?

• Chromatin begins to condense and chromosomes become visible

• Along each chromosome are chromomeres, localized condensations that resemble beads on a string

• Homology search occurs, a process essential to the initial pairing of homologs

What occurs during, Zygonema, in prophase 1 in meiosis?

• Chromosomes continue to condense

• Homology search continues and homologs are lined up end to end

• Synaptonemal complex forms (protein complex)

  • Variably (though visually) required for homolog pairing and recombination (crossing over) to occur

• At the end, homologs are closely associated and called bivalents (not apparent as double structures yet)

What occurs during, Pachynema, in prophase 1 in meiosis?

• Homologs become more closely associated and undergo synapsis

• Genetic exchange between chromosomes occur. The two more distal chromatids do not undergo exchange

What occurs during, Diplonema, in prophase 1 in meiosis?

• Homologs separate slightly but are still held together at points called chiasmata (sites where recombination occurred)

What occurs during, Diakinesis, in prophase 1 in meiosis?

• Chiasmata move to the ends of chromosomes (terminalization)

• Nucleolus and nuclear envelope breakdown

• Spindle attaches to centromere of each homolog

How does Meiosis contribute to genetic variation?

• For any gamete, each letter has a 50% chance of being maternal and 50% chance of being paternal

• Each chromosome aligns independently of all others in meiosis 1

• Each position is essentially a independant coin flip, making the total number of possible combinations 2²³ = 8,388,608 gamete combinations

  • With recombination and mutation this number is of possible gametes a parent can make is actually much higher

  • the larger number then needs to be squared since both contribute gametes to the offspring (>64 trillion combinations)

How does Meiosis differ in males and females?

Males:

• 1 spermatogonium → (Growth) → primary spermatocyte → (M1) → Secondary spermatocytes → (M2) → 4 spermatids → (differentiate) → 4 spermatozoa

Female

• Oogonium → (growth) → Primary oocyte → (M1) → First polar body and secondary oocyte → (M2 for secondary oocyte) → Second polar body and ootid → (differentiation for ootid) → Ovum