Cells & Genes Capstone Review

Compiled using Cells & Genes study guides . BI498

What defines what a cell is?

• It’s a living unit of the body

• Carries out essential processes

• Have genetic info and make energy

• Smallest unit of life

The central dogma of molecular biology

DNA → RNA → Protein

Eukaryotes vs. Prokaryotes

Eukaryotes: Can be multicellular, have chromosomes, a membrane-bound nucleus, and membrane-bound organelles.

Prokaryotes: Unicellular, have plasmids for DNA, no true nucleus.

What do cells generally do?

• Make energy

• Protein synthesis

• Respiration

• Divide

• Phagocytosis

Endosymbiotic theory

posits that eukaryotic cells evolved when large prokaryotic cells engulfed smaller, energy-producing bacteria, which then lived inside the host and evolved into organelles like mitochondria

Function of the nucleus

DNA storage

Function of mitochondria

Power plant

Function of the rough endoplasmic reticulum

Protein synthesis

Function of the Golgi apparatus

Package, sort, traffic

Function of lysosomes

Acidic enzymes used for protein breakdown

The function of peroxisomes

oxidizing breakdown

Function of the nucleolus

rRNA & ribosome construction

How does the Golgi apparatus function?

protein/lipds enter the vesicles, then often get decorated before being sent back out.

Rank bonds by largest to smallest: Covalent, Ionic, H bond, Vander Waals.

1. Vander Waals

2. Ionic

3. H bond

4. Covalent

Rank bonds by strongest to weakest: Covalent, Ionic, H bond, Vander Waals.

1. Covalent

2. Ionic

3. Hydrogen

4. Vander Waals

What are the 4 macromolecules of a cell?

• Carbohydrates

• Proteins

• Lipids/Fats

• Nucleic acids

Sugars are defined by…

Carbon backbone and OH groups

Monosaccharides can combine into disaccharides via a…

Glycosidic bond

What kind of reactions allow the polymerization of biochemicals

Dehydration synthesis

True or False: fats are polar molecules

False. They are nonpolar

Two key traits of a fatty acid

1. Hydrophilic carboxylic acid head

2. Hydrophobic hydrocarbon tail

What distinguishes triacylglycerol from phospholipids?

Triacylglycerols have three fatty acid tails for energy storage and are hydrophobic, while phospholipids have two fatty acid tails and a phosphate group

The 4 components of an amino acid:

1. An amino group

2. A carboxyl

3. an alpha carbon

4. a side chain

What is the main role of enzymes?

To act as catalysts

Why are fatty acids important to the cell?

1. Insulation

2. Long-term energy

3. membrane formation

Chaperone proteins

Help polypeptide chains properly fold

The most common protein folding motif

alpha helix

Example of a structural protein

Actin

True or False: Enzymes are not consumed in a reaction

True

The “helpers” of enzymes

Cofactors

Transferases

Transfers a functional group. aka kinases

Ligase function

Join two molecules with covalent bonds

Describe G-Protein-GTP hydrolysis

Protein “on” with GTP → GTP hydrolysis, phosphate falls off → Protein has GDP and is inactive → GDP slowly falls off → New GTP steps in to activate protein!

What 3 general strategies does an enzyme use when it’s interacting with its

substrate to make a reaction happen?

1. Binds two substrates close together to ‘encourage’ them to bond

2. Rearranges charges

3. Strain the bonds (make it transition!)

Describe a phospholipid

Has a hydrophilic head composed of phosphate and glycerol. Also has a fatty acid tail that is hydrophobic.

Where are phospholipids made?

Inside the endoplasmic reticulum

How do membranes get more membrane?

The ER delivers vesicles

If you have a bunch of phospholipids in a tube of water, what will happen?

They will automatically form a bilayer.

What kind of micrograph is this?

Scanning Electric Microscopy

What kind of micrograph is this?

Confocal fluorescence microscopy

What kind of micrograph is this?

Transmission electron microscopy

What do scientists often use to solubilize membrane proteins?

Detergent

What gets through the cell membrane?

• Small hydrophobic molecules (O2, CO2)

• Small uncharged polar molecules (H2O, -ols)

How are ion channels often created?

Aqueous pore becomes bound by alpha helices

3 things ions can use to go against their gradient

1. Coupled transport

2. ATP-driven pump

3. Light driven pump

Name the highest concentrations of ions inside and outside the cell

Inside: K⁺

Outside: Cl^- & Na⁺

Na+ / K+ ATPase Pump function

Active transports 3 the Na+ against gradient, while bringing in 2 K+. Maintains cellular homeostasis.

Glycolysis ATP investment/net

Invest: 2

Net: 2

TCA ATP invest/net

Invest: 0 ATP

Net: 2 ATP

What is the A band on a sarcomere comprised of?

Overlapping myosin and actin

What is the I band of a sarcomere comprised of?

Only thin, actin filaments

What is the H zone on a sarcomere comprised of?

Thick, myosin filaments

Describe the steps leading up to muscle contraction.

1. An action potential moves down a motor neuron

2. Once at the terminal end, voltage-gated Ca+ ion channels open

3. The influx of Ca+ makes vesicles dump Acetylcholine

4. Ach is received by receptors on muscle cell membrane via the Ach receptor

5. Na+ rushes into the muscle cell through receptor channels

6. An action potential goes down the muscle membrane

7. Ryanodine receptors on the sarcoplasmic reticulum open

8. Ca+ rushes out of SR

9. Ca+ binds to troponin

10. Troponin leaves myosin & actin connections

11. ATP hydrolysis allows connection and power strokes on myosin heads

Describe what methylation and acetylation do to histones

• Methylation - tightens, no transcription

• Acetylation - loosens, transcription welcome

In the electron transport chain, what does complex I do?

• NADH dehydrogenase

• Receives 4 electrons from NADH, pumps out 4 H+ protons

In the electron transport chain, what does complex II do?

• Succinate Dehydrogenase

• Receives electrons from FADH2, oxidizes succinate to fumarate. Does not pump protons.

In the electron transport chain, what does complex III do?

• Cytochrome bc1 Complex

• Receives electrons from reduced ubiquinol, pumps 4 protons, and reduces cytochrome c

In the electron transport chain, what does complex IIII do?

• Cytochrome c Oxidase

• Receives electrons from cytochrome c, pumps 2 protons, and reduces oxygen to water

In the electron transport chain, what does complex IV do?

• ATP Synthase

• Uses proton gradient generated by the complexes (I, III, & IV) to synthesize ATP from ADP

• Whirling dervish!

Where do light-dependent reactions occur? What are their inputs & outputs?

• Location: Thylakoid membrane

• Input: light & H₂O

• Output: ATP, NADPH, and O2

What are the mobile carriers of the ETC?

Cytochrome c & ubiquinone

Where do light-independent reactions occur? What are their inputs & outputs?

• Location: Stroma

• Input: ATP, NADPH, & CO₂

• Output: Sugar! Aminos, fatty acids.

What types of signal transduction pathways exist?

1. Endocrine

2. Neuronal

3. Paracrine

4. Contact-dependent

Anterior pituitary gland

Secrete ‘starter hormones’

Adrenal gland

secretes stress hormones

Gonads

Secretes estrogen, testosterone

Paracrine function

Effectively function as local mediators

At what phase of life is contact dependent signaling most prevalent?

Embryonic development

What are the two main molecular on/off switches?

1. Phosphorylation/ dephosphorylation

2. G proteins (like GTP)

What is the direction of replication?

5’ to 3’

Who starts replication?

Helicase

Initiation of DNA Synthesis Requires a…

Primer

RNA polymerase (primase) function

synthesizes primers

Elongation of DNA strands is easier in what direction?

The leading strand (5’ to 3’)

What are the steps of DNA replication in a cell?

1. Single-Stranded Binding Proteins open the replication bubble

2. Helicase unzips

3. Primase makes primer

4. DNA polymerase III copies DNA

5. Replace RNA primers with DNA

6. Ligase seals gaps

What are the steps to DNA replication in a tube (PCR)?

1. Use heat to melt open the double helix

2. Add primers to the tube

3. Taq DNA polymerase III copies the DNA

If you wanted to actually replicate DNA, which DNA polymerase would you choose?

Polymerase III

What enzyme can be used to stop supercoiling?

DNA gyrase

True or false: DNA Polymerase III synthesizes only in the 5’ to 3’ direction

True

True or False: The leading strand is associated with Okazaki fragments

False! it’s the lagging strand

DNA Polymerase II function

Repairs mistakes and proofreads

True or False: RNA uses Uracil

True!

mRNA function

Codes for proteins

rRNA function

acts as a ribozyme to catalyze protein synthesis

tRNA function

transfers RNA amino acids onto growing peptide chain in translation

What 3 things must happen for transcription to be complete?

1. 7 methyl guanosine cap on 5’ end

2. Introns must be spliced out

3. Polyadenylate the 3’ end