Mech 483 Quiz 1

Front 1

What is the basic unit of life?

What do all these units of life have in common?

Back 1

Cells

They share a similar chemistry

Front 2

How is the flow of information described for the basic units of life?

Back 2

The Central Dogma

Front 3

Cells reproduce by duplicating their DNA and then dividing.

Briefly explain how this enables different species to retain their distinct characteristics, and the role played by mutations (copying errors in cell division) for the adaptability and continued survival of the species.

Back 3

• DNA duplication happens with very small error rates, so daughter cells are typicallyidentical copies of the parent cell and germ cells are combined well enough that distinct characteristics are conserved.
• Mutations create offspring that are sometimes better able to survive a harsh change in theenvironment than their peers. This enables selected members of the species to survive, though withslightly altered (adaptations) genetic material.
  

Front 4

Define mutations

Back 4

occasional defects in the genetic information passed on

Front 5

Describe evolution

Back 5

Evolution is the record of adaptive survival or "survival of the fittest".

Front 6

Label the organelles

Back 6

1. Mitochondrion

2. Peroxisome

3. Golgi apparatus

4. Endoplasmic reticulum (ER)

5. Vesicle

6. Nuclear envelope

7. Lysosome

8. Rough ER

9. Plasma membrane

10. Nucleolus

Front 7

What is cytosol and what is it's function?

Back 7

• the part of the cytoplasm not contained within intracellular membranes (aka not enclosed inside membrane-bound organelles).
  
• in most cells, it's the largest single compartment
  
• contains enough large & small molecules that it acts more like a gel than a fluid
  
• site of many chemical reactions like the creation of proteins by ribosomes
  

Front 8

What is the plasma membrane?

Back 8

the protein-containing lipid bilayer that surrounds aliving cell

Front 9

Describe the nucleus and nuclear envelope. What are their functions?

Back 9

nucleus: is enclosed by the nuclear envelope and contains DNA

nuclear envelope: double membrane surrounding the nucleus; consists of inner & outer envelope, perforated by pores

Front 10

Describe a mitochondrion and its function.

What is the probable origin of the mitochondrion? Why?

Back 10

Mitochondria generate usable energy from food to power the cell (ATP production aka cellular respiration).

• present in essentially all eukaryotes
  
• enclosed in two membranes, the inner being all folded up
  

Origin: probably an engulfed bacteria that had a symbiotic relationship with a modern-day eukaryotic ancestor cell. This theory is suggested by the fact that they reproduce themselves by dividing in two within the cell.

Front 11

What are chloroplasts?

Back 11

• large green organelles
• found only in the cellsof plants and algae
  
• more complex than mitochondria
• contain chlorophyll
• carry out photosynthesis
• same theorized origin as mitochondria

Front 12

Describe the endoplasmic reticulum.

What is the smooth endoplasmic reticulum's function?

What is the rough endoplasmic reticulum's function?

Back 12

ER: irregular maze of interconnected spaces enclosed by a membrane; much larger for cells that specifically produce proteins.

It is the site where most cellular membrane components and export goods are made.

SER:

RER:

Front 13

What is a Golgi apparatus? Describe it's function.

Back 13

• Stacks of flattened membrane-enclosed sacs (yum)
  
• modifies & packages molecules made in the ER for export from the cell or transport w/in the cell

Front 14

What is the cytoskeleton?

Back 14

The cytoskeleton is a network of protein filaments that helps define cellular shape and are responsible for directed cell movements.

Three types of filaments:

• actin filaments (thinnest type)
• microtubules (thickest type)
• intermediate filaments

Front 15

What is the function of a lysosome?

Back 15

Small, irregularly shaped organelles in whichintracellular digestion occurs:

• releases nutrients from ingested food particles
• breaks down unwanted molecules
• either for intracellular recycling or excretion from the cell

Front 16

What is the function of a peroxisome?

Back 16

Peroxisomes are small, membrane-enclosed vesicles that provide a safeenvironment for a variety of reactions in which hydrogen peroxide isused to inactivate toxic molecules.

Front 17

What is the function of a vesicle?

Back 17

transport vesicles ferry materials between one membrane-enclosed organelle and another

Front 18

Describe the nucleolus and give its function.

Back 18

structure within the nucleus where ribosomalRNA is transcribed and ribosomal subunits areassembled

Front 19

What is the difference between prokaryotic and eukaryotic cells?

Back 19

Prokaryotes lack a distinct nucleus because they don't have a nuclear envelope, so the DNA free floats within the cell.

Front 20

What is a nucleic acid?

Back 20

Macromolecule that consists of a chain of nucleotidesjoined together by phosphodiester bonds; RNA orDNA.

Front 21

How do mitochondria and chloroplasts resemble bacteria?

What's an interesting note about mitochondrion?

Back 21

both resemble bacteria in many ways, for ex. they containtheir own DNA and reproduce by dividing in two.

interesting fact: mitochondrion containDNA. Unlike nuclear DNA, is not changed by the fusion of DNA from parent cells, and is passed onfrom the mother -hence it allows tracking of mother-daughter lineages and migration patterns. Alsothis presents the possibility of 3 parent embryos.

Front 22

What are tensegrity structures?

Back 22

those in which tensile and compressive forces are distributed andbalanced within the structure (no bending moment)

Front 23

What are some advantages of tensegrity use in man-made structures.

Back 23

• typically support a high load per unit mass of structure
• local loading causes a response (forcedistribution) throughout the structure
• failure modes are restricted to yielding in tension andbuckling in compression
  

Front 24

Give some man-made examples (2) and some biological examples (4) of tensegrity structures.

Back 24

man-made structures:

• geodesic domes
• the Needle Tower
  biological structures:
• bones in compression
• muscles in tension
• cytoskeleton and extra-cellularmatrix
• protein molecules

Front 25

List the three types of bonds described in class (& be able to draw them).

What are some biological examples of where these bonds form?

Back 25

Covalent: joining subunits together to form macromolecules

Ionic: in proteins, joining subunits together to form tertiary proteins

Hydrogen: in phospholipids along the "tails" causing them to be hydrophobic

Front 26

Give some prefixes, suffixes, and words that suggest the presence of sugars or sugar groups in larger molecules.

Back 26

• (Glyco)proteins
• (glycol)gen
• rib(ose)
• fruct(ose)
• (glyc)erin
• poly(saccharide)
• peptide(glycan)
  

Front 27

Which sugar molecules act as high-tensile strength fibre?

Back 27

Cellulose

Front 28

Which sugar molecules act as a hard exoskeleton?

Back 28

Chitin

Front 29

Which sugar molecules act as a long-term storage of energy?

Back 29

Glycogen, starch

Front 30

Which sugar molecules act as signalling and recognition labels?

Back 30

Glycolipids, glycoproteins

Front 31

Why is it more difficult to determine the arrangement of sugars in a polysaccharide than thenucleotide sequence in a DNA molecule?

Back 31

The chemistry of polysaccharide synthesis causes many possible configurations of molecules: *

• highly branched molecules
• can form bonds at different points in their ring structures

Also until recently, there was no standardization for namingpolysaccharides due to the diversity of sugars (unlike DNA which is made up of 4 different types ofnucleotides).

* In other words a monosaccharide has multiple free hydroxyl groups available to link to another monosaccharide that allow branching of molecules.

Front 32

What's special about an amino acid at pH = 7.0?

Back 32

They can become ionized. (add more )

Front 33

What causes the structural (as opposed to electrical) polarity of a polypeptide chain?

Back 33

The linking nature of peptides to form a polypeptide result in a C-terminus (carboxyl group) and an N-terminus (amino group).

They link together such that there is always a C-terminus on one end and an N-terminus on the other end.

Front 34

Name four types of forces or bonds (non-covalent) that are important for stable proteinconformation in cells.

Back 34

• Hydrogen bonds
• electrostatic bonds
• van der Waals attraction
• hydrophobic forces (ionic bonds... is this the same thing?)

Front 35

What is the type of bond used to “staple” and maintain the conformation ofproteins that must function outside the regulated environment of the cell?

Back 35

Disulfide bond

Front 36

Define primary structure for proteins.

Cite one example of this structure in a suitable protein.

Back 36

The primary structure is the sequence of residues in the polypeptide chain.

aka: the amino acid sequence.

Example: insulin

Front 37

Define secondary structure for proteins.

How & where is it formed? What are the most common shapes?

Cite one example of this structure in a suitable protein.

Back 37

Secondary structure is a local, regularly occurring structure in proteins

• mainly formed throughhydrogen bonds between backbone atoms
• includes alpha helices and beta pleated sheets.
  

Example: fibroin

Front 38

Define tertiary structure for proteins.

What bonds does it include?

Cite one example of this structure in a suitable protein.

Back 38

• The packing of alpha-helices, beta-sheets and random coils with respect toeach other on the level of one whole polypeptide chain.
• includes non-repeating interactions likeionic bonds or disulfide bridges
  

Example: the coiled coil in theenzyme triosephosphateisomerase (hahahaha good luck remembering that)

Front 39

Define quaternary structure for proteins.

What bonds does it include?

Cite one example of this structure in a suitable protein.

Back 39

Quaternary structure isa multi-complex of multiple polypeptide chains; an example is hemoglobin.

• exists only if there is 2+ polypeptide chains present in a complexprotein.
• describes the spatial organization of the chains
  

Example: hemoglobin

Front 40

What is a coiled coil?

Back 40

• tertiary structure protein
  
• made up of intertwined α-helices which wrap around each other due to differences inpolarity in the amino acid sequence
  

Front 41

What is the difference between protein domains and protein subunits?

Give examples!

Back 41

Protein domains: a segment of a polypeptide chain that can fold independentlyinto a compact, stable structure and can contain typically 40-350amino acids in a secondary structure.

It is a modular subunit from which larger proteins are constructed.

Example: The bacterial protein called cataboliteactivator protein has two domains.

Protein subunits: Asubunit is a protein itself, and usually combines with other proteins whichbecome subunits when they form a large multi-protein complex.

They are single protein chains in a multiple chain complex. Each single chain is called a subunit and each subunit may have multiple domains.

Hemoglobin is anexample.

Front 42

What are protein families?

Are antibodies a protein family?

Are motor proteins a protein family?

Back 42

• A group of proteins where each member closely resembles theother in terms of their amino acid sequence and 3D conformation (shape).
• Antibodies are a proteinfamily because they have a similar shape and a close amino acid sequence.
• Motorproteins are not a family as they vary greatly in shape and mechanism.
  

Front 43

What is an antibody?

Back 43

Proteins produced by the immune system in response to foreign molecules.

• Y-shaped molecules with two identical binding sites complementary to a small portionof the antigen.
• All have the Y-shape conformation; small amino acidchanges in the binding sites create the wide variety of antibodies.
  

Front 44

What is a motor protein?

Back 44

Generate the forces responsible for muscle contraction & the dramaticmovements of cells; their major function is to move other molecules.

• conformational changes arepowered by the hydrolysis of ATP.
• Have varying structures, for example Kinesins, Dyneins, & Myosins have different structures.
• do not fit the definition of a proteinfamily.
  

Front 45

What makes the ubiquity of the α-helix and β-sheet structures possible?

Back 45

Both formed by H-bonds between N-H and C=O groups inthe polypeptide backbone (which is a common repetitive structure),

therefore the side chains of the amino acids areindependent of the structure’s formation.

This means that a protein can easilytake on these structures regardless of it’s amino acid sequence.

Front 46

The α-helix shown has a pitch of0.54nm. What leads to a fixed value for the pitch?

Why doesn't the helix collapse on itself under the tensile force of the H-bonds?

Is this an exampleof a tensegrity structure?

Back 46

The C-N bond in the polypeptide backbone inhibits rotation, making the helix serve as a torsionalspring where the spring force balances the force due to the regularly spaced H-bonds between thesame backbone atoms, leading to a fixed pitch.

Tensegrity?? Yes? or No?

Front 47

Giveone example of fibrous proteins.

How does their structure enable function?

Back 47

Collagen fibril; α-keratin

(length enables it to serve as structural protein)

Front 48

Give one example of sheet-like proteins.

How does their structure enable function?

Back 48

elastin

(elastic sheet that can return to its original form once stretched)

Front 49

Give one example of globular proteins.

How does their structure enable function?

Back 49

actin and tubulin

(act as subunits that polymerize to form longer fibres)

enzymes

(globular shape promotes transport)

Front 50

Briefly outline the three mechanisms by which enzymes can encourage the catalysis for the conversion of substrate molecules.

Back 50

1. Controlling the orientation and position of two substrate molecules to promote the creation ofbonds at specific sites.

2. Upon binding, creating a change in the charge distribution on the surface of the substrate moleculethat is helpful for the reaction.

3. Straining the bound substrate towards a transitional state to promote reaction.

Front 51

List three functions of nucleotides in the cell, naming the specific nucleotides involved.

Back 51

1. Nucleotides provide a way of storing (DNA) and delivering information (RNA) in cells. (ATP, TTP,GTP, CTP, UTP)
2. Nucleotides can serve as energy carriers due to the high energy nature of their bonds. ATP
3. They can act as signalling molecules (cyclic AMP)
   

Front 52

What is meant by the 3’ end or the 5’ end of a nucleic acid chain?

Back 52

• the 3’ or the 5’ carbon of thesugar available at that end for further linkage through bonding.
  

Front 53

Explain how the phosphodiester bond between successive units of the DNA backbone facilitates the generation of the double-helix.

Back 53

The phosphodiester links 3’ and 5’ carbons of adjacent nucleotides, which creates a lateral displacement between the sugar units of the DNA backbone, causing formation of the double helix structure.

Front 54

What is the chief difference between the A-T and G-C pairs of nucleotides?

Back 54

They form different numbers of hydrogen bonds

A-T forms two, G-C forms three

Front 55

Which of the A-T and G-C pairs would you expect to find at replication origins and why?

Back 55

A-T

fewer bonds to break, easier to open out the DNA for replicating

Front 56

Which of the A-T and G-C pairs might be more prevalent in the DNA of organisms living at very hightemperatures near ocean hydrothermal vents and why?

Back 56

G-C

more bonds to stabilize the molecule

Front 57

Define gene

Back 57

a unit of heredity containing the instructions that dictate the characteristics or phenotype of anorganism

Front 58

Define genome

Back 58

the total genetic information carried by all the chromosomes of a cell or organism

Front 59

Define gene expression

Back 59

the process by which a gene makes a product that is useful to the cell or organismby directing the synthesis of a protein or an RNA molecule with a characteristic activity

Front 60

Define genetic code

Back 60

set of rules by which the information contained in the nucleotide sequence of a geneand its corresponding RNA molecule is translated into amino acid sequence in a protein

Front 61

Define DNA transcription

Back 61

Process in which RNA polymerase uses one strand of DNA as a template tosynthesize a complementary RNA sequence

Front 62

Define DNA translation

Back 62

process by which the sequence of nucleotides in a messenger RNA molecule directsthe incorporation of amino acids into protein

Front 63

What is the length of fully extended human DNA, and what is the nucleus size?

Back 63

2 m, (~10 μm dia)

Front 64

Describe or draw how DNA is packaged using a multi-level hierarchy of folding, in eachchromosome.

Include histone proteins, nucleosomes, chromatin beads, chromatin fibres and theirtypical length scales.

Back 64

A complex of DNA and protein is calledchromatin, which is mostly comprised of chromosome fibres each about 30nm in diameter, where the DNA chain is folded into a compact structure.

Theproteins used to bind into the primary level – the nucleosome - of thefolded chromosome structure are histone proteins.

The nucleosomes resemble beads on a string along the chromatinstrand if it is unfolded, where the string would be the DNA chain, and the chromatinbeads are nucleosome core particles. The distance from one chromatin beadto the other is roughly 50 nm.

Front 65

Define nucleosome

Back 65

The nucleosome has DNA wrapped around eight histones which act as a protein core for the structure.

It is the primary level of DNA packaging.

Front 66

Define histone proteins

Back 66

histones

Front 67

What is epigenetic inheritance?

Back 67

When traits are passed on from parent to offspring by mechanisms not directly involving nucleotidesequences.

Nucleotide sequences are unchanged.

Front 68

For human DNA, state the following:

1. number of base pairs
2. number of chromosomes
3. number of genes
   

Back 68

1. ~3.2 billion
2. 46
3. ~25,000

Front 69

What are homologous and nonhomologous chromosomes in human DNA?

Back 69

Homologous chromosomes has one maternal and one paternal chromosome paired in a cell during the meiosis process, which have complementary information (matching chromosomes); therefore they contain alleles for same type of genes {onefrom sperm and one from egg} or can be called similar.

Nonhomologous chromosomes contain alleles for different type of genes - the chromosomes are not matching (therefore nonhomologous chromosomes are only the sex chromosomes in males because they inherit a paternal Y chromosome and a maternal X chromosome).

Front 70

What are haploid and diploid cells?

Back 70

Haploid cells have one set of chromosomes.

Diploid cells have two sets of chromosomes.

Front 71

Assume a length of DNA that has one replication origin at its centre and is 3 billion nucleotidepairs in length with a replication speed of 100 nucleotides per second.

1. How long would it take to replicate?
2. How many replication origins would be needed if the DNA were to be replicated in 24 hours?
   

Back 71

1. 1.5x107 seconds = 174 days
   
2. If L = total length of the DNA, one replication origin involves replicating L/2 on either side, andcorresponding time t = VL/2, where V is the average replication speed.

In general, replication takesplace for a length x (and corresponding time t = xV) on either side of each replication origin. For Nreplication origins, 2Nx =L, x=L/2N and time t =VL/2N, or 1/N th of the time with one origin.

Front 72

Draw a simplified schematic representation of a DNA molecule as a string of labeled bases and two(straight) backbones.

Use it to explain the statement “DNA acts as a template for its ownreplication”.

Back 72

Front 73

What characteristic of DNA helps it to act as it's own template for replication?

Back 73

The paired nature of DNA makes it easy for it to unzip and act as its own template for replication.

Front 74

What are the two special abilities of DNA polymerase that enable it to accurately replicate DNA?

Back 74

1. carefully monitors the base-pairing between the incoming nucleotide and the templatestrand. Only correct matches are catalyzed to be added to the strand.
2. has the ability to proofread – it checks to ensure the correct base was added. If awrong base is added, it can remove it and add the appropriate base.
   

Front 75

How is DNA replication initiated?

Back 75

The process of DNA synthesis is begun by initiator proteins that bind tospecific DNA sequences called replication origins.

Front 76

How many replication origins would a

• bacterial genome have?
• human genome have?

Back 76

Bacterial genome: (which is typically contained in a circular DNA molecule of several million nucleotide pairs), has a single replication origin.

Human genome: has approximately 10,000such origins—an average of 220 origins per chromosome.

Front 77

What is a replication fork?

Why is DNA replication in eukaryotes and bacteria called bidirectional?

Back 77

DNA molecules in the process of being replicated contain Y-shapedjunctions called replication forks.

The forks move away from each other as the DNA unzips, which is why eukaryotic and bacterial DNA replication is called bidirectional.

Front 78

Which enzyme is at the heart of the DNA replication machine?

What does this enzyme do?

Back 78

DNA polymerase.

• catalyzes the addition of nucleotides to the 3􏰀 end of a growing DNA strand, using one of the original (parental) DNA strands as atemplate.
  

Front 79

Why is the replication fork asymmetrical?

Back 79

Because the DNA double helix is antiparallel, at each replication fork, one new DNA strand is made on a template running in one direction (3􏰀 to 5􏰀), & the other new strand is madeon a template running in the opposite direction (5􏰀 to 3􏰀).

The replication fork is therefore asymmetrical.

Front 80

Why are the two strands in the DNA double helix antiparallel?

Back 80

The sugar–phosphate backbone of each strand of a DNA double helix has a unique chemical direction (polarity) determined by the way each sugar residue is linked to the next, and the two strands in the double helix are antiparallel; that is, they run in opposite directions.

Front 81

What is the nucleolus?

Back 81

• structure within the nucleus where ribosomal RNA is transcribed and ribosomal subunits are assembled.
  

Front 82

What is the order of the central dogma?

Back 82

DNA > transcription in nucleus to mRNA

>translation at ribosomes in cytoplasm to proteins