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Biology - SBI4U1 > Unit 1 - Biochemistry > Flashcards

Unit 1 - Biochemistry Flashcards

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1
Q

cell (plasma) membrane

A
  • phospholipid bilayer with embedded protein and carbohydrate molecules that surround the cell
  • is a semi-permeable membrane that allows only certain substances to enter (e.g. nutrients) and exit (e.g. metabolic wastes)
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2
Q

cell wall

A
  • found in plant cells only
  • made of cellulose
  • provides structural support
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3
Q

nucleus

A
  • separated from the cytoplasm by a double membrane called the nuclear envelope
  • spherical
  • “control center” of the cell
  • contains DNA
  • contains the nucleolus, which produces ribosomes
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4
Q

cytoplasm

A
  • consists of cytosol, an aqueous solution, and organelles
  • contains various chemicals and molecules (ions, amino acids, enzymes, ATP, carbohydrates, etc.)
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5
Q

vacuole

A
  • membrane-bound sac
  • much larger in plant cells
  • stores starch, molecules, water, and wastes
  • provides structural support to plants
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6
Q

ribosome

A
  • dense-looking, spherical granule
  • free-floating in cytoplasm or attaches to RER
  • synthesizes proteins (where amino acids are assembled into proteins)
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7
Q

endoplasmic reticulum (ER)

A
  • RER (rough endoplasmic reticulum): have ribosomes; are the site of protein synthesis
  • SER (smooth endoplasmic reticulum): don’t have ribosomes; manufacture lipids
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8
Q

golgi apparatus

A
  • flattened stack of membranes
  • receives and modifies fats and proteins produced by the ER
  • packages fats and proteins into vesicles for transport out of the cell (exocytosis)
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9
Q

lysosome

A
  • found in animal cells only
  • is a membrane-bound sac (vesicles) produced by the golgi apparatus and ER
  • contains hydrolytic enzymes
  • are like mini-stomachs
  • breaks down molecules and old organelles/cells, digests food particles, and destroys microorganisms
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10
Q

mitochondrion

A
  • rod-shaped
  • site of cellular respiration
  • glucose molecules are broken down to produce ATP
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11
Q

chloroplast

A
  • found in plant cells only
  • double-membrane
  • contains chlorophyll
  • site of photosynthesis
  • enables plants to convert sunlight, CO2 and H2O into glucose (C6H12O6)
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12
Q

molecular polarity

A
  • symmetrical arrangement of polar covalent bonds = non-polar molecule (e.g. CCl4)
  • asymmetrical arrangement of non-polar bonds = non-polar molecule (e.g. O3)
  • asymmetrical arrangement of polar bonds = polar molecule (e.g. NH3)
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13
Q

electronegativity

A

a measure of an atom’s ability to attract electrons of a covalent bond (fluorine (F) is the most electronegative, francium (Fr) is the most electropositive)

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14
Q

molecular shapes

A
  • tetrahedral (e.g. CH4)
  • pyramidal (e.g. NH3)
  • angular (e.g. H2O)
  • linear (e.g. HCl)
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15
Q

applications of radioisotopes

A

1. radiometric dating; measuring the carbon-12/carbon-14 ratio of dead organism or fossil
2. radioactive tracers in biological research; radioisotopes which flag various molecules and trace their path in vivo
3. radioactive tracers in nuclear medicine; diagnosis and treatment of various diseases

  • iodine-125 for bone density measurements
  • iodine-131 for thyroid monitoring
  • technetium-99
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16
Q

isotopes

A
  • atoms of an element with the same atomic number, but a different atomic mass (e.g. carbon-12 and carbon-14

EXAMPLE OF USEFULNESS: sulfur-33 used in human genome research

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17
Q

isomers

A
  • molecules that have the same atomic mass, but different atomic rearrangement (e.g. glucose and fructose (C6H12O6))

EXAMPLE OF USEFULNESS: used in clinical pharmacology, due to difference in properties

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18
Q

intermolecular forces of attraction

A
  • a.k.a. “van der Waals” forces
  • bonds amongst molecules
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19
Q

London forces

A
  • weakest intermolecular force of attraction
  • is between all molecules
  • e.g. methane (CH4(g))
  • number of associations determine the state of matter (more forces = g→s; and vice versa)
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20
Q

dipole-dipole attractions

A
  • “average-strengthed” intermolecular force of attraction
  • between polar molecules
  • e.g. between hydrogen chloride (HCL) molecules
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21
Q

hydrogen bonds

A
  • strongest intermolecular force of attraction
  • between polar molecules containing nitrogen, oxygen, or fluorine (H-N, H-O, or H-F)
  • e.g. between water (H2O) and ammonia (NH3) molecules
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22
Q

intramolecular forces of attraction

A

bonds within molecules

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23
Q

ionic bond

A
  • type of intramolecular bond
  • electrostatic attraction between oppositely charged ions
  • electrons are transferred
  • e.g. between sodium (Na) and chlorine (Cl) in sodium chloride (NaCl)
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24
Q

covalent bond

A
  • type of intramolecular bond
  • electrostatic attraction between nuclei and valence electrons of natural atoms
  • electrons are shared
  • e.g. between nitrogen atoms (N) in nitrogen gas (N2)
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25
Q

polar covalent bond

A
  • type of intramolecular bond
  • covalent bond with an electronegativity difference (EN) of 0-1.7
  • e.g. water (H2O); ΔEN = 1.24
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26
Q

acids

A
  • substances that release H+ ions in solution (proton donors)
  • e.g. HCL
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27
Q

bases

A
  • substances that accept H+ ions (proton acceptors), and sometimes produce OH- (hydroxide donors) in solution
  • e.g. NaOH
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28
Q

pH

A
  • the unit of measurement that describes the acidity or basicity of a solution
  • as [H+] concentration increases, acidity increases, and pH decreases
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29
Q

buffers

A
  • chemical systems that resist significant changes in pH; releasing H+ in solutions too basic, and absorbing H+ in solutions too acidic
  • usually consist of specific conjugate acid-base pairs (HCO3-(aq))
  • proteins may also act as buffers (e.g. hemoglobin)
  • e.g. carbonic acid/bicarbonate buffer system found in kidneys to resist significant changes of pH in bloodstream:

H2O(ℓ) + CO2(aq) ⇄ H2CO3(aq) ⇄ HCO-3(aq) + H+(aq)

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30
Q

ionization

A

the strength of an acid or base is relative to their ionization (breakdown)

Examples:

  • HCl → H+ + Cl-; ∴ strong acid (complete ionization)
  • CH3 → H+ + CH3COO-; ∴ weak acid (partial ionization)
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31
Q

neutralization

A
  • when an acid and a base react, a neutralization reaction occurs: the acid and base lose their acidic and basic properties respectively, producing water and a salt
  • e.g. HCL(aq) + KOH(aq) → H2O(ℓ) + KOH(aq)
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32
Q

oxidation-reduction reactions

A
  • a.k.a. REDOX reactions
  • the process in which electrons are transferred from one substance to another; the molecule which accepts electrons is “oxidized” (oxidation = loss of electrons), and the molecule which gives away electrons is “reduced” (reduction = gain of electrons)
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33
Q

functional groups

A
  • groups of elements that contribute to the formation of products in biochemical reactions
  • allow the interaction between biomolecules
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34
Q

hydroxyl

A

⎯ OH

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35
Q

carboxyl

A

⎯ COOH

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36
Q

amino

A

⎯ NH2

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37
Q

sulfhydryl

A

⎯ SH

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38
Q

phosphate

A

⎯ PO4

39
Q

aldehyde

A

⎯ COH

40
Q

ketone

A

⎯ CO ⎯

41
Q

dehydration synthesis

A

the formation of a covalent bond between two molecules with the production of a water molecule

42
Q

hydrolysis

A

the breakdown of a covalent bond, due to the addition of a water molecule

43
Q

carbohydrates

A
  • macromolecules composed of carbon, hydrogen, and oxygen atoms
  • simplest and quickest sources of energy
  • either simple (mono/disaccharides), or complex (polysaccharides)
44
Q

monosaccharides

A
  • simple carbohydrates
  • ratio of C:H:O = 1:2:1
  • e.g. glucose
45
Q

monosaccharide classification

A

classified according to the number of carbons or the functional group

number of carbons:

  • triose sugars; have 3 carbons
  • pentose sugars; have 5 carbons
  • hexose sugars; have 6 carbons

functional group:

  • aldoses; have an aldehyde (⎯ COH)
  • ketoses; have a ketone (⎯ CO⎯)
46
Q

disaccharides

A
  • simple carbohydrates composed of two monosaccharadies, combined via α 1-4 glycosidic linkages (dehydration synthesis)
  • formula for disaccharides = C12H22O11

MUST-KNOW EXAMPLES:
α-glucose + α-glucose = maltose
α-glucose + fructose = sucrose
α-glucose + galactose = lactose

47
Q

polysaccharides

A
  • complex carbohydrates (carbohydrate polymers) composed of many monosaccharides via α 1-4 glycosidic linkages, and sometimes α 1-6 glycosidic linkages
  • number of particles - 1 = number of linkages

MUST-KNOW EXAMPLES:
many α-glucoses = starch (amylopectin)
many β-glucoses = cellulose

48
Q

examples of polysaccharides in biology

A
  • glycogen is used for temporary storage in the liver
  • cellulose gives structure and form to plants
  • chitin is found in the exoskeleton of insects
49
Q

lipids

A
  • macromolecules composed of carbon, hydrogen, and oxygen atoms, with a high proportion of non-polar carbon–hydrogen bonds
  • store energy and regulate hormones

4 main types:
1. triglycerols/triglycerides
2. phospholipids
3. steroids
4. waxes (only one not made up of fatty acids)

50
Q

fatty acids

A
  • made of a carboxylic acid as the head, and a hydrocarbon tail
  • max amount of H’s = saturated; solid at room temperature (e.g. butter)
  • not the max amount of H’s = unsaturated; carbon-carbon double bonds, and “kink” (bend) in the tail; liquids at room temperature (e.g. olive oil)
51
Q

triglycerides

A

lipids composed of a glycerol molecule (C3H8O3) and three fatty acids linked by ester bonds via esterification (dehydration synthesis)

52
Q

phospholipids

A
  • lipids composed of a glycerol molecule (C3H8O3), two fatty acids, and a phosphate group with a R group; linked by ester bonds via esterification (dehydration synthesis)
  • made of a hydrophilic head (phosphate and glycerol), and hydrophobic tails (fatty acids); are polar molecules
53
Q

lipid bilayers

A
  • made up of hydrophilic heads directed towards aqueous solutions, and hydrophobic tails tucked away from aqueous solutions, interacting with each other
  • found in micelles and the cell membrane
54
Q

steroids

A
  • lipids composed of four attached carbon-based rings
  • are chemical messengers
  • aid in cell-to-cell communication
  • a lot of them are hormones

EXAMPLES:

  • cholesterol (pre-cursor steroid)
  • estradiol (an estrogen)
  • testosterone (an androgen; mostly in males)
  • progesterone (a progestin; mostly in females)
55
Q

proteins

A
  • macromolecules composed of amino acid monomers linked by covalent bonds
  • are folded and functional polypeptides (peptide bonds link amino acids together)
  • serve many functions: including acting as enzymes, providing structural support, regulating passage of substances across the cell membrane, and maintaining pH levels
56
Q

denaturation

A

the process in which proteins can potentially unfold

57
Q

amino acids

A
  • an organic molecule composed of an amino group (amino), a central carbon atom, an R group, and a carboxyl group (acid)
  • humans have 20 amino acids (proteins are made of up to 20 different types of amino acids
  • can be ionized (H3N+ amino group), or crystalline (H2N amino group)
58
Q

4 levels of protein structural organization

A

1. primary structure

  • linear sequence of amino acids

2. secondary structure

  • hydrogen bonding between amino acids result in a coil-like shape (α-helix) or a fan-like shape (β-pleated sheet)

3. tertiary structure

  • composed of one folded polypeptide
  • e.g. myoglobin

4. quaternary structure

  • composed of many polypetides
  • found in bigger proteins
  • e.g. hemoglobin (composed of 4 subunits (polypeptides))
59
Q

types of amino acids

A

nonpolar

  • composed of H or CH3, and aliphatic (open-chained) R-groups
  • hydrophobic

polar

  • composed of O, NH2, or SH
  • hydrophilic

electrically charged

  • acidic (negative charge) or basic (positive charge) composed of a negative or positive change in the R-group respectively
60
Q

protein synthesis

A

amino acids are joined together via peptide bonds and dehydration synthesis; DNA specifies the order in which the amino acids follow one another

61
Q

protein shape

A
  • either globular (e.g. hemoglobin) or fibrous (e.g. keratin)
  • polypeptide forming occurs in the Golgi bodies

things that affect the shape of a polypeptide:

  • hydrogen bonds: between two polar amino acids (can be broken with high temperature)
  • proline kink: formation of a bend in a proline amino acid, as it folds in on itself
  • hydrophobic and van der Waals interactions: hydrophobic association between two non-polar amino acids (can be broken with high temperature)
  • disulfide bridge: covalent linkage between two cysteine amino acids (very strong; needs a REDOX agent to break it)
  • ionic bonds: associations between two oppositely charged amino acids (can be broken with high temperature)
62
Q

nucleic acids

A
  • macromolecules composed of nucleotide monomers
  • DNA or RNA
  • are acidic; H+ donors
  • carry genetic information
63
Q

nucleotides

A

organic molecules composed of a phosphate group, a pentase sugar, and a nitrogenous base

64
Q

DNA

A
  • contains deoxyribonucleotide monomers; A, G, T, C
  • contains deoxyribose
  • serves as a guide to make proteins
  • homes the genetic code of an organism
65
Q

RNA

A
  • contains ribonucleotide monomers; A, G, U, C
  • contains the sugar ribose
  • many functions and forms (mRNA, tRNA, mtRNA, rRNA, gRNA, etc.)
66
Q

Benedict’s reagent

A

an indicator used to identify the presence of monosaccharides and some disaccharides; turns a different colour depending on the sugar concentration

  • blue colour: nil
  • light green colour: 0.5%-1.0% concentration
  • green to yellow colour: 1.0%-1.5% concentration
  • orange colour: 1.5%-2.0% concentration
  • red to red brown colour: 2.0%< concentration
67
Q

Lugol’s solution

A

an indicator used to identify the presence of complex carbohydrates; turns from a brown to a blue-black colour in the presence of starch (complex carbohydrates)

68
Q

Sudan IV solution

A

an indicator used to identify the presence of lipids; turns from a pink to a red colour in the presence of lipids

69
Q

Biuret reagent

A

an indicator used to identify the presence of proteins; turns a different colour depending on the relative amounts of peptide bonds (from “-“ (none) to “+++”)

  • blue: -
  • pink: +
  • violet: ++
  • purple: +++
70
Q

The Fluid Mosaic Model of Cell Membranes

A
  • the accepted model of the cell membrane
  • “Fluid”: parts move around (dynamic nature; not static)
  • “Mosaic”; made up of many different components

features of the model:

  • carbohydrate chains: make up glycoproteins, which can recognize harmful cells
  • protein chains: can act as receptors
  • phospholipid bilayer: separates the extracellular fluid (E.C.F) and the intracellular fluid (I.C.F.)
  • cholesterol: stabilizes the cell membrane
  • globular proteins: can act as transport channels
71
Q

micelles

A
  • non-specific vehicles which can carry hydrophobic substances - even nucleic acid - for gene therapy and vaccination administration
  • made of phospholipids
72
Q

permeability factors of the cell membrane

A
  • phospolipids are not static; they move laterally, or - rarely - flip flop

The degree of fatty acid tail hydrogen saturation will dictate cell membrane permeability:
* unsatured hydrocarbon tails with kinks are more porous, and therefore more permeable
* saturated hydrocarbon tails with no kinks are less permeable

The amount of cholesterol within the phospholipids will also dictate cell membrane permeability:
* more cholesterol means more permeability
* less cholesterol means less permeability

73
Q

functions of integral proteins

A
  • transport channel: can transport substances into the cell
  • enzyme: acts as a biological catalyst to speed up reactions
  • receptor site: ligands bind to receptors (e.g. hormones) and change shape; the causes a cascade of reactions called “signal transduction”
  • cell identity marker: carbohydrate chains that protude from glycoproteins enable cells to recognize each other, and therefore identify “intruders”; can be used to detect various cancers and infections
  • cell adhesion: used for tissue formation
  • attachment of cytoskeleton: maintain cell shape and form (proteins, microfilaments, microtubules and spindle fibers, etc.)
74
Q

The Genetic Dogma

A

the process of which DNA is USED (not TRANSFORMED) to create proteins

1. DNA replication: DNA is replicated during the S phase of the cell cycle within the nucleus
2. DNA transcription: a strand of DNA is copied into a molecule of messenger RNA (mRNA) within the nucleus
3. DNA translation: mRNA is used in the process of protein synthesis within the RER, and polypeptide folding (packaging and modifying of proteins) within the Golgi bodies; the new protein is then excreted outside of the cell membrane via exocytosis and vesicles

75
Q

enzymes

A
  • organic substances that speed up biochemical reactions; is mostly proteins
  • are specific to substrates
  • e.g. amylase
76
Q

substrates

A
  • the reactant that an enzyme acts on
  • e.g. amylose
77
Q

enzymatic action

A
  • follows the “induced-fit model” (a.k.a. the “hand in glove model”), NOT the “lock and key model”; the enzyme/substrate changes shape to fit the other

EXAMPLE: (maltose → glucose + galactose)
1. Maltase (the enzyme) binds with maltose (the substrate) at the active site.
2. Hydrolysis takes place, and there is a conformation change of the enzyme.
3. The enzyme recycles (reverts to it’s original shape), and the glucoses (the products) are released.

78
Q

factors that affect enzyme activity

A

pH

  • enzymes tend to have an optimal pH level in which they work

temperature

  • increase in temperature means the enzyme denatures and theres a loss of activity
  • decrease in temperature means the activity is reduced, but is restored when the temperature is raised (is reversible)

concentration

presence of co-factors and co-enzymes

  • co-factors are inorganic non-proteins (e.g. ions; Zn2+, Mg2+)
  • co-enzymes are organic non-proteins (e.g. vitamins; Vitamin B3, NAD+, NADP)
79
Q

characteristics of enzymatic action

A

1. optimal conditions: each enzyme operate at optimal conditions

  • e.g. pepsin (in stomach; digests proteins) will operate best at pH3
  • e.g. trypsin (in duodenum; digests proteins) will operate best at pH8

2. specificity: every enzyme is specific for it’s substrate

  • e.g. amylase breaks down amylose

3. sensitivity: refers to an enzyme’s binding affinity (degree of attraction) to it’s substrate

80
Q

enzymatic regulation

A

1. Competitive inhibitors: the active site of the enzyme is blocked directly by the competitive inhibitor; prohibiting the substrating from binding with the enzyme
2. Non-competitive inhibitors: the non-competitive inhibitor binds allosterically (not in the active site; causing a change in the shape of the active site, and prohibiting the substrate from binding with the enzyme
3. Allosteric activators and inhibitors
* allosteric activators bind to the active site of an enzyme and keep an enzyme active, or cause an increase in activity (ACTIVE FORM)
* allosteric inhibitors bind to the active site of an enyzme and causes the enzyme to be inactive, or cause a decrease in activity (INACTIVE FORM)

81
Q

biochemical pathways

A

A –(Ase)-> B –(Base)-> C –(Case)-> D

(If there’s too much/not enough product (D), it can act as an allosteric activator/inhibitor to produce less/more activity at A.)

82
Q

enzymes in society

A

1. food industry; e.g. lactase in dairy/cheese
2. sanitation; e.g. enzymes in detergents (doesn’t work in higher temperatures), lipases
3. ethanol production; e.g. maltases

83
Q

diffusion

A

the net movement of substances from an area of higher to lower concentration

84
Q

osmosis

A

the movement of water from an area of higher to lower concentration, across a semipermeable membrane

85
Q

passive transport

A

the movement of substances from an area of higher to lower concentration, without the input of energy

86
Q

active transport

A

the transport of a solute across a membrane against the concentration gradient

87
Q

endocytosis

A

process where the cell membrane ingulfs extracellular material to bring it inside the cell

88
Q

phagocytosis

A

endocytosis of solid particles

89
Q

pinocytosis

A

endocytosis of liquid particles

90
Q

exocytosis

A

process in which a vacuole fuses with the cell membrane, and releases its contents outside of the cell

91
Q

isotonic solution

A
  • equal osmotic pressure
  • no net movement of water
92
Q

hypotonic solution

A
  • lower osmotic pressure
  • water enters the cell; the cell grows
93
Q

hypertonic solution

A
  • higher osmotic pressure
  • water leaves the cell; the cell shrinks
94
Q

hydrogenation

A

adding more hydrogen atoms to unsaturated fats

Biology - SBI4U1 (5 decks)

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