1
Q
what is life
life is complex and dynamic explain
A
all organisms are made of the same set of chemical elements
primarily our biomolecules (CHNOPS)
2
Q
what is life
life is organized and self susatining explain
A
organisms are heirarchirally organized with a pattern from smallest (atom) to largest (organism)
3
Q
what is life
life is cellular explain
A
cells are the basic unit of living organisms
4
Q
Life is organized and self sustaining
biomolecules are composed of _______ which in turn are formed from _______
A
biomolecules are composedf of atoms which in turn are formed from subatomic particles
5
Q
life is organized and self sustaining
certain biomolecules (CHNOPS) become linked to form polymers calledd
A
macromolecules
6
Q
macromolecules examples include
A
nuceleic aciods, proteins, and polysacchardies
7
Q
nucleic ackids are macromolces formed from
A
nucleotides
8
Q
proteins are forned from
A
amino acids
9
Q
the sum or all reactions in a living organism is reffered to as
A
metabolism
10
Q
polysaccharides arfe formed from
A
sugars (monosacch)
11
Q
the ability of organisms to regulate metabolic procesess (reaction biochem pathways) despite internal and external is
A
homeostasis
12
Q
life is cellular
cells differ widely in structure and function BUT each is surrounded
A
by a membrane that controls the transport of substances into and out of thje cell
13
Q
cell membrane ourpose
A
controls transport of substances into and out of cell
also mediates response of the cell to the extracellular environment
14
Q
life is cellular
cells arise only from
A
the division of exisiting cells
15
Q
life is information based
A
organization requires information
16
Q
life is information based
DNA stored in genes is the linear seqeunce of nucleotides which then in turn does what to amino acids and preoteins
A
in turn that specifies the linear sequence of amino acids in proteins and how and when they arew synthesized
17
Q
whagt allows proteins to interact with a specific moldcules
A
their unique three dimensional shape allow it to bind with a specific molecule
18
Q
what is liufe
life adapts and evolves
A
all life on earth has a common origin with new forms arising from older forms
19
Q
life adaprs and evolves
what can happen when an individual oreganism in a population reproduces itself
A
mutations or sequence changes can arise a
20
Q
why do mutations arise
A
as a result of stress induce DNA modifications and erroes when DNA molecules were copied
21
Q
most mutations are
A
silent
they either are repaired or have no effect
22
Q
CHNOPS can readily form
A
stable covalent bonds (the kind that allow for formation of important moleciules and proteimns)
23
Q
the structural complexity and diversity of organic molecules are made possibly by carbons ability to
A
form four strontg single covalent bonds
to either other carbons atoms or to atoms of other elemetns
24
Q
hydrocarnons and hydrogen and carbon containing molecules that are
A
hydrophobic or insoluble in water
25
the chemical properties of backbones attached to hydrocarbons are determined by
the specific arrangment of atoms called functional groups
26
alcohol
Hydroxyl group
polar (watersoluble) and form h bonds
27
aldehyde
carbonyl group
polar and found in some sugars
28
ketone
carbonyl group
polar and found in some suagrs
29
acids
carboxyl group
weakly acidic and bears a negative charge when it donates a proton
30
amine
amino group
weakly basic bears a positive charge whem it accepts a proton
31
32
thiol
thiol group
33
34
35
cells contain four families of smal molecules
amino acids sugars fatty acids and nucleotides
36
amino acids form what polymer and function
protein and function as catalysts and structural elements
37
sugars form what polymer and have what general functionm
form carbohydrates and function for energy sources and structural elements
38
fatty acids gen function
energy sources and strctural elements of complex lipid molecules
39
nucleotides form wehjat polymers amd general functions
form DNA and RNA
DNA=Genetic info
RNA= protein synthesis
40
there are hundreds of amino acid groups each of which contains
an amino group and a carboxyl group
41
amino acids are classified as alpha beta or y thingey based off
the location of the amino group in refernce to the carboxyl group
42
in alpha amino acids (most common) the amino group is attached to the
alpha carbon (immediately adjacent to the carboxyl group)
43
# in
in B and y amino acids the amino group attached
to the second and third carbon respictivelyt from the carboxyl group
44
also attached to the alpha carbon thert is a side chain or
R group
45
The chemical properites of each amino acid (once in protein) are determined largely by the properties on
its side chain (r group)
For example, some side chains are hydrophobic (i.e., they have low solubility in water),
whereas others are hydrophilic (i.e., they dissolve easily in water)
| For example, some side chains are hydrophobic (i.e., they have low solub
46
many naturally occuring amino acids are not
alpha amino acids
example: β-alanine and γ-aminobutyric acid (GABA)
47
amino acid molecules are used primarily in the syntehsis opf
long complex polymers known as polypeptides
proteins consist of one or more polypeptide
48
polypeptides are connected by
peptide bonds
49
peptide bonds are amide linkages that form in what rxn
nucleophilic substitution rxn
in which the amino group nitrogen of one amino acid attacks the carbonyl carbon in the
activated carboxyl group of another.
50
51
sugars (smallest carbohydratres) contain what functiona groups
alcohol and carbonyl
52
sugars that posses an aldehyde are called
aldoses
53
# suga
sugars that posess a ketone group are called
ketoses
54
fatty acids are represented chemical formula
R-COOH
55
there are two types of fatty acids
saturated amd unsatuirated
56
saturated fatty acids contain
no carbon-carbon double bonds
57
# unsatu
unsturated fatty acids have
one or more double bonds
58
under physiological conditions the cafrboxyl group of fatty acids exsists
in the ionized state R--COO-
59
lipids are
a diverse group that are soluble in organic solvents but not soluble in water
60
each nuceltoide contains three components
a five carbon sugar (either ribose or deoxyribose) a nitrogenous base and one or more phosphate groups
61
the bases in nucleotides are
heterolytic aromatic rings with a variety of substituents
the two classes are bycyclic purine and monocyclic pyrimidines
62
in a nucleic acid doenzto millions of
nucleotides are linked by phosphodiester linkages to forn long polynuceltoide chains
63
what are the two types of nucleic acid
DNA and RNA
64
in addition to the pentose sugar deoxyribose and phosphate dna contains bases of four typoes
the purines adenine and guanine
]the pyrimidines thymune and cytosine
A pair with T
G pair with c
65
why does the double helix of DNA form
because of complementary pairing between the bases due to hydrogen bonding
66
an organisms entire sret of dna sequence
genome
67
DNA has both coding and noncoding sequences coding is non is
coding is genes: they specify structure of gene products (RNA)
some noncoding have regulatory functions (controlling synthesis of certain proteins) while some we have no idea
68
RNA differs from DNA by
contains the sugar ribose instead of deoxirobose and has a base uracil instead of T
69
RNA molecules are synterhsized by process named
transcription
70
mRNA does
has information that codes directly for the amino acid sequence in a specific polypeptide
71
rRNA does
convert mRNA base sequence into the amino acid of a polypeptide
72
tRNA
deliver activated amino acids to the ribosome during protein synthesis
73
snoRNAs assist in the
maturation of ribosomal RNA
74
snRNAs facilitate the process by which
mRNA precursor molecules are made to functional mRNA
75
gene expression controls when or if
the information encoded in a gene will be accessed
76
transcription is the mechanism where the
base sequence is used to synthesize a gene product
77
a class of proteins called transcription factors regulates
the expression of protein coding genes when they bind to specific regulatory DNA sequences reffered to as response elements
78
autopoiseis
basically that each organism is autonomous self organizing and self maintaining entity (self regulation)
79
primary functions of metabolism
getting and then using energy
making of molecules needed for cell structure and function
growth development
removal waste products
80
nucleophilic sub rxn
one atom or group is substitued for another
attacker= nuc phile (anion or neutral with non bonding electrons)
electrophile is the acceptor (e neg defficient)
leaving grou[ leaves with e pair
81
hydrolysis rxn
nucleophilic acyl. sub rxn in which oxygen of a water serves as nuc phile
82
elimination reaction
forms a double bond
removal of H2O from biomolecules containing alcohols is a common rxn
83
addition reactions
two molecules combine to form a single product
hydration is one of the most common (water added to an alkene and alcohol)
84
isomerization rxns
atoms or groups undergo intramolecular shifts
85
oxidation reduction (redox)
when there is a transfer of electrons from a donor (reducing agent) to an electrong acceptor (oxidizing agent)
86
donates electrons and becomes oxidized after in redox
reducing agent
87
accepts electrons and becomes reduced in redox
oxidizing agent
88
how to determine what is oxidized and reduced in redox
OIL RIG
1. oxidation has occured if a carbon gains oxyggen or loses hydrogen
2. redeuction has occured if carbon loses oxyggen or gains hydrogen
89
what rxn type do cells use to generate most of their energy
redox rxns where electrons are transferred from an oxidizable molecules to an electron deficient molecule
90
the more reduced a molecule is the more
H atoms it posseses meaning the more H= more energy
91
when a electron is transferred energy is
lost/released
92
autotroph
transform energy of the sun (photosynth.) or chemicals (chemosynth.) into chemical bond energy
93
In living organisms, energy, the capacity to move matter(energy), is usually generated by
redox rxns
94
there are 2 types of metabolic pathways
anabolic and catabolic
95
In anabolic pathways
larger molecules are synthesized from smaller precursors
96
In anaboilic pathweays bulding block molecules (amino acids, sugars, fatty acids) (produced or aquiured from dietr) are made into
larger more complex molecules
97
catabolic pathways
large complex molecules are degraded into smaller simpler products
98
some catabolic pathways release energy and a fraction of this energy is captured and used to drive what
anabolic rxns
99
signals transduction pathways let cells
recieve and respond to signals from their surroundings
100
what is the first phase of the signal transduction pathway
the receptions phase a signal molecule (hormon or nutrient molecule) binds to a receptor protein
101
In the signal transductipn pathway once a signal molecule has binded to a receptor protein what is the next step
the binding starts the transduction phase which isd a cascade of intracellular rxns that triggedr cells response to the original signal
102
there are 3 classses of biochemical pathways
metabolic (anabolic, catabolic) energy transfer and signal transduction
103
biological order 4 categories
synthesis of biomolecules
transport across membranes
cell movement
waste removal
104
in living organisms processes of highly ordered complexity are sustained by
a constant input of energy
105
What is **reductionism** in biochemistry and biology?
A method of inquiry that studies complex living systems by breaking them down into their individual components to understand their chemical and physical properties.
## Footnote
Reductionism aims to simplify complex systems for better understanding.
106
What is the major **limitation of reductionism**?
Knowing all the parts does not necessarily explain how the whole system functions dynamically.
## Footnote
This limitation highlights the complexity of interactions in biological systems.
107
What is **systems biology**?
An approach that studies living organisms as integrated systems whose interactions produce biological function over time.
## Footnote
Systems biology emphasizes the relationships and interactions between components.
108
How do **biological systems** differ from human-engineered systems?
* Evolved by trial and error
* Overlapping and flexible component functions
* Contain unavoidable interactions between components
## Footnote
These differences contribute to the complexity and adaptability of biological systems.
109
Why is **systems biology necessary** for understanding living organisms?
The human mind cannot analyze hundreds of simultaneous biochemical reactions without computational and mathematical models.
## Footnote
This necessity arises from the complexity of biological interactions.
110
What tools do **systems biologists** use to study living systems?
* Mathematical models
* Computer simulations
* Large datasets of biomolecule concentrations and reaction rates
## Footnote
These tools help in analyzing complex biological interactions and functions.
111
What is **emergence** in systems biology?
The appearance of new properties or behaviors that arise from interactions among system components and cannot be predicted from the parts alone.
## Footnote
Emergence illustrates how complex systems can exhibit behaviors not evident from individual components.
112
What is **robustness** in biological systems?
The ability of a system to maintain function despite changes, disturbances, or incomplete components.
## Footnote
Robustness is crucial for the survival and adaptability of biological systems.
113
114
What is **emergence** in complex biological systems?
Emergence is when new, unanticipated properties arise from interactions among system components that cannot be predicted from the properties of the individual parts alone.
## Footnote
Emergent properties are a key concept in understanding complex systems.
115
Why can’t **emergent properties** be explained by studying parts in isolation?
Because emergent properties depend on the organization, interactions, and dynamics of the entire system, not just the chemical properties of individual components.
## Footnote
This highlights the importance of studying systems as wholes rather than just their individual parts.
116
How does **hemoglobin** demonstrate an emergent property?
The amino acids surrounding the iron-binding site protect Fe²⁺ from oxidation, even though free iron normally oxidizes—this protection arises from the system’s structure, not the iron itself.
## Footnote
This example illustrates how the arrangement of components can lead to new functions.
117
Key exam takeaway about **emergence**
Structure + interaction = new function that is not obvious from the parts alone.
## Footnote
Understanding this equation is crucial for grasping the concept of emergence in complex systems.
118
Memory trick for understanding emergence: Parts don’t predict behavior — _______.
interactions do.
## Footnote
This mnemonic helps to remember the essence of emergent properties in complex systems.
119
120
What does **robustness** mean in biological systems?
The ability of a system to remain stable and functional despite fluctuations, damage, or perturbations.
## Footnote
Robustness is crucial for the survival of biological systems in changing environments.
121
Why must **robust systems** be complex?
Preventing failure requires multiple interacting components and automatic fail-safe mechanisms.
## Footnote
Complexity allows systems to manage unexpected challenges effectively.
122
How do **human-engineered systems** achieve robustness?
Through redundancy, using duplicate or backup parts (e.g., backup generators in aircraft).
## Footnote
Redundancy ensures that if one component fails, others can take over.
123
How do **living systems** primarily achieve robustness?
Through degeneracy, where structurally different components perform the same or similar functions.
## Footnote
This allows for flexibility and compensation in biological functions.
124
How is the **genetic code** an example of degeneracy?
Multiple codons can encode the same amino acid, which protects against harmful effects of base substitution mutations.
## Footnote
This redundancy in the genetic code contributes to the stability of protein synthesis.
125
Provide a biological example of robustness beyond the **genetic code**.
Loss or inactivation of one hormone receptor can be compensated by other receptors with overlapping functions.
## Footnote
This demonstrates how biological systems can maintain functionality despite individual component failures.
126
How is **biochemistry** defined?
The study of the molecular basis of life.
## Footnote
Biochemistry explores the chemical processes and substances that occur within living organisms.
127
What five major insights about life have **biochemists** contributed?
* Life is complex and dynamic
* Organized and self-sustaining
* Cellular
* Information-based
* Capable of adaptation and evolution
## Footnote
These insights highlight the intricate nature of biological systems.
128
What proportion of a cell is made up of **water and ions**?
Water makes up 50–90% of cell mass; ions (Na⁺, K⁺, Ca²⁺) account for about 1%.
## Footnote
Water is essential for cellular processes and maintaining structure.
129
What type of **biomolecules** make up most of the remaining cellular material?
Organic biomolecules, especially proteins.
## Footnote
Proteins play crucial roles in cellular functions.
130
What are the major roles of **proteins** in cells?
* Transport
* Structure
* Catalysis (enzymes)
## Footnote
Proteins are vital for various cellular functions and processes.
131
What are the four major families of **small biomolecules** found in cells?
* Amino acids
* Sugars
* Fatty acids
* Nucleotides
## Footnote
These biomolecules are fundamental building blocks of life.
132
What is **DNA** and what is its function?
DNA is a double-stranded, antiparallel polynucleotide that stores genetic information.
## Footnote
DNA is essential for inheritance and the blueprint for protein synthesis.
133
What are **genes**?
Coding sequences within DNA that specify functional products.
## Footnote
Genes are the basic units of heredity.
134
How does **RNA** differ from DNA?
* RNA is single-stranded
* Contains ribose instead of deoxyribose
* Uses uracil instead of thymine
## Footnote
RNA plays a key role in translating genetic information into proteins.
135
What is **gene expression**?
The regulation of whether and when a gene is transcribed.
## Footnote
Gene expression is crucial for cellular differentiation and function.
136
What role do **transcription factors** play in gene expression?
They bind to regulatory DNA sequences (response elements) to control transcription.
## Footnote
Transcription factors are essential for the precise regulation of gene activity.
137
What catalyzes all **biochemical reactions** in living systems?
Enzymes.
## Footnote
Enzymes lower the activation energy required for reactions, facilitating metabolic processes.
138
What are common types of **biochemical reactions**?
* Nucleophilic substitution
* Elimination
* Addition
* Isomerization
* Oxidation-reduction
## Footnote
These reactions are fundamental to metabolic pathways.
139
What is a **biochemical pathway**?
A stepwise sequence of enzyme-catalyzed reactions converting a reactant into a product.
## Footnote
Biochemical pathways are essential for metabolism and cellular function.
140
Why do living organisms require a constant flow of **energy**?
To prevent disorganization and maintain internal order.
## Footnote
Energy is crucial for sustaining life processes.
141
What is the main way cells obtain **energy**?
Oxidation of biomolecules or certain minerals.
## Footnote
This process is vital for cellular respiration and energy production.
142
What is **metabolism**?
The sum of all chemical reactions in a living organism.
## Footnote
Metabolism encompasses both catabolic and anabolic pathways.
143
What are the two main types of **metabolic pathways**?
* Catabolic (break down molecules)
* Anabolic (build molecules)
## Footnote
These pathways are essential for energy management and biosynthesis.
144
What are **signal transduction pathways** and their three phases?
* Reception
* Transduction
* Response
## Footnote
These pathways allow cells to respond to external signals and maintain homeostasis.
145
How do cells maintain **internal order**?
* Synthesizing biomolecules
* Transporting substances
* Producing movement
* Removing waste
## Footnote
These processes are critical for cellular health and function.
146
What is **systems biology**?
A field that uses mathematical and computational models with large biological datasets to understand living systems.
## Footnote
Systems biology integrates various biological data to reveal complex interactions.
147
What key concepts has **systems biology** helped reveal?
* Emergence
* Robustness
* Modularity
## Footnote
These concepts are important for understanding biological complexity and system behavior.
BioChem
flashcards
Decks in class (28)
# Cards
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in class day 113
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ch117
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ch1 solutions49
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ch1 solutionsd148
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c h1 solutionsd from him48
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ch 1 test bank0
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yaya30
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ch 2chatgpt60
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quiz 2 book98
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ch2 study guide for quiz chat bru67
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questionsfrombookch2butcxhatcondenseddownfromstudygudise74
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chapter 1 me147
-
;ec 32
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chapter 2 me165
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chapter 1 activity 140
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chapter 1 activity 255
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chapter 2 lecture 1 activity41
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chapter 2 lectuer part 2 activity63
-
chapter 2 lecture 2 actviity 345
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quiz 3 study guide ]92
-
condensed questions268
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quizzes20
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quizzes chat other56
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quizzes COPY20
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archea otter chat82
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chapter 2 lecture 1 activity COPY41
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chapter 3 l3ctuure 2 actibvity 244
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chapter 5 overview11
