Final Study Guide- Cumulative Material

Question 1

explain the major differences between eukaryotic and prokaryotic cells

Answer 1

-Eukaryotic cells found in animals, plants, fungi
-have organelles.

-prokaryotic cells only in bacteria and archaea
-do not have organelles or true nucleus

Question 2

Describe the functions of the major components of prokaryotic cells

Answer 2

-cell (cytoplasmic) membrane: thin sheet of lipid and protein that surrounds cytoplasm
-bacterial chromosome or nucleoid: condensed

DNA molecules; contains genetic info and codes for all proteins

-ribosomes; protein synthesis sites

-cytoplasm: water-based solution filling the cell

Question 3

Describe the difference between Gram-positive and Gram-negative cells

Answer 3

Gram Positive
-many thick layers of peptidoglycan cell wall
-lack an outer membrane
-has lipoteichoic and teichoic acid which increases wall flexibility

Gram Negative
-thin peptidoglycan cell wall
-has outer membrane with lipopolysaccharide
-has porin proteins

Question 4

Describe how eukaryotes evolved

Answer 4

Endosymbiotic hypothesis - identify the lines of evidence
[indicates origins of mitochondrion and chloroplast]
Mitochondria evolved from a Rickettsia
Chloroplast evolved from a cyanobacteria

-nucleus has a double membrane
-Mitochondria have their own cell membranes, just like a prokaryotic cell does.
-DNA — Each mitochondrion has its own circular DNA genome, like a bacteria’s genome, but much smaller.
-Reproduction — Mitochondria multiply by pinching in half — the same process as by bacteria; chloroplast also independently divided
-mitochondria and chloroplast act as separate entities & have their own circular DNA (similar to bacterial chromosomes)
-mitochondria and chloroplast have their own ribosomes

Question 5

Describe the functions of the common external structures found on eukaryotes.

Answer 5

Eukaryotic flagella
-10x larger than prok. Flagella.
-has a cell membrane
-9 pairs of microtubules surrounding 2 single microtubules (figure 5.4)
-whips back and forth
-find these in some protozoa, some algae (not in fungi).

Cilia
-shorter, hair-like (same as eukaryotic flagella, just numerous, covering entire cell)
-only found in one type of protozoa called ciliates & animal cells.
-movement

Glycolalyx layer (sticky surface layer)
-made of polysaccharides
-can be a slime layer or capsule
-for sticking, not movement. Prevents dehydration/water loss.

Cell wall [protozoa & animal cells do not have a cell wall]
Fx: structural support and shape
-algae cell walls- made of cellulose
-fungi cell walls- made of chitin

Cell membrane- selective permeability
Sterols, sugars, proteins, phospholipids
In animal cells- cholesterol
In fungal cells- ergosterols

Question 6

Describe the general structure of a virus, both inside and outside.

Answer 6

Outer:
Capsid, may have an envelope
Capsid made of capsomers; helical and icosahedral
With dna/rna in capsid = nucleocapsid
Can be naked (no envelope) or enveloped (surrounded by membrane)
~~~Most viruses have the envelope [made of phospholipids and embedded proteins] 13/20
~~Viral spikes can be inserted into the envelope, or be in the capsid in a naked virus [Viral spikes- responsible for attaching to a host cell- determined host range [which organisms can it affect] - determines tropism]]

inside:
Core - nucleic acid molecules either DNA or RNA, may contain matrix protein enzymes
nucleic acid types inside: dsDNA, ssDNA, dsRNA, ssRNA
ds= double-stranded, ss = single-stranded

Question 7

Describe the steps of viral replication.

Answer 7

Adsorption- using viral spikes, will attach to host cell; glycoprotein attachment

Penetration- being engulfed or [direct fusion only w/ enveloped viruses, envelope fuses with]

Uncoating- the dissolving of vesicle, envelope, and capsid

Synthesis- making all the parts of virus [capsomers, nucleic acid copying, spikes…]

Assembly- bringing all parts together, capsid forms from capsomers, nucleocapsid, spikes inserted in membrane or nucelocapsid

Release- virion buds off

Question 8

Describe what a prion is and what makes it so unique.

Answer 8

infectious protein that can replicate; associated with the slow virus spongiform encephalopathies of humans and animals

[a misfolded protein that can transmit its misfolded shape onto normal variants of the same protein. Prions are the causative agent of several transmissible and fatal neurodegenerative diseases in humans and other animals]

-lacking nucleic acids

BSE mad cow disease
-scrapie -CJD -vCJD -Kuru -fatal familial insomnia–

Question 9

What are the different ways microbes bring molecules into their cells? Which requires energy?

Answer 9

endocytosis - requires energy
group translocation - requires energy
ion pumps- requires energy
facilitated diffusion - no energy
osmosis - no energy

Question 10

Draw a population growth curve and explain what is happening at each step.

Answer 10

-label axis if asked to draw curve/graph
Bottom X axis - time
Side Y axis: living cells

4 phases
-Lag- looks like nothing is happening; cell is gearing up for cell division; it is copying its DNA which takes long time…DNA replication
-Log rhythmic/ log/ exponential— growth; optimal rate of growth will continue if there is nutrients & space…
-Stationary — growth levels out, division slowed, cell death is increasing; population remaining the same; running out of food and space
-Death – due to build-up of waste products (toxic, poop, salt…)— does not go to Zero

—doubling time is 30-60 minutes
-E coli is usually 30 minutes to reproduce

Question 11

Describe the ways scientists count the number of microorganisms in a sample.

Answer 11

Viable cell count: just counting living cells ; cannot figure out how many dead cells; accurate and cheap; can take at least a day
—CFU colony forming units

-turbidity- looking for cloudiness in a liquid culture = rough estimate how many dead and living cells there are

-spectrophotometer: passes light through culture/test tube; the more light reaches through, the less cloudy, and the less growth you have; relative scale of cloudiness to obtain doubling time; very inaccurate; dead and living cells.; immediate reading, $200

-Direct cell count- slide cytometer- more expensive-0- very accurate, immediate, but counting living and dead cells

-Flow cytometer– research labs; too expensive for hospitals; detect how big and dense cell is…laser beams shines on a single cell dropping out of a narrow tube..costs millions of dollars, extremely precise; differentiate between living and dead cells and different cell types

Question 12

What are the inputs and outputs of glycolysis?

Answer 12

Input: 1 glucose and 2 ATP [ATP not required to be included… but you can]
Output: 2 ATP, 2 NADH, 2 pyruvic acids

Question 13

What are the inputs and outputs of the TCA cycle?

Answer 13

Input: 1 ACETYL-COA per TCA cycle; 2 Acetyl CoA per glucose
Output: 4 CO2, 6 NADH, 2 ATP, 2 FADH2 PER GLUCOSE (cut in half for per turn)

Question 14

What are the inputs and outputs of the respiratory chain?

Answer 14

Input: 10 NADH, 2 FADH2, 6 O2 (oxygen gas molecules)
Outputs: 34 ATP, 6 H2O

Question 15

What are the inputs and outputs of fermentation?

Answer 15

Input: 1 glucose
Output: ethanol & Co2 OR lactic acid, … 2 ATP

Question 16

Where does each step of cellular respiration take place in the prokaryotic cell?

Answer 16

Glycolysis- cytoplasm
TCA- cytoplasm
Electron transport- plasma membrane

Question 17

Where does each step of cellular respiration take place in the eukaryotic cell?

Answer 17

Glycolysis- cytoplasm
TCA- mitochondrial matrix
Electron transport- mitochondrion cristae

Question 18

What is the purpose of ATP synthase? How does it function and what does it need to function?

Answer 18

catalyzes the synthesis of ATP from ADP and phosphate

-it needs proton motive force to function, uses proton motive force and spins; creates covalent bond between ADP and inorganic phosphate

Question 19

What does it mean to say DNA is a charged, polar molecule whose strands are anti-parallel and replicates in a “semi-conservative” fashion?

Answer 19

2 nucleic strands attached to each other by hydrogen bonds; basic acid is a nucleotide that consists of a pentose sugar, a phosphate, and a nitrogenous base
Antiparallel because strands are growing in opposite directions

According to the semiconservative model, after one round of replication, every new DNA double helix would be a hybrid that consisted of one strand of old DNA bound to one strand of newly synthesized DNA.

Question 20

Name the six enzymes involved in DNA replication and describe, in order, what their roles are.

Answer 20

Gyrase: uncoiling supercoil + supercoiling

Helicase: unzipping the DNA helix

Primase: synthesizing an RNA primer

DNA Polymerase III: adding bases to the new DNA chain, proofreading the chain for mistakes

DNA polymerase I: removing RNA primers, replacing gaps between Okazaki fragments with correct nucleotides, repairing mismatched bases

Ligase: final binding of nicks in DNA during synthesis ; phosphodiester bonds

Question 21

Describe the process of translation for prokaryotic organisms.

Answer 21

Take mRNA, using tools of ribosomes and tRNA to make proteins

-Initiation- small subunit binds, initiator tRNA, large subunit; have a shine-delgarno sequence found throughout the prok. mRNA.; several recipes/genes
-Elongation- next tRNA enters A site ; has anticodon that pairs with codon after start codon; ribozyme grabs first amino acid in P site or peptide and forms peptide bond to amino acid in A site; translocation: mRNA pulled thru by 3 nucleotides
termination
-Protein folding- this happens during elongation; happens as protein is being made; if protein loses its structure later, it can’t regain structure bc its being folded as it is being made
-Protein processing- changing protein to make it function- such as by adding functional groups to make enzymes function better, also maybe adding a cofactor like metal ions/vitamins, or in the case of insulin, needs to be cut and pieces removed to be functional

Question 22

How does the entire process of transcription and translation differ between prokaryotes and eukaryotes?

Answer 22

Euk- only 1 gene per RNA; occurs in nucleus

Prok- several recipes per RNA; occurs in cytoplasm

Question 23

Describe the five different types of point mutations and explain how they differ in the effects on the organism.

Answer 23

Wild-type (nonmutated) sequence [normal sequence found in most organisms] [THE BIG BAD CAT ATE THE FAT RED CAT]
Substitution mutation

Missense- usually, tolerated and fine.. 1 nucleotide change/ Small change; may or may not make huge impact on protein = [THE BIG MAD CAT ATE THE FAT RED BUG]

Nonsense- converts codon to stop codon; premature termination of protein synthesis; usually severe effect; [THE BIG BAD XXX (STOP)]

Inversion mutation- adjacent letters exchange places; can result in significant changes

Frameshift mutation– extreme effects; every amino acid after this is very impacted
-Insertion- addition of letter
-Deletion- deletion of letter

Reverse mutation- happens in mutants that change the mutated sequence back to wild-type

Silent mutation- change in nucleotide from one to another nucleotide that does not affect the primary amino acid sequence— no significant negative effect

Worst mutations- frameshift & nonsense
Best- silent (no bad effects)

Question 24

Describe three methods other than sexual reproduction whereby organisms recombine their genetic sequences.

Answer 24

Conjugation- using protein bridge (pilus); sending a plasmid from one cell to another; plasmids are advantageous genes ex) metal resistance, toxin/enzyme production, iron uptake…

Transformation- done by competent cells; taking naked DNA from any source and trying it out; most cells are not naturally competent.

Transduction- involving viruses; accidental;

Transposons- happens in all organisms including our cells… individual DNA pieces that move around on their own inside our cells (some can replicate) they are single, jumping genes. Can move from 1 location to another, sometimes copy themselves, or escape and leave cell… = Mutation or change in DNA = genetic evolution

Question 25

Explain the process and purpose of PCR and describe how polymerase chain reaction is similar to and different from the Sanger method of DNA sequencing reactions.

Answer 25

PCR (Polymerase Chain Reaction) is a lab technique that makes many copies of a specific DNA segment. It involves three steps: denaturation (separating DNA strands), annealing (binding DNA primers), and extension (synthesizing new DNA strands). These steps are repeated in cycles to amplify the targeted DNA. PCR is fast and produces a large amount of DNA.

Sanger sequencing determines the order of nucleotides in a DNA molecule. It uses chain-terminating nucleotides and a different DNA polymerase to halt DNA synthesis at specific positions. Sanger sequencing is slower and requires separate reactions for each DNA fragment being sequenced.

In summary, PCR amplifies DNA, while Sanger sequencing determines DNA sequence. PCR is quick and makes many copies, while Sanger sequencing is slower and determines the order of nucleotides in a DNA molecule.

Question 26

What is the difference in ionizing versus non-ionizing radiation? Give examples of each and explain how each would act differently on a microorganism.

Answer 26

Ionizing: electromagnetic waves (x-ray or gamma) or high-speed electrons that cause dislodgement of electrons on target molecules, which creates ions; can break covalent bonds;
MOA=lot of energy= can slice thru DNA = large scale DNA mutations [foods like raspberries can be treated with radiation]
~if DNA bonds broken, can kill / greatly impact cell
-can penetrate liquids
-used by food industry, requires labeling

Non ionizing: A type of low-energy radiation that does not have enough energy to remove an electron (negative particle) from an atom or molecule.
– creating new, unusual covalent bonds between thymines and cytosines & produces deletion mutations on DNA
~visible, infrared, and ultraviolet light; microwaves; radio waves; and radiofrequency energy from cell phones.

Question 27

MOA of soap:

Answer 27

lifting and suspending oil, dirt, and debris from hands so they can be rinsed down the drain

Question 28

MOA of bleach:

Answer 28

breaking disulfide bonds in proteins

Question 29

MOA of alcohol:

Answer 29

alcohols of over 50% concentration dissolve membrane lipids and denature proteins by coagulation [protein denaturation with water]

Question 30

MOA of hydrogen peroxide:

Answer 30

forms hydroxyl free radicals; oxidizes other molecules in the cell, forming radicals; does this with any molecule (will attack components like DNA, RNA, proteins, cell membranes…); toxic to endospores at high concentrations

Question 31

MOA of antiviral drugs:

Answer 31

3 MOAs depending on type:
-Inhibiting viral adsorption
-Inhibit the nucleic acid synthesis
-inhibiting proper release

Question 32

MOA of penicillin and cephalosporin:

Answer 32

block cross-linking of peptidoglycan.

Question 33

MOA of sulfanomides:

Answer 33

block folic acid synthesis.

Question 34

Describe the major ways in which bacteria can defend themselves from antibiotics.

Answer 34

Drug inactivation- R gene makes a protein that is an enzyme that destroys antibiotic (breaks covalent bonds) EX) penecillinase, betalactamase

Decreasing cell permeability; R gene makes a protein that keeps antibiotic out

Activation of drug pumps- R gene produces a protein that pumps antibiotic out of the cell using ATP [MDR multi drug resistant pumps]

Change in drug binding site on target [binding site on target [ribosome] is altered, so drug has no effect]

Use of alternative metabolic pathways

Question 35

Describe the functions of the common internal structures found in eukaryotes.

Answer 35

Nucleus- has chromosomal DNA; houses and protects DNA; It is MEMBRANE BOUND by the nuclear envelope.
~Double membrane layer- allow molecules to move across using nuclear pores (large protein pumps in envelope, allows large molecules to move like RNA)
-Nucleolus (Granular mass of RNA; dark staining region inside nucleus; dark color is result of so many molecules, very dense; makes ribosomes).
-Chromatin: DNA (in the form of chromosomes) wrapped by histones (inside the nucleus)

Endoplasmic reticulum (ER) - extensions of nuclear envelope, but just made of 1 membrane layer; factories
Rough ER- Has ribosomes; makes proteins in here
Smooth ER- Makes fats, lipids.

Golgi apparatus
-hangs out next to rough ER, but separate organelle
-hollow stack of pancakes
-receives transport vesicles from rough ER (fuses with golgi and dumps synthesized proteins into golgi)

Lysosome
-fx: destruction/digestion/breaking down; contains harsh enzymes
-breaks down food, bacteria in cell, viruses & damaged tissue

Vacuoles
-storage organelles; food, water, toxins, waste, bacteria

Mitochondria
-energy-converting organelle [does not MAKE energy, converts]
-Fats and sugars > ATP (energy currency of cell for doing most tasks)
2 membranes: folds in inner membrane = cristae
-fluid-filled space inside inner membrane in the mitochondrial matrix
-outer membrane has more of a euk. Protein chem structure
-where aerobic cellular respiration occurs

Chloroplast
-energy conversion; more complex; converts solar/light/photon energy to chemical energy in form of sugars; photosynthesis; produces oxygen gas as toxic waste byproduct
-only algae and plants have this.
-3 membranes : outer membrane (euk) , inner membrane (prok,), thylakoid membrane (very similar to thylakoid in cyanobacteria)
-contains DNA in circular structure in stroma (fluid filled space inside the chloroplast) also has prokaryotic ribosomes.
-has Granum- gives pigment/color

Ribosomes
-NOT an organelle, bc not surrounded by membrane
-Ribosome = 80s; small subunit = 40s; large subunit = 60s
-can be attached to rough ER when assembles, and subunits only floating in cytoplasm
-made of ribosomal proteins/RNA

Cytoskeleton
-not an organelle, but important structure
-made of proteins; involved in cellular movement & cell divison
-3 components
a)microfilaments- made of small actin filaments ; permeate entire cell; actin microfilaments can move cytoplasm and organelles by moving cell and cell membrane(during cell division)
b)microtubules: made of tubulin, small hollow tubes (largest structure here) go thru entire cell and membrane and cytoplasm; involved in cell movement (like a train track) and division [divison- spindle fibers, pull DNA apart in anaphase) (involved w movement of flagella/cilia).
c)intermediate filaments- support, shape..