Cell Structure Final Exam Cumulative Section

Ch.1: What are the different types of chemical bonding/interactions? Rank them from strongest to weakest.

Strongest to Weakest:

• * Ionic bonds: exchange of pos. or neg. charge

• * Covalent bonds: sharing orbital e-

• Di-Sulfide: type of covalent (S-S)

• * Hydrogen bonds: where a hydrogen atom, covalently bonded to a highly electronegative atom (like O, N, or F), is electrostatically attracted to a lone pair of electrons on another nearby electronegative atom

• Van derWaals forces: attraction due to charge

• * Hydrophobic Interactions

Ch.1: Describe the important features of water for life.

• Most abundant molecule in a cell (75-85% of total mass)

• * Water molecules have a polar chemical structure that is the context for living cells (can readily form hydrogen bonds with other water molecules & other polar molecules)

  • High heat stabilization

  • * The abundant solvent of living systems

Ch.2:

1. * What are the building blocks of macromolecules?

2. * What type of reactions covalently link them together?

3. What has to happen to these building blocks before the reaction can occur?

1. Monomers

2. Successive condensation reactions (release water)

3. They have to be activated by coupling them to a carrier molecule (carbon) using energy from ATP

Ch.3: * Describe the 4 different levels of structure for proteins.

What * different chemical bonding do the different levels require?

1. Primary structure: a sequence of amino acids linked together by peptide bonds, forming a polypeptide

   • Covalent peptide bonds

2. Secondary structure: local regions of the polypeptide coiled into an alpha helix or beta sheet

   • Hydrogen bonds between NH and CO groups of peptide bonds in the backbone

3. Tertiary structure: regions of the secondary structure (R-groups) associate in a specific manner to form a tertiary structure, which is the final folding of the polypeptide

   • Covalent disulfide bonds, hydrogen bonds, ionic bonds, Van der Waals interactions & hydrophobic interactions

4. Quaternary structure: association of 2 or more polypeptides as they interact to form a functional multimeric protein

   • same as tertiary

Ch.4: How do enzymes catalyze (or speed up) chemical reactions?

They lower the activation energy required for the reaction to proceed (more molecules will have the energy needed to overcome the barrier).

Binding reactants to a surface and bringing them close together so their interaction will be favored.

Ch.4: What is an enzyme’s active site?

A cluster of amino acids formed by 3D folding (induced fit model) where specific substrates bind & catalysis takes place.

Ch.5: Describe the general DNA/RNA structure and the chemical bonding that forms them.

• DNA is a double helix

• RNA can form diverse higher-level structures - like tRNA cloverleaf (using hydrogen bonding)

• Hydrogen bonding between the bases of the 2 DNA strands to hold together the DNA double helix

Ch.6: Many lipids, such as phospholipids, are ________, meaning they have a polar end and a nonpolar end.

What is their main function?

amphipathic

Contribute greatly to membrane structure & fluidity (lipid bilayer)

Ch.7: What is the structure/function of the following organelles/cell components:

1. Nucleus

2. Ribosomes

3. Cytoskeleton

4. Plasma Membrane

5. ER (smooth and rough)

6. Golgi Apparatus

7. Mitochondria

1. Nucleus:

   • Structure: Nuclear envelope, nuclear pores, nucleolus, nucleoplasm, chromatin

   • Function: Information center of the eukaryotic cell (houses DNA)

2. Ribosomes:

   • Structure: Small & large subunit

   • Function: Synthesizes proteins

3. Cytoskeleton:

   • Structure: 3D array of interconnected proteinaceous structures (MTs, MFs, IFs) - in euk cells

   • Function: provide structure, perform mechanical functions, mediate transport

4. Plasma Membrane:

   • Structure: Lipid bilayer with membrane proteins (typically glycoproteins) on the external side of the membrane; lipid rafts

   • Function: Boundary & permeability barrier, organization & localization of functions (organelle membranes), transport processes, signal detection, cell-to-cell interactions

5. ER: Structure: ER cisternae are the physical sacs or tubules of the ER, and the continuous space within them where proteins & lipids are folded & processed is the ER lumen.

   1. Smooth ER:

      • Structure: No ribosomes, smooth tubular structures

      • Function: steroid/membrane lipid synthesis, drug detoxification, carbohydrate metabolism, calcium storage

   2. Rough ER:

      • Structure: studded w/ ribosomes, large flattened sheets

      • Function: site for protein synthesis, processing (glycosylation), folding, sorting, recognition & removal of misfolded proteins, & assembly of multimeric proteins

6. Golgi Apparatus:

   • Structure: Cis-Golgi Network (CGN): oriented towards ER, Medial cisternae, Trans-Golgi Network (TGN): oriented away from ER; golgi stacks

   • Functions: Processing, sorting, packaging, & trafficking of newly synthesized membrane & secretory proteins & lipids from the ER

7. Mitochondria:

   • Structure: Outer membrane, inner membrane, matrix, inter-membrane space, cristae (foldings that increase surface area)

   • Function: Site of aerobic respiration, generates energy

Ch.8: What are the 3 functions of membranes?

1. Separation of cell from environment

2. Separation of some cellular components from others

3. Concentration of certain enzymes in particular useful locations

Ch.8: Describe the plasma membrane structure in more detail.

• Fluid lipid bi-layer (hydrophilic heads facing aqueous environments, hydrophobic tails forming hydrophobic interior of bi-layer)

• Made from proteins (mostly glycoproteins) and lipids

• Asymmetric/non-homogenous

Ch.9: What are the differences between active and passive transport across membranes?

• Active transport requires energy, passive does not

• Passive can be facilitated (uses proteins), or simple diffusion

• Active moves molecules up their concentration gradient (from lower to higher concentration), Passive moves molecules down their gradient (from higher to lower concentration)

Ch.10: What are the 5 components of the endomembrane system and what do they do?

1. Endoplasmic reticulum: sites for protein synthesis, processing & sorting (rough ER), & lipid synthesis (smooth ER)

2. Golgi complex: membrane lipid & protein sorting, packaging, & trafficking

3. Endosomes: carry & sort material brought into cell

4. Lysosomes: digest ingested material & unneeded cell components

5. Vesicles: traffic material between the ER and Golgi and to and from both the plasma membrane and other membrane bound organelles

*All have double membranes

Ch.10: In the endomembrane system, where and how are materials such as proteins & lipids trafficked?

In vesicles:

1. To different compartments within the cell, or

2. To the plasma membrane (if secreted or embedded within the membrane, such as a receptor on the exterior of the cell)

Ch.11: * What do localization signals on proteins do?

What are some examples of these?

Dictate where proteins end up in a cell.

Ex:

• ER-Retention tag: prevent proteins from leaving ER

• Retrieval tag: Retrieves proteins from the Golgi back to the ER

• NLS (nuclear localization signal): allows protein to be shuttled into the nucleus

• NES (nuclear export signal): targets a protein for export out of the nucleus

Ch.14: Cytoskeleton components are ______ structures. They are continuously assembled & disassembled.

dynamic

Ch.14: What are the general functions of microtubules in cells?

• Provide structure, organization for cell

• Provide structure of flagella/cilia (for motility)

• Participate in Mitosis (spindle)

• Provide “roadway” to transport materials throughout the cell

Ch.14: What are the general functions of microfilaments in cells?

• Provide structure, shape, organization for cell (cell cortex beneath plasma membrane)

• Participate in cytokinesis of cell division

• Participate in cellular movement (e.g. crawling)

• Participate in contraction (in muscles)

Ch.15: Motor proteins physically bind to what?

They produce ________ work.

Cytoskeleton components (MTs, MFs)

Mechanical

Ch.15: Motor proteins play a role in what kinds of movement?

1. Transport of cargo along microtubules

2. Movement of flagella/cilia

3. Mitosis

4. Cellular crawling

5. Muscle cell contraction

Ch.17: What does it mean that the basic DNA structure is like “beads on a string”?

Nucleosomes: DNA (negatively-charged) wrapped around histone proteins (positively-charged) like beads on a string

Purpose: first step of condensing DNA so it fits in the cell & nucleus

Ch.17: What are the levels of chromatin compaction?

1. Nucleosome formation: DNA wound around histone octamers → chromatin

2. Chromatin forms thicker chromatin fiber (irregular, 3D zigzag structure), facilitated by H1 histone

3. Fibers fold into DNA loops stabilized by cohesin protein

4. Loops form heterochromatin

5. Heterochromatin condenses into chromosome

Ch.17: What does the nuclear envelope (double-membrane) separate?

Material contained within the nucleus from cytoplasmic material

Ch.17: Only certain molecules can pass through channels in the nuclear envelope called ______________.

nuclear pores

Ch.18: DNA replication is __________: one strand of each new DNA molecule is derived from the parent molecule, and the other strand is newly synthesized.

semi-conservative

Ch.18: Describe the general roles and direction of DNA polymerase in DNA replication.

• DNA polymerase synthesizes a complementary DNA strand from each parent strand during DNA replication

• Synthesis occurs in the 5’ to 3’ direction.

• DNA polymerase has proofreading capabilities to make sure each daughter cell receives close to a perfect copy of genome.

Ch.19: What are the general properties of the 5 stages of mitosis?

1. Prophase:

   • Begins when individual chromosomes become visible

   • Centrosomes (MTOCs) begin to migrate away from e/o

   • They act as nucleation sites for MTs (mitotic spindle)

     • Aster MTs form near each centrosome

   • Nucleolus starts disappearing

2. Prometaphase:

   • Begins with the fragmentation of the nuclear envelope

   • Centrosomes complete movement to opposite sides of the nucleus & form the spindle pole

   • The spindle MTs contact the condensed chromosomes & attach to the kinetochores in the centromere region

3. Metaphase:

   • Chromosomes are fully condensed & align at metaphase plate

     • Sister chromatids are actively tugged towards opposite poles to line them up

4. Anaphase:

   • Anaphase A: sister chromatids separate & chromosomes are pulled towards spindle poles by shortening of kinetochore MTs

   • Anaphase B: spindle poles themselves move away from e/o as polar MT’s lengthen and dissociate from each other

5. Telophase:

   • Begins when daughter chromosomes arrive at the poles of the spindle

   • Chromosomes uncoil into interphase chromatin

   • Nucleoli reappear, nuclear envelope starts to reform

Ch.19: What are the differences between the G1, S, G2, and M phases during mitosis?

Interphase: where most of cell’s time is spent

• G1 phase

  • Major decision is made about if cell should divide again: G1 checkpoint

  • G0: cell is arrested in G1 & waits for signal to move forward

  • Cells that exit cell cycle undergo terminal differentiation & never divide again.

• S phase

  • DNA is replicated

  • Centrosomes duplicate

  • Cell is now committed to divide or die

• G2 phase

  • Last chance for cell to opt out of mitosis if DNA is damaged: G2 checkpoint

    • Apoptosis if not allowed through

  • DNA begins to condense into sister chromatids for each chromosome

M phase: when cells divide

• Mitosis: nuclear division

• Cytokineses: cytoplasm division

Ch.20: * What is the purpose of various checkpoints in the cell cycle?

What are these checkpoints, and which cues are cells monitoring to determine whether or not to progress?

* For cells to ensure they are ready before progression to the next phase.

G1 Checkpoint (Restriction Point):

• Cells ask, “Are we ready to divide?”

  • Make sure cell size is large enough, there’s enough energy & nutrients, there’s growth factors, & there’s no DNA damage

G2 Checkpoint (G2-M Transition):

• Cells ask, “How’s our DNA?”

  • Make sure chromosomes have been replicated correctly & DNA isn’t damaged, check cell size

M Checkpoint (Metaphase-Anaphase Transition):

• Cells ask, “How’s our chromosome alignment?”

  • Make sure chromosomes are attached correctly to the spindle