Exam 2 Flashcards
1
Q
what is metabolism
A
chemcial reactions that organisms use to break down subtances and to release subtances
2
Q
3 categories of metabolic pathways
catabolic pathways
A
breakdown of subtances and release energy
3
Q
3 categories of metabolic pathways
anabolic pathways
A
comebine energy and molecules to build new subtances
4
Q
3 categories of metabolic pathways
amphilboic pathways
A
can be used for both breaking down and building subtances
5
Q
How can we differentiate catabolic, anabolic and amphibolic reactions
A
Catabolic = hydrolytic, anabolic = biosynthetic (dehydration synthesis)
6
Q
importance of ATP
A
is the cash that cells get when they break down nutrients (CANNOT BE SAVED UP)
7
Q
How ATP is used in catabolic and anabolic rxns
A
is made by catabolic rxns, provides energy for anabolic rxns
8
Q
enzyme
A
proteins that help speed up a reaction
9
Q
Characteritics of enzymes
A
Catalysts, effective in small amounts, act on specific substrates to generate specific products
10
Q
why enzymes are catalysts
A
increases rxn rate, only needed in small amounts to make rxn happen
11
Q
how ezymes reduce energy required for a rxn to occur
A
hold reactants in their proper orientation and lower energy required
12
Q
enzyme classfication
A
names usually end in -ase
Ligase (joining of 2 molecules), hydrolase (hydrolysis)
13
Q
what is a substrate
A
molecules that an enzyme acts upon
14
Q
what is an active site
A
the site where substrate binds the enzyme
15
Q
cofactor
A
non-protein components that enzymes sometimes need
Ex: Iron
16
Q
aponenzyme
A
an enzyme without a cofactor (inactive form)
Ex: Urease
17
Q
holoenzyme
A
an enzyme with its cofactor
Ex: DNA polymerase
18
Q
coenzyme
A
organic cofactors
Ex: NAD+
19
Q
riboenzyme
A
Specialized catalytic RNA molecules
20
Q
what type of substrate do riboenzymes metabolize
A
act on RNA molecules
21
Q
what factors can modify enzymes
A
cofactors, temp., pH, presence of inhibitors, phosphorlaytion state
22
Q
how does temp affect enzyme activity
A
lowering temp will lower enzyme activity, warmer temp increases, temps above optimal temp reduce activity
high temps can cause Denature
23
Q
how does pH affect enzyme activity
A
pH above or below optimal pH with alter enzyme structure by disrupting bonds, extreme changes can also lead to denaturation
24
Q
enzyme saturation affect on rxn rates
A
rate of product formation depends on how many active sites are available
25
difference between kinases and phosphatases
kinases = add Phosphate groups, phosphatases = remove phosphate group
26
competive inhibiton
slow rxn by competing with a substrae for active site
27
non-competive inhibtion
decrease enzyme activity by binding to enzyme at site and not active site
28
feedback inhibtion
slows down or turn off biochemical pathways to help cells be efficient
29
oxidation rxn
atom or molecule loses electrons
30
reduction rxn
atom or molecule gains electrons
31
common oxidizing rxn agents
oxygen
32
common reduction rxn agents
hydorgen
33
redox rxn
Involve oxidation and reduction rxns
33
why are redox rxn tied to phosphorlaytion rxns
they recharge ADP to ATP
34
substrate level phosphorlaytion
occurs when enzyme tranfers a phosphoryl group from donor to ADP to make ATP
35
purpose of ETC
to fuel phosphorlaytion of ADP to ATP
36
36
oxidative phosphorlation
collection of redox rxns
37
what is phorphorlaytion and what organisms can do it
attachment of phosphate group to an ion, EU cells can do it
38
primary way cells extract energy from carbs
respiration and fermentation
39
main difference in cellular repiration in EU and pro
EU occurs mostly in mitochondria and pro occurs in cytoplasm
40
end products of glycolysis
2 pyruvate 2 ATP, 2 NADH
## Footnote
no oxygen, requires glucose
41
end products of intermediate step
pyruvic acid is made, converts into acetyl-CoA
## Footnote
not directly Required
42
end products of kerbs
3 NADH, FADH2, ATP
## Footnote
does need oxygen indirectly
43
end products of ETC
ATP, H20, regenerated NAD+ and FAD
## Footnote
oxygen is required
44
what molecules can be used for electron acceptors in areboic and anaerobic respiratory chains
oxygen and nitrate
45
elements needed in a respiratory chain
occurs in inner mito membrane and needs electron donors, proteins, proton pumping
46
How many types of electron transport chains can a bacteria have and how can we use that diversity to identify them?
can have several, the oxidase test can detect if carrier has cytochrome c oxidase
47
name of enzyme responsible for recharing ADP and ATP
ATP synthase
48
where is ATP synthase in EU and pro
EU in inner mito membrane, pro in plasma membrane
49
what is chemosis
movement of ions across selective permeable membrane, helps drive phosphorylation rxns that recharge ADP to ATP
50
difference between electron carrier and electron acceptors
e-carriers transport electrons to molecules, e-acceptors receive electrons do not pass further
51
is glycolysis the only way cells oxidize sugars? Explain
no, there are other pathways that cells used to break down sugars and extract energy. if there is oxygen is available cellular respiration continues after glycolysis to extract more sugar
52
fermentation purpose
sustain ATP production by glycolysis when respiration are not available
53
two types of lactic acid fermentation
homolatic and heterolactic
54
final products for Alcohol fermentation
ethanol, CO2, ATP, NAD+
55
final products for mixed acid fermentation
formic acid, acetic acid, succnic acid, ethanol, CO2, H2
56
final products for homolatic Fermentation (latic acid)
2 ATP molecules
57
final products for heterolactic fermentation (latic acid)
minor amounts of acidic end products, 1 ATP
58
what type of cells can fermenation occur
EU cells and a variety of pro cells
59
main differences between fermentation and cellular respiration
fermentation does not require oxygen while cellular respiration does
60
How do bacteria catabolize lipids, proteins, and nucleic acids
Initial catabolism happens extracellur, large molecules most be broken down into smaller molecules to be transported into the cell
61
difference between gluconeogenesis and glycogenesis
gluconeogenesis is the chemical process of building glucose from non-suagr starting materials, glycogenesis is the production of glycogen
62
essential vs non-essential amino acids
essential amino acids must be obtained from the enviorment, non-essential amino acids can be made
## Footnote
in both EU and PRO cells
63
building blocks needed for the formation of both nucleic acids and energy carrying molecules
nucelotides
64
how are metabolic pathways regulated
enzyme regulation and feeeback inhibtion and hormonal control
65
How are organisms classified according to their metabolism
if they are phototrophs (havest ATP from light), chemotrophs (harvest energy by chemical bonds to make ATP), or mixtrophs (switch between modes of metabolism)
66
3 examples of tests used to identify bacteria and explain the principle behind the
test
amino acid catabolism tests, fermentation tests, catalase test
67
genetics vs genomics
genetics is the study of heredity and inheritance-genomics is study of organsims entire genome
68
how genetic material can be organized in a cell
in chromosomes
69
chromosomes
cellular structure composed of neatly structued DNA
70
EU chromosomes vs PRO chromosmes
located in nucleus in EU cells can be diploid or haploid, in PRO cells singular and circular chromosomes
71
gene
basic informational packages
72
genotype vs phenotype
genotype is the sum of all genes, phenotype is the expression of those genes
73
do all organisms contain the same number of genes
no, there is variation in genome size
## Footnote
human cell 23,000 genomes and 46 chromosomes
74
basic unit of DNA
nucleotide and made of phosphate, deoxyribose sugar, nitrogenous base
75
nitrogenous bases
prunies and pyrimidines -- AT and GC
76
antiparalle arrangment
one side of the helix runs in the opposite direction of the other
## Footnote
5' to 3' in one direction 3' to 5' in other direction
77
semiconservative replication of DNA
each daughter molecule is indentical to the parent in composition
78
enzymes in DNA replication and fucntion
helicase (unzips helix), primase (Synthesis of RNA polemer), ligase (binding), DNA polyermerase I (removes primer), DNA polymerase III (adding bases to new DNA), Topoisomerase I (making single strand DNA break), Topoisomerase II and IV (making double stranded DNA break)
79
replication fork
place in helix where strands are unwound
80
primer
length of an RNA inserted before being replaced by DNA
81
leading strand
strand of new DNA synthesized continuously from 5' to 3'
82
lagging strand
strand of new DNA synthesized in short segments from 3' to 5'
83
Okazaki fragments
short DNA segments synthesized from 5' to 3' then later to 3' to 5'
84
similarties between EU and PRO cells in DNA replication
replication in both directions, use a variety of polymerases
85
central dogma
genetic information only flows in one direction
86
why is central dogma incomplete
Many genetic malfunctions that cause human disease are found in regulatory RNA, not in genes for proteins
87
gene-protein connection
connection between DNA and organisms traits
88
Proteomics
study of an organism’s complete set of expressed proteins
89
codon
a series of triplet bases that hold messages of transcribed mRNA
90
ribosome involvment in synthesis
interaction of rRNA and protein create 2 subunites of ribosome that help in final genetic code
91
central principles of translation
mRNA nucleptides read in codons, condon dictates which amino acids are added, this code is universal for bacteria, archaea, EU, and vriuses
92
redundancy
certain amino acids are represented by multiple codons
93
wobble
only first 2 nucleotides are required to encode the correct amino acid, 3rd does not change -- permits variation or mutation without altering
94
elements needed to synthesize proteins
start codon (AUG), stop codon (UAA, UAG, UGA), translocation
95
co-translation
translation only occurs in bacteria and archaea
96
introns
intervening sequences of bases that do not code for protien
97
exons
coding regions
98
spliceosome
recognizes exon-intron junctions and enzymatically cuts through them
99
operon
coordinated set of genes regulated as a single unit
## Footnote
catabolic operons inducible by substrates
100
repressible operons
contain conding for anabolic enzymes
## Footnote
repressedby the product of synthesized enzymes
101
recombination event
an event in which one bacterium donates DNA to another
102
horizontal gene transfer
any transfer of DNA that results in aquiring new genes
103
types of horizontal gene transfer
conjunction, transformation, transduction
104
competent cells
cells that are capable of accepting genetic material through transformation
105
mutations
any change to nucleotide sequence in genome
## Footnote
wild type, mutant strain
106
photo activation
light repair of damage caused by ultraviolet radiation
107
excision repair
mutations are excised by a series of enzymes that remove incorrect bases and add correct ones
108
ames test
used to rapidly detect chemicals with carcinogenic potential
## Footnote
allows easy observation and monitoring of gene expression
109
innate immunity
routine protection present at birth
110
lnnate lines of defenes
* protective barrier -- 1st line, skin and mocus membranes
* eater cells -- 2nd line, NK cells and macrophages
* smart cells-- 3rd line, antibodies, B and T cells
111
antimicrobial subtances
* lysozyme degrade peptioglycan
* peroxidases form antimicrobials
* antimicrobial peptides (AMPs)
112
dysbiosis
microbial imbalance or maladaptation on or inside body
113
main components of innate defenses
* interferon-- secreted with viral infection
* phagocytes-- engulf microbes or cell debris by phagocytosis
* fever-- intefers with pathogen growth and enhances immune responses
114
blood cells
* red blood cells -- carry O2
* platelets -- involved in clotting
* white blood cells -- important in host defenses
115
low levels of neutrophils
neutropenia -- may be congenital or due to leukemia
116
high levels of neutrophils
neutrophilia -- indicates possible microbial infection
117
cytokines
proteins that help control inflammation in the body
## Footnote
Ex in humans: interferons and lymphokines
118
inflammation
localized tissue response to injury producing signs and symmptoms
119
acute inflammation
short term, mainly neutrophils and macrophages -- clean up damage by ingesting dead cells and debris
120
chronic inflammation
macrophages, giant cells accumulate and granulomas form
121
damaging effects of inflammation
prevents spread, but damanges body (usually minimal but can be severe)
122
when is a person considered immuniocompromised
if any part of the innate or adaptive immune system is impaired
123
immunological memory
secondary exposure to the same antigen is rapid and effective
124
divisions of adaptive immune system
ceullar reponse (T cells) , humoral response (B-cells and antibodies)
125
steps on activating adaptive immune system
* stage 1 antigen presentation -- dendritic cells, macrophages, and B-cells acts as antigen presenting cells
* stage 2 lymphocyte activation-- are activated by collection of released signaling cytokines
* stage 3 Lymphocyte Proliferation
and Differentiation -- activated B and T cells undergo rounds of cell division to make more
* stage 4 antigen elimination and memory -- once threat passes effector cells die
126
B cells
develop in bone marrow, mainly in lymphoid tissues
127
clonal expansion
rapid reproduction of genetically indeitcal cells from parent cells
128
antigens
compounds that provoke a specific immune response
129
molecules that are antigens
capsules, cell wall, flagella, toxins
130
role of MCH genes
encode cell surface proteins that help body recognize foreign subtances
131
MCH class I
allow for recognition of self and the regulation of the immune reactions, present endogenous anitgens
132
MCH class II
involved in presenting antigens to T cells during cooperative immune reactions
133
differnece between T cytotoxic cells and T helper cells
T cytotoxic cells directly kill infected cells, T helper cells coordinate the immune response by activating other immune cells
## Footnote
T helper cell = CD4, T cytotoxic cell CD8
134
plasma cells
produce antibodies
135
nature of antibody
2 heavy chains, 2 light chains
136
T dependent
can bind to multiple receptors
137
IgG
fix complement, in blood and intestine, enhance phagocytosis, 80% of serum
138
IgM
fix complement, 5-10% of serum, in blood and B cells, produced in response to infection
139
IgA
10-15% of serum, in secretions, mucosal protection
140
IgE
0.002% of serum, on mast cells and basophils
141
IgD
0.2% of serum, in blood and B cells, initaite immune response on b cells
142
naturally aquired active immunity
resulting from infection
143
naturally aquired passive immunity
transplacental
144
artifically acquired active immunity
injection of a vaccine
145
artifically acquired passive immunity
when you get antibodies for you to fight an infection
