1
Q
what type of cells are prokaryotic and eukaryotic
A
Pro: bacteria and achea
Eukar: Protisits, animals, fungi, plants
2
Q
where is dna located in pro and eukaryotic
A
prokary: nucleoid (no nucleus)
Eukaryote: nucleus
3
Q
Plasmid vs chromosone
A
plasmid is small and carries extra genes and helps adpat to unsual enviroments (poisin)
chromosone is longer and main dna
both supercoiled
4
Q
how many chromosone in prok and euk
A
prokaryotes: 1 chromosone
Eukaryotes: multipule
5
Q
bacterial and archeal phospholipids
A
bacterial (fatty acids) archeal (isoprenoids)
both bound to glycerol
6
Q
DNA ______ to fit inside a cell
A
supercoils
7
Q
ribosomes are responsible for what step of central dogma
A
2nd
8
Q
central dogma
A
genetic information flow DNA->(transcription)RNA-> (translation) Protein
9
Q
cytoskeloten
A
long, thin, filaments in cytoplasm of bacteria and archea. looks like spiderweb structure
ESSENTIAL FOR CELL DIVISON AND SHAPE
10
Q
Ribosomes
A
PROTEIN MANUFACTURING CENTER
11
Q
Nucleoid hold
A
chromosones: DNA clusters of genetic material
12
Q
photosynthesis
A
chemical reactions converting sunlight -> chemical energy stored in sugars
13
Q
cell membrane folds inward to…
what is it called….
A
INVAGINATION/endocytosis
make extra surface area, holding PROTEIN and pigments to capture light for PHOTOSYNTHESIS
Extensive surface area allows for more photoynthesis thus increases ability to make food!!!!!!!
14
Q
does photosynthesis occur in pro or eukarotes
A
both!
15
Q
how do cells move and attach (embedded in plasma membrane)
A
flagellum: movement
fimbriae: attachment
eukaryotes dont have fimbriae
16
Q
cell wall
A
protective “exoskeleton”
17
Q
what holds proteins and pigments
A
photosynthetic membrane
18
Q
which cell lack membrane bound organelles
A
prokaryotes (less complex than eukaryotes)
19
Q
inheritance of viral traits is carried by the…
A
molecules injected into the host!
20
Q
Nucleic Acids are ___, just as proteins are _____
A
N.A. = Nucleotides Protein=amino acids, polymers
21
Q
secondary structures of nucleic acids results from complementary base pairing (defining feature) between
A
purine (A&G) and pyrimidine (TorU&C) bases.
Purine + Pyrimidine
A (big) + T/U (small)
G (big) + C (small)
Keeps the helix the right width
22
Q
DNA and RNA Primary structures
A
DNA:
Sequence of deoxyribonucleotides; bases are A, T, G, C
RNA:
Sequence of ribonucleotides; bases are A, U, G,
23
Q
nucleotide Secondary structures
A
DNA:Two antiparallel strands into a double helix (drawn as two straight lines), stabilized by hydrogen bonding, hydrophobic interactions, and van der Waals interactions
RNA: Most commonly, a single strand folds back on itself to form a double-helical “stem” and an unpaired “loop”
24
Q
nucleotide Tertiary:
A
DNA: Most commonly, a single strand twists back on itself (more than secondary) to form a double-helical “stem” and an unpaired “loop”
RNA:Secondary structures fold to form a wide variety of distinctive three-dimensional shape
ex. pseudoknot
25
viruses shape evolution of organism through...
natural selection, influencing genetic makeup
26
lateral gene transfer
picking up genes from one organism of the same species or different
27
epidemic
dz that rapidly transfers in specific region or population
28
pandemic
global outbreak affects multiple continents
29
bacteria are CELLS because they have...
membrane, cytoplasm, ribosome
30
which is localized infections and which is whole body immune response
localized=bacteria
whole body = virus
31
all viruses have...
genetic material (DNA, RNA)
Protein coat (capsid) to protect DNA
32
viruses cannot replicated without...
host (very selective!)
33
Describe virus replication cycles
Lytic:Virus attaches to the host cell
Injects viral DNA
Viral DNA takes over the cell
Cell makes viral DNA + viral proteins (transcription, translation)
New viruses assemble
Cell bursts (lysis) and dies
Viruses infect new cells
Key idea:
Host cell dies
Happens right away
Makes lots of viruses fast
Lysogenic: Virus attaches
Injects viral DNA
Viral DNA integrates into host DNA (becomes “prophage”)
Virus DNA is copied every time the cell divides
Cell stays alive and normal-looking
⚠️ Later:
Stress (UV light, chemicals, starvation) triggers virus
Virus leaves host DNA
**Switches into lytic cycle
Cell eventually bursts
Key idea:
Cell does NOT die at first
Virus is silent
Spreads by cell division, not bursting
34
what do plants have that animals lack
cell wall
chloroplast
large central vacuole
for support and photosynthesis
35
plant or animal cells are more flexible and mobile
Animal!
36
bacteria organize genetic material in the _______ with a single ______ and they isolate internal contents via a _______.
bacteria organize genetic material in the NUCLEOID with a single CIRCULAR CHROMOSONE, and they isolate internal contents via a PLASMA MEMBRANE or sometimes protective cell wall.
37
Eukaryotes have much larger cells than Prokaryotes.
Increased diameter = decreased surface area-to-volume ratio=???
Small cell 🟢
Has some surface area
Has some volume
Enough surface area to exchange nutrients/waste
Bigger cell 🔵
Has more surface area
BUT way more volume
Not enough membrane relative to what’s inside
So diffusion becomes inefficient.
Increased diameter = decreased to -surface-are-ratio = SLOWER SUBSTANCE EXCHANGE
surface area is where cells exchange substances with environment.
38
How do eukaryotes overcome decreased surface area to volume ratio?
ORGANELLES!
39
organelles...
compartmentalize volume into many small bins
cytosol is only a fraction on the cell volume
40
small vol. of cytosol....
offsets effects of decreased surface area:volume ratio
41
Advantages of compartmentalization
1. incompatible chemical reaction separated.
2. chemical reactions become more efficient
42
where does the 1st step in central dogma happen
nucleus
43
nuclear envelope
studded with pore openings, inside linked to FIBOROUS PROTEINS FORMING LATICE LIKE SHEET (nuclear lamina)
44
nuclear lamina
stiffens double membrane maintains organelle shape
45
nucleolus
manufactures and processes RNA to make ribosomes
46
lumen
interior of any sac-like structure
47
after proteins are processed, they either
function in the rough ER or sent off to be packaged into transported cargo (golgi)
48
Smooth endoplasmic reticulum is associated with....
LIPIDS!
contains enzymes catalyzing rxns w/ lipids and store ca2+ ions
49
cisternae:
stacked, flattened membrane sac (like pancakes)
CIS SIDE (longer) is top and TRANS is bottom (shorter)
50
endomembrane system!
modify, sort proteins and lipids!
lysosome, golgi, ER
51
cristae
sac-like inside mitochondria
52
mitochondrial matrix
inner membrane
53
mtDNA
mitochondrial DNA responsible for organelle function
54
thylakoids
inside networks in stacks (grana) for photosynthesis... in chloroplasts
55
endosymbiosis theory
how mitochondria and chloroplasts came to be inside eukaryotic cells. bacteria lives inside host cell in a mutually beneficial relationship, overtime became part of cell permanently.
56
extracellular matrix
animal cells lack cell walls, makes up for it
57
lipids
carbon containing compound, insoluble in water (hydrophobic) due to high proportion of c-c and c-h bonds
58
hydrocarbons
non polar molecules containing only carbon and hydrogen atoms
59
fatty acid
simple lipid of hydrocarbon chain bonded to polar carboxyl groups(-COOH)
60
saturated fatty acid
NO DOUBLE BONDS (straight chains)
61
unsaturated fatty acid
1 or more double bonds (bonds create bends/kinks in chain)
62
types of lipids found in cells
1. steroids
2. fats
3. phospholipids
63
steroids
lipid
4 ring structure'hormone cell signaling testosterone, estrogen)
64
fats
nonpolar, 3 fatty acids linked to 1 glycerol, aka triacylglycerols.
energy is primary function, can store 2x as much chemical energy as carbs
hydrophobic
65
ester linkage
GLYCEROL(-OH) AND FATTY ACIDS (-COOH) BECOME JOINED
only happens in monomers- not nucleotides
66
glycerol
3 carbon alcohol forming backbone of many lipids
67
phospholipids
consist of glycerol, crucial to plasma membrane
HYDROPHILIC
2 fatty acids linked to 1 glycerol, 1 phosphate
ampipathic!
68
membrane lipids and water
membrane lipids are ampithetic
- store chemical enrgy
- pigments capture sunlight
-waterproof coatings
-vitamins
- FORM MEMBRANES!!!!!!!!!
69
although lipids are nonpolar, hydrophobic; membrane-forming lipids have polar, hydrophilic regions called
hydrophilic heads
70
ampipathic
both hydrophobic and hydrophilic.... responsible for plasma membrane!
71
nucleic acid =
D NA/ RNA
72
3 components of nucleic acid
1. phosphate group
2. 5- carbon sugar
3. nitrogenous base (phosphate group is bonded to sugar, which is bonded to the nitrogenous base
73
______ is the central component of nucleotide
sugar
74
monomers of RNA =
monomers of DNA =
monomers of RNA =ribonucleotides
monomers of DNA= deoxyribonucleotides
75
sugar of RNA=
sugar of DNA=
sugar of RNA = ribose
sugar of DNA = deoxyribose (lacking oxygen)
76
RNA base=
DNA base=
Rna base= uracil (U)
DNA base = Thymine (T)
77
RNA nucleotides=
DNA nucleotides=
Rna nucleotides= A,G,C,U
DNA nucleotdes= A,G,C,T
78
once nucleotides form, how do they polymerize to form nucleic acids?
condensation rxns!
two molecules join together and lose a water molecule
79
phosphodiester linkage
bridge formed by phosphate group
connect 3' carbon to 5' carbon of another nucleotide
- joins ribonucleotides: produces RNA
- joins deoxyribonucleotides: produces DNA
80
DNA and RNA strands are...
one-directional
(unlinked phosphate) ----> (unlinked hydroxyl)
5'-------------->3'
81
how does adding phosphate groups raise the potential energy?
phosphates are negatively charged, like charges repel!
linking 2 or more phosphates generates covalent bonds that carry a lot of potential energy due to strong repulsive forces.
the energy is released when phosphates form new, more stable bonds w other atoms
82
chains of linked sugars and phosphates in a nucleic acid act as a....
backbone
83
dna structure
sugar-phosphate back bone made by phosphodiester linkages
sequence of any 4 nitrogenous bases extending from it.
84
ATP stores potential energy in the bonds between its phosphate groups. When ATP is hydrolyzed, one phosphate bond is broken and replaced by a ___________.
lower-energy bond, releasing energy.
85
Secondary structure empirical rules
1) # of purines in DNA = # pyrimidines
2) DNA has = # of T's and A's and = # of C's and G's
86
secindary structurethe addition of phosphate groups....
raises potential energy
87
Purine - Pyrimidine pairing allows hydrogen bonds to form only between certain bases, _________.
Complementary bases
88
double stranded DNA backbones must run in what direction
antiparallel
89
double stranded DNA twist together to form..
double helix
90
complementary base pairing
A-T
G-C
or, "watson-crick pairing"
91
whats the purpose of twisting into a helix
to minimize contact between hydrophobic bases and surrounding molecules.
92
base stacking
further stabilization- stacks bases like coins
93
DNA secondary structure consists of ......
2 antiparallel strands twisted into a DOUBLE HELIX
94
double helix is shaped and stabilized by...
hydrogen bonds between complementary base pairs.
95
secondary structure of protein often leads to compact...
tertiary structure
96
the need for compaction...
the total length of DNA in each cell is ~6 feet long!
97
2 forms of compaction
Supercoils: DNA is wound too tightly, it can twist on itself, supercoiling.
Tertiary: DNA in eukaryotes wrap around specialized DNA binding proteins, histones. Compact into discrete, movable units during cell division. Store and transmit info.
98
DNA contains information required for a copy of itself to be made. What are the steps in this?
1. double helix strands seperate by breaking hydrogen bonds
2. free deoxyribonucleotides form H-bonds on original strand of DNA (template strand). Sugar phosphates form phosphodiester linkages to create a new strand (complementary strand)
3. complementary base pairing allows each strand of DNA to copy exactly, producing 2 identical daughter molecules (polymerization)..
99
The DNA double helix is ______ because complementary base pairing and hydrogen bonding hold the _________ together, allowing DNA to store genetic information reliably and ____________accurately.
The DNA double helix is STABLE because complementary base pairing and hydrogen bonding hold the TWO STRANDS together, allowing DNA to store genetic information reliably and REPLICATE accurately.
100
RNA primary structure
4 types of bases extending backbone
101
DNA vs. RNA
🔑 Why DNA is more stable
Double-stranded
No reactive 2′-OH group
Thymine instead of uracil
➡️ Ideal for long-term information storage
🔬 Why RNA is less stable
Single-stranded
Has a reactive 2′-OH
More flexible
➡️ Good for temporary messages & catalysis
102
Thymine pyrimidine base doesnt exist in _______; it contains a closley related pyrimidine base; _______.
Thymine pyrimidine base doesnt exist in RNA; it contains a closley related pyrimidine base; URACIL.
103
2'-OH group makes ______ much less stable than _____, but as also support ___________.
2'-OH group makes RNA much less stable than DNA, but as also support CATALYZATION.
104
Teritary
when secondary structures fold into complex slopes
105
RIBOZYMES
RNA molecules that act as enzymes- catalyzing chemical rxns without proteins.
106
name the biomolecules... aka macromolecules
- carbohydrates
- lipids
- proteins
- Nucleic acids
107
monomer
building block; usually referring to some type of "block" that makes up something larger
108
carbohydrates
monomer = monosaccharide
ROLE: energy, cell wall
109
lipids
monomer = glyceryol and fatty acids
ROLE: phospholipid bilayer! long term energy storage and insulation (myelin sheath), hormones (chemical messengers)
110
proteins
monomer = amino acid
ROLE: make up structures (hair, muscle, collagen), protein channels, receptors, enzymes, antibodies
111
nucleic acids
DNA, RNA
monomer=nucleotide
ROLE: genetic information- coding traits
112
What are proteins made of?
Polymers composed of amino acids.
113
How many common amino acids are found in cells?
20
114
What type of macromolecule are proteins?
Polymers of amino acids (polypeptides).
115
What is the central carbon in an amino acid called?
The alpha (α) carbon.
116
What four groups are always bonded to the α-carbon?
Hydrogen, amino group, carboxyl group, and R-group (side chain).
117
What determines the identity of an amino acid?
The R-group (side chain).
118
all amino acids share common _________ but different _________
all amino acids share common CORE STRUCTURES but different R-GROUPS
119
what do amino acids make...
protein polymers!
120
peptide bonds
short chains of AA. Formed by dehydration synthesis. Broken by hydrolysis
121
polypeptides
long chain of AA. Joined by peptides bonds. Folds into functional protein.
122
Which functional group acts as a base in amino acids?
The amino group (–NH₂ / –NH₃⁺).
123
Which functional group acts as an acid in amino acids?
The carboxyl group (–COOH / –COO⁻).
124
Why are amino acids called amino acids?
Because they contain both an amino (basic) and carboxyl (acidic) group.
125
carbon has valence = ?, so the geometry is always conserved!
carbon valence = 4
126
In what form do amino acids exist at physiological pH (~7)?
Ionized (zwitterion) form.
127
What charge does the amino group have at pH 7
Positive (–NH₃⁺).
128
What charge does the carboxyl group have at pH 7?
Negative (–COO⁻).
129
Why is ionization important for amino acids?
It increases solubility and affects reactivity and interactions.
130
What is an R-group?
The variable side chain that makes each amino acid unique.
131
What properties of amino acids are determined by R-groups?
Size, shape, charge, polarity, and reactivity.
132
Which R-groups rarely participate in chemical reactions?
Nonpolar R-groups made only of carbon and hydrogen.
133
Name functional groups that can appear in R-groups.
Carboxyl, amino, hydroxyl, and sulfhydryl.
134
What is the role of disulfide bonds?
They stabilize protein structure.
135
Which amino acid R-groups are hydrophilic?
Polar and charged R-groups
136
Which amino acid R-groups are hydrophobic?
nonpolar r-groups
137
What are the three main categories of amino acid R-groups?
Charged, polar (uncharged), and nonpolar.
138
What makes an amino acid acidic?
A negatively charged R-group (loss of a proton).
139
What makes an amino acid basic?
A positively charged R-group (gain of a proton).
140
What bond links amino acids together?
peptide bond
141
How is a peptide bond formed?
By dehydration synthesis between the carboxyl group of one amino acid and the amino group of another.
142
What type of bond is a peptide bond?
covalent bond
143
What molecule is released during peptide bond formation?
Water (H₂O).
144
What are the ends of a polypeptide called
N-terminus (amino end) and C-terminus (carboxyl end).
145
What reaction builds polypeptides?
dehydration synthesis (condensation)
146
What reaction breaks peptide bonds?
hydrolysis
147
does hydrolysis break covalent bonds
yes
148
Do all amino acids have the same core structure?
strong covalent bonds
149
What primarily drives protein folding in water?
interactions among R-groups, especially hydrophobic affects
150
What are the two functional groups present in every amino acid?
An amino group (–NH₃⁺) and a carboxyl group (–COO⁻).
151
What is the general structure of an amino acid?
A central (alpha) carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and an R-group (side chain).
152
What does the R-group determine?
The chemical properties of the amino acid, including polarity, charge, and reactivity.
153
How can you tell if an uncharged R-group is polar?
If it contains an oxygen (or sometimes nitrogen), which forms polar covalent bonds.
154
Why does oxygen make an R-group polar?
Oxygen is highly electronegative and creates polar covalent bonds.
155
Give an example of an uncharged polar amino acid
Serine.
156
How do nitrogen atoms contribute to polarity?
They are electronegative and can form polar covalent bonds.
157
How is overall R-group polarity determined?
By the number of highly polar covalent bonds relative to nonpolar bonds.
158
What makes an amino acid nonpolar?
The R-group lacks a positive charge, negative charge, and oxygen atoms.
159
Give an example of a nonpolar amino acid.
Methionine.
160
How do amino acids link together to form proteins?
Through a bond between the carboxyl group of one amino acid and the amino group of another.
161
What type of reaction forms a peptide bond?
A condensation (dehydration) reaction.
162
What covalent bond is formed in peptide bond formation?
A carbon–nitrogen (C–N) bond.
163
What is this C–N bond called?
peptide bond
164
After condensation, what happens to the functional groups?
The carboxyl group becomes a carbonyl (C=O) and the amino group becomes –NH–.
165
Why are peptide bonds unusually stable?
: Because nitrogen can donate unshared electrons to form partial double-bond character.
166
What does electron sharing between N and C cause?
The peptide bond to have characteristics of a double bond.
167
What happens to electrons in the carbonyl group during resonance?
Electrons shift to the oxygen, forming an oxygen anion (C–O⁻).
168
What is resonance in peptide bonds?
The oscillation between single- and double-bond configurations.
169
What structural consequence does resonance cause?
The peptide bond is planar.
170
Why is planarity important?
It limits rotation and constrains protein structure.
171
What are amino acids called once they are linked in a chain
Residues.
172
Why are they called residues?
They differ chemically from free amino acid monomers after condensation.
173
What structural framework do peptide bonds create?
The polypeptide backbone.
174
Why is R-group orientation important?
It allows interactions with other R-groups and with water.
175
What are the two ends of a polypeptide called?
The N-terminus and the C-terminus.
176
: What defines the N-terminus?
The end with the free amino group (–NH₃⁺).
177
What defines the C-terminus?
The end with the free carboxyl group (–COO⁻).
178
In what direction are amino acid sequences written?
From N-terminus to C-terminus.
179
Why is sequence directionality important?
Proteins are synthesized starting at the N-terminus.
180
Can the peptide bond rotate?
No, due to its partial double-bond character.
181
Which bonds can rotate in a polypeptide?What does this allow?
The single bonds on either side of the peptide bond.
Overall flexibility of the polypeptide chain.
182
What is a peptide or oligopeptide?
A chain with fewer than 50 amino acids.
183
how many AA in polypeptide?
A chain with 50 or more amino acids.
184
What is a protein (formal definition)
The complete, functional form of one or more polypeptide chains.
185
Can proteins have multiple subunits?
Yes, some proteins are functional only when multiple polypeptides interact.
186
Why do proteins have such diverse functions?
Because they vary enormously in size, shape, and amino-acid side-chain chemistry.
187
How is protein shape related to function?
The 3D shape determines what molecules a protein can bind and what reactions it can perform.
188
Which type of protein is typically long and fibrous?
Structural proteins (e.g., collagen).
189
Which type of protein is typically globular?
Enzymes and many binding proteins.
190
What is a protein’s primary structure?
Its unique linear sequence of amino acids.
191
Why is primary structure critical?
It determines all higher levels of structure and ultimately protein function.
192
How can a single amino acid change affect function?
It can alter folding and interactions, dramatically changing protein behavior.
193
What defines secondary structure?
Local folding patterns stabilized by hydrogen bonds in the backbone.
194
What groups form hydrogen bonds in secondary structure?
Carbonyl (C=O) oxygen and amino (N–H) hydrogen in the backbone.
195
Name the two main types of secondary structure.
α-helix and β-pleated sheet.
196
What characterizes an α-helix?
A coiled structure stabilized by hydrogen bonds every 4 residues.
197
What characterizes a β-pleated sheet?
Backbone segments folded into the same plane, connected by hydrogen bonds.
198
Why is proline rarely found in α-helices?
: Its rigid structure introduces kinks that disrupt helix formation.
199
Why are secondary structures stable despite weak bonds?
Many hydrogen bonds act together to create strong overall stability.
200
What is tertiary structure?
The overall 3D shape of a single polypeptide.
201
What interactions stabilize tertiary structure?
Interactions between R-groups and/or backbone segments.
202
List the five major interactions stabilizing tertiary structure.
Hydrogen bonds
Hydrophobic interactions
van der Waals interactions
Disulfide bonds
Ionic bonds
203
Why do hydrophobic R-groups cluster inside proteins?
Water excludes them, forcing them into the interior.
204
Which amino acid forms disulfide bonds?
Cysteine.
205
Why are van der Waals interactions important?
Individually weak but collectively stabilize folded proteins.
206
What is quaternary structure?
The interaction of multiple polypeptide subunits to form a functional protein.
207
What are protein subunits?
Individual polypeptide chains in a multi-chain protein.
208
What is a dimer?
protein made of two subunits
209
Difference between homodimer and heterodimer?
Homodimer = identical subunits; heterodimer = different subunits.
210
What is a tetramer?
A protein made of four subunits.
211
Give an example of a protein with quaternary structure.
Hemoglobin (2 α + 2 β subunits).
212
Why is protein structure described as hierarchical?
Each level depends on the previous one (primary → secondary → tertiary → quaternary).
213
What ultimately directs protein folding?
The amino acid sequence (primary structure).
214
Do proteins fold spontaneously?
Yes, under proper cellular conditions.
215
What happens if protein folding is disrupted?
Loss of function (often leading to disease).
216
What are macromolecular machines?
Large complexes of proteins (sometimes with nucleic acids) that perform specific functions.
217
Give an example of a macromolecular machine.
The ribosome.
218
phosphodiester is for..
ester bonds are for...
phosphodiester = nucleotides
ester = monomers
Molec and Cell Bio
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