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BIOL112 > Biochem > Flashcards

Biochem Flashcards

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1
Q

Buffer

A

Makes the overall solution resistant to pH change because it reacts with both added bases and acids

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2
Q

Law of mass action

A

Addition of reactants accelerates the reaction. Likewise, removal of products accelerates the reaction.

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3
Q

Hydroxyl

A

R—OH; Alcohols; Highly polar so makes compounds more soluble through hydrogen bonding with water. May also act as weak acid and drop proton

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4
Q

Phosphate

A

O
||
R—O—P—O- ; Organic Phosphate;
|
O-
When several phosphate groups are linked together, breaking O—P bonds between them releases large amounts of energy

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5
Q

Sulfhydryl

A

R—SH; Thiols; When present in proteins, can form disulfide (S—S) bonds that contribute to protein structure

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6
Q

Amino

A

R
|
H—N—H ; Amines; Acts as a base—tends to attract a proton to form R—NH3

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7
Q

Carbonyl

A

O
||
R—C—H ; Aldehydes ; react with certain compounds to produce larger molecules with ending =O —H

R—C—R ; Ketones
||
O

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8
Q

Carboxyl

A

O
||
R—C—OH ; Carboxylic acids; Acts as an acid—tends to lose a proton in solution to form =O —O-

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9
Q

Marcromolecule

A

Large molecule containing a very large number of atoms (e.g. proteins, nucleic acids, carbohydrates)

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10
Q

Polymerisation

A

bonding together of monomers

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11
Q

Condensation reaction

A

Monomer bonded to HO in, H2O out (all monomers also bonded to H -> HO—Monomer—H)

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12
Q

Hydrolysis

A

H2O in, monomer bonded to HO out (all monomers also bonded to H -> HO—Monomer—H)

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13
Q

Protein

A

Polymers of amino acids
Range in size from a few amino acids to thousands (typical protein = 200-300)(largest protein = 33,000)

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14
Q

Polypeptide chain

A

String of amino acids connected together by peptide bonds.
Make up proteins.
Start with amino group and end with carboxyl group.

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15
Q

Numbering system

A

Start at N-terminus (5’) and end at C-terminus(3’)

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16
Q

Peptide bond

A

Polypeptides flex because groups on either side of each peptide bond can rotate about their single bonds

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17
Q

Tertiary structure

A

Fully folded protein arrangement
Side chain interactions determine tertiary structure

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18
Q

Coiled coils

A

Arise when two a-helices have hydrophobic amino acids at every 4th position. Fibrous structural proteins (e.g. keratins) consist mainly of a-helices arranged as coiled coils.

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19
Q

Disulfide bonds

A

Covalent interactions formed between the sulfur atoms of two cysteine residues

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20
Q

Dimer

A

Polymer formed from two molecules of a monomer

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21
Q

Transcription factor

A

Protein that help turn specific genes “on” or “off” by binding to nearby DNA

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22
Q

Tetramer

A

Polymer formed from four monomers (e.g. hemoglobin)

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23
Q

Ribonuclease

A

Cuts RNA

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24
Q

Protein turnover

A

Half-life. Occurs constantly in cells

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25
Chaperones
Specialised proteins that help keep other proteins (temporarily exposed hydrophobic regions) from interacting inappropriately with each other. Do this by isolating/hiding some newly synthesised proteins to give them time to fold
26
Nitrogenous Bases
Pyrimidines (Cytosine, Thymine, Uracil) - 1 aromatic ring Purines (Guanine, Adenine) - 2 aromatic rings
27
Phosphodiester linkage
ester bonds that form between sugar and phosphate to form the backbone of nucleic acids. *Always 3' hydroxyl group to 5' phosphate group*
28
Metabolism
All the chemical reactions that take place in the body
28
Anabolic reactions
Link simple molecules together to make complex ones. Energy storing reactions (require energy)
28
Catabolic reactions
Break down complex molecules into simpler ones (release energy)
29
First Law of Thermodynamics
Energy is neither created nor destroyed
29
Second Law of Thermodynamics
The dispersing of energy is the driving force for energy conversions
30
Exergonic Reaction
ΔG < 0 always
31
Endergonic
ΔG > 0 always
32
Transferring energy in cells
- All living cells use adenosine triphosphate (ATP) for capture, transfer, and storage of energy. - Some of the free energy released by exergonic reactions is captured in ATP which then can drive endergonic reactions
33
Catalyst
- Substance that speeds up a chemical reaction without being used up itself. - Most biological catalysts are proteins called enzymes (some can be RNA but rarely [e.g. in the ribosome]). - Only reactions with overall -ΔG can be catalysed
34
Enzyme cofactors
Anything that is not an amino acid attached to an enzyme. Can be metal ions (e.g. zinc, copper), small organic molecules temporarily binding, and small organic molecules that are permanently bound to the protein (heme)
35
Catalysis
Increase in rate of a chemical reaction due to a catalyst
36
3 Ways of Catalysis
1) orientation (optimise bond formation) 2) charged environment (enzymes can carry charge which can interact with the substrate) 3) strain (facilitates breaking of covalent bond)
37
Enzyme Saturation
When all the binding sites are occupied. Depends on turnover rate of enzyme
38
Major categories of carbohydrates
1) Monosaccharides 2) Disaccharides 3) Polysaccharides
39
Monosaccharides
Singular sugar molecules. Generally multiples of CH2O. Functional groups: hydroxyl groups (alcohol groups). Difference is sugars have carbonyl group which has one O less than carboxyl of alcohols. Gives sugar unique identity and typically occurs at the end of the sugar
40
Glycosidic linkage
Polymerisation between the carbonyl C1 and any O in the hydroxyl group. 2 matter to us: B14 (carbon atom 1 to hydroxyl of carbon 4) and A14
41
Starch
Polysaccharide -> unbranched long chain (can occasionally be branched). In plants called amylose. When highly branched is amylopectin in plants and glycogen in animals (found in liver and muscles).
42
Cellulose
Alternating orientation of B14 links. Very stable structure so very hard to digest.
43
Oligosaccharides
On the outside of cell often attached to proteins. Determine things like blood groups
44
Lipids
NOT POLYMERS. Very bunched group of molecules that are insoluble in water.
45
Roles of lipids
1) Energy storage (fats and oils) (most energy dense molecules [just consist of carbon and oxygen]) 2) Phospholipids in cell membranes 3) Capture light energy (Carotinoids) 4) Hormones and vitamins 5) Thermal insulation 6) Electrical insulation of nerves
46
Fatty Acid vs Fat
Fatty acid is triglyceride (3 fatty acids bound covalently via ester linkages to glycerol)
47
Amphiphilic
Both hydrophobic and hydrophilic. An alpha helix forms which can integrate into lipid bilayers
48
Phospholipids
49
Lipid bilayer shape
Forms into spheres so that the edges are not exposed
50
Lipid bilayer motion
Very fluid, constantly moving around but cannot invert.
51
Lipid bilayer temperature
In humans stays about the same but in animals like fish, colder temperatures means more rigid and warmer more fluid. When more rigid, they can't work well so they increase ratio of hydrocarbon tails with kinks in them (unsaturated) in order for the bilayer to become more fluid (kinks leave more space between phospholipids allowing them to move more).
52
Integral membrane proteins (trans membrane protein)
Proteins that cross the lipid bilayer
53
Leaflet
Half of lipid bilayer (top or bottom)
54
Diffusion
Passive mixing of substances resulting in net transport along a concentration gradient
55
Diffusion rate
Determined by temperature, size, and steepness of concentration gradient
56
Osmosis
Diffusion of water across a selectively permeable membrane
57
ATP hydrolysis
Can overcome ΔG to transport something against the concentration gradient
58
Primary active transport
Transport that directly hydrolyses ATP and couples it to the transport of the membrane
59
Secondary active transport
Use established gradients to move substances (e.g. glucose)
60
Lysosome
Membrane-enclosed organelles that contain an array of enzymes capable of breaking down all types of biological polymers
61
Lumen
When something is enclosed by membranes
62
Thylakoid
Stack of membranes functionally similar to cristae. Internal photosynthetic membrane systems of chloroplasts which can be extracted from green leaves like spinach. Have a two-layer membrane which separate their lumen from stroma of cytosol
63
Cristae
Folds in the inner mitochondria membrane which increase surface area
64
Cytoskeletal filaments
Actin filaments (smallest), intermediate filaments, microtubules (biggest)
65
End product inhibition
When the final product inhibits an enzyme involved in the initial reactions
65
Intermediate filaments
Form rope-like structures in cells that provide mechanical strength to cells or nucleus. NO POLARITY NO MOTOR PROTEINS
66
Extracellular matrix
All the proteins that fill up the extracellular space. Not rigid but provides some form of structure
67
Focal Adhesions
Hundreds of Integrins in one spot
68
Integrins
Dynamic molecules that bind indirectly to the cortical actin cytoskeleton and on the outside bind to extracellular matrix proteins
69
Cell recognition
One cell specifically binds to another cell of a certain type. This can lead to phagocytosis, DNA exchange, sperm-egg fusion
70
Cell Junctions
Tight junction, gap junctions
71
Continuous variation
there are a seemingly infinite number of traits for a given character (e.g. height, skin colour)
72
Discrete variation
there are only two or a few traits for a given character (e.g. fur colour in mice)
73
First rule of proability
The probability of two independent events both occurring is the product of the probability of each event occurring
74
Second rule of probability
The probabilities of mutually exclusive events sum
75
Wild type allele
Predominant allele (>99%) in a population
76
Mutant allele
a change from the wild type allele, typically the result of a recent mutation. Also can refer to alleles that cause disease
77
Polymorphic allele
Allele that is present in >1% of the population
78
Recombination rate
Measure of physical distance along the chromosome
79
Synapsis
Fusion of chromosome pairs
80
Plasmid
Small, circular, double-stranded DNA molecule that is distinct from a cell's chromosomal DNA. Naturally exist in bacteria and carries genes
81

BIOL112 (2 decks)

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