Module 1 - Basic Biochemistry Flashcards
1
Q
Life
A
Reproduction
Independent acquisition of material + energy
2
Q
Central dogma of molecular biology
A
Replication (DNA synthesis)
Transcription (RNA synthesis)
Translation (Protein synthesis)
3
Q
Heredity
A
Parent organism hands down detailed info specifying the characteristics the offspring will have
4
Q
What distinguishes life from other processes?
A
Heredity
5
Q
Heredity info
A
Machinery needed to gather raw materials from the environment to construct a new cell in its own image w/ a new copy of heredity info
6
Q
What is heredity info comprised of?
A
Comprised in the linear code of DNA
7
Q
Nucleotide
A
Sugar + phosphate + base
8
Q
Nucleoside
A
Sugar + base
9
Q
Nucleobase
A
A T G C U
10
Q
Bases in DNA
A
A T G C
11
Q
Bases in RNA
A
A U G C
12
Q
Backbone of DNA?
A
Sugar-phosphate backbone
13
Q
What type of bond ties the bases together in single strands of DNA?
A
Hydrogen-based
14
Q
What process creates double-stranded DNA?
A
Templated polymerization
15
Q
What shape does DNA have?
A
Double helix
16
Q
What is the process of DNA synthesis called?
A
Replication
17
Q
What is the process of RNA synthesis called?
A
Transcription
18
Q
What is the process of protein synthesis called?
A
Translation
19
Q
What links the sugars to in the backbone of DNA?
A
Phosphate groups
20
Q
A T G and C are what kind of bases?
A
Nitrogenous
21
Q
Nucleotides within each strand of DNA are linked by ___ bonds
A
Covalent bonds
22
Q
A binds to _
A
T
23
Q
T binds to _
A
A
24
Q
C binds to _
A
G
25
G binds to _
C
26
Bases are linked by __ bonds and nucleotides by __ bonds
"Strong" "Weak"
Weak, Strong
27
Transcription
a templated polymerization in which segments of the DNA sequence (= represent genes) are used as templates for the synthesis of RNA
28
Function of mRNA
Act as intermediates in the transfer of genetic info
29
Sugar in DNA
deoxyribose
30
Sugar in RNA
ribose
31
True or false: the backbone in DNA and RNA is the same
True
32
Is DNA single-stranded or double-stranded?
double-stranded
33
Is RNA single-stranded or double-stranded?
single-stranded?
34
Advantage of single-strand
flexible, can bend back on itself to form weak bonds with another part of the same molecule
35
Sequence of RNA...
determines its shape
36
Advantage of RNA over DNA
mass-produced and disposable
37
What reads out mRNAs sequence?
tRNA
38
Codon
3 nucleotides that codes for an amino acid
39
How does tRNA read mRNA sequence?
in groups of 3 nucleotides (codons)
40
What codes for a single amino acid?
codon
41
Where are proteins synthesized?
ribosome
42
What synthesizes proteins?
rRNAs
43
How do rRNAs synthesize new proteins?
Latches onto the end of an mRNA molecule, trundles along capturing tRNA molecules and stiching amino acids together
44
Purpose of DNA
contains genetic and herdity info of cells, holding the instructions to make proteins
45
Purpose of RNA
synthesizes proteins by lining up amino acids and binding them
46
Is the chain of nucleotides in DNA short or long?
long
47
Is the chain of nucleotides in RNA short or long?
short
48
Lifetime of DNA
long
49
Lifetime of RNA
short
50
4 functions of proteins
1) maintain structures
2) act as catalysts
3) generate movement
4) sense signals
51
What forms most of the cell mass following water?
Protein
52
Proteins bind with __ specificity to other molecules
high
53
What are enzymes
proteins that mediate chemical reactions?
54
What do enzymes do?
make-or-break covalent bonds
55
How do enzymes break covalent bonds in polysaccharides?
1) Catalytic sites are formed at grooves
2) A polysaccharide molecule binds to it
3) Amino acids lining the groove causes a covalent bond-breaking reaction
4) Polysaccharide is broken
56
What are the 2 parts of amino acids
1) Same core structure
2) A side group giving them a distinctive character
57
Similarity of proteins to DNA and RNA
Carry info in the form of a linear sequence of symbols
58
What is meant by life being an autocatalytic process?
Catalysis of a reaction by one of its products
59
What does the enveloped nucleus contain?
Chromosomes (DNA)
60
Where are ribosomes?
endoplasmic reticulum
61
What is the function of the golgi apparatus?
the storage and transport of proteins and other biomolecules produced in the endoplasmic reticulum
62
What is the function of mitochondria?
energy production
63
What are the 2 parts of the cytoskeleton?
1) action + intermediate filaments
2) microtubules
64
What is the function of microtubules in the cytoskeleton?
transport
65
What kind of bilayer is the cell membrane made up of?
Phospholipid
66
Where is the genetic material stored in prokaryotes?
cytoplasm
67
True or false: prokaryotes have no mitochondria
true
68
Ribosomes in prokaryotes are __
disperesed
69
Gene
segment of DNA sequence transcribed into an mRNA molecule
70
Genes code for __
proteins
71
True or false: genes can only be processed in one way to produce 1 version of a protein
false
72
What is the function of regulatory DNA
Regulates the expression of individuals genes - the cell adjusts the rate of transcription and translation of different genes independently according to need instead of manufacturing its full repertoire of proteins simultaneously
73
Genome
totality of a cells genetic info embodied in its DNA sequence
74
2 functions of atp
1) building block in DNA + RNA synthesis
2) carrier of free energy needed to drive intracellular chemical reactions
75
Plasma membrane has a __ membrane
selective
76
3 functions of plasma membrane
1) concentrate nutrients gathered from the environment
2) retain products it synthesizes for its own use
3) excrete waste products
77
Amphiphilic
one part hydrophobic, one part hydrophilic
78
Hydrocarbon is hydro___
hydrophobic
79
Phosphate is hydro___
hydrophilic
80
Phospholipids have __ heads and __ tails
hydrophilic, hydrophobic
81
Oil droplets in water form
small-closed vesicles
82
Membrane transport proteins function
1) transport of specific molecules from one side to the other
2) determine which molecules may enter
83
Actin filaments
give structure - grow and disassemble quickly
84
Intermediate filaments
give structure - more permanent and essential
85
Chromatin
complex of DNA + proteins forming chromosomes
86
What forms chromosomes?
Chromatin
87
Extracellular matrix
Large network of proteins and other molecules that surrond, support cell
88
Atomic number
number of protons
89
Relative atomic mass (atomic weight)
Ratio between average mass of an atom to unified atomic mass unit (AMU)
Protons + neutrons of nucleus
90
Protons are __
positive
91
Neutrons are __
neutral
92
Electrons are __
negative
93
Unit of atomic weight
Dalton
94
AMU of a carbon-12 atom
1/12th
95
Number on the top left of an element
atomic number
96
Number on top right of an element
atomic mass
97
What are molecules comprised of?
atoms
98
Atoms make __ bonds to form molecules
strong
99
What 2 bonds do atoms form to make up molecules?
covalent and ionic
100
Through what bonds to molecules interact with each other?
non-covalent
101
Covalent bond
Sharing of electrons
102
H2O is an example of a ___ bond
covalent
103
Electronegativity
tendency of atomic nuclei to attract electrons
104
Non-covalent bond
105
What is the nucleus of an atom made up of?
protons and neutrons
106
Isotope
members of a family of an element that all have the same number of protons but different number of neutrons e.g. radioactive isotopes - carbon-14 and hydrogen-3
107
Ion
atom or molecule with a net electric charge
108
Net electric charge
equal numbers of protons to electrons
109
What charge do ions have?
net electric charge
110
How are ions formed?
loss or gain of 1 or more electrons
111
Example of an ion?
sodium
112
Elements in the periodic table are ordered by __
atomic number
113
elements in the same vertical column ..
show similar properties
114
Single covalent bond
1 electron from each of the 2 atoms is shared
115
Double covalent bond
a total of 4 electrons are shard between 2 atoms
116
Atoms joined by 2 or more covalent bonds can or cannot rotate freely around the bond axis?
can
117
Polar covalent bond
asymmetrical molecules that interact with ions or other polar molecules at the sites of opposite charge
118
Non-polar
symmetrical molecules with no unshared electrons
119
Ionic bond
transferring an electron -> one that gave it is now (+) charged and the one that received is (-) charged
120
Hydrogen bonds
H atom is sandwiched between 2 electron-attracting atoms (e.g. O)
121
Hydrogen bonds have __ the strength of covalent bonds
1/20th
122
amino acids are held together by
peptide - covalnt bonds
123
van der Waals attraction
when 2 masses are close together they tend to attract one another but if too close or too far they repel
124
Hydrophobic interactions
water forces hydrophobic molecules together because doing so minimizes their disruptive effects on the hydrogen-bonded water network
125
Electrostatic interactions
interactions between ions and polar molecules or between 2 polar molecules
126
Acids
release hydrogen ions into a solution - more FREE hydrogens
127
Carboxyl group (-COOH) is an example of a ___
weak acid
128
Bases
substances that reduce the number of H ions in a solution - less FREE hydrogens
129
What are the 2 ways bases reduce H ions in a solution?
1) combining directly with H ions
2) indirectly by making OH- ions and then combining directly with H ions
130
Many bases/acids are only partially dissociated in the cell making them
weak
131
pH
acidity of a solution - defined by the concentration of H ions
132
Hydrophilic molecules
substances composed of ions or polar molecules that attract water molecules through electrical charge effects
133
Hydrophobic molecules
uncharged molecules with few or no hydrogen bonds and many non-polar bonds
134
Solute
dissolved substance
135
Solvent
substance that dissolves
136
Solute + solvent
solution
137
Hydrocarbons are comprised of ...
carbon skeletons
138
Carbon skeletons in hydrocarbons can take on 3 shapes...
1) chain
2) branched trees
3) rings
139
Resonance
double bonds on alternate carbon atoms cause the bonding electrons to move within the molecule, stabilising the structure
140
Alternating double bonds in a ring can generate
stable structure
141
Carbon chains absorb
visible light
142
carbon rings absorb
UV light
143
Methyl group
H2C
144
Hydroxyl group
-OH
145
Carbonyl
C double bonded to O
146
Hydroxyl groups found in
alcohol
147
Carbonyl group found in
aldehyde and ketone
148
Carboxylic aci
-COOH
149
Esters
C3O2 + H2O
150
Esters are formed by combining...
alcohol and acid
151
Unsaturated fatty aicds have double bonds
true
152
Double bond makes the chain
rigid and creates a kink - chain is free to rotate around the other C-C bonds
153
Triacylglycerols/triglycerides
fatty acids are stored as an energy reserve through an ester linkage to glycerol to form these
154
Trioses monosaccharides have __ carbons
3
155
Pentoses monosaccharides have __ carbons
5
156
Hexoses monosaccharides have __ carbons
6
157
Aldoses monosaccharides have a __ group
aldehyde (CHO - O double bonded to C)
158
Ketoses monosaccharides have a __ group
C and O double bonded
159
Glucose is an example of a
Hexoses aldoses
160
Ribose is an example of a
Pentoses aldoses
161
Fructose is an example of a
Hexoses ketoses
162
Number of avogrado
1 mole of a substance (6x10^23)
163
Molecular mass/weight
mass of 1 mole of a molecule (gram/mole)
164
Molarity
number of moles per volume (M = 1 mole/litre)
165
Law of lambert beer
Transmittance (T) = measured light intensity / initial light intensity
166
Absorbance ...
-log T or the wave-length dependent absorption coefficient x path length x analyte concentration
167
Absorbance is proportional to
substance concentration
168
Are hydrocarbons polar or non-polar?
non-polar (neutral)
169
Are hydrocarbons hydrophobic or hydrophilic?
hydrophobic
170
Oligosaccharides
short chains of repeating sugar subunits
171
Polysaccharides
long chains of repeating sugar subunits
172
Good transmittance means __ absorption
bad
173
Good absorption means __ transmittance
bad
174
Nucleus of an atom is __ charged
positively
175
Nucleus is surrounded by
a cloud of negatively hcarged electrons
176
Are electrons big or small?
small
177
Are protons big or small?
big
178
First orbit of an atom can only contain _ electrons to keep it stable
2
179
The second orbit of an atom can only contain _ electrons to keep it stable
4
180
The third orbit of an atom can only contain _ electrons to keep it stable
8
181
What determines how stable an atom is?
Number of electrons on the last orbit
182
Saccharides consist of a __, __ and __
a carbon skeleton, hydroxyl group and an oxygen group on the end
183
Acid dissociation constant: Ka
= amount of H atoms that are being released * amount of molecules that has released it divided by the combined molecule by itself
184
If the Ka is higher
the equilibrium is going to the right à more strong acid, it tends to give away more H atoms
185
If the Ka is lower
the equilibrium is going to the left à it won’t be easy to give away a H atom; it is not a strong acid or it is not an acid at all
186
Function of phosphate-buffered saline (PBS)?
osmolarity and ion concentration match those of the human body making it non-toxic to most cells.
187
PBS is a __ based solution
water
188
PBS is isotonic meaning
it has the same osmotic pressure as some other solution, especially one in a cell or body fluid
189
Advantage of PBS being isotonic
Prevents cells rupturing or shriveling up due to osmosis when being examined – this property makes it useful in substance dilution, separating cells (w/ EDTA) and cell container rinising
190
How does PBS resist change following the addition of an acid or base?
Neutralizes small amounts of the added acid or base helping to maintain the pH of the solution relatively stable
191
How to calculate amount of compound needed
[Concentration needed (mM/for volume needed) x volume of buffer (L)] x molecular weight (Mw)
192
Purpose of magnetic stirrer
Dissolve compounds
193
Why do we use ionized water?
its the purest
194
What is PBS comprised of?
Sodium Chloride (NaCl)
Potassium Chloride (KCI)
Sodium Hydrogen
Phosphate (Na2HPO4)
Potassium Dihydrogen Phosphate (KH2PO4)
195
How do you calibrate the pH meter?
Place electrode into an acidic and basic solution (rinising with distilled water in between)
196
What do you add to make a solution more basic?
Sodium hydroxide
197
What do you add to make a solution more acidic?
Hydrochloric acid
198
Optimal wavelength for Eosin Dilution Series
490 nanometers
199
Standard curve y-axis
absorbance
200
Unit of absorbance
nanometers
201
Standard curve of x-axis
concentration
202
Unit of concentration on standard curve
%
203
How to calculate concentration of unknown solution
sub into x of standard curve formula
204
Coefficient of variation of concentration
variation of absorbance values of that concentration
205
Formula for coefficient of variation of concentration
%CV = (SD/mean)x100
206
pH of PBS
7.4
