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BIO 110 > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

Comparative Experiment

A

use data from the outside world, would not be possible as a controlled experiment

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2
Q

Independent Variable

A

the variable manipulated

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3
Q

Dependent Variable

A

the variable being measure, changes in response to IV

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4
Q

Negative control

A

no phenomenon is expected

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5
Q

Positive Control

A

a group where the phenomenon is expected

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6
Q

Null Hypothesis

A

there is no relationship between the two variables. Any difference is the result of random chance

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7
Q

Hypothesis

A

A hypothesis can not be proven. If it is supported by evidence, we reject the null hypothesis. If it is not supported by evidence, we fail to disprove the null hypothesis

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8
Q

Structure of Water

A

Water is a bent molecule with electrons unequally shared (different electronegativity). Oxygen is more electronegative than the hydrogens, so it pulls on the shared electrons more. Resulting in the oxygen having a slight negative charge and hydrogen having a slight positive charge.

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9
Q

Hydrogen Bonding

A

Hydrogen bonds explain the high melting and boiling points of water.Water can form hydrogen bonds with up to 4 other water molecules

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10
Q

Polarity of Water

A

Water pulls apart ionic compounds (salts) due to its polarity

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11
Q

Hydrophobic Effect

A

The dipole nature of water creates the hydrophobic effect (entropically driven exclusion from water).
Hydrophobic effect: tendency for hydrophobic molecules to clump together in polar solutions.
When nonpolar molecules are apart, it takes more energy than if all of the molecules were together. Since it requires less energy when the molecules are clumped, they proceed to the state that is thermodynamically favorable

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12
Q

Water Uses

A

Water is an important part of most biomolecules and can be crucial for the structure and function of an active site of an enzyme.
Water is often used to make and break covalent bonds
Hydrolysis: Water is used to break a bond
Condensation: water is produced as a result of a bond forming

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13
Q

weak interactions hold together complex biological molecules

A

covalent bonds
Hydrogen bonds: sharing of H atom (between polar molecules)
ionic bonds: attraction of opposite charges, charges are full
hydrophobic interactions: interaction of nonpolar substances in the presence of polar substances
van der Waals forces: interaction of electrons of non polar substances. Electrons are constantly moving, causing negative and positive regions (unequal distribution of electrons)

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14
Q

Energy

A

Endergonic: requires energy to occur (activation energy), Ereactants< Eproducts
Exergonic: releases energy, Ereactants> Eproducts
Free energy (ΔG) = [Energy]products - [Energy]reactants
energy in living systems is found in many forms (covalent bonds, electron carriers, proton
gradients, ATP)
ATP is the energetically rich energetic currency used by many reactions within a cell
the hydrolysis of ATP (a favorable reaction) is coupled with unfavorable reactions to push them forward

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15
Q

Structure of Carbohydrates, Lipids, Fatty Acids, and Triglycerol

A

Carbohydrates: made of carbon and hydrogens. Cn(H2O)n. Chain of carbons connected by single bonds, if there are more than 5 carbons carbon rings form.
Lipids: nonpolar molecules
Fatty acids: long nonpolar hydrocarbon chain with a terminal polar carboxyl functional group
Triacylglycerol: Simple lipid. 1 glycerol group and 3 fatty acid tails (hydrocarbon+acid on tp)

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16
Q

Carboydrates VS Lipids

A

Energetic differences between carbohydrates and lipids
Lipids are more efficient at storing energy than carbohydrates. More energy per carbon (less oxidized). They take up less space per carbon (water doesn’t bind to lipids)

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17
Q

Saturated versus unsaturated fatty acids

A

Saturated fatty acids: all carbon bonds are single bonds. Packs efficiently, solid at room temperature
Unsaturated fatty acids: some carbons have double bonds, causing kinks in the chain. Liquid at room temperature, can not pack efficiently. Causes membranes to be more fluid

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18
Q

Amino Acids: why these 20?

A

Because amino acids were present before life existed on earth, so life chose the 20 simplest and most common amino acids to synthesize proteins with. Only 20 amino acids are used because they have enough diversity.

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19
Q

Amino Acids: why one isoform? Why L?

A

Amino acids are almost exclusively the L isoform because their structures have to be consistent so that the proteins made folds the correct way.

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20
Q

What are the unique properties of each?

A

Nonpolar, uncharged: hydrophobic, tend to cluster together
Polar, uncharged: hydrophilic, can form hydrogen bonds
Aromatic group: nonpolar, can participate in hydrophobic interactions, made of carbon rings
Positively charged: hydrophilic
Negatively charged: hydrophilic

more carbon = more phobic

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21
Q

Protein Folding

A

Peptides are polymerized amino acids, usually synthesized at the ribosome.
All the information necessary to properly fold a protein is contained in primary sequence
If denature agents are removed, structure and function are restored

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22
Q

Primary Structure

A

The linear sequence of amino acids in a peptide

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23
Q

Secondary structure

A

Interactions between nearby amino acids give rise to regular repeating structures called secondary structure.
Secondary structure is maintained by hydrogen bonding.
α-helix by intramolecular H-bonds. For spiral regions. Full revolution every 3.6 residues, hydrogen every 4 residues.
β-sheet by intermolecular H-bonds. Form pleated sheets

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24
Q

Tertiary structure

A

the 3D structure of a folded peptide
Non-covalent forces (H bonds, hydrophobic effect, ionic interactions, Van der Waals) and disulfide bonds stabilize both Tertiary and Quaternary structures.

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25
Quaternary structure
the 3D structure of a protein composed of more than one polypeptide. Non-covalent forces (H bonds, hydrophobic effect, ionic interactions, Van der Waals) and disulfide bonds stabilize both Tertiary and Quaternary structures.
26
Antifreeze Proteins
Evenly spaced hydroxyl groups on the flat side allows for H bonds with water crystals. This makes it thermodynamically unfavorable for water molecules to add to the ice layer. This prevents the ice layer from growing too large
27
Mucins
Large, relatively unfolded glycoproteins. Consisting of about 80% carbohydrates, carbohydrates bind to water, causing the protein to take up a lot of space. Mucins bind to each other via dimerization domains and disulfide bridges. Hydrophobic alpha helix at the end embeds them into membranes
28
Enzymes
Enzymes are proteins that catalyze reactions, increase the rate of reactions
29
Coenzymes
molecules that bind to enzymes and put them in their functional form
30
Induced Fit Model
when a substrate binds to the active site, there is a conformational change in the enzyme, along with the substrate (catalysis)
31
Enzymes Facts
Enzymes do not change the equilibrium of a reaction, they only allow the reaction to go faster Enzyme activity can be regulate be binding something to change the shape of the active site or blocking the active site
32
T.H.Morgan
Recognized that the inheritance of the sex chromosomes in Drosophilia closely followed the inheritance of the white-eye phenotype. Concluded genes are on chromosomes
33
Oswald Avery
Information necessary for causing virulence survived heat treatment and was able to transform non-deadly virus strand. Concluded DNA, not proteins, are the material of heredity.
34
Hershey Chase
Bacter was radioactive with 32P, so the bacteriophage injected bacteria with DNA. Concluded DNA is the material of heredity.
35
Chargaff’s Rule
The number of adenosine residues is equal to the number of thymidine residues (A=T). The number of guanine residues is equal to the number of cytidine residues (G=C). Purines: adenosine and guanosine Pyrimidines: Cytidine and thymidine
36
Watson & Crick
Hydrophilic sugar phosphate backbone are antiparallel strands. Run from 5’ to 3’. Hydrogen bonds between complementary bases (A-T 2, G-C 3). 10 bases/full rotations Nucleotide=sugar+phosphate+base
37
Dickerson Dodecamer
3D structure of DNA varies with sequence. Differences in twist, roll, propeller twist, displacements (different in many minor features). Departure from B form DNA so important because need to locate specific sequences in our genomes in order to regulate genes (every DNA sequence is a different ligand (the specific thing a protein binds to))
38
Prediction
If ___, then ___
39
Osmotic Effect
high concentration water goes to low concentration water
40
sugars
carbon:water (1:2) more connected = less soluble remove water to form bond, add water to break
41
join 2 sugars
formed by a condensation reaction, splitting of water
42
branching
more branches = more efficiency with adding and subtracting glucose
43
lipid functions
energy storage (more energy per carbon in lipids because of how oxidized carbon is, and no water needed so better than carbohydrates) basic structural unit of cellular membranes
44
triglycerides
glycerol attached to 3 fatty acids energy storage and insulation when connect no more OH groups, and becomes hydrophobic (and destroys part of the fatty acid that is hydrophilic)
45
cis fats vs trans fats
natural, artificial
46
membrane lipids
need hydrophobic and hydrophilic parts remove 1 fatty acid add in something hydrophilic
47
amino acids
hydrogen, amino group, carboxyl group, and r group attached alpha carbon building blocks of proteins neurotransmitters energy source
48
protein where is the hydrophilic and hydrophobic parts?
hydrophobic inside hydrophilic outside
49
proteins (primary structure)
linear sequence of amino acids (encoded in DNA) determines fold and therefor function
50
proteins (secondary structure)
hydrogen bonds between amino acids form alpha helices and beta sheets
51
proteins (tertiary structure)
heme picket helps carry oxygen throughout the body
52
proteins (quaternary structure)
2+ polypeptide chains form one functional molecule with subunits
53
protein shape and function
defense (protect body from disease by recognizing and binding to foreign molecules) structure (collagen forms strong triple helix for structural support throughout body) communication (insulin can easily maintain its shape while traveling through the blood and helps regulate blood and sugar levels) transport (calcium pump moves ions across cell membranes) enzymes storage
54
protein structure
protein structure determined by protein structure protein structure determined by amino acid sequence
55
how do proteins know how to fold?
hydrophobic effect hydrogen bonds, ionic bonds, vander waals, disulfide bonds all of these forces help stabilize the 3d structure of proteins bonds depend on each other
56
cooperativity of folding
changing one part of the protein changes the other parts of the protein change by binding something to the protein
57
alpha helix
a repeated structure in proteins caused by hydrogen bonds between different elements of the backbone every 3.6 residues stable because of the hydrogen bond between the C and O of one amino acid and the N and H of another one side very positive, other is very negative
58
antifreeze proteins
prevent death by freezing prevent ice from expanding without --> keeps small common features: bind to ice (flat regular side) evenly spaced OH groups on the flat side allows for H bonds with water crystals humans don't have antifreeze proteins
59
mucins
binds to and traps foreign things protective layer heavy with proteins sequence is very repetitive (largely unfolded) extracellular glycoproteins both membrane bound and secreted mucins share many common features. Both are highly glycosylated consisting of 80% carbohydrates
60
sodium potassium pump
uses ATP protein found in cell membranes, used to generate a gradient of ions sodium out, potassium in for each ATP that is broken down, 3 sodium out, 2 potassium in (removal of phosphate group + bind to protein which causes a structural change)
61
Lock and Key Model
explains specificity of the enzyme but does not explain the stability of the transition state for it would require more energy to reach the transition state complex, and is more rigid
62
Induced Fit Model
enzymes put strain on substrate, catalysts, begin reaction causes conformational change and structural adaptation that makes this binding site more complementary and lighter molecules mold into precise formation so that there is an induced fit where the enzyme can perform maximum catalytic function
63
what do enzymes do?
bond between the enzyme and substrate creates energy that can be used to reduce activation energy in order to make reactions more likely to occur)
64
how do you regulate enzyme activity?
change the structure, change function covalent modification (another enzyme do the work) allosteric modulators (activator or repressor, non-covalent, cells prefer because not using ATP) more regulated = more important
65
Gregor Mendel
provides first evidence for a heredity material
66
T.H.Morgan
provides evidence that chromosomes are the material of heredity sex determination related to the inheritance of x or y chromosome inheritance of sex chromosome similar to inheritance of white-eye phenotype alleles for the red/white eyes are carries on x chromosome
67
Griffiths, and Avery
MICE smooth vs rough (live or die)
68
Watson & Crick
DNA structure
69
Gene
the functional unit of hereity
70
allele
a specific form of a gene at a given location on a chromosome, among multiple possible forms
71
denaturing of a protein
hydrogen bond is broken, protein back to primary structure, when rebinds together not native shape if remove denaturing agent, can get back to original shape
72
A and G are what?
purines (two rings)
73
T and C are what?
pyrimidines (one ring)
74
Structure of DNA
Base-Sugar ---- Phosphate over and over again bases bind together via H-bonds

BIO 110 (1 decks)

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