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Biology - SBI4U > Unit 1 - Biochemistry > Flashcards

Unit 1 - Biochemistry Flashcards

1
Q

Biochemistry Definition

A

the study of the activity and properties of biologically important molecules

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2
Q

Matter/Elements

A

All matter is composed of elements -substances that cannot be broken down into simpler substances by ordinary chemical methods.

Only 6 elements are the chemical foundation for the diversity of life: C, H, N, O, P, S

An Element is a substance made up of one type of atom- atoms are made up of subatomic particles; protons, electron, neutrons

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3
Q

Ions (definition)

A

Atom or group of atoms that has gained or lost electrons in order to be stable
Cation: loses e- results in + charged particle
Anion: gains e- results in - charged particle

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4
Q

INTRAmolecular Bond

A

interactions between atoms WITHIN a molecule.

bonds can be ionic, polar covalent, or non-polar covalent depending on the difference in electronegativity

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5
Q

INTERmolecular Bond

A

interactions BETWEEN molecules
- between different molecules or different parts of the same molecule
-much weaker than intramolecular forces
-VERY IMPORTANT for biological systems
-Ex. Hydrogen Bonding

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6
Q

Hydrogen Bonding

A

a weak association between an atom (O, N, or F) with partial negative charge and hydrogen atom with partial positive charge.

Help maintain proper structure and function of the molecule.

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7
Q

Hydrophobic Interactions

A

NON-POLAR molecules that do NOT have attractive interactions with water molecules. (water fearing)

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8
Q

Hydrophilic Interactions

A

POLAR molecules that DO have attractive interactions with water molecules. (water loving)

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9
Q

Ions in Biological Systems

A

important part of living systems and are critical to many biological processes including cellular respiration, transport mechanisms across cell membranes and muscle contraction.

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10
Q

Functional Groups

A

atom or group of atoms attached to a molecule that gives the molecule particular chemical and physical properties. Determine the properties of a molecule
-provide the molecules they are bonded to the same chemical properties (polar, acidic, etc)
-Contains atoms such as O, N, P, S
-more reactive than hydrocarbon portion

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11
Q

Hydrocarbons

A

Organic Molecules that are made up of only carbon and hydrogen atoms.
-non-polar, do not dissolve in water, relatively low boiling points, flammable
-covalent bonds between C and C, as well as, between C and H are “energy-rich” as breaking the bonds releases a lot of energy

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12
Q

Molecular Formula vs Structural Formula

A

Molecular: shows # of each type of atom in an element or compound. Ex. H2O

Structural: shows how different atoms of a molecule are bonded together

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13
Q

Macromolecules (definition and 4 main)

A

-large, complex molecules, composed of repeating units of smaller molecules covalently linked together
-many are polymers
4 main: Carbohydrates, Proteins, Lipids, Nucleic Acids

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14
Q

Polymer

A

large molecules composed of repeating units of smaller molecules called monomers

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15
Q

Monomer

A

smallest repeating unit of a polymer

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16
Q

Organic Molecules

A

carbon containing molecules in which C atoms are bonded to each other and to H
-C is essential to all life on earth (“carbon backbone”)

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17
Q

Carbohydrates (function, structure, characteristics)

A

-Used as short-term energy storage and structural support
-Contain C,H,O in 1:2:1 ratio
-lots of hydroxyl and carbonyl groups, making most carbs POLAR (Therefore, dissolving in water)

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18
Q

Monosaccharides (structure, common examples)

A

Simple sugars composed of between 3 and 7 C atoms
-3 common monosaccharides have same molecular formula, but different structural arrangements, called ISOMERS of each other.
-3 monosaccharides: glucose, fructose, galactose

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19
Q

Disaccharides (definition, bond name, common examples)

A

When 2 monosaccharides join together, covalent bond between them is called a GLYCOSIDIC LINKAGE
-Examples: sucrose (glucose+fructose), Maltose (glucose+glucose), lactose (glucose+galactose)

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20
Q

Polysaccharides (definition, function, structure, examples)

A

Carbohydrate polymer composed of many monosaccharides
-complex carbs
-straight or branched chains
-used for energy storage and structural support
-Examples: starch, glycogen, cellulose. all composed of glucose monomers but organized differently, different 3D shapes and functions

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21
Q

Starch vs Glycogen

A

Starch: energy storage in PLANTS, branched or non-branched
Glycogen: energy storage in ANIMALS, HIGHLY branched.
Both can be digested by humans but glycogen can be broken down more rapidly since there are more branches

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22
Q

Cellulose

A

Structural support in plants, component of plant cell walls, indigestable for humans since we do not have the enzyme that recognizes their glycosidic linkages

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23
Q

Lipids (characteristics/structure, functions, examples)

A

-Hydrophobic and insoluble
-Contain C,H,O
-Many energy rich C-H bonds
Functions: energy storage, form cell membranes, chemical signalling molecules, insulation, protection.
-Triglycerides (fat), phospholipids, steroids, waxes

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24
Q

Triglycerides (structure, components, bond name)

A

-Composed of: glycerol backbone and 3 fatty acid(F.A.) chains
-each hydroxyl of glycerol bonds with carboxyl of F.A.
-Bond called ESTER BOND

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25
Q

Fatty Acids (saturated vs unsaturated, characteristics of each)

A

Saturated: only single bonds between carbons, linear. fit closely together, solid at room temp (ex. butter)

Unsaturated: one or more double bonds between carbons (monounsaturated: one double bond, polyunsaturated: 2 or more double bonds). space between them due to “kinks” so its liquid consistency at room temp. (ex. olive oil)

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26
Q

Phospholipid (definition, components, lipid bilayer)

A

Main component of cell membranes
- made up of glycerol molecule, 2 fatty acid chains, and phosphate group, and R
-Phosphate group is HYDROPHILIC, and the ‘head region’, faces outward in lipid bilayer.
-Fatty Acid Chains are HYDROPHOBIC, ‘tail region’, faces inward in lipid bilayer

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27
Q

Steroids (structure, function)

A

Contain 4 fused HC rings and several functional groups
Function: to communicate change, cellular/chemical signalling

28
Q

Waxes (structure, function)

A

Long fatty acid chains linked to alcohols or C rings
-hydrophobic, solid, firm/pliable consistency
-good for waterproof coatings on plants and animal parts

29
Q

Protein (functions, structure, components)

A

Functions: structural building blocks for muscles, enzymes, transport across cell membrane, chemical messengers, muscle movement, and antibodies.
Composed of Amino Acids
Contain: C,H,O,N
Can be polar, non-polar, or charged

30
Q

Amino Acids (structure, essential, non-essential)

A

Structure: amino group, carboxyl group, Hydrogen, and R variant
20 common amino acids, 8 considered essential A.A’s, meaning you must get from diet, 12 considered non-essential A.A’s, meaning your body can build them from non-protein food sources

31
Q

Polypeptides (component, bond name)

A

many amino acids joined together, bonds between are called PEPTIDE BONDS

32
Q

How to make Functional Protein

A
  1. Primary Structure: join A.A’s together in specific order.
  2. Secondary Structure: p.p chain (as it is being formed) coils and folds (due to H bonds) into a-helix or b-pleated sheet
  3. Tertiary Structure: supercoiling of secondary structure that is stabilized by side-chain interactions including covalent bonds. Different for every protein. Some proteins are functional at this stage, such as insulin
  4. Quarternary Structure: two or more p.p subunits come together to form functional protein, ex. hemoglobin.
33
Q

Denaturation (definition, practical and detrimental example)

A

Protein is placed in an environment it is normally NOT in (ex. extreme temps, pH conditions, or harsh chemicals), it can become DENATURED -unfolds or changes shape and will NOT be able to perform its normal function.
May or may not be permanent depending on severity and time it is exposed, as long as primary structure is not destroyed it should be able to function again.

Practical example: heating hair to straighten or curl it
Detrimental example: changing pH of various parts of digestive tract

34
Q

Nucleic Acid (components, types, structures)

A

Two types: DNA or RNA
composed of Nucleotide base pairs
DNA: double stranded helix structure, anti-parallel strands, sugar-phosphate backbone, nucleotide interior
RNA: single stranded

35
Q

Nucleotides (components, bond name between them)

A

Consists of: 5 carbon sugar (ribose or deoxyribose), Phosphate group, and a nitrogenous base (A,T/U,C,G)
Bond between nucleotides is called a PHOSPHODIESTER BOND

36
Q

Neutralization Reactions

A

Chemical rxn between and ACID and a BASE, producing water and a salt
-an ACID produces H+ ions when dissolved in water
-a BASE produces OH- ions when dissolved in water
-pH scale classifies aqueous solutions as acidic, basic, or neutral.

37
Q

Buffers

A

A substance that minimizes changes in pH by donating or accepting H+ ions
-Chemical rxns in the body can only take place within a narrow range of pH values
-To maintain optimal pH ranges, organisms rely on buffers

38
Q

REDOX Reactions

A

A Chemical rxn that involves the transfer of electrons from one substance to another.
-molecule that loses electrons is OXIDIZED
-molecule that gains electrons is REDUCED
LEO says GER

39
Q

Condensation Reaction

A

-covalent bond is created and two molecules JOIN together
-Water is always formed
-ABSORBS energy
-ANABOLIC rxn: building larger molecules from smaller molecules

40
Q

Hydrolysis Reaction

A

-Water molecule is used to BREAK a covalent bond
-Water provides H atom to one subunit and OH group to the other
-energy is RELEASED
-CATABOLIC rxn: breaking larger molecules into smaller molecules

41
Q

Activation Energy

A

-Any chemical rxn requires a certain amount of energy to begin
-Amount of energy required for rxn to begin
-A large activation energy means the rxn will be slow

42
Q

Enzyme (definition/function)

A

A molecule that catalyzes (speeds up) chemical rxns in biological systems, MOST are proteins.
-Lowers the activation energy required for a rxn
-reusable to a point, not used up in rxn
-very specific, almost all chemical rxns are facilitated by enzymes

43
Q

Enzyme Binding to Substrate

A

Enzymes have Active Sites - where substrates (reactant) can bind to it
-binding of enzyme to substrate causes enzyme to change shape created induced fit between molecules, like a hug, called the ENZYME-SUBSTRATE COMPLEX

44
Q

How Enzymes Lower Activation Energy

A

-cause bonds to stretch or bend so they are easier to break
-bring two substrates together in correct position for rxn to occur
-transfer electrons/hydrogen ions to or from substrate, destablilizing to making it more likely to react

45
Q

Factors affecting Rates of Reaction

A

-Temperature
-pH
-Substrate concentration

46
Q

Inhibition (definition, function, and 2 types)

A

-Inhibitors are molecules that reduce the activity of enzyme by decreasing its ability to interact with substrates
-Temporary, to conserve energy
Competitive and Non-competitive

47
Q

Competitive Inhibition

A

Compete with substrate for binding to the same active site.
-Numbers game, if there are more inhibitors they will bind more, if there are more substrates they will bind more

48
Q

Non-Competitive/Allosteric Inhibition

A

Binds to ALLOSTERIC site on enzyme, causes shape of active site to change so that it reduces the ability for the substrate to bind to enzyme

49
Q

Allosteric Activation

A

allosteric activator binds to allosteric site fixing the distorted shape of active site and allowing for the substrate to bind to the active site.

50
Q

Biochemical Pathways and Feedback Inhibition

A

A series of rxns in which the product of one rxn becomes the substrate of the next rxn
-regulated by feedback inhibition, where end product of the pathway is an allosteric inhibitor of an earlier enzyme in the pathway.
-occurs when there is too much end product to temporarily prevent end product from being made, saving energy

51
Q

Cell Membrane

A

-helps maintain stable internal conditions of cell, maintains homeostasis
-All living cells exist in aqueous medium
-maintains integrity of the cell by regulating the passage of molecules and ion into and out of cell
-Phospholipid Bilayer

52
Q

Fluid Mosaic Model (structure/components)

A

-consists of semi-fluid phospholipid bilayer with proteins, cholesterol, and carbohydrates
-Polar ‘heads’ cluster together facing the water molecules, while the non-polar ‘tails’ are shielded from the water
-membrane lipids “fluid” - can move around a little
-held together by weak INTERmolecular forces, can move around freely
-if there is puncture phospholipids will quickly rearrange to seal the area

53
Q

Fluid Mosiac Model (functions)

A

Protective barrier
Transport: controls what goes in and out of cell (selectively permeable)
Rxn Catalysis
Cell Recognition: carb chains on outside recognize other cells
Signal Reception and transduction
Provides building site for enzymes

54
Q

Factors effecting fluidity of model

A

-Temperature: Increase in temp causes bilayer to be too fluid, decrease in temp causes bilayer to become too gel-like and prevent molecules from crossing
-Presence of double bonds: increased double bonds, too many kinks, less tightly packed, increases fluidity
-Length of F.A tail: long F.A tails increase intermolecular attractions, reducing fluidity
-Presence of cholesterol: at room temp or above it reduces fluidity, keeps human cells from being too fluid at body temp, at lower temp prevents bilayer from turning into solid gel-like state.

55
Q

Proteins in Bilayer

A

Integral: embedded in membrane, assist in transport

Peripheral: loosely attached to outer regions of the membrane

56
Q

Passive Transport (definition, types)

A

Movement of molecules across a membrane from a region of high to low concentration (ALONG its concentration gradient), WITHOUT the input of energy.
Types: Diffusion, Osmosis, Facilitated Diffusion

57
Q

Diffusion (definition and factors affecting rate of diffusion)

A

The net movement of ions or molecules from an area of higher concentration to lower concentration

Factors affecting rate:
-molecule size; decreases with increased molecule size
-molecule polarity; small polar molecules can cross, but at a lower rate than non-polar molecules of the same size
-molecule/ion charge: usually charged molecules/ions CANNOT diffuse across cell membrane
-temperature and pressure: increased temp and pressure increases rate of diffusion.

58
Q

Osmosis (definition, types of solutions, what plant/animal cells prefer)

A

The movement of water from area of high to low concentration, the movement of water toward an area of high SOLUTE concentration.

Isotonic solution: 2 solutions have SAME osmotic concentrations
HypERtonic solution: solution with higher solute concentration
HypOtonic solution: solution with lower solute concentration

Water moves through aquaporins TOWARD the hypERtonic solution.

Plant Cells: hypOtonic, cell wall stops cells from bursting
Animal Cells: isotonic

59
Q

Facilitated Diffusion (definition, 2 types of proteins)

A

Movement of molecule from high to low concentration across a cell membrane with the help of a protein (integral proteins).

Channel Proteins: polar interior, allowing SMALL polar molecules or ions to pass through, some remain open all the time, some dont, highly specific size and shape to determine what can go through
Carrier Protein: bind to specific LARGER polar molecules (such as glucose) to facilitate its passage, lower rates of diffusion than channel, as they can only transfer a few molecules at a time.

60
Q

Active Transport (definition, types)

A

Transport of a SOLUTE across a membrane AGAINST its concentration gradient, from low to high concentration. REQUIRES energy (ATP).
Types: Primary and Secondary

61
Q

Primary Active Transport (example and how it works)

A

Uses ATP directly
Sodium-Potassium Pump
-3 Na+ bind to integral/carrier protein from inside cell -ATP is hydrolyzed becoming ADP + P
-P attaches to protein, changing proteins shape to allow 3Na to exit the cell against its concentration gradient
-2K+ from outside cell want to go into the cell against their concentration gradient, bind to integral protein
-P group deattaches from protein, changing its shape, allowing the 2K to enter the cell
-Creates imbalance of Na+ and K+

62
Q

Secondary Active Transport (example and how it works)

A

Uses an electrochemical gradient as a source of energy to transport molecules or ions across a cell.
Electrochemical gradient: difference in charge and concentration, imbalance of charge against cell membrane, which is stored energy.

Hydrogen-Sucrose Pump
- needs primary to establish the electrochemical gradient
-H+ is transported out of cell by primary (low to high)
-then they use the H+ gradient and bring H+ back into cell (along gradient), releasing energy
-sucrose is needed in the cell and no ATP is available
-use energy from H+ diffusion to transport sucrose into the cell from low to high concentration

63
Q

Membrane-Assisted Transport (definition and types)

A

Sometimes molecules are too large to move through a channel protein or by using a carrier protein. Cells form vesicles around material using cell membrane.
Types: endocytosis and exocytosis, both require ATP from cells

64
Q

Endocytosis (definition and types + their definitions)

A

When cell engulfs material by folding cell membrane around it, then pinching off to form vesicle inside cell. Brings material INTO the cell.

Types:
-Phagocytosis: cell takes in SOLID particulate matter (cell-eating)
-Pinocytosis: cell takes in fluid (cell drinking)
-Receptor-mediated: specific molecules are taken in after they bind to a receptor, receptors are recycled for later use.

65
Q

Exocytosis (definition, uses)

A

Vacuole fuses with the cell membrane and releases its contents outside the cell. Brings materials OUT of cell. Used in animals to secrete hormones, neurotransmitters, digestive enzymes, and other substances.

Biology - SBI4U (4 decks)

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