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Molecular Cell Bio > EXAM 1 Ch 1,2, 4-6, 9 > Flashcards

EXAM 1 Ch 1,2, 4-6, 9 Flashcards

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Biology 101 flashcards
1
Q

What are the four points of Cell Theory?

A
  • All living organisms are made of cells.
  • The cell is the fundamental unit of structure and function in living organisms.
  • All cells are essentially the same in chemical composition.
  • All cells come from other cells.
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2
Q

What is the general flow of genetic information?
Central dogma:

A

DNA is transcribed into RNA which is translated in proteins.
Reverse transcriptase is an exception and can do RNA to DNA.

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3
Q

Are viruses Alive?

A

No! They cannot reproduce on their own.
They also don’t have growth.

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4
Q

DNA to RNA?

A

Transcription!!!

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5
Q

RNA to Protein?

A

Translation!!

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6
Q

What molecule was likely not present on earth at first?
When was it produced?

A

Primitive earth likely lacked O2 and started with anaerobic organisms. It wasn’t until photosynthesis that earth became abundant in O2 primarily from cyanobacteria.

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7
Q

What were the three processes of early earth allowing for production of organic molecules?

A
  • Heat (sun)
  • Electric Discharge (lightning)
  • Cooling System (Molecules to liquid form.)
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8
Q

What four molecules were produced by “Early Earth Experiments”

A
  • Aldehydes
  • Simple Acids (ammonium NH4+)
  • Complex Acids (amino acids)
  • Long Hydrocarbon Chains. (Fatty Acids.)
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9
Q

After organic molecules were produced by the earths atmosphere what likely came next?

A

Abiotic Earth self replicating macromolecules. RNA world hypothesis. Discovered certain RNA could self replicate.

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10
Q

RNA molecule that can also act as an enzyme (usually folded in some way.)

A

Ribozyme.

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11
Q

What are three activities of ribozymes?

A
  • RNA splicing
  • Ligation
  • Polymerization.
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12
Q

Where are ribozyme catalyzed reactions observed?

A
  • Genome replication in some RNA viruses.
  • Some protozoan intron splicing.
    -Functions in translations are rRNA.
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13
Q

What is a ribosome composed of?

A

rRNA and rProteins.

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14
Q

What are the types and functions of RNA?

A

mRNA- Messenger transcribed RNA that leaves the nucleus with code for proteins.
tRNA- Transfers amino acids to ribosome during translation.
rRNA- Ribosomal RNA, main component of ribosome. in combination with proteins forms large and small sub units that build polypeptide chains.

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15
Q

What ribozyme is part of the large ribosomal subunit and assists in forming peptide bonds?

A

peptidyl transferase.

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16
Q

how might ribozymes interact with other RNA molucules?

A

Ribozymes can cleave RNA (if mRNA, this stops production of that protein.)
Ribozymes can also base pair, and this allows for cleavage at specific sites of the substrate.

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17
Q

How did DNA come about?

A

Hypothesis: Some RNA can self replicate using ribozymes. These RNA’s eventually became able to produce proteins. DNA is more stable than RNA but requires many proteins to replicate.

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18
Q

What limits the size of cells? excluding frog eggs.

A

The size of a cell requires more membrane to be produced per unit of volume.

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19
Q

Three characteristics of smaller cells in relation to larger cells.

A
  • Smaller cells can interact with surroundings more efficiently.
  • Smaller cells lose more heart/ energy to surroundings.
  • Smaller cells have higher metabolic rate.
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20
Q

Three things prokaryotes lack?

A
  • Cytoskeleton
  • Nuclear envelope
  • Membrane bound organelles
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21
Q

Distinguishing feature of eukaryotes?

A

Nuclear envelope.

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22
Q

Most diverse cell type?

A

Prokaryotes.

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23
Q

Do photosynthetic bacteria have chloroplasts?

A

NO organelles!! That have a system of membranes where photosynthesis occurs.

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24
Q

What is chemosynthetic?

A

Derives energy from oxidation of H2S

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25
Q

Explain mitochondria?

A

Power house.
Contains mtDNA that is only inherited from mothers side in humans. Thought to have evolved via endosymbiont in an oxygen rich world.
Enclosed by a double membrane very similar to prokaryote, not other organelles, and has circular DNA.

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26
Q

Explain chloroplasts

A

Photosynthesis in eukaryotes, non-animal cells. Believed to be attained via endosymbiont post mitochondria (no plant ancestry W/O mitochondria.)

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27
Q

What are the steps of exocytosis?

A

Product is formed, usually within RER, and “bud” from the membrane as vesicles & travel to the golgi apparatus for packaging, from they travel to the outer membrane of the cell where the vesicle will become part of the cell membrane and release it’s contents. They use the cytoskeleton filaments as tracks to the outer membrane.

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28
Q

You come across a cell that has organelles, is this cell a eukaryote?

A

No, cannot know without knowing if the cell has a nucleus

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29
Q

Name one things animals cells have plant cells don’t, what is their alternative?

A

Centrioles, used to organize microtubules.
Plant cells have a microtubule organizing center.

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30
Q

What are 8 basic properties cells contain?

A
  • Complexity
  • Genetics
  • Replication
  • Metabolism
  • Biochemistry
  • Function
  • Response
  • Homeostasis
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31
Q

What are the four building blocks of the cell?

A

Sugars, Fatty Acids, Amino Acids, and nucleotides.

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32
Q

What are the four larger building units of the cell?

A

Polysaccharides, fats, lipids, membranes, proteins, nucleic acids.

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33
Q

What is a condensation reaction?

A

Think Dehydration synthesis, water by product. Endergonic (requires energy.) Builds a product.

34
Q

What is a hydrolysis Reaction?

A

When water is added break down a molecule. Usually adds an H and OH to each piece.

35
Q

What happens when two monosaccharides go through a condensation RXN?

A

Dehydration reaction, will combine the monosaccharides and have H2O by product, builds a Disaccharide bonded via Glycosidic (covalent) bond.

36
Q

What are the two parts of a fatty acid?

A

Hydrophilic carboxylic head and Hydrophobic hydrocarbon tail.

37
Q

Difference between a saturated and unsaturated fat?

A

Saturated= Saturrated W/ Hydrogens- Alkane.
Unsaturated = Double bond/s somewhere- Alkene.

38
Q

How to fatty acids link to glycerol?

A

an ester bond.

39
Q

Types of fats and differences?

A
  • Saturated fats: Bad, tightly packed, build up in arteries.
  • Unsaturated trans fats: WORST unsure how these get processed, raise bad cholesterol, not natural.
  • Unsaturated Cis Fats: Raise good cholesterol,
40
Q

Oleic Acid Vs. Elaidic Acid?

A

Oleic Acid- Cis fat
Elaidic acid- Trans fat
isomers of each other.

41
Q

Describe phospholipid:

A

Fatty acids + glycerol. Two non-polar tails, one is usually cis bond, other is saturated.
Hydrophilic phosphate group, with a polar group at the head (usually choline)
The more saturated= more rigid.
more unsaturated= more fluidic.

42
Q
A

Amino Acid.
In the body a (+) on the Amine (NH2) and a (-) on the Carboxylic Acid (COOH)
The R-group Defines the type of amino acid.
The carbon the R-group is attached to is the alpha carbon.

43
Q

How are amino acids bonded?

A

Through (covalent) peptide bonds, usually formed via condensation (Dehydration).
The blue is by product H20
The Carbon will attach to the Nitrogen.
This creates a Carbon nitrogen backbone with a C and N terminus. (N-C-C)

44
Q

What is ATP?

A

Adenosine triphosphate, a nucleotide containing Nitrogenous base (adenine), Ribose sugar and triphosphate.

45
Q

Difference between deoxyribose and ribose?

A

Deoxyribose has lost an Oxygen on the beta carbon. OH group is only on the 3’. Think, DNA can only replicate to the 3’ side (5’–>3’ direction)

46
Q

What is a nucleotide composed of?

A

Nucleoside + Phosphate group.

47
Q

How do nucleotides attach?

A

Always in the 5’ Phosphate to 3’ OH.
The 5’ Phosphate will attach to the 3’OH. These are joined by phosphodiester (covalent) bonds.
The Nitrogenous bases will be joined by hydrogen bonds.
This is now a nucleic acid.

48
Q

What is a nucleoside?

A

5 Carbon Sugar backbone (D or R) + nitrogenous base.

49
Q

ATP and ADP?

A

Adenosine (tri- or di- ) phosphate.
ADP has 1 less phosphate group.
Cellular respiration produces ATP, a stored form on energy (currency), When around H20 the third phosphate group will readily separate releasing energy as the OH group adds to the now diphosphate group.
This is a hydrolysis reaction.

50
Q

Hydrolysis Vs Condensation RXN.

A

Hydrolysis:
-consumes H20
-releases energy.
-breaks things down.
Condensation:
-H20 byproduct
-uses energy.
-attaches molecules.

51
Q

What is a polymer?

A

A chain of monomeric subunits.

52
Q

What type of bonds mediate bonds of macromolecules and compatible groups?

A

Non-covalent bonds.

53
Q

Bonds from subunits to macromolecule production?

A

Covalent bonds.

54
Q

Bonds building macromolecules into macromolecule complexes?

A

Non-covalent bonds.
(H-bonds, Electrostatic, vanderwals, ionic bonds.)

55
Q

When does a polypeptide become a protein?

A

When the polypeptides come together to a shape that is functional.

56
Q

Does the polypeptide backbone primary structure have free rotation?

A

The side chain R-groups are able to rotate freely but due to the resonance between O-C-N the C-N back bone bond is rigid.

57
Q

What type of bonds stabilize folding proteins?

A

weak non-covalent bonds, MANY.

58
Q

Sequence of amino acids protein structure?

A

Primary.

59
Q

Localized conformations of the polypeptide backbone structure?

A

Secondary. Alpha helix (H-bonding between every 4 peptide bonds.) & beta sheets, non-covalent bonds such as H-bonding.
No R-group side chain interactions.

60
Q

Folding pattern of an entire polypeptide chain to produce it’s
3-dimensional structure.

A

Tertiary Structure.
Side chain orientation: Hydrophobic non-polar stay to inside.
Hydrophilic polar go to outside of the structure.
cysteine and disulphide covalent bonding.
Structure will determine function.

61
Q

Multiple polypeptides arranged in a specific way Structure?

A

Quaternary structure. non-covalently bound/ electrostatic interactions.
Usually has sub units that will determine it’s function.

62
Q

When non-synonymous mutations occur that affect the amino acids side chains what might happen?

A

When amino acids side chains are changed, this can affect the intramolecular forces of the protein & subsequently how it folds, which affect it’s function.
EX: Sickle cell is just a mutation for Valine instead of glucose & changes the folding pattern at that location & the shape of hemoglobin at large which causes the disc shape which clogs blood vessels and severely limits O2 supply.

63
Q

Name and why special?

A

Cysteine, non-polar. The H-S

64
Q

What type of amino side chains stay towards the outside of the protein as it folds?

A

The Polar and Charged amino acids. They are chemically reactive if an aqueous environment.

65
Q

5 steps of protein maturation?

A
  1. Correct Folding
  2. Proteolytic Cleavage- cuts off unneeded bits.
  3. Chemical Modifications.
  4. Formation of Quaternary structures.
  5. Association W/ Co factors.
66
Q

In Tertiary structure folding what occurs that allows 3-d folding to begin that was preventing it before?

A

Chaperones which were bonded to nascent (new) polypeptide during synthesis will begin to release and allow proper folding.

67
Q

Bonds that begin to form in tertiary structures that will be becoming quaternary structures that are very strong and will hold together the proper shape of the protein.

A

Cysteine, Disulfide bonding, links domains of the same or different polypeptides.

68
Q

What are cross links?

A

Links between the side chains that can be elastic and help hold together the protein, most common in the disulfide bonding of cysteine. Think of collagen, as they stretch out over time.

69
Q

What can break disulfide bonds?

A

Reducing agents such as Beta-mercaptoethanol

70
Q

What is urea?

A

an excrete toxic ammonia metabolic waste product of mammals. A reversible denaturant.

71
Q

What are TSE’s?

A

Transmissible Spongiform Encephalopathies. They are caused by Prions, an infectious agent these are incorrectly folded proteins. They are not recognized to be degraded and are able to alter normal proteins and lead to protein aggregate plaque.
They do not transmit genetic info.

72
Q

What are the two levels of protein regulation?

A
  • Regulation of gene expression: think on/ off for transcription.
  • Regulation of protein function- restricted according to the needs of the cell.
73
Q

What is regulation by binding of specific ligands?

A
74
Q

What is kinase activity?

A

Phosphorylation, think ATP. This usually requires a binding regulator that will have a binding constant that will affect when kinase activity is active.

75
Q

What are the 6 protein activity regulation types?

A
  1. Reg by location
  2. Reg by binding activation
  3. Allosteric feed back +/-
  4. Phosphorylation- Kinase-uses ATP.
  5. GTP binding- hydrolysis GTP-GDP
  6. Proteolytic degradation & ubiquitylation.
76
Q

Ubiquitin regulation:
Mono:
Multi:
Poly:

A

Mono: histone reg
Multi: Endocytosis.
Poly proteasomal degradation usually or DNA repair. Uses ATP.

77
Q

Where is rRNA transcribed?

A

Nucleolus

78
Q

Where are ribosomes made?

A

Nucleolus

79
Q

LAD and NAD?

A

Laminar and nucleolus associated domain. Both are heterochromatin.

80
Q
A

Molecular Cell Bio (2 decks)

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