Exam 1 Review

Question 1

What are some advantages and disadvantages of light microscopy as compared to electron microscopy?

Answer 1

In light microscopy, the cell will not die or be mutilated during the process, but there are convolution, resolution, and transparent cell issues.

Question 2

What are basic features of a cell?

Answer 2

1. cell membrane and cytosol
2. A way to store information (DNA)
3. A way to make components (ex. Ribosomes make protein)
4. A way to create fuel (ATP)
5. Means of copying information for reproduction

Question 3

What has been a driving force in our understanding of cells?

Answer 3

microscopy

Question 4

What are some ways features within a cell can be labeled in light microscopy?

Answer 4

stains/dyes, specific antibodies coupled to a fluorophore, genetic fusions between a gene encoding a protein of interest and a fluorescent protein

Question 5

How does fluorescence work? Be able to explain the following: fluorophore, excitation wavelength, emission wavelength

Answer 5

1) How does fluorescence work? Be able to explain the following: fluorophore, excitation wavelength, emission wavelength

First, a fluorophore is a fluorescent molecule that is fused with the DNA in a target cell. This will allow the cell to reflect a specific color light. All color light waves come from the light source. All colors are filtered through an excitatory filter and then the one color remaining is reflected by a beam splitting mirror except for the excitatory color (wavelength). This will light up fluorophores that react with that color. The sample reflects the wanted color onto the eyepiece, which is called the emission wavelength which is filtered through the emissions filter.

Question 6

What is “resolution” in the context of microscopy? What is the numerical resolution limit of light microscopy? In basic terms, what aspect of the nature of light causes this limitation?

Answer 6

Resolution is the ability to tell 2 objects apart from each other. The numerical limit is 200 nm. The diffraction limit of light causes this limitation.

Question 7

What are super-resolution light microscopy techniques designed for?

Answer 7

Super-resolution light microscopy techniques are designed to overcome the resolution limitations of light microscopy. Some approaches have increased the resolving power by a factor of 10 (20 nm)

Question 8

The diffracted light produces a “convoluted” signal can be…

Answer 8

deconvolved to reduce blurring effect

Question 9

What has evolved to form a fluorophore from an amino acid?

Answer 9

Fluorescent proteins like green fluorescent protein (GFP) have evolved to form a fluorophore from amino acids and can be molecularly modified to improve the signal.

Question 10

How can a fusion protein be used to study the localization of a protein in a living cell by fluorescence microscopy?

Answer 10

The DNA sequence for a fluorescent protein can be fused to the DNA sequence for another protein of interest. The modified gene is introduced into the cell and the location of the fusion protein can be observed and tracked.

Question 11

What does “confocal” fluorescence microscopy do differently than non-confocal fluorescence microscopy? What is an optical section?

Answer 11

Confocal microscopes exclude light above and below the focal plane, capturing “optical sections”*
Two features: 1. Laser excitation, 2. Pinhole aperture

Question 12

What is special about electron microscopy?

Answer 12

Resolution of electron microscopy is not limited by its wave-like nature (as its wavelength is much smaller than light). EM can achieve resolutions >1,000x higher than light microscopy.

Question 13

What would be different about the images of a cell when taken by TEM vs SEM?

Answer 13

In TEM, the image will be 2D and it will have been created by electrons that are passing through the sample to create the image.
In SEM, the image will be 3D and it will be the electrons reflecting off the sample.

Question 14

Role of the Nucleus

Answer 14

Information store of the cell. Dark spots are the subdomain where ribosomes are made.

Question 15

Role of the Rough ER

Answer 15

encloses lumen in membrane compartments. has docked ribosomes that move proteins through ER membrane. Produces most membrane proteins.

Question 16

Role of the Smooth ER

Answer 16

Smooth appearance and has no ribosomes. Synthesis of lipids & steroids. Regulation of calcium concentrations. Detoxification of drugs and poisons

Question 17

Role of the Golgi Appartatus

Answer 17

has flattened membrane-enclosed disks. Cis (close to ER) and trans (close to membrane) Golgi. It sends out proteins and lipids to the lysosomes, the membrane, and the vesicles. Abundant in plants. Has enzymes for breaking down proteins.

Question 18

Role of the mitochondria

Answer 18

generate ATP from sugar, fatty acids, and ketone bodies in the cytosol with aerobic respiration.

Question 19

Role of the lysosome

Answer 19

contain enzymes for degradation and recycling of biomolecules. it must be packaged because it is an oxidizing environment.

Question 20

Role of the peroxisome

Answer 20

contain hydrogen peroxide and are sites of certain chemical reactions such as inactivation of toxins. Peroxisomes are the sites in which yeast and plants break down fats. Animal cells also do this in their mitochondria.

Question 21

Role of the chloroplast

Answer 21

endosymbiosis as well.

Question 22

Role of transport vesicles

Answer 22

storage and movement around the cell

Question 23

Process of endocytosis

Answer 23

moving things into the cell

Question 24

Process of exocytosis

Answer 24

moving things out of the cell

Question 25

Explain how amyloid structures form and discuss some of the consequences of their improper folding and aggregation.

Answer 25

A group of proteins that form beta‑pleated sheets which are resistant to proteolysis. When amyloids are misfolded, they form aggregates of hundreds and more monomeric peptides into long fibers. These form amyloid plaques that accumulate in brain tissues and are toxic and Contribute to neurodegenerative disorders - Alzheimer’s and Huntington’s disease - Not contagious from one individual to another

Question 26

Describe the structure of a glycerol-containing phospholipid. What is the backbone and what three things does this attach to?

Answer 26

Fatty acid, glycerol, phosphate group, choline. the backbone is a hydro-carbon chain a part of the fatty acid.

Question 27

What is meant by the term “amphipathic?”

Answer 27

This means the molecule has a hydrophillic and a hydrophobic end

Question 28

What is endosymbiosis?

Answer 28

Early eukaryotes acquired their mitochondria through endocytosis of an aerobic bacteria, bring the more efficient aerobic metabolism to eukaryotes. Previously, they were strictly anaerobic and largely consumed prokaryotes for energy

Question 29

Actin Filaments Basics:

Answer 29

abundant in muscle cells where they are used in contraction

Question 30

Intermediate filaments

Answer 30

provide structural support in animal cells

Question 31

What is the relationship between the number of valence electrons and the number of covalent bonds an atom can form? What does this suggest for carbon, nitrogen and oxygen?

Answer 31

• Most stable/lowest energy state
• Valance shell filled
• Octet rule: H and He exceptions to the rule
  -Covalent bond: When atoms share electrons
  This suggests that C, N, and O bond well with many other molecules.

Question 32

Be able to describe what a covalent bond means, and how a single covalent bond differs from a double/triple covalent bond with respect to freedom of movement.

Answer 32

Covalent bonds are sharing of electrons, single bonds allow for movement and double/triple bonds allow for less movement.

Question 33

Why are some molecules polar while others are non-polar? Include the role of electronegativity.

Answer 33

Electrons are often shared unequally in covalent bonds, forming a polar molecule with partial charges.
Electronegativity: the degree to which an element tends to gain electrons and form negative ions in chemical reactions

when two electronegative atoms “share” a hydrogen atom. This is an attraction of opposite partial charges.

Question 34

What is an ionic bond? Do these form between atoms with partial or full charges?

Answer 34

• Know that water able to separate sodium and chloride ions to dissolve salt
• Ionic is a type of chemical bond where atoms are bonded together by the attraction between opposite charges. Bond between metal and non-metal

Question 35

How do Van der Waals interactions work? Dipole-dipole charges

Answer 35

weak interactions between nearby atoms, and are formed by slight induced dipoles (uneven charge) as their electrons repel one another. The only reason we know its happening is millions happen at a time.

Question 36

Understand the hierarchy of bond strength and its strength in water.

Answer 36

Covalent (377 kJ/mole) > ionic (12.6 kJ/mole) > hydrogen bonds (4.2 kJ/mole) > Van der Waals (.4 kJ/mole)

Question 37

What do amino acid side chains do?

Answer 37

the different amino acid side chains can contribute to the non-covalent interactions which occur within a protein to determine its final, most stable structure, as well as the interactions the protein can form with other proteins or molecules.

Question 38

Define a protein’s primary, secondary, tertiary, and quaternary structures.

Answer 38

Primary: amino acids joined by peptide bonds
Secondary: alfa helix or beta pleated sheets
Tertiary: Can find - α-Helix or β-pleated sheets or a combination of both
Quaternary: when 2 or more folded polypeptide chains (subunits) come together into one complex

Question 39

Explain how amyloid structures form and discuss some of the consequences of their improper folding and aggregation.

Answer 39

A group of proteins that form beta‑pleated sheets which are resistant to proteolysis. When amyloids are misfolded, they form aggregates of hundreds and more monomeric peptides into long fibers. These form amyloid plaques that accumulate in brain tissues and are toxic and Contribute to neurodegenerative disorders - Alzheimer’s and Huntington’s disease - Not contagious from one individual to another

Question 40

What is a prion? What are the consequences of the change from alpha-helices to beta-pleated sheets in prion structure?

Answer 40

A normal structural component of the nervous system Proteinatous material (without RNA or DNA) - yet contagious among individuals When misfolded they form a subclass of amyloids Normal prion has alpha-helical is converted into beta‑pleated isoform Amyloid fibers are formed by the beta‑sheet stabilization of the abnormally folded proteins. Causes Creutzfelt-Jakobs disorder (neurodegenerative)

Question 41

Explain how noncovalent interactions and specific protein conformation play in allowing proteins to recognize and bind specifically to their ligands.

Answer 41

protein conformation, acts for a slot that the ligand can fit into. Puzzle piece with analogy. Pretend the pieces has magnets on it as well.

Question 42

Explain how and why feedback control might be used to regulate enzyme activity.

Answer 42

feedback control allows regulation because it allows a product of a system loop around and halt production of that system by binding to a site on the protein that is not an active site.

Question 43

Explain how the binding of a ligand at a regulatory site can alter the activity of a protein or enzyme, allosteric regulation.

Answer 43

Allosteric regulation of a protein means that a ligand or other protein will bind to it and produce a subtle change in the proteins structure. * This commonly can switch an enzyme on or off, or change its catalytic rate.

Question 44

Explain the difference between a tumor suppressor and an oncogene in light of loss of heterozygosity and dominant negative effects

Answer 44

Tumor supressor: Its gene product suppresses tumorigenesis (slows down the cell cycle) * All you need is one good copy * If heterozygous (one copy is good and one is bad) - OK

Oncogene: Its gene product promotes cell division * All you need is one bad copy, it is dominant negative

Question 45

Describe the structure of a glycerol-containing phospholipid. What is the backbone and what three things does this attach to?

Answer 45

Fatty acid, glycerol, phosphate group, choline. the backbone is a hydro-carbon chain a part of the fatty acid.

Question 46

What is meant by the term “amphipathic?”

Answer 46

This means the molecule has a hydrophillic and a hydrophobic end

Question 47

What is the difference between saturated and unsaturated lipid tails?

Answer 47

Saturated lipids have single carbon bonds and unsaturated lipids have a double carbon bond which makes the bond ridged.