Midterm 1 Flashcards
1
Q
What does cell theory (old one) state:
A
- all organisms are composed of 1 or more cells
- the cell is the structural unit of life
- cells can only arise by division from pre existing cells
2
Q
what does the updated cell theory state?
A
- life: most basic property of cells
- cells are highly complex and organized
- cell possess a genetic program and the means to use it
- cells acquire and use energy
- cells carry out a variety of chemical reactions
- cells engage in mechanical activities
- cells are able to adapt and respond to stimuli
- cells are capable of self regulation
- cells evolve
3
Q
what is metabolism
A
the sum total of all chemical reactions in cells
4
Q
how is organization in cells achieved
A
though processes that are random
5
Q
where is genetic info kept in cells
A
in chromosomes in either the nucleus (eukaryotes) or nucleoid (prokaryotes)
6
Q
what do cells convert glucose into
A
ATP
7
Q
what do virtually all chemical changes in a cell require ?
A
enzymes
8
Q
what initiates cellular activity?
A
Based on mechanical changes within cells, which are often initiated by changes in shape of motor proteins
9
Q
what bring cell back to the appropriate state
A
feedback circuits
10
Q
what are the differences between prokaryotes and eukaryotes distinguished by
A
size and the type of organelles they contain
11
Q
what do procaryotes and eukaryotes share, and why
A
because of shared ancestry
- identical genetic language
- common set of metabolic pathways
-many common structural features
12
Q
what are the two types of organization that eukaryotes have for biochemical events
A
temporal and spatial arrangements
13
Q
what is the size range of bacteria cells
A
1-5 um (micro meter)
14
Q
what is the size range of animals cells
A
10 - 100 um (micro meter)
15
Q
what limits the size of a cell
A
-SA to volume ratio
-need to maintain adequate local concentrations of substances required for cellular function
- rates at which molecules diffuse
16
Q
what is lower size limit of cells because
A
due to cell needing enough volume to hold all its stuff
17
Q
what is the upper size limit of cells because
A
due to rates of diffusion (bigger cells = slower diffusion)
18
Q
how do cells overcome size limitations relating to nutrient uptake and release of waste
A
active transport
morphological specializations
19
Q
what determines the amount of exchange a cell needs to make
A
cell volume
20
Q
what is the cytoplasm
A
the volume of the cell excluding the nucleus
21
Q
what is diffusion
A
unassisted motion that relies on concentration gradients
22
Q
what is active transport
A
specialized machinery can move molecules/vesicles along the cytoskeleton from one place to another
23
Q
what is a virus
A
an infectious agent that can only replicate inside a living cell
24
Q
what is a virion
A
a complete viral partice, which includes the genome, capsid, and in some cases am envelope
25
what is a viroid?
an infectious agent that is composed solely of RNA (ie no coat proteins)
26
what is a prion
an infectious protein that can transmit its folded shape to other native folded proteins
27
in general what do virus particles (virions) consist of
nucleic acids (DNA or RNA) enclosed in a protein coat
28
what are the 3 types of proteins that all viral genomes encode
- for replication
- for packaging and delivery
-for modification of host cell
29
what are covalent bonds
strong bonds formed by the sharing of electrons between adjacent atoms
30
what are ionic bonds
attractions between charged atoms
31
what do polar covalent bonds have, and where will electrons go to
unequal electron sharing
electron will go to more electronegative atom
32
where in a cell, are ionic bonds stronger
stronger in core of protein, since water is often excluded
33
what are hydrogen bonds
weak attractive interactions between an electronegative atom and a hydrogen atom that is covalently linked to a second electronegative atom
(the electronegative atom owns the hydrogen electron, creating an electropositive hydrogen
34
is hydrogen bond strength additive
yes
35
are hydrophobic interactions a bond or attraction
no, neither
based on desire of hydrophobic molecules to not interact with each other
36
are polar molecules hydrophobic to hydrophilic
hydrophilic
37
are non-polar molecules hydrophobic or hydrophilic
hydrophobic
38
what are van der waals forces
weak attractive forces between uncharted molecules that are very close to each other
39
does it take more energy to break covalent bonds or non-covalent bonds
covalent
40
is more energy used to break single bond or double/triple bonds
double/triple
41
what is the universal solvent in biological systems
water
42
how many bonds can a water molecule form simultaneously
4
43
what allows water to dissolve a large variety of substances
its polarity
44
what is the hydrophobic effect and why is it energetically favourable
the tendency of non-polar molecules and non-polar portions of molecules to aggregate in water
aggregated form has less order = more entropy = energetically favoured (less order since more free water)
45
why does water have a high specific heat
most of the energy used to disrupt H-bonds rather than increase the molecular motion (ie increase temp)
46
how efficient are metabolic reactions and what happens to "wasted" energy
50% efficient
wasted energy warms body
47
what do acids and bases of in regards to protons
acids: release protons
bases: accept protons
48
what is a amphoteric molecule
and what is an example
can act as acid or base
ex: water
49
what do buffers do
resist changes in pH
50
why are hydrocarbons less common in living cells
they are of limited importance since they aren't soluble in water
51
what is a macromolecule
large highly organized molecules that form cellular structures and carry out the activities of cells
52
what are the 4 major categories or macromolecules
- proteins
- nucleic acids
- polysaccharides
- lipids
53
are most macromolecules short lived
yes
expect DNA which is continually broken down and replaced
54
what is the most abundant form of organic matter on earth
carbohydrates
55
what are the roles of carbohydrates
energy
metabolic intermediates
structural components of DNA/RNA
structural components of cell walls (bacteria and plants)
glycoproteins and glycolipids
56
what is the structure of sugar's backbone
backbone of carbons linked in a linear array of single bonds
57
when is it a ketose
if carbonyl group is located at internal position
58
when is it an aldose
if carbonyl is located at end of molecule
59
what happens to sugars with more than 5 carbons
they self react to form a ring containing molecule
60
what is the anomeric carbon
carbon derived from the carbonyl (C=O) of the open chain form of the carbohydrate molecule
61
what are glycosidic bonds
formed between OH groups on 2 separate monosaccharides (or monosaccharide + another molecule)
62
what is a polysaccharide
long chain polymers of sugars and sugar derivatives
63
what are the functions of polysaccharides
storage
structural
signalling
64
what do the multiple OH groups in monosaccharides participate in
glycosidic bonds
65
what is cellulose
plant product made of unbranched polymers (glucose)
66
what re GAGs
composed of 2 different sugars found in intracellular space
67
what do alpha - glycosidic bonds allow for
spontaneous formation of helical shapes
68
what do beta - glycosidic bonds form
rigid linear rods
69
what are glycoconjugates
signalling carbohydrates covalently joined to a protein or lipid
(glycoproteins or glycolipids)
70
what are blood types determined by
cell surface carbohydrates of red blood cell
71
what are nucleic acids and what do they do
linear polymers of nucleotides
they store, transmit, and express genetic info
72
what direction are nucleotide sequences written
5' to 3'
73
how many hydrogen bonds does AT form
2
74
how many hydrogen bonds does GC form
3
75
what is coenzyme A notable for
its role in the synthesis and oxidation of fatty acids
76
what cAMP
second messenger for intracellular signal transduction in many different organisms
77
what is the central dogma of MBB
DNA males RNA, RNA makes protein
78
what are the non-coding RNAs
small nuclear/nucleolar RNA
microRNA (miRNA)
transfer RNA (tRNA)
rRNA
long non coding RNA (lncRNA)
79
are lipids formed by the same type of linear polymerization as proteins, nucleic acids, and polysaccharides
no
80
why are lipids considered macromolecules
because of their high molecular weight and importance in membranes
81
lipids are a heterogenous category, what classifies them together
solubility properties (hydrophobic)
82
what are the functions of lipids
energy storage
membrane structure
specific biological functions (ex: signal transmission)
83
what are the 6 classes of lipids
fatty acids
triacyglycerols
phospholipids
steroids
glycolipids
terpenes
84
what is a fatty acid
long unbranched hydrocarbon with a carboxyl group at one end
85
why are even numbers of carbons favoured
because fatty acid synthesis occurs via the stepwise addition of 2 carbon units to growing chain
86
why do fatty acids release a high amount of energy upon oxidation
since they are highly reduced
87
what is a saturated fatty acid like
long and straight
no double bonds
88
what is an unsaturated fatty acid like
bent
at least 1 double bond
89
what is the orientation around the double bond in unsaturated fatty acids
cis
since they reduce van der Waals interactions
90
what is hydrogenation
chemical process by which hydrogen atoms are added to unsaturated fats to reduce number of double bonds
allows the chains to pack more closely together to form a solid structure
91
what kind of bond does hydrogenation create
trans bonds
92
why are phospholipids important to membrane structure
due to their amphipathic nature (has both hydrophobic and hydrophilic parts)
93
what is a diacylglycerol
phospholipid molecule that has 2 fatty acid chains (not 3) attached to a glycerol backbone
94
what is a steroid
derivatives of 4 ringed hydrocarbon skeleton
95
are steroids non polar or polar
non polar = hydrophobic
96
what is the most common steroid in animals cells
cholesterol
97
what is cholesterol the starting material for
the synthesis of steroid hormones ( sex hormones, glucocorticoids, mineralocorticoids)
98
what is membrane fluidity determined by
phospholipid/steroid content
length and degree of saturation of fatty acyl chains and temperature
99
what are terpenes synthesized from
5 carbon compound: isoprene
100
what are involved in almost every cellular pathway
proteins
101
what are the 4 levels of protein organization
primary structure : amino acid sequence
secondary structure: folding of polypeptide backbone
tertiary structure: describes conformation of entire polypeptide
Quaterary structure: assembled subunits
102
what do all amino acids have
carboxyl group
amino group
single carbon atom ( alpha carbon)
r group
103
what happens to the carboxyl group and the amino group at pH 7
carboxyl group looses a proton (negatively charged)
amino group accepts a proton (positively charged)
104
what kind of amino acids are used in the synthesis of a protein on a ribosome
L-amino acids
105
what charge do acidic amino acids have
negatively charged
106
what charge do basic amino acids have
positively charged
107
where do polar amino acids tend to be found
surfaces of proteins
108
where do non-polar amino acids tend to be found
buried in the core of proteins or membranes
109
what are the unique amino acids and what do they do
glycine: flexible and can tightly pack
cysteine: disulphide bond formation
proline: breaks secondary structures
110
what kind of reaction are involved in the addition new amino acids
condensation (dehydration reaction)
111
when does a polypeptide become a protein
after it has assumed a unique 3D stable shape and is biologically active
(after folding)
112
what is protein synthesis
the process of elongating a chain of amino acids
113
where is all info necessary for secondary structure contained
primary structure
114
what is the difference between configuration and conformation
configuration: molecular composition
conformation: proper shape
115
what kind of bond are necessary for a protein to adopt its proper shape
covalent and non-covalent bonds
116
what generates secondary structure
hydrogen bonding between amino acids (polypeptide backbone)
117
what is an alpha helix
spiral in shape, consisting of the peptide backbone wth the R groups jutting out from the spiral
118
how may amino acids are there per turn of an alpha helix
~3.6
119
is an alpha helix hydrophilic or hydrophobic
can be either
120
in an alpha helix where do the H-bonds occur
between the NH group of one and the CO or another that is one turn from the first
121
what are the 4 constraints affecting formation/stability of am alpha-helix
-electrostatic repulsion/attraction between successive amino acid residues with charged R groups
-bulkiness of adjacent R group
-helix forming amino acids (leucine, methionine, glutamate)
-helix breaking amino acids (proline and glycine)
122
what is a beta sheet
extended sheet like conformation with several segments of a polypeptide (strand) lying side by side in a folded or pleated formation
123
where do R groups jut out in beta sheets
on alternating sides of the sheet
124
what amino acids are beta sheet formers
isoleucine, valine, phenylalanine
125
what are the major internal supportive elements in a protein
alpha helices and beta sheets
126
where on the polypeptide chain is there the greatest biological activity
hinges, turns, loops, or finger like extensions (most flexible parts)
127
what is a motif
unit of secondary structure that consist of short stretches of alpha helices and beta sheets connected by turns and loops
128
what do people use to classify proteins into protein families
motifs
129
what is tertiary structure stabilized by
covalent and non-covalent binds between R groups
130
what does the weak nature of stabilizing forces result in for proteins
being able to change shape
131
what give proteins considerable stability to proteins
disulphide bonds
132
what is often used to decide if 2 proteins have similar structure/function
primary sequence
133
what is a domain
discrete locally folded unit (substructure) of the overall tertiary structure, usually with a specific function
134
Are proteins static and inflexible
no
135
what accompanies nearly every activity that a protein takes part in
conformational changes
136
what is quaternary structure
assembled subunits
137
what is a homodimer
protein composed of 2 identical subunits
138
what is a heterodimer
protein composed of 2 non-identical subunits
139
what are monomeric proteins
proteins that consist of a single polypeptide
140
what are multimeric proteins
consist of 2 or more polypeptides
141
what is native conformation
a stable 3D structure for a particular polypeptide
lowest energy
142
what are the two categories that proteins are divided into
fibrous: have extensive regions of secondary structure, giving them a highly ordered repetitive structure
- most common in structural material that resides outside of cell
globular: different segments of polypeptide chain (or multiple chains) fold back on each other generating a compact structure
-most proteins within cell are globular
143
what is denaturation
unfolding of a protein
144
how do proteins get their final conformation
explore a range of conformations, then funnel down to the most energetically favourable state
145
what do molecular chaperons do
bind to short structures of hydrophobic amino acids that are exposed in non-native proteins to facilitate proper folding
(having these regions exposed is unfavourable since proteins can stick together when they are not supposed to)
146
where are larger polypeptides transferred to to provide a proper folding environment
chaperonins
