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dat exam study > bio ch 1: molecules and fundamentals of biology > Flashcards

bio ch 1: molecules and fundamentals of biology Flashcards

1
Q

matter

A

anything that takes up space and has mass

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2
Q

element

A

a pure substance that has specific physical/chemical properties and can’t be broken down into a simpler substance

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3
Q

atom

A

the smallest unit of matter that still retains the chemical properties of the element

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4
Q

molecule

A

two or more atoms joined together

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5
Q

intramolecular forces

A

attractive forces that act on atoms within a molecule

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6
Q

intermolecular forces

A

forces that exist between molecules and affect physical properties of the substance

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7
Q

monomers

A

single molecules that can potentially polymerize

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8
Q

polymers

A

substances made up of many monomers joined together in chains

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9
Q

polymerization

A

any process in which relatively small molecules, called monomers, combine chemically to produce a very large chainlike or network molecule

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10
Q

carbohydrates

A

contains carbon, hydrogen, and oxygen atoms (CHO)
- comes in the form of monosaccharides, disaccharides, and polysaccharides

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11
Q

monosaccharides

A

carbohydrate monomers with an empirical formula of (CH2O)n
- “n” represents the number of carbons

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12
Q

ribose

A

five carbon monosaccharide

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13
Q

fructose

A

six carbon monosaccharide

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14
Q

glucose

A

six carbon monosaccharide

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15
Q

relationship between fructose and glucose

A

isomers- same chemical formula, different arrangement of atoms

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16
Q

disaccharides

A

contain two monosaccharides joined together by a glycosidic bond

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17
Q

glycosidic bond

A

a type of covalent bond that joins a carbohydrate (sugar) molecule to another group
- the result of a dehydration (condensation) reaction

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18
Q

dehydration (condensation) reaction

A

reaction where a water molecule leaves and a covalent bond forms

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19
Q

hydrolysis reaction

A

a covalent bond is broken by the addition of water

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20
Q

sucrose

A

disaccharide made of glucose + fructose

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21
Q

lactose

A

disaccharide made of galactose + glucose

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22
Q

maltose

A

disaccharide made of glucose + glucose

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23
Q

polysaccharides

A

contain multiple monosaccharides connected by glycosidic bonds to form long polymers

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24
Q

starch

A

form of energy storage for plans and is an alpha bonded polysaccharide

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25
Q

amylose

A

linear form of starch

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26
Q

amylopectin

A

branched form of starch

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27
Q

mnemonic to remember amylose vs amylopectin

A

amylopectin has more branching letters (y, l, p, t) than amylose (y, l)
- making amylopectin the more branched form

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28
Q

glycogen

A

form of energy storage in animals
- alpha bonded polysaccharide
- has more branching between starch

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29
Q

bonds found in both starch and glycogen

A

a-1,4-glycosidic bonds
a-1,6-glycosidic bonds

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30
Q

cellulose

A

structural component in plant cell walls
- beta bonded polysaccharide
- linear strands are packed rigidly in parallel

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31
Q

chitin

A

structural component in fungi cell walls and insect exoskeletons
- beta bonded polysaccharide with nitrogen added to each monomer

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32
Q

proteins

A

contain carbon, hydrogen, oxygen, and nitrogen atoms (CHON)

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33
Q

amino acids

A

the monomers of proteins
- formed from carbon, hydrogen, oxygen, and nitrogen atoms
- twenty different kinds, each having a different r-group

structure of a.a.
- amino group
- hydrogen
- carboxyl group
- r-group (varies)

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34
Q

polypeptides (proteins)

A

polymers of amino acids, joined by peptide bonds
- done through dehydration (condensation reactions)
- hydrolysis reactions break peptide bonds, polypeptide becomes an amino acid chain that contains two end terminals on opposite sides (N and C)

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35
Q

proteome

A

refers to all the proteins expressed by one type of cell under one set of conditions

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36
Q

N-terminus (amino terminal)

A

the side of a polypeptide that is the side that ends with the last amino acid’s amino group

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37
Q

C-terminus (carboxyl terminal)

A

the side of a polypeptide that is the side that ends with the last amino acid’s carboxyl group

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38
Q

conjugated proteins

A

proteins that are composed of amino acids and non-protein components
- examples: metalloproteins, glycoprotein

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39
Q

metalloproteins

A

proteins that contain a metal ion cofactor
- e.g. hemoglobin

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40
Q

glycoprotein

A

proteins that contain a carbohydrate group
- e.g. mucin

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41
Q

primary structure of a protein

A

sequence of amino acids connected through peptide bonds

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42
Q

secondary structure of a protein

A

intermolecular forces between the polypeptide backbone (not R-groups) due to hydrogen bonding
- forms alpha helices or beta pleated sheets

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43
Q

tertiary structure of a protein

A

3D structure due to interactions between R-groups
- can create hydrophobic interactions based on the R-groups
- hydrogen bonding and and ionic bonding between R groups also hold together the tertiary structure

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44
Q

disulfide bonds

A

part of tertiary structure
- created by covalent bonding between the R-groups of two cysteine amino acids

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45
Q

quaternary structure

A

multiple polypeptide chains come together to form one protein

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46
Q

protein denaturation

A

describes the loss of protein function and higher order structures
- only the primary structure is unaffected

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47
Q

causes for protein denaturation

A
  • high or low temperatures
  • pH changes
  • salt concentrations

ex: cooking an egg in egg in high heat will disrupt the intermolecular forces in the egg’s proteins, causing it to coagulate

48
Q

protein function: storage

A

reserve of amino acids

49
Q

protein function: hormones

A

signaling molecules that regulate physiological processes

50
Q

protein function: receptors

A

proteins in cell membranes which bind to signal molecules

51
Q

protein function: structure

A

provide strength and support to tissues (hair, spider silk)

52
Q

protein function: immunity

A

antibodies that protect against foreign substances

53
Q

protein function: enzymes

A

regulate rate of chemical reactions

54
Q

catalysts

A

increase reaction rates by lowering the activation energy of a reaction
- reduces the energy of the transition state
- does not shift a chemical reaction or affect spontaneity

55
Q

transition state

A

the unstable conformation between the reactants and the products

56
Q

enzymes

A

act as biological catalysts by binding to substrates (reactants) an converting them into product
- binds at active sites of substrates, these active sites are specific for the substrate that it acts upon
- most enzymes are proteins
- protein enzymes are susceptible to denaturation, they require optimal temperatures and pH for function

57
Q

specificity constant

A

measures how efficient an enzyme is at binding to the substrate and converting it to a product

58
Q

induced fit theory

A

describes how the active site molds itself and changes shape to fit the substrate when it binds
- outdated theory: “lock and key” model

59
Q

ribozyme

A

RNA molecule that can act as an enzyme (a non-protein enzyme)

60
Q

cofactor

A

non-protein molecule that helps enzymes preform reactions

61
Q

coenzyme

A

organic cofactor (i.e. vitamins)
- inorganic cofactors are usually metal ions

62
Q

holoenzymes

A

enzymes that are bound to their cofactors

63
Q

apoenzymes

A

enzymes that are not bound to their cofactors

64
Q

prosthetic groups

A

cofactors that are tightly or covalently bonded to their enzymes

65
Q

ways that enzymes catalyze reactions (4):

A
  1. conformational changes that bring reactive groups closer
  2. the presence of acidic or basic groups
  3. induced fit of the enzyme-substrate complex
  4. electrostatic attractions between the enzyme and substrate
66
Q

phosphatase

A

cleaves a phosphate group off of a substrate molecule

67
Q

phosphorylase

A

directly adds a phosphate group to a substrate molecule by breaking bonds within a substrate molecule

68
Q

kinasse

A

indirectly adds a phosphate group to a substrate molecule by transferring a phosphate group from an ATP molecule
- these enzymes do not break bonds to add the phosphate group

69
Q

feedback regulation of enzymes

A

the end product of an enzyme-catalyzed reaction inhibits the enzyme’s activity by binding to an allosteric site

70
Q

competitive inhibition

A

occurs when a competitive inhibitor competes directly with the substrate for active site binding.
- in competitive inhibition, adding more substrate can increase enzyme action

71
Q

noncompetitive inhibition

A

occurs when the noncompetitive inhibitor binds to an allosteric site that modifies the active site
- in noncompetitive inhibition, the rate of enzyme action cannot be increased by adding more substrate

72
Q

allosteric site

A

a location on an enzyme that is different from the active site

73
Q

enzyme kinetics plot

A

used to visualize how inhibitors affect enzymes
1. x-axis represents substrate concentration [X], while the y-axis represents reaction rate or velocity (V)
2. Vmax is the maximum reaction velocity
3. Michaelis Constant (Km) is the substrate concentration [X] at which the velocity (V) is 50% of the maximum reaction velocity (Vmax)
4. saturation occurs when all active sites are occupied, so the rate of reaction does not increase anymore despite increasing substrate concentration (causes graph plateaus)

74
Q

competitive inhibition (on enzyme kinetics plot)

A
  • Km increases
  • Vmax stays the same
75
Q

noncompetitive inhibition (on enzyme kinetics plot)

A
  • Km stays the same
  • Vmax decreases
76
Q

lipids

A

contains carbon, hydrogen, and oxygen atoms (CHO)
- similar to carbohydrates
- have long hydrocarbon tails that make them very hydrophobic

77
Q

triacylglycerol (triglyceride)

A

lipid molecule with a glycerol backbone (three carbons and three hydroxyl groups) and three fatty acids (long hydrocarbon tails)

78
Q

what are glycerol and the three fatty acids connected by in triglyceride

A

ester linkages

79
Q

saturated fatty acids

A

have no double bonds and as a result pack tightly (solid at room temp)

80
Q

unsaturated fatty acids

A

have double bonds
- can be divided into monounsaturated fatty acids (one double bond) and polyunsaturated fatty acids (two or more double bonds)

81
Q

cis-unsaturated fatty acids

A

have kinks that cause the hydrocarbon tails to bend
- as a result they do not pack tightly

82
Q

trans-unsaturated fatty acids

A

have straighter hydrocarbon tails
- as a result they pack tightly

83
Q

phospholipids

A

lipid molecules that have a glycerol backbone, one phosphate group, and two fatty acid tails
- the phosphate group is polar, while the fatty acid tails are nonpolar
- they are amphipathic
- can spontaneously assemble to form lipid bilayers

84
Q

amphipathic

A

both hydrophobic and hydrophilic

85
Q

cholesterol

A

an amphipathic lipid molecule that is a component of the cell membranes
- most common precursor to steroid hormones (lipids with four hydrocarbon rings)
- starting material for vitamin D and bile acids)

86
Q

factors that influence membrane fluidity

A
  1. temperature: an increase in temperature increases fluidity, a decrease in temperature decreases fluidity
  2. cholesterol: holds membrane together at high temperatures and keeps membrane fluid at low temperatures
  3. degrees of unsaturation: saturated fatty acids pack more tightly than unsaturated fatty acids, which have double bonds that may introduce kinks
87
Q

lipoproteins

A

allow the transport of lipid molecules in the bloodstream due to an outer coat of phospholipids, cholesterol, and proteins

88
Q

low-density lipoproteins (LDLs)

A

have low protein density and work to deliver cholesterol to peripheral tissues
- sometimes considered “bad cholesterol” because it can cause vessel blockage and heart disease

89
Q

high-density lipoproteins (HDLs)

A

have high protein density and take cholesterol away from peripheral tissues
- considered “good cholesterol” because they deliver cholesterol to the liver to make bile (reduces blood lipid levels)

90
Q

waxes

A

simple lipids with long fatty acid chains connected to monohydroxy alcohols (contain a single hydroxyl group) through ester linkages
- used mainly as hydrophobic protective coatings

91
Q

carotenoids

A

lipid derivatives containing long carbon chains with conjugated double bonds and six-membered rings at each end
- functions mainly as pigments

92
Q

sphingolipids

A
  • have a backbone with aliphatic (non-aromatic) amino alcohols and have important functions in structural support, signal transduction, and cell recognition
93
Q

glycolipids

A

lipids found in the cell membrane with a carbohydrate group attached instead of a phosphate group in phospholipids
- like phospholipids, they are amphipathic and contain a polar head and a fatty acid chain

94
Q

nucleic acids

A

contains carbon, hydrogen, oxygen, nitrogen, and phosphorus atoms (CHONP)
- contains nucleotide monomers that build into DNA and RNA polymers

95
Q

nucleosides

A

contain a five-carbon sugar and a nitrogenous base

96
Q

nucleotides

A

contain a five-carbon sugar, a nitrogenous base, and a phosphate group

97
Q

deoxyribose sugars

A

found in DNA have a hydrogen at the 2’ carbon while ribose five-carbon sugars (in RNA) have a hydroxyl group at the 2’ carbon

98
Q

nitrogenous bases found in DNA

A

(A) adenine
(T) thymine
(C) cytosine
(G) guanine

99
Q

what nucleotide replaces thymine in RNA

A

uracil (U)

100
Q

what nitrogenous bases are purines

A

A and G
- they have a two-ringed structure

101
Q

what nitrogenous bases are pyrimidines

A

C, U, and T
- they have a one-ringed structure

102
Q

PUR As Gold

A

PURines are Adenine and Guanine

103
Q

CUT the PY

A

Cytosine, Uracil, and Thymine are PYrimidines

104
Q

phosphodiester bonds

A

formed through a condensation reaction where the phosphate group of one nucleotide (at the 5’ carbon) connects to the hydroxyl group of another nucleotide (at the 3’ carbon) and releases a water molecule as a by-product

105
Q

what creates the sugar-phosphate backbone

A

a series of phosphodiester bonds
- with a 5’ end (free phosphate) and a 3’ end (free hydroxyl)

nucleic acid polymerization proceeds as nucleoside triphosphates are added to the 3’ end of the sugar-phosphate backbone

106
Q

antiparallel double helix

A

two complementary strands with opposite directionalities (positioning of 5’ ends and 3’ ends) twist around each other

107
Q

nitrogenous bases and H-bonding

A
  • adenine can only H-bond to thymine (using two hydrogen bonds)
  • guanine can only H-bond to cytosine (using three hydrogen bonds)
108
Q

mRNA

A

messenger RNA
- single stranded after being copied from DNA during transcription
- in RNA, uracil binds to adenine, replacing thymine

109
Q

miRNA

A

micro DNA
- small RNA molecules that can silence gene expression by base pairing to complementary sequences in mRNA

110
Q

rRNA

A

ribosomal RNA
- formed in the nucleolus of the cell and helps ribosomes translate mRNA

111
Q

dsRNA

A

double stranded RNA
- some viruses carry their code as double stranded RNA
- dsRNA must pair its nucleotides, so it must have equal amounts of A/U and C/G

112
Q

tRNA

A

transfer RNA
- small RNA molecule that participates in protein synthesis

113
Q

modern cell theory (7 points)

A
  1. all lifeforms have one or more cells
  2. the cell is the basic structural, functional, and organizational unit of life
  3. all cells come from other cells (cell division)
  4. genetic information is stored and passed down through DNA
  5. an organism’s activity is dependent on the total activity of its independent cells
  6. metabolism and biochemistry (energy flow) occurs within cells
  7. all cells have the same chemical composition within organisms of similar species
114
Q

central dogma of genetics

A

information is passed from DNA –> RNA –> proteins
- there are a few exceptions to this (e.g. reverse transcriptase and prions)

115
Q

each cell consists of what

A
  • nucleic acids
  • cytoplasm
  • cell membrane
116
Q

specialized organelles

A

organelles that have specific functions within the cell
- mitochondria
- chloroplasts

dat exam study (2 decks)

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