BIO 151 - EXAM 1

Van der Waals forces

Attractive/repulsive forces between molecules

Early experiment that shows biomolecules operate by the same rules of chemistry as nonliving systems.

Friedrich Wohler in 1828 synthesized urea (a compound found in and made in living organisms) using inorganic synthesis to show that biomolecules operate under the same chemical laws as non-living things.

Polysaccharides (purpose, types, bonds and examples)

Purpose:

1. Structural - provide structural support to cell

2. Storage - broken down for energy as needed

Types:

• Linked monosaccharides

• Linked amino sugars

Bonds - monosaccharides bond via dehydration reactions to form glycosidic linkages

Examples:

• Starch: storage polysaccharide, linked monosaccharide (branched)

• Chitin: structural polysaccharide, amino sugar (linear)

Polypeptides (bond type, formation and structure)

Polypeptides - linked amino acids via peptide bonds

Formed by dehydration reaction of C and N terminus of 2 amino acids

New AAs added to C terminus

Protein structures (1st, 2nd, 3rd and 4th)

Primary - linked sequence of amino acids via peptide bond (formed by dehydration reaction between C and N terminus of 2 AAs)

Secondary - alpha helices and beta sheets, determined by H-bonding interactions

• Alpha helix - each carbonyl group of an AA H-bonds with an aide group 4 subunits away

• Beta-sheet - h-bonds form between carbonyl and amide groups of different parts parts the polypeptides

Tertiary - folded 3-D shape of protein (single polypeptide linkage!!)

Quaternary - consists of several polypeptides, folded together in space

Denaturing of protein (def and experimental evidence that some proteins renature)

Process resulting in the breakdown of the 3-D folded shape of a protein.

Denaturing can be reversible or irreversible

Experiment:

Anfinsen experiment (Urea added - denatured, urea removed - re-folded to tertiary structure)

Hydrolysis reaction vs dehydration reaction

Hydrolysis - water consumed, breaks bond

Dehydration - water consumed, forms bond

Dehydration linkage (def and biology examples)

Water is taken away to form a bond

EX - formation of the following bonds:

• glycosidic linkage (bonds between monosaccharides)

• peptide bond (bonds between amino acids to form proteins)

• phosphodiester bond (bonds between nucleotides to form nucleic acids, 5’ phosphate and 3’ H/OH)

Nascent polypeptides

Mnemonic: “newborn” proteins

A growing chain of amino acids still being translated by the ribosome/mRNA (“off the assembly line”)

Nascent polypeptides begin to start taking their tertiary shape (folded shape) due to their primary structure (sequence of amino acids)

Molecular chaperones

Proteins that help mis-folded proteins re-fold into their needed shape. Usually requires energy (ATP) to do so.

Prions (def and ex)

Mis-folded proteins that cause other proteins to mis-fold, negatively affecting their purpose.

EX: cause PrP protein to fold into beta sheets and not their desired alpha-helix

• Also Mad cow disease

X-ray crystallography

Process to determine a proteins structure

Process:

• Crystallize a protein and point an X-ray on it

• Diffraction pattern analyzed to show protein structure

Nucleotide (Structure, bonds, base identifications)

Components: 5C sugar (Ribose - RNA, Deoxyribose - DNA) + 5’ phosphate group + nitrogenous base + 3’ OH/H (OH - RNA, H - DNA) group off 2’ C on 5C sugar

Bond: phosphodiester bond (between 5’ phosphate and 3’ OH/H)

Bases:

• Pyrimidines (1 ring): Cytosine, Thymine, Uracil

• Purine (2 rings): Guanine, Adenine

Mnemonic: pyrimidines CUT the pie & pure AGony

Nucleotides added in 5’ to 3’ direction

DNA shape (purpose, base pairing)

Alpha-helix

Base Pairings:

• Adenine and Thymine (2H bonds)

• Guanine and Cytosine (3 H bonds)

Hydrogen bonding and base stacking allows for stable shape

RNA shape

RNA has more complicated shape than DNA

EX: tRNA

Lipids (Structure, saturated vs unsaturated)

Structure: long hydrocarbon chains with a carboxyl group on one end

Packing:

• Saturated: all single bonds (less fluid as can pack closer together)

• Unsaturated: at least 1 double bond (more fluid as cannot pack as closely together)

Longer fatty acids → less fluidity

Trans vs Cis Fats

Trans vs Cis structures

Trans fats are worse for human health as can pack closer together

Low density lipoproteins (LDLs) vs high density lipoproteins (HDLs)

LDLs: triacylglycerols surrounded by phospholipids with cholesterol and other proteins, accumulates cholesterol in arteries (bad cholesterol - “low density” high volume → lots of fat volume bad)

• Chylomicrons - large diameter

HDLs: regulates LDL storage, promotes excretion

Cell Membrane (functions, structure, fluidity, cholesterol)

Functions: semi-permeable barrier, segregation of cellular components, transporting material in and out of cell, detecting signals, cell-cell and cell-matrix interactions

Structure: phospholipids - hydrophilic head & hydrophobic tail

Packing:

• Saturated: all single bonds (less fluid as can pack closer together)

• Unsaturated: at least 1 double bond (more fluid as cannot pack as closely together)

• Longer fatty acids → less fluidity (longer lipids: higher VDW forces: tighter packing)

Cholesterol is amphipathic, allowing it to stabilize the cell membrane from being too fluid or too rigid

Membrane Associated Proteins (Types, purpose)

Types:

• Transporter - transports ions/species across the cell membrane

• Receptor - receives signaling into the cell

• Enzymes - catalyzes reactions in the cell

• Adhesion - adhesizes protein to other surfaces

Integral membrane proteins - permanently embedded in cells

• Commonly alpha-helix structure

Peripheral membrane proteins - temporarily attach to cells

Diffusion Types

Simple diffusion: diffusion of small, non polar molecules across the cell membrane with the concentration gradient (high to low)

• Osmosis: simple diffusion but for water

Facilitated diffusion: diffusion of molecules, through a membrane protein, across the cell membrane with the concentration gradient (high to low)

• Cotrasnporters:

  • Symport: same way (EX: glucose/Na coupling)

  • Antiport: two different ways

Active diffusion: moving molecules across the cell membrane against the concentration gradient (low to high)

• Primary: uses ATP

• Secondary: uses electrochemical charge difference

Aquaporins (Purpose, experimental evidence)

Purpose: release water quickly from cell

Experimental evidence: oocytes (frog eggs) do not swell in water

Eukaryotes vs Prokaryotes

Eukaryotes:

• Membrane bound Nucleus

• Compartmentalizes organelles

Prokaryotes:

• No membrane bound nucleus

• Less organization of organelles

Lysosome (Purpose)

Lysosome - degrades unwanted/unneeded macromolecules in the cell

• Has proton pumps on it’s surface which keeping the inside of lysosomes acidic, allowing it to break down substances

Exocytosis vs Endocytosis (Purpose and steps)

Exocytosis - exports substances from Golgi Apparatus out of cell

• Steps:

  • Vesicles produced (budded from Golgi apparatus) → vesicles transported to needed placed via microtubules → vesicles dock at cell membrane → vesicle contents pushed out of cell and vesicle is recycled into cell membrane

• Lysosomes rely on this

Endocytosis - imports out of cell substances into the cell

• Steps:

  • Cell membrane pinches off to form vesicle around incoming contents → contents are moved to desired place

• Types:

  • Receptor mediated endocytosis - endocytosis dictated by a receptor binding to the cell

Endomembrane System (Organelles purpose of each) ** Draw out

Order from in to out:

Nuclear Envelope - double membrane surrounding nucleus

• Has complex channel of nuclear pores (small molecules can enter via diffusion & large molecules enter via facilitated diffusion)

Endoplasmic Reticulum - site of lipid and protein synthesis, continuous with nuclear envelope

• Rough ER - studded with ribosomes, protein synthesis

• Smooth ER - lipid synthesis

Golgi Apparatus - modifies proteins and lipids created in ER, sorts and ships proteins/lipids to different parts of cell (in vesicles) and synthesizes carbohydrates

• Structure: series of flattened sacs called “cisternae”

Lysosomes - special vesicles from GA which degrade damaged/unneeded macromolecules from the cell

Mitochondria (purpose, basic features)

Purpose - extracts energy from metabolites, place of ATP synthesis

Has double outer membraned, has own circular DNA, divides separately from rest of cell (endosymbiotic theory)

Chloroplast (purpose, basic features)

Purpose - place of photosynthesis (sun energy → carbon containing compounds for cellular respiration)

Has double outer membraned, has own circular DNA, divides separately from rest of cell (endosymbiotic theory)

Endosymbiotic theory (def and evidence)

Theory stating that the mitochondria and chloroplast were originally prokaryotic cells that were consumed by a larger cell, eventually turning into the organelles they are today over evolution.

Evidence - both mitochondria and chloroplast:

• Have two membranes (inner membrane resembles bacteria membrane)

• Has own circular DNA (circular DNA seen in bacteria)

• Have ribosomes that resemble bacterial ribosomes

• Multiply indecently from cell in binary fission process

• Endosymbiosis occurs today (with two eukaryotic cells)

Cytoskeletal polymers (types, subunits, purposes, molecular motors, dynamically assembled)

In order from smallest to largest

General purpose: provide internal structure to cell (all 3) and allows for transport in cell (actin and microtubules)

Types:

• Microfilament - involved in cytokinesis and allows cell to crawl

  • Subunit: actin monomer

• Intermediate filament - structural support

  • Subunit: protein subunit

• Microtubule - aids in chromosome segregation during cell division, allow for vesicle transport and beating of cilia and flagella

  • Subunit: tubulin dimers

  • Molecular motors:

    • Kinesin: moves vesicles - → + end on microtubules

    • Dynein: moves vesicles + → - end on microtubules

    • Myosin: aids in muscele contraction by walking on microfilaments

Dynamic assembly:

• Microtubules and microfilaments:

  • - end in middle of cell, + end towards outer edge of cell

  • Growth occurs more quickly at + end

Protein sorting (general idea, example)

Protein sorting - allows proteins to be sent desired part of cell

• Based on: specific sorting sequence (specific amino acid chain of peptide backbone), which is bound by mRNA binds to determine where goes

ER secreted proteins are either secreted in aqueous vesicles to be transferred out of ER or remain inserted in piece of vesicles and become inserted into a membrane

ER targeted signal sequence:

• Proteins meant for secretion from ER or to membrane follow these steps:

  • As protein is being translated by a ribosome, its sorting sequence determines where it goes.

  • The sorting sequence is read by an mRNA and directed towards the ER membrane.

  • At the ER membrane, the sorting sequence is bound by a signal recognition particle (SRP), pausing translation until the SRP receptor on the ER membrane is attached.

  • Translation finishes and protein is funneled into the ER lumen.

  • SRP dissociates

Transmembrane protein (what are they, general creation and movement to cell membrane)

Created in rough ER

Its orientation and embedded nature is preserved as it’s created, meaning that the part inside the transporting vesicle eventually becomes the part of the protein sticking out of the cell.

(Orientation: inside vesicle → outside cell membrane)

Affects of high and low temperatures of cell membrane

High temperature: more fluid

Low temperature: less fluid

Animals have evolved to counteract negative changes in its cell membrane fluidity due to temperature. (“homeoviscous adaptation”)

Cell adhesion systems

Cadherins - connect to other cell cadherins to create cell-to-cell adhesion

Integrins - connect cell to extracellular-matrix

Intercellular junctions (types, functions, example of importance)

Tight junction - permeability barrier, sealing sheet to restrict solute movement

Adherin junctions - have cadherins

Desomosomes - connect intermediate filaments to form webs between cells

Gap junctions - allow passages of small molecules between cells

Example of importance:

• Epidermolysis bulls simplex - disease from genetic mutation → makes skin fragile

Gibbs Free energy

ΔG = ΔH - TΔS

ΔG = amount of free energy available to do work

ΔH = amount of heat released from a reaction

ΔS = amount of disorder of a system

Induced fit (def and ex)

Process of an enzyme that when it binds a substrate, it holds the enzyme closer to it

EX: hexokinase - enzyme that catalyzes 1st step of glycolysis

Optima

Concept that certain enzymes are optimized/only work to act under certain conditions (temp, pH)

Enzymatic inhibition (types)

Competitive inhibition - when a substance can bind to the active site of an enzyme preventing it from binding to the substrate, preventing it’s action

Non-competitive inhibition - when a substance can bind to a non-active site of an enzyme changing it’s shape so that it can still bind to the substrate, but will have a reduced rate of reaction

Allosteric inhibition - any molecule binding at a site other than the active site and changing the enzyme's activity. Binding can activate(allosteric activators) or inhibit (allosteric inhibitors

Benefit of controlled stepwise processes

More precise, more efficient and creates more energy overall

Aerobic Cellular Respiration (Purpose, steps, locations, output **draw out locations)

Purpose: synthesize ATP from glucose

Steps:

1. Glycolysis: glucose → Pyrvuate (Cytosol)

2. Pyruvate Oxidation: pyruvate → Acetyl-CoA (Mitochondrial matrix)

3. Citric 0Acid Cycle: Acetyl-CoA → NADH reducing power (Mitochondrial matrix)

4. Oxidative Phosphorylation: NADH reducing power → ATP synthesis (Inner membrane and inner membrane space)

Output: 30-32 ATP

**check drawing

Glycolysis (purpose, steps, intermediate names, C#s and NADH/ATP #s)

Glycolysis - breakdown of glucose to pyruvate, 1st step of cellular respiration

Steps:

1. Investment: Glucose (6C) + 2ATP → Fructose 1,6-bisphosphate (6C) + 2ADP

2. Splitting: Fructose 6-bisphosphate (6C) → 2x Glyceraldehyde 3-Phosphate (3C)

3. Payoff: Glyceraldehyde 3-Phosphate (3C) → Pyruvate (3C) + 4ATP + 2NADH

Net gain: 2ATP & 2NADH

Pyruvate Oxidation (purpose, steps, C#s and NADH/ATP #s)

Purpose: pyruvate → Acteyl-CoA

Steps:

• 2x Pyruvate (2x from glycolysis) → 2CO2 + 2NADH + 2 Acetyl-CoA

Location: Mitochondrial matrix

Citric Acid Cycle (purpose, initial/final carbon steps in and out of cycle, main output)

Purpose: Acteyl-CoA → NADH for Oxidative Phosphorylation

Initial Step: Acteyl-CoA binds 2Cs to 4Cs of oxaloacetate

Final step: 1 CO2 leaves cycle and 1CO2 stays to carry on cycle

Per 1 Acetyl-CoA: 3 NADH, 1 FADH2, 1ATP, 2CO2

Electron Transport Chain (purpose, location, steps, final electron acceptor, ATP synthase details, output, experimental evidence of ATP synthase)

Purpose: reduced power → ATP

Location: inner membrane and inner membrane space

Steps:

• NADH donates electrons to Complex 1

• Coenzyme Q is a mobile electron carry to complex 2

• FADH2 donates electrons to complex 2

• Coenzyme Q is a mobile electron carry to complex 3

• Cytochrome C moves electrons to complex 4

• Complex 4 transfers electrons to final electron acceptor (O2), generating H2O

• All of these steps generate proton gradient, which flow through ATP synthase to generate ATP (oxidative phosphorylation) (26-28 ATP from single glucose)

ATP synthase (**draw out):

• Potential energy from proton gradient generates mechanical energy, rotating F0

• Rotation of F0 catalyzes F1 to generate ATP from ADP

Net output: 26-28 ATP per 1x glucose molecule

Experimental evidence of ATP synthase: fluorescent actin attached to F0, and witnessed to be rotating

Substrate Level Phosphorylation vs. Oxidative Phosphorylation

Substrate level phosphorylation - phosphorylation reaction of ADP → ATP

Oxidative phosphorylation - phosphorylation reaction driven by proton gradient to create ATP

Chemiosmosis (def and experimental evidence)

Use of a ion gradient to generate ATP

Experimental evidence: bioengineered bacterial proton pump to allow for active proton gradient and synthesis of ATP. Light powered by proton gradient attached to membrane and remained powered (showed active proton gradient powering ATP synthesis)

Anaerobic cellular respiration (types, differences from aerobic cellular respiration, steps, ** Draw out)

2 types:

• Lactic acid fermentation cycle:

  • Glucose + NAD+ + ADP→ Pyruvate +2ATP + NADH → NAD+ + Lactic acid → NAD+ for glucose reaction step → …

  • Reaction: Glucose + 2ADP + 2Pi ←→ 2 lactic acid + 2 ATP + 2H2O

• Ethanol fermentation cycle (in plants only):

  • Glucose + NAD+ + ADP→ Pyruvate +2ATP → Acetaldehyde + NADH → NAD+ + ethanol → NAD+ for glucose reaction step → …

  • Reaction: Glucose + 2ADP + 2Pi ←→ 2 ethanol + 2 ATP + 2H2O

Cyanide effect on ETC

Cyanide binds to Fe/Cu center of complex 4, preventing it from accepting electrons and breaking down ATP production of the ETC

Alternative pathway of cellular respiration used by some cancer cells (name, purpose, steps, output, **draw it out)

Name: Warburg Effect

Purpose: allows cells to divert as many resources as possible to cell division rather than aerobic respiration

Steps: Glucose → pyruvate → lactate

Output: 4 ATP

Where main categories of macromolecules enter cellular respiration

Carbohydrates: can be broken down into monosaccharides which can act as intermediates in glycolysis

Lipids: broken down and enter at: glycerol in glycolysis and fatty acid tails broken down and enter via Acetyl-CoA

Proteins: broken down to amino acids and enter as intermediates in Citric acid cycle

Photosynthesis (general process/steps, locations and overall reaction)

General process: turn sunlight + CO2 → glucose (for cellular respiration)

Steps:

• Light reactions: light energy → ATP + NADPH for Calvin cycle

  • Location: thylakoid

• Calvin cycle: ATP + NAPD + CO2 → glucose for cellular respiration

  • Location: Stroma

Overall reaction: Energy (sunlight) + 6CO2 + 6H2O → glucose (6C) + 6O2

Light Reactions of photosynthesis (steps, locations, **draw it out)

Steps:

• Light energy received in Photosystem 2.

• Central “special pair” of chlorophyll A’s become excited and strip electrons from H2O, also yielding O2.

• Electrons from this stage are moved through e- transport chain:

  • Linear:

    • Electrons carried from PS2 by Pq (Plastoquine) to cytochrome complex

    • Electrons carried from cytochrome complex by Pc (Plastocyanine) to PS1.

    • Electrons from PS1 carried by Fd to NADPH+ reductase to give NADPH for Calvin cycle

    • As this is happening protons accumulate inside the thylakoid space, to ATP synthase, creating ATP which is also sent to Calvin cycle

  • Cyclic:

    • electrons recycled from PS1 to Fd and pq to create more ATP and less NADPH to match exact demands of Calvin cycle and reduce light stress on plant

**Check drawing

Calvin Cycle (steps, locations, **draw it out)

Steps:

1. Carbon Fixation: CO2 attaches to Ribulose bisphosphate (RuBP) (5C), catalyzed by RUBISCO → 6C intermediate splits into 2× 3-phosphoglycerate (6 3-phosphoglycerate)

2. Reduction: Each 3-phosphoglycerate phosphorylated by 6 ATP and recede by 6 NADPH → 3C sugar glyceraldehyde-3-phosphate (6 G-3-P) and 1 G-3-P leaves to cellular respiration

3. Regeneration: 5 G-3-P + 3ATP → 3 5C RuBP (3RuBP )

Experimental evidence that the source of oxygen in photosynthesis is the splitting of water

2 test tubes were placed with one having O18 O2 and the other having O18 H2O with algae. The test tubes were left to undergo photosynthesis. The result was that the test tube with O18 H2O yielded glucose with O18.

Why leaves appear green?

They have chlorophylls in them which absorb red and blue light, reflecting green light.

Experimental evidence for main wavelengths absorbed by chloroplasts

A lens of algae was placed on a slide under different colored lights and underwent photosynthesis. The algae under the red and blue light proceed more O2, indicating there was more energy absorbed.

Special pair of chlorophylls in PS2 (general process, why it’s needed)

Special pair of chlorophylls (chlorophyll As) in PS2 absorb energy, exciting their electrons. This makes them a great electron donator, allowing them to oxidize water, releasing O2 and allowing the electron transport process to begin.

The oxygen in water is very electronegative. This means it holds not its electron very tightly. Therefore, to be able to oxidize the electrons of water, the special pair of chlorophyll, must become excited to a new energy level to be able to strip the electrons of the water molecule.

Why is PS1 needed when PS2 already absorbs energy?

The electrons excited in PS2 gradually lose their energy across the electron transport chain, meaning that by the time they hit PS1, they need to be re-excited by light energy in order to reduce NADP+ to NADPH for the Calvin cycle.

Z-scheme

Where are trioses incorporated into sugars and starch in higher plant cells?

Trioses from Calvin cycle have 2 fates:

1. Can be assembled as starch for storage in starch granules in the chloroplast

2. Exported to cytosol and assembled into sucrose for nutritional purposes

RUBISCO (purpose, its 2 reactions, inefficiency)

Purpose: catalyze carbon fixation reaction of RuBP and CO2 to yield 3-phosphoglycerate

• VERY SLOW!!

2 reactions:

• Carboxylase (good): yields 3-Phosphoglycerate

• Oxygenase (bad): yields phosphoglycolate

  • Creates need for photorespiration

Photorespiration (purpose, input and output, recovery %)

Purpose: Allows plant to recycle the Rubisco inefficient oxygenase produced product (phosphoglycolate) back into 3-Phosphoglycerate.

Inefficiency:

• Uses ATP (energy depleting)

• Input: O2 + phosphoglycolate | Output: CO2 + water + 3-Phosphoglycerate

For every 2 phosphoglycolate (4Cs) that enter process, 1 3-Phosphoglycerate molecules (3Cs) recovered: 75% recovery

C4 and CAM plants (purpose, general strategy)

Purpose: Evolved to reduce water waste due to photorespiration process. Photorespiration process requires stomata to be open, causing water lose - these plants minimize this as they exist is hot, drought-common areas.

C4: Spatially separates initial steps of carbon fixation from Calvin cycle process.

• Produces 4C compounds instead of 3-PG in carbon fixation process.

• 4C compounds transferred to bundle sheath cells and converted to pyruvate and CO2.

• CO2 levels remain high in bundle sheath cells and is used in Calvin cycle

CAM: time separation of initial steps of carbon fixation from Calvin cycle process

• CAM plants only keep their stomata open at night and convert CO2 into organic acids that are stored in vacuoles.

• Then during the day, CO2 can be released from the internal organic acids to be used in the Calvin cycle.

2 main events of cell division and what they accomplish

Mitosis - replication of genetic material

Cytokinesis - separation of cell in two cells

Main Phases of Cell Cycle (each/purpose)

G1 - metabolic growth and activity

S - metabolic growth, activity and DNA synthesis

G2 - metabolic growth, activity and preparation for cell division

M:

• Mitosis: distribution f chromosomes into 2 daughters nuclei

• Cytokinesis: division of cytoplasm, creating 2 daughter cells

Interphase: G1, S and G2

Chromosome (Parts/Termonology, replication process)

Chromosome - humans have 46 (23 pairs)

• Homologous chromosomes - 2 different chromosomes (one from each parent) that carry the same genes

Chromatids - 1 double helix strand of a double helix

• Sister chromatids - 2 identical copies of a replicated chromosome

Haploid - cells that carry one set of chromosomes (EX: gametes)

1. G1: Each chromosome is a single chromatid (a "line"), uncondensed.

2. S phase: DNA replicates, so each chromosome now has two sister chromatids joined at the centromere. Still uncondensed, and still the same number of chromosomes (46 in humans).

3. Prophase (mitosis): The replicated chromosomes condense, and now the X shape is visible.

4. Anaphase: Sister chromatids separate. Each is now its own chromosome (92 chromosomes briefly in the cell).

5. After cytokinesis: Two daughter cells, each with 46 single-chromatid chromosomes.

Mitosis (Purpose, Stages, **draw each and label)

Purpose - distribution of chromosomes into 2 daughter cells

Before:

• G2 of interphase

Stages (Mnemonic: please pay me and thank customers):

• Prophase

• Prometaphase

• Metaphase

• Anaphase

• Telophase

• Cytokinesis

Major cytoskeletal system vital for mitosis and cytokinesis

Microtubules

Anaphase mechanism (stages)

Stags:

• Cohesins degrade

• Sister chromatids seperate and move to opposite side of cell, via the movement of microtubules:

  • Kinetochore microtubules - are attached to sister chromatids and shorter to pull sister chromatids to opposite sides of the cell

  • Non-kinetochore microtubules - overlap with over non-kinetochore Mts and push each other away

  • Astral microtubules - pulled towards plasma membrane by other mechanism

Cytoplasmic cell cycle regulators (def, experimental evidence)

Def - specific signaling molecules that drive cell cycle progress and are present in the cytoplasm

Experimental evidence: 2 mammalian cells at different phases of the cell cycle were fused to form a single cell with 2 nuclei. Signals in cytoplasm allowed/caused both cells to enter same phase of cell cycle

Cyclin / Cyclin-dependent kinases (Cdks) (purpose, concentration, process, experimental evidence)

Purpose: promote the entry into the mitosis phase (M-phase promoting factor - MPF)

Cyclin: concentration fluctuates in cell, peaking at mitosis

CDK: concentration constant in cell

Process:

• Cyclin binds to CDK forming cyclin-CDK complex

• Cyclin-CDK complex binds to protein

• Protein promotes mitosis

• Cyclin degrades

Experimental evidence: radioactive methane added to sea urchin eggs, eggs fertilized and allowed to grow. Radioactive methane would be incorporated as proteins in cell-division were expressed. One protein had a cyclic expression pattern over time (cyclin)

Cell cycle checkpoints (purpose, types)

Purpose - ensure cell is ready to move onto next stage of cell division

Types:

• G1 checkpoint - end of G1

  • Checks if growth signal received. If so: continue on. If not: cell goes to G0

  • p53 - checks if DNA is damaged. If so, it becomes phosphorylated, which signals the turning on of genes to inhibit cell cycle to give cell time to repair DNA damage (“guardian of the genome”)

• G2 checkpoint - end of G2

  • Checks if all DNA is replicated

• Spindle-assembly checkpoint - before anaphase

  • Checks if all chromosome attached to the spindle

p53 (purpose)

At G1 checkpoint:

• Checks if DNA is damaged.

• If so, it phosphorylates it, turning on genes to inhibit cell cycle to give cell time to repair DNA damage

• (“guardian of the genome”)

Intracellular vs cell-surface receptors (purpose and modes of action)

Intracellular receptor:

• Small, non-polar molecule diffuses through cell membrane, attaches to the intracellular receptor, signaling a desired action

Cell-surface receptor:

• Polar signaling molecule cannot pass cell membrane → attaches to trasnmembrane protein to cause signal for desired action.

Signal transduction pathway (basic idea)

Way by which a signal is transmitted through the cell.

General idea: ligand binds to receptor → signal transduction pathway → response → signal termination

Oncogenes vs Tumor suppressors (def, examples)

Both are mutations!!

Oncogenes - results from mutations in the proto-oncogenes. Mutations cause hyperactive signaling.

• EX: Ras

Tumor suppressors - encode proteins that normal activities inhibit cell division. When a tumor suppressor gene is mutated, the “brakes” on cell division are removed.
- Ex: p53

Proto-oncogenes

Gene that promote cell division and tumor suppression genes that inhibit cell division

Eukaryotic chromatin is composed of which of the following macromolecules?

DNA and proteins

What is the name of the microtubule-organizing center found in animal cells as an identifiable structure present during all phases of the cell cycle?

Centrosome

Centrosome vs aster

Centrosome - microtubules organizing center (where the MTs come from in Mitosis)

Aster - star shaped cellular structure encompassing the centrosome and sprouting MTs in Mitosis (the spiky bits with the centrosome in the middle)

ATP (where is energy stored, bond)

Energy stored in phosphoanhydride bonds of last 2 phosphates

Inner mitochondrial membrane (structure relating to ATP synthase, terms)

Inner mitochondrial membrane is highly folded, increasing it’s surface area, allowing for more ATP synthase complexes to exist.

Cristae - infolding of inner membrane

Porins - outer membrane channels

Plant anatomy (terms - mesophyll, stomata, chloroplast, thylakoids, grand, chlorophyll, veins, stroma)

Mesophyll - interior issue of leaf (where chloroplasts are found)

Stomata - microscopic pores where CO2 and O2 enter/leave the plant from

Chloroplast - has envelope of two membranes surrounding a dense fluid called the stroma

Thylakoids - connected acs in the chloroplast, can be stacked in columns called grana

Chlorophyll - pigment that causes green color, found in thylakoid membranes

Veins - transport water from roots and export sugar to non photosynthetic parts of the plant

Calvin cycle experiment

Team added CO2 with radioactive 14CO2 to algae.

Assessed where 14CO2 1st appeared.

Appeared in trioses.

Concluded that CO2 is fixed into carbohydrates through production of 3-Carbon sugars.

Physical separation of cells (process of animals vs plants vs bacteria)

Animals - cytokinesis

• Cytokinesis occurs through process called “cleavage”

  • First sign of cleavage is appearance of cleavage furrow, caused by a contractile ring of microfilaments and myosin

Plants - assembly of cell wall splits daughter cells

• Cell wall constituted to separate daughter cells.

• Microtubules transport vesicles to the site where a new cell wall will form.

• Cell plate grows outwards from middle eventually splitting cell

Bacteria - binary fission

• As chromosome replicated, the plasma membrane pinches inward, diving cell in two

• Protein called FtsZ accumulates at fission site

• Mitochondria and chloroplasts also use this mechanism

Cell-cell signaling (types)

endocrine - long range signals, in blood stream

paracrine - short range signals, not in blood stream