Chapter 1 Flashcards
1
Q
what is biochem?
A
the interface of biology and chemistry
2
Q
what are the 4 main small biomolecules?
A
- amino acids
- nucleotides
- simple sugars
- fatty acids
3
Q
where is biochem often studied? what does this mean?
A
in vitro, or outside a living cell
4
Q
what are catalysts?
A
biomolecules that increase the rate (catalyze) of reactions dramatically
5
Q
what are catalysts essential for?
A
all living cells
6
Q
give 5 of the many processes that catalysts are responsible for
A
- digestion
- fermentation
- metabolism
- apoptosis
- biofuel production
7
Q
list and describe 2 examples of catalysts
A
- enzymes: proteins that catalyze reactions
- ribozymes: catalytic RNA
8
Q
how do catalysts increase the rate of reactions?
A
by lowering the activation energy
9
Q
how is biochem an applied science?
A
used to create methods that exploit cellular processes and enzymatic reactions
10
Q
what are the 3 categories of the building blocks of life?
A
- main elements
- trace elements
- essential ions
11
Q
what are main elements?
A
the elements that make up most of organisms
12
Q
what 4 (plus an additional sometimes 5th) elements are super important in amino acids?
A
carbon, nitrogen, oxygen, hydrogen, sometimes sulfur
13
Q
what are trace elements?
A
make up less than 1% of living things
14
Q
how do trace elements work/are used?
A
used as cofactors, work with main elements for better and proper functioning
15
Q
what are essential ions?
A
charged elements
16
Q
what are essential ions involved in?
A
- signaling
- neurochemistry
17
Q
give 5 examples of essential ions
A
- Ca2+
- Cl-
- Mg3+
- K+
- Na+
18
Q
describe bare bones what a chemical bond is
A
atoms share electrons
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
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
21
Q
describe rotation around a pi (double) bond
A
impossible, like trying to rotate a board stuck in a wall with two nails
22
Q
see flashcards for functional groups!!
A
go see them!!
23
Q
what is the main function of amino acids?
A
build proteins
24
Q
list 3 additional amino acid functions other than building proteins
A
- neurotransmission
- nitrogen metabolism
- energu conversion (BUT NOT A MAIN ENERGY SOURCE, INEFFICIENT)
25
what is the main function of nucleotides?
build nucleic acids (DNA and RNA)
26
list 3 additional functions of nucleotides other than building nucleic acids
1. energy conversion
2. signal transduction
3. enzyme catalysis
27
what is the main function of simple sugars (CHOs)?
energy conversion
28
list 3 additional functions of simple sugars other than energy conversion
1. cell wall structure
2. cell recognition
3. nucleotide structure
29
what is the main function of fatty acids?
linking noncovalently to form cell membranes both around and within cells
30
what do amino acids, nucleotides, and simple sugars all have in common?
they are monomers that link covalently to form polymers
31
what determines the identity of an amino acid?
the side chain; is the only variable part
32
how are amino acids linked?
covalently by peptide bonds
33
what do amino acids link covalently through peptide bonds to form?
peptides
34
what are large polypeptides called?
proteins
35
what is another name for simple sugars?
carbohydrates
36
what 3 atoms do carbohydrates contain?
C, H, O
37
what is the ratio of hydrogen atoms to oxygen atoms in carbohydrates?
2:1; 2 hydrogens for every oxygen
38
how are carbohydrates linked? what do they form when they link?
covalently through glycosidic bonds; form polysaccharides
39
what is a monosaccharide?
1 simple sugar
40
what a disaccharide?
two simple sugars linked
41
what type of molecules are fatty acids? what does this mean?
amphipathic; have a hydrophilic polar head group attached to a hydrophobic hydrocarbon chain
42
how do fatty acids assemble? what does this form?
via noncovalent interactions to form membranes
43
what do fatty acids act as?
a storage form of energy
44
list 2 ways to describe macromolecules
1. large molecules; functional units
2. polymers: many units of monomers covalently linked together
45
what are polymers?
many units of monomers covalently linked together
46
what are 3 types of polymers and what are they made of?
1. proteins: amino acid polymers
2. nucleic acids: nucleotide polymers
3. polysaccharides: sugar polymers
47
what is the reaction that forms the peptide bonds that link amino acids to form proteins?
condensation (dehydration synthesis)
48
how do you read amino acids?
from N-terminus to C-terminus
49
where are new amino acids added?
to the C terminus
50
what 3 atoms are the cue to recognize a full amino acid?
NCC
51
what are the 2 ways to describe macromolecules?
1. as large molecules; functional units
2. as polymers; many unites of monomers covalently linked together
52
what macromolecules are considered the workhorses of life that perform most biological functions?
proteins
53
what is very important to the function of a protein?
the structure!
54
give 3 examples of proteins performing biological functions
1. enzymes like lipase metabolize fat
2. antibodies like immunoglobulins kill bacteria and viruses
3. transport proteins like hemoglobin deliver oxygen to cells
55
define nucleic acids as macromolecules
genetic material that determines everything about an organism
56
contrast the shape of DNA and RNA
DNA is double helix and RNA is single helix
57
contrast the ribose sugar in DNA and RNA
DNA has deoxyribose sugar (hydrogen at 2' carbon) and RNA has oxyribose sugar (OH at 2' carbon)
58
how are polymers of nucleotides (DNA and RNA) formed?
by covalently linked nucleotides via phosphodiester bonds from the 5' to 3' end
59
during transcription, where are nucleotides added?
to the 3' end, NEVER the 5' end
60
what are polysaccharides?
complex carbohydrates
61
list and describe the 3 functions of polysaccharides
1. structure: gliding motion in joints
2. biomarkers: sugar flags for blood typing and virus detection
3. energy: glycogen degradation
62
how are simple sugars linked to form polysaccharides?
via variable glycosidic bonds
63
what is key to the identification and chemical properties of a polysaccharide? (2)
orientation and position of the glycosidic bond
64
give 2 types of glycosidic bonds
a-1,4 and a-1,6 linkages
65
what is always the same about a glycosidic bond?
2 carbons (one from each ring) are connected via an oxygen outside the ring
66
what are metabolites?
small biomolecules that serve as both reactants and products in biochemical reactions within cells
67
what is metabolic flux?
the rate at which reactants and products are interconverted in a metabolic pathway
68
what is influx?
the entry of metabolites into a pathway
69
what it efflux?
the flow of metabolites out of a pathway
70
what are the 3 types of metabolic pathways?
1. linear
2. forked
3. cyclic
71
how is cellular communication accomplished? (main actors)
proteins mostly
72
give the general process of cellular communication
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
what are the two types of nitrogenous base pairs?
purines and pyrimidines
74
what are the 2 purines of DNA?
adenine and guanine
75
what are the two pyrimidines of DNA?
cytosine and thymine
76
which purines pair with which pyrimidines in DNA?
guanine with cytosine and
adenine with thymine pyrimidine
77
what are the 2 purines of RNA
same as DNA, adenine and guanine
78
what are the two pyrimidines of RNA?
cytosine and uracil
79
what purines pair with which pyrimidines in RNA?
guanine with cytosine and
adenine with uracil
80
which purine-pyrimidine bond is stronger and why?
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
which way do you read DNA?
5' to 3'
82
what is a gene?
a stretch of DNA that will eventually code for a protein
83
what is a nucleosome?
a string of negatively charged DNA wrapped tightly around a postively charged histone; tightly packed to prevent damage
84
what is chromatin?
multiple nucleosomes tightly packed together
85
what is a chromosome?
tightlt packed chromatin
86
what is a nucleus?
tightly packed chromosomes with a protective membrane
87
give the levels of genetic structure from smallest to largest (5)
1. gene
2. nucleosome
3. chromatin
4. chromosome
5. nucleus
88
give the central dogma
DNA is transcribed into mRNA that is translated into proteins that do jobs
89
will noncoding DNA ever become a protein?
no!
90
what makes a codon?
3 nucleotide bases
91
what are the 2 types of mutations?
1. germ-line cell
2. somatic cell
92
describe germ-line cell mutations (2)
1. passed from parents to offspring
2. can result in inherited genetic diseases (ex. sickle cell anemia)
93
describe somatic cell mutations (3)
1. not inherited by offspring
2. limited to individual organism
3. can result in developed diseases (ex. cancer)
94
what is the danger of mutation?
mutations can change the sequence and moleculer structure of proteins, which can affect function (could be real bad)
95
what is an advantage of mutation?
evolution! could make organisms more fit for the environment
96
how are phylogenetic trees created?
using bioinformatics
97
describe how similar human DNA is to chimpanzee DNA (2)
1. 98% is identical
30% of proteins have the exact same sequence
98
what are orthologous genes?
1. similar genes in different species
2. conserved sequence and function
3. likely from common ancestral gene
99
give an example of an orthologous gene
G6P dehydrogenase
100
what are paralogous genes?
similar genes in the SAME species
101
how are paralogous genes created?
through gene duplication, as there are only 3 possible outcomes for a codon
102
give an example of a paralogous gene
nuclear receptors
103
what is a genome?
a collection of all an organism's genes
104
what is a transcriptome?
a collection of all DNA transcripts (RNA products) generated by DNA transcription
105
what is a proteome?
collection of all proteins produced by mRNA translation
106
describe the determination of biomolecular structure and function
sequence determines structure determines function
