CMB: The Dynamic Cell

Cells were first name by who? Looking at what kind of Cell?

Robert Hooke, observing cork cells.

The size cell humans can see without a microscope?

500 micrometers

Indivisual cells do these five things:

grow, reproduce, process info, respond to stimuli, carry out chemical reactions

Levels of organization of cells:

molecules → cells → tissues → organs → systems → organism

Define cell

The basic living unit of a biological system.

True or False: All cells composed of the same types of chemical molecules and employ similar principles of organization at the cellular level.

True

Life and cells are based off of what element?

Carbon

Cell and molecular biology studies how cells do what five things?

develope, operate, communicate, control activities, go awry

The smallest type of cell and its size:

Bacterial cell: 0.2-0.3 micrometers

The biggest type of cell and its size:

Nerve cell: >1 meter long

Common range of cell size for bacteria:

1-5 micrometers

Common range of cell size for Eukaryotes:

10-50 micrometers

What is the most fundamental difference between prokaryotes and eukaryotes?

Eukaryotes have membrane bound organelles, prokaryotes do not.

True or false: There are more similarites between prokaryotes and eukaryotes than differences.

True

Four classes or eukaryotes:

plants, animals, protists, and fungi

The two categories of prokaryotes are:

Eubacteria (most bacteria and cyanobacteria) + Archaebacteria (methanogens, halophiles, thermo-acidophiles)

How the genetic info is stored in a eukaryote vs prokaryote:

Eukaryote → membrane bound nucleus. Prokaryote → not membrane bound nucleoid.

3 reasons why Eukaryotic cells compartmentalize the functions within the cell:

1. To maintain an adequate concentration of essential compound and catalysts (being that a two fold change in the diameter of a cell requires an eight fold change in the amount of reactants and enzymes).

2. The organelles are indivisually specilized for certain functions so it requires compartmentalization.

3. Allows different processes happening within the cell to occur simultaneously.

Which parts of the cell produce ATP and whats the difference between the two?

Mitochondria + Cytoplasm: The mitochondria produces aerobic respiration while the cytoplasm does not.

How does E. Coli fulfill oxidative phosphorylation without any mitochondria?

E. Coli uses its plasma membrane which holds ATP synthase (enzyme) + the electron transport chain (ETC)

The only eukaryote that can produce anaerobic respiration?

Yeast (fungi): Ex. petite mutants

What 3 proteins are involved in maintaining proper structure of the cytoskeleton, motility, and contraction within the Eukaryotic cell?

Microtubules (within cilia and flagella), microfilaments (within actin and myosin of muscle fibers), and intermediate filaments (creates support in stress areas of the cell).

Define Endocytosis and Exocytosis. What kind of cells utilize these methods?

Eukaryotes.

These processes are for exchanges material between the organelle or in and out of the cell.

Endocytosis: formation of vesicals containing materials within the cell.

Exocytosis: release of materials outside of the cell by the vesicles.

How do prokaryotes and Eukaryotes oragnize genetic info differntly?

Prokaryotes: Few associated proteins - Circular DNA packed into the nucleoid region.

Eukaryotes: Many associated proteins - Linear DNA fragmented packed into chromoses which are then packed into the membrane bound nucleus. (all chromosomes from one person combined and stretched would be 2.6 meters long)

How much more DNA is there in a Eukaryotic cells than in E. Coli

1000 fold

Humans have what number of basepairs, encoded proteins, + types of chromosomes?

Basepairs: 3.3 billion

Encoded proteins: 20,800

Chromosomes: 24 types

How do prokaryotes and eukaryotes differ in how they divide?

Prokaryotes: Binary fission

Eukaryotes: Mitosis and meiosis

Stages of the cell cycle:

G0 - Cycle arrest (ex: neurons, no longer dividing)

G1 - RNA, lipid, and protein synthesis, cellular components are duplicated

S - Each chromosome is replicated

G2 - RNA, lipids, and proteins are synthesized. Duplicated chormosomes repaired if need be. Chromosomes divide in preperation for mitosis

M - mitosis: Cell division

How does gene expression differ in prokaryotes and eukaryotes?

Prokaryotes: do not (or barely) process their RNA, transcription and translation are coupled, ribosomes are smaller.

Eukaryotes: RNA undergoes processing, transcription and translation not couples, ribosomes are larger.

3 stages of RNA processing in Eukaryotes:

1. ‘5 cap - 7 methyl guanosine cap added (helps avoid degredation)

2. RNA splicing (second step in larger genes with more introns, third step in smaller genes with fewer introns)

3. cleavage and ‘3 polyadenylation

Name 7 differences between Eukaryotes + Prokaryotes:

1. Bound vs unbound organelles

2. Nucleus vs nucloid region

3. Compartmentalization of organelles vs none

4. Tubules and filaments vs none

5. Ability to perform exo/endo cytosis vs not

6. Linear vs circular DNA

7. Mitosis and meiosis vs binary fission

8. Lengthy process for gene expressions vs short

Metazoan:

An organism composed of multiple cells.

Humans today have up to what percent of their DNA genome derived from Neanderthals as a result of matings thousands of years ago.

2%

Translation:

The process in which mRNA is used as a template to join the amino acids of a polypeptide chain in the correct order.

Protein synthesis occurs in:

the cytoplasm

Role of mRNA, tRNA, + rRNA

mRNA: carries genetic info that was transcribed into a linear form. Uses codons as keys

tRNA: deciphers codons and links amino acids to the polypeptide chain. Uses anticodons to pick up the specific amino acid needed. The N bonds to the C of the growing chain. 

rRNA: helps form ribosomes + helps for the peptide bonds found between amino acids. Large and small unit each contain rRNA.

Four major structural features of a eukaryotic cell:

1. Nucleus

2. Plasma Membrane

3. Organelles

4. Cytoplasm

5. (Plants - cell wall)

The two parts of the cell membrane:

Glycolipids + Glycoproteins

4 Functions of the cell membrane?

1. Holds enzymes

2. Anchors the cytoskeleton

3. Transport

4. Receptors

4 parts of the nucleus:

1. Interior (aka nucleoplasm) - holds chromosomes

2. Nuclear envelope - double membrane containing pores

3. Pores - transports ribosomes, mRNA, enzymes, and proteins

4. Nucleoli - rRNA production, assembly of ribosomes

The inner membrane of the nucleus is supported by?

A structural network composed of lamins + intermediate filament proteins.

The outer membrane of the nucleus is connected to?

The Endoplasmic Reticulum

What is the role of the endoplasmic reticulum and what cells are most likely to have them?

Makes and processes proteins (that will be secreted from the cell or part of membranes) and lipids

Cells that produce macromolecules (ex. Pancreatic Acinar cells that produce digestive enzymes).

The mitochondria is the size of:

A bacterial cell

Most oxidative reactions that produce ATP within the cell occur in:

Mitochondria

Mitochondria have their own:

Ribosomes, DNA, synthesize their own protein

What are cristae and what are their roles?

Inner folding of the mitochondria - harbor intermediates involved in the transport of electrons from the food molecules to o2.

The semifluid inside the mitochondria is called:

Matrix - fat oxidation + TCA (citric acid cycle AKA krebbs) cycle happen here → getting energy from food

β-oxidation generates acetyl-CoA from fatty acids, while the Krebs cycle oxidizes acetyl-CoA to produce reduced cofactors (NADH, FADH₂) for ATP production.

The largest and second to largest organelle?

Largest = nucleus

Second = chloroplasts

Photosynthesis does what?

Sugar is made from co2 and h2o

What reactions occur in the Thylakoid Membrane system vs. Stroma

Thylakoid Membrane - light dependant reaction

Stroma - other reactions

2 parts of the ER:

1. Cisternae - network of interconnected tubular membranes and flattened sacs

2. Lumen - space enclosed by the ER membrane (where ribosomes are located on the rough ER)

ER is connected to the outer membrane of the nuclear envelope

Properties of the smooth ER:

1. No ribosomes or protein synthesis

2. Sythesizes lipids and steroids

3. Inactivates and detoxifies drugs and other compounds

What is a Leydig cell?

A specialized cell for testostrone production. Contain more smooth ER.

Properties and functions of the golgi:

1. Properties: contains stacks of flattened golgi vesicles that contain proteins that go through processing. Once processed they bud off of the cell and form secretory vesicles. The secretory vesicles leave, fuse with cell membranes and dispense the contents.

2. Functions: Process and package secretory proteins + synthesis of pollysaccharides.

Funtion of the lysosomes:

Store hydrolases (enzymes that are capable of digesting specific biological molecules like proteins, fats, carbohydrates).

Lysasomal enzymes are synthesized in? Transported to and activated by? Enclosed in?

Rough ER

Golgi

Lysosomes

Primary vs Secondary Lysosomes:

Primary - Enclose and contain hydrolytic enzymes, bud off from golgi

Secondary - A fusion of primary lysosomes with vaculoles containing food. Hydrolytic enzymes digest these contents (only in the secondary) until they’re small enough to pass through the membrane into the cytosol.

What are Peroxisomes?

(aka Microbody) Organelles that contain catalase enzymes which convert toxic peroxide radicals into h2o2 which is then further broken down into water and oxygen.

Animal Peroxisomes are found where and have what three functions?

Found mainly in kidney and liver cells.

1. Detoxes h2o2, methanol, ethanol, formate, formaldehyde.. harmful compounds.

2. Can catabalize substances like D-amino acids found in some pathogenic bacterial cell walls.

3. Can oxidize fatty acids

What is ALD?

Adenoleukodystrophy - a genetic disorder involving the peroxisomes. The enzyme for degrading fatty acid is defective or missing and can lead to neurological debilitation and cause death.

2 types of plant peroxisomes:

1. Glycoxysomes - convert stored fat into carbs

2. Leaf peroxisomes - photorespiration - light dependant respiration.

What are vacuoles and what is the differene between the central vacuole and the contractile vacuole?

Used for temporary storage or transport

Central vacuole - less storage more helping in intracellular digestion + maintains turgur pressure

contractile vacuoles - maintain osmolarity by acting as pumps and expelling water.

What organelle is not membrane bound?

Ribosomes

Ribosomes are the site of:

Protein synthesis (measures in S)

What is Cytosol?

The semifluid in the cytoplasm where the organelles are suspended. This is where cellular activies like protein synthesis, fat synthesis, and glycolysis occur.

What are the four major kind of biomolecules in the cell?

1. Fats → Lipids

2. Sugars → Polysaccharides

3. Amino Acids → Proteins

4. Nitrogenous Bases → Nucleic Acids

What is the RNA world hypothesis?

RNA is the original molecule of life rather than DNA or protein.

Four steps of gene expression:

1. Activation of genes

2. Transcription

3. Processing

4. Translation

Cis Vs Trans gene regulation?

Cis - regulation is performed by motifs on the DNA strand itself (often with the help of outside - trans - molecules. ex: TATAWAW box). W = T or A

Trans - regulation performed by outside molecules (ex: Transcription factor)

The TATAWAW box and transcription factor work together.

mRNA is composed of these 3 segments:

‘5 UTR - CDS - ‘3 UTR

What is the Shine Delgarno sequence and where is it located?

Located within the ‘5 UTR, it is the sequence in which rRNA within the small unit of the ribosome recognizes and latches onto within the mRNA to initiate protein synthesis. It is a Cis element of regulation.

How many amino acids are coded in a 90 bp long sequence of DNA?

29 - the stop codon is not included.

How does the ribosome bind to the SDS?

The small subunit of the ribosome contains an anti bases and it binds through normal basepairing.