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Biochemistry > Chapter 1 > Flashcards

Chapter 1 Flashcards

1
Q

what is biochem?

A

the interface of biology and chemistry

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2
Q

what are the 4 main small biomolecules?

A
  1. amino acids
  2. nucleotides
  3. simple sugars
  4. fatty acids
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3
Q

where is biochem often studied? what does this mean?

A

in vitro, or outside a living cell

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4
Q

what are catalysts?

A

biomolecules that increase the rate (catalyze) of reactions dramatically

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5
Q

what are catalysts essential for?

A

all living cells

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6
Q

give 5 of the many processes that catalysts are responsible for

A
  1. digestion
  2. fermentation
  3. metabolism
  4. apoptosis
  5. biofuel production
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7
Q

list and describe 2 examples of catalysts

A
  1. enzymes: proteins that catalyze reactions
  2. ribozymes: catalytic RNA
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8
Q

how do catalysts increase the rate of reactions?

A

by lowering the activation energy

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9
Q

how is biochem an applied science?

A

used to create methods that exploit cellular processes and enzymatic reactions

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10
Q

what are the 3 categories of the building blocks of life?

A
  1. main elements
  2. trace elements
  3. essential ions
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11
Q

what are main elements?

A

the elements that make up most of organisms

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12
Q

what 4 (plus an additional sometimes 5th) elements are super important in amino acids?

A

carbon, nitrogen, oxygen, hydrogen, sometimes sulfur

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13
Q

what are trace elements?

A

make up less than 1% of living things

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14
Q

how do trace elements work/are used?

A

used as cofactors, work with main elements for better and proper functioning

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15
Q

what are essential ions?

A

charged elements

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16
Q

what are essential ions involved in?

A
  1. signaling
  2. neurochemistry
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17
Q

give 5 examples of essential ions

A
  1. Ca2+
  2. Cl-
  3. Mg3+
  4. K+
  5. Na+
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18
Q

describe bare bones what a chemical bond is

A

atoms share electrons

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19
Q

how many times can carbon bond before filling it octet? what geometry is this?

A

4 times; if all four bonds used is called tetrahedral geometry

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20
Q

describe rotation around a sigma (single) bond and give an analogy

A

is easy, like sticking a board to a wall with one nail, can rotate easily

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21
Q

describe rotation around a pi (double) bond

A

impossible, like trying to rotate a board stuck in a wall with two nails

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22
Q

see flashcards for functional groups!!

A

go see them!!

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23
Q

what is the main function of amino acids?

A

build proteins

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24
Q

list 3 additional amino acid functions other than building proteins

A
  1. neurotransmission
  2. nitrogen metabolism
  3. energu conversion (BUT NOT A MAIN ENERGY SOURCE, INEFFICIENT)
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25
Q

what is the main function of nucleotides?

A

build nucleic acids (DNA and RNA)

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26
Q

list 3 additional functions of nucleotides other than building nucleic acids

A
  1. energy conversion
  2. signal transduction
  3. enzyme catalysis
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27
Q

what is the main function of simple sugars (CHOs)?

A

energy conversion

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28
Q

list 3 additional functions of simple sugars other than energy conversion

A
  1. cell wall structure
  2. cell recognition
  3. nucleotide structure
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29
Q

what is the main function of fatty acids?

A

linking noncovalently to form cell membranes both around and within cells

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30
Q

what do amino acids, nucleotides, and simple sugars all have in common?

A

they are monomers that link covalently to form polymers

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31
Q

what determines the identity of an amino acid?

A

the side chain; is the only variable part

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32
Q

how are amino acids linked?

A

covalently by peptide bonds

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33
Q

what do amino acids link covalently through peptide bonds to form?

A

peptides

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34
Q

what are large polypeptides called?

A

proteins

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35
Q

what is another name for simple sugars?

A

carbohydrates

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36
Q

what 3 atoms do carbohydrates contain?

A

C, H, O

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37
Q

what is the ratio of hydrogen atoms to oxygen atoms in carbohydrates?

A

2:1; 2 hydrogens for every oxygen

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38
Q

how are carbohydrates linked? what do they form when they link?

A

covalently through glycosidic bonds; form polysaccharides

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39
Q

what is a monosaccharide?

A

1 simple sugar

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40
Q

what a disaccharide?

A

two simple sugars linked

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41
Q

what type of molecules are fatty acids? what does this mean?

A

amphipathic; have a hydrophilic polar head group attached to a hydrophobic hydrocarbon chain

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42
Q

how do fatty acids assemble? what does this form?

A

via noncovalent interactions to form membranes

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43
Q

what do fatty acids act as?

A

a storage form of energy

44
Q

list 2 ways to describe macromolecules

A
  1. large molecules; functional units
  2. polymers: many units of monomers covalently linked together
45
Q

what are polymers?

A

many units of monomers covalently linked together

46
Q

what are 3 types of polymers and what are they made of?

A
  1. proteins: amino acid polymers
  2. nucleic acids: nucleotide polymers
  3. polysaccharides: sugar polymers
47
Q

what is the reaction that forms the peptide bonds that link amino acids to form proteins?

A

condensation (dehydration synthesis)

48
Q

how do you read amino acids?

A

from N-terminus to C-terminus

49
Q

where are new amino acids added?

A

to the C terminus

50
Q

what 3 atoms are the cue to recognize a full amino acid?

A

NCC

51
Q

what are the 2 ways to describe macromolecules?

A
  1. as large molecules; functional units
  2. as polymers; many unites of monomers covalently linked together
52
Q

what macromolecules are considered the workhorses of life that perform most biological functions?

A

proteins

53
Q

what is very important to the function of a protein?

A

the structure!

54
Q

give 3 examples of proteins performing biological functions

A
  1. enzymes like lipase metabolize fat
  2. antibodies like immunoglobulins kill bacteria and viruses
  3. transport proteins like hemoglobin deliver oxygen to cells
55
Q

define nucleic acids as macromolecules

A

genetic material that determines everything about an organism

56
Q

contrast the shape of DNA and RNA

A

DNA is double helix and RNA is single helix

57
Q

contrast the ribose sugar in DNA and RNA

A

DNA has deoxyribose sugar (hydrogen at 2’ carbon) and RNA has oxyribose sugar (OH at 2’ carbon)

58
Q

how are polymers of nucleotides (DNA and RNA) formed?

A

by covalently linked nucleotides via phosphodiester bonds from the 5’ to 3’ end

59
Q

during transcription, where are nucleotides added?

A

to the 3’ end, NEVER the 5’ end

60
Q

what are polysaccharides?

A

complex carbohydrates

61
Q

list and describe the 3 functions of polysaccharides

A
  1. structure: gliding motion in joints
  2. biomarkers: sugar flags for blood typing and virus detection
  3. energy: glycogen degradation
62
Q

how are simple sugars linked to form polysaccharides?

A

via variable glycosidic bonds

63
Q

what is key to the identification and chemical properties of a polysaccharide? (2)

A

orientation and position of the glycosidic bond

64
Q

give 2 types of glycosidic bonds

A

a-1,4 and a-1,6 linkages

65
Q

what is always the same about a glycosidic bond?

A

2 carbons (one from each ring) are connected via an oxygen outside the ring

66
Q

what are metabolites?

A

small biomolecules that serve as both reactants and products in biochemical reactions within cells

67
Q

what is metabolic flux?

A

the rate at which reactants and products are interconverted in a metabolic pathway

68
Q

what is influx?

A

the entry of metabolites into a pathway

69
Q

what it efflux?

A

the flow of metabolites out of a pathway

70
Q

what are the 3 types of metabolic pathways?

A
  1. linear
  2. forked
  3. cyclic
71
Q

how is cellular communication accomplished? (main actors)

A

proteins mostly

72
Q

give the general process of cellular communication

A
  1. a ligan binds to an extracellular receptor and causes a conformational change in the receptor protein to an active state
  2. once active, the receptor protein does its thang
  3. since the ligand is bound reversibly to the receptor protein, it detaches and causes another conformation change of that receptor protein back to inactive state
73
Q

what are the two types of nitrogenous base pairs?

A

purines and pyrimidines

74
Q

what are the 2 purines of DNA?

A

adenine and guanine

75
Q

what are the two pyrimidines of DNA?

A

cytosine and thymine

76
Q

which purines pair with which pyrimidines in DNA?

A

guanine with cytosine and
adenine with thymine pyrimidine

77
Q

what are the 2 purines of RNA

A

same as DNA, adenine and guanine

78
Q

what are the two pyrimidines of RNA?

A

cytosine and uracil

79
Q

what purines pair with which pyrimidines in RNA?

A

guanine with cytosine and
adenine with uracil

80
Q

which purine-pyrimidine bond is stronger and why?

A

G-C pair is stronger than A-T because there are 3 bonds between G-C and only 2 bonds between A-T or A-U

81
Q

which way do you read DNA?

A

5’ to 3’

82
Q

what is a gene?

A

a stretch of DNA that will eventually code for a protein

83
Q

what is a nucleosome?

A

a string of negatively charged DNA wrapped tightly around a postively charged histone; tightly packed to prevent damage

84
Q

what is chromatin?

A

multiple nucleosomes tightly packed together

85
Q

what is a chromosome?

A

tightlt packed chromatin

86
Q

what is a nucleus?

A

tightly packed chromosomes with a protective membrane

87
Q

give the levels of genetic structure from smallest to largest (5)

A
  1. gene
  2. nucleosome
  3. chromatin
  4. chromosome
  5. nucleus
88
Q

give the central dogma

A

DNA is transcribed into mRNA that is translated into proteins that do jobs

89
Q

will noncoding DNA ever become a protein?

A

no!

90
Q

what makes a codon?

A

3 nucleotide bases

91
Q

what are the 2 types of mutations?

A
  1. germ-line cell
  2. somatic cell
92
Q

describe germ-line cell mutations (2)

A
  1. passed from parents to offspring
  2. can result in inherited genetic diseases (ex. sickle cell anemia)
93
Q

describe somatic cell mutations (3)

A
  1. not inherited by offspring
  2. limited to individual organism
  3. can result in developed diseases (ex. cancer)
94
Q

what is the danger of mutation?

A

mutations can change the sequence and moleculer structure of proteins, which can affect function (could be real bad)

95
Q

what is an advantage of mutation?

A

evolution! could make organisms more fit for the environment

96
Q

how are phylogenetic trees created?

A

using bioinformatics

97
Q

describe how similar human DNA is to chimpanzee DNA (2)

A
  1. 98% is identical
    30% of proteins have the exact same sequence
98
Q

what are orthologous genes?

A
  1. similar genes in different species
  2. conserved sequence and function
  3. likely from common ancestral gene
99
Q

give an example of an orthologous gene

A

G6P dehydrogenase

100
Q

what are paralogous genes?

A

similar genes in the SAME species

101
Q

how are paralogous genes created?

A

through gene duplication, as there are only 3 possible outcomes for a codon

102
Q

give an example of a paralogous gene

A

nuclear receptors

103
Q

what is a genome?

A

a collection of all an organism’s genes

104
Q

what is a transcriptome?

A

a collection of all DNA transcripts (RNA products) generated by DNA transcription

105
Q

what is a proteome?

A

collection of all proteins produced by mRNA translation

106
Q

describe the determination of biomolecular structure and function

A

sequence determines structure determines function

Biochemistry (20 decks)

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