Unit 1 BIO 2 Flashcards
(185 cards)
1
Q
What is a structural isomer?
A
Molecules that have the same chemical formula but different bond arrangements.
2
Q
What are cis isomers?
A
A type of geometrical (stereoisomerism) where two identical or similar groups are on the same side of a double bond or ring structure.
3
Q
What are trans isomers?
A
A type of geometrical isomer, where two identical or similar groups are on opposite sides of a double bond or ring structure.
4
Q
What are enantiomers?
A
A type of stereoisomer that consists of two non-superimposable mirror images of each other.
5
Q
What are diastereomers?
A
Stereoisomers that are not mirror images of each other and are not superimposable (same order of bonds but not mirror image)
6
Q
What is a hydroxyl group? (structure+characteristics)
A
OH, hydrophilic (polar) and can make H bonds.
7
Q
What is a carbonyl group?(structure+characteristics)
A
(C=O), interacts with H bonds via dipole dipole int but is not very polar.
8
Q
What is a carboxyl group?(structure+characteristics)
A
C=O(O)H, hydrophilic (polar), acidic and can form H bonds
9
Q
What is an aldehyde group?(structure+characteristics)
A
CH=(O), is hydrophilic and can from dipole dipole interactions
10
Q
What is an amino group?(structure+characteristics)
A
NH2, hydrophilic (polar), forms H bonds and is a base.
11
Q
What is a sulfidryl group?(structure+characteristics)
A
SH, will form sulfidryl bridge if it is near another sulfidryl group (covalent bond). It is also slightly polar and will show moderate interest in making H bonds
12
Q
What is a phosphate group?(structure+characteristics)
A
O=(O)P(O)=O, large in size, are very hydrophilic (polar) and are charged
13
Q
What is a methyl group?(structure+characteristics)
A
CH3, very hydrophobic(non polar) when is a chain
14
Q
What is the function of carbohydrates in biological organisms?
A
Fuel and structure
15
Q
What is the general formula of carbohydrates?
A
C(n)H(2n)O(n)
16
Q
What happens to hexose linear strands of sugar when they are places in solution? How does this occur?
A
The formation of a ring occurs when a hydroxyl group (-OH) from one of the sugar’s carbons attacks the carbonyl carbon, creating a new covalent bond This closes the line up and makes the first carbon an anomeric carbon.
17
Q
What differentiates ketone sugars from aldose sugars?
A
The key difference between ketone sugars (ketoses) and aldose sugars (aldoses) lies in the position of their carbonyl (C=O) group:
Aldoses have an aldehyde (-CHO) group at carbon 1 (C1) in their open-chain form. Example: Glucose, Ribose
Ketoses have a ketone (C=O) group at carbon 2 (C2) in their open-chain form. Example: Fructose, Ribulose
18
Q
What differentiates alpha isomers from beta isomers?
A
The position of their hydroxyl group on the anomeric carbon. If it is pointing in the same direction as the CH2OH the sugar is a beta sugar. If they point in opposite directions the sugar is an alpha sugar.
19
Q
What are anomers?
A
Anomers are stereoisomers that differ
at the anomeric carbon (the carbon in
carbs that “opens and closes”)
20
Q
What are the monomers that make maltose? What bond unites these two monomers?
A
alpha Glucose+ alpha Glucose.
An alpha 1-4 glycosidic bond
21
Q
What are the monomers that make up sucrose? What bond unites these two monomers?
A
alpha Glucose+ beta fructose
An α-1,β-2-glycosidic bond
22
Q
What are the monomers that make up lactose?
A
Beta Galactose + alpha glucose
A β1-4 glycosidic bond
23
Q
What are the two types of sugars? What are their relationship and which ones are useful for human consumption?
A
D sugars and L sugars
They are stereoisomers. Only the D sugars are edible for humans.
24
Q
What is the difference between amylose and amylopectin?
A
Amylose is a long chain of alpha glucose only connected through alpha 1-4 glycosidic bonds which gives it a linear form. Whereas amylopectin is connected through alpha 1-4 and alpha 1-6 bonds which gives it a branched appearance.
25
What is the polysaccharide used in animals to store energy? What does it structure ressemble? Where is it stored in humans?
Glycogen
It is highly branched and made of alpha 1-4 bonds and 1-6 bonds.
It is stored in the liver and in the muscles.
26
What are some functions of polysaccharides?
Storage of sugars and structural support
27
What is a particularity that makes cellulose recognizable?
Very linear strand of beta glucose linked via glycosidic bonds.
28
What makes chitin recognizable?
Long chain of beta 1-4 glycosidic bondages of N glucosamine. (there are N-acetylglucosamine groups on it)
29
What organisms can break down cellulose?
Prokaryotes, Termites, Certain fungi
30
What is the main functions of nucleic acids?
Store genetic information
31
What reaction links carbohydrate monomers into polymers?
A dehydration (or condensation) reaction, which removes a water molecule during bond formation.
32
33
How do D- and L- designations apply to sugars?
They indicate the overall stereochemistry of the molecule, with only D-sugars used in biology.
34
How does amylose differ from amylopectin?
Amylose is a long, unbranched chain of glucose linked by α1-4 bonds.
35
What is cellulose?
A structural polysaccharide composed of D-glucose molecules linked by β1-4 bonds.
36
What three components make up a nucleotide?
A phosphate group, a pentose sugar, and a nitrogenous base.
37
What sugars are found in RNA and DNA respectively?
RNA contains ribose; DNA contains deoxyribose.
38
What is the difference between a nucleoside and a nucleotide?
A nucleoside is a nitrogenous base attached to a sugar; a nucleotide also has one or more phosphate groups.
39
Which bases are purines?
Adenine (A) and guanine (G), which have two-ring structures.
40
Which bases are pyrimidines?
Cytosine (C), thymine (T) in DNA, and uracil (U) in RNA; they have a single-ring structure.
41
What are Chargaff’s rules?
In DNA, the amount of A equals T and the amount of G equals C.
42
Why is base stacking important in nucleic acids?
It stabilizes the double-helix structure through interactions between adjacent base rings.
43
How does the deoxyribose in DNA differ from ribose in RNA?
Deoxyribose lacks an OH group at the 2’ carbon, making DNA more chemically stable.
44
What role do enzymes play in forming the phosphodiester bond?
Enzymes like DNA polymerase facilitate the formation of the bond during nucleic acid synthesis.
45
How does hydrogen bonding contribute to the structure of the double helix?
It holds the two complementary strands together through specific base pairing.
46
What are the common structural components of every amino acid?
An amino group, a carboxyl group, a hydrogen atom, and a variable “R” group attached to a central α-carbon.
47
How many different amino acids are used in proteins?
20
48
What is a peptide bond?
A covalent bond that forms between the carboxyl group of one amino acid and the amino group of another.
49
In what direction is a protein synthesized?
From the N-terminus (amino end) to the C-terminus (carboxyl end).
50
What is meant by the primary structure of a protein?
The linear sequence of amino acids in a polypeptide chain.
51
Why is the primary structure critical?
It determines all higher levels of protein structure and ultimately its function.
52
What are the characteristics of glycine?
It has a single hydrogen as its side-chain and is the only amino acid without a stereocenter.
53
How does alanine differ from glycine?
Alanine has a methyl group as its side-chain, making it slightly larger and less flexible than glycine.
54
What is special about proline’s structure?
Its side-chain bonds to the backbone, creating a rigid structure and often inducing bends in protein chains.
55
What does it mean for an amino acid to be amphipathic?
It contains both hydrophilic (polar) and hydrophobic (nonpolar) regions.
56
What is secondary protein structure?
The regular folding patterns in proteins, such as α-helices and β-sheets, stabilized by hydrogen bonds. This structure is generated by backbone interactions.
57
How is an α-helix formed?
By hydrogen bonds between the carbonyl oxygen of one amino acid and the amide hydrogen of another, forming a coiled structure.
58
What is a β-sheet?
A structure formed by linking β-strands side-by-side through hydrogen bonds to form a sheet-like arrangement.
59
What defines tertiary structure?
he three-dimensional folding of a single polypeptide, determined by interactions among its side chains.
60
Which interactions contribute to tertiary structure?
Hydrogen bonds, ionic bonds, van der Waals interactions, hydrophobic interactions, and disulfide bridges.
61
What is a disulfide bridge and which amino acid is involved?
A covalent bond formed between the sulfur atoms of two cysteine residues.
62
What is quaternary structure?
The association of two or more polypeptide chains to form a functional protein complex.
62
Give an example of a protein with quaternary structure.
Hemoglobin, which is composed of four subunits.
63
How does protein folding relate to function?
The folded structure of a protein determines its active sites and how it interacts with other molecules.
64
What is meant by “denaturation” of a protein?
The loss of the native structure (and thus function) of a protein due to disruption of noncovalent bonds.
65
Can protein denaturation be reversed?
Often yes, if the primary structure remains intact and conditions become favorable for refolding.
66
What role do chaperones play in protein folding?
Prevent aggregation by binding unfolded proteins
Assist refolding using ATP-driven mechanisms (e.g., Hsp60)
Guide folding pathways (e.g., PPIases aid proline isomerization)
Help transport proteins by unfolding/refolding
Protect against stress (e.g., heat shock proteins)
Tag misfolded proteins for degradation (ubiquitin-proteasome system)
67
What is a prion?
An infectious protein that, when misfolded, can induce misfolding in normal proteins.
68
How do side-chain properties affect protein structure?
They determine the hydrophobic or hydrophilic character and can form ionic or hydrogen bonds that stabilize the protein.
69
What does the isoelectric point (pI) of a protein mean?
The pH at which the protein has a net charge of zero.
70
What is a zwitterion?
A molecule that has both a positive and a negative charge but an overall neutral charge.
71
How does pH influence the charge on amino acids?
pH changes affect the protonation state of amino and carboxyl groups, altering their net charge.
72
What is the effect of a protein’s net charge on its solubility?
Proteins with a net charge repel each other and remain soluble; at their pI, they tend to aggregate.
73
How do basic amino acids differ from acidic ones?
Basic amino acids (e.g., lysine, arginine) can accept protons, while acidic amino acids (e.g., glutamate, aspartate) can donate protons.
74
Why is stereochemistry important in amino acids?
It affects the three-dimensional structure of proteins; nearly all biological amino acids are in the L-conformation.
75
How might a mutation in the primary structure affect a protein?
It can change side-chain interactions, potentially leading to misfolding and loss of function.
76
What is the peptide bond’s effect on the polarity of the amino acid backbone?
Formation of the peptide bond removes the free amino and carboxyl groups from participating in hydrogen bonding, altering local polarity.
77
Why are hydrophobic interactions important in protein folding?
Hydrophobic side chains tend to cluster away from water, driving the folding of the protein into a compact structure.
78
What is the role of salt bridges in proteins?
Salt bridges (ionic bonds) form between oppositely charged side chains and help stabilize tertiary structure.
79
How can enzyme function be affected by protein misfolding?
Misfolding may alter the active site, reducing or eliminating catalytic activity.
80
How does myoglobin use its prosthetic group?
It uses heme to bind and transport oxygen.
81
What is the relationship between protein structure and enzyme specificity?
The specific folding of an enzyme creates an active site that fits only particular substrates.
82
How is protein structure analyzed experimentally?
Methods include X-ray crystallography, NMR spectroscopy, and bioinformatics comparisons.
83
Why might two proteins with similar primary sequences fold differently?
Even small variations can lead to different intramolecular interactions, altering the folding pathway.
84
How do pKa values of side chains influence protein structure?
They determine the ionization state of side chains at different pH levels, affecting interactions and folding.
85
What is the main characteristic that defines lipids?
They are hydrophobic molecules, generally composed of hydrocarbons.
86
What are fatty acids?
Long hydrocarbon chains with a terminal carboxylic acid group.
87
How do saturated and unsaturated fatty acids differ?
Saturated fatty acids have no double bonds, whereas unsaturated ones have one or more double bonds.
88
What effect does a cis double bond have on a fatty acid?
It creates a kink in the chain, reducing the ability to pack closely.
89
How does a trans double bond differ from a cis double bond?
A trans double bond allows a more linear structure, similar to a saturated fatty acid.
90
What is a triglyceride?
A molecule composed of one glycerol linked to three fatty acids via ester bonds.
91
What is saponification?
A reaction that breaks ester bonds in triglycerides to produce soap (fatty acid salts).
92
What are phospholipids?
Lipids with two fatty acids and a phosphate group attached to a glycerol backbone.
93
What structural feature gives phospholipids amphipathic properties?
They have a hydrophilic (polar) head and hydrophobic (nonpolar) tails.
94
How do phospholipids arrange themselves in an aqueous environment?
They form a bilayer with heads facing outward and tails inward.
95
What are eicosanoids?
Lipid molecules derived from 20‑carbon fatty acids that act as signaling molecules.
96
What roles do eicosanoids play in the body?
They help regulate inflammation, immunity, and other signaling pathways.
97
What distinguishes waxes from other lipids?
They consist of long-chain fatty acids esterified to long-chain alcohols and are highly hydrophobic.
98
What are sphingolipids?
A class of lipids based on a sphingosine backbone, found in cell membranes and particularly in the brain. They are also involved in signal transduction,
and cell-recognition.
99
How do sphingolipids differ structurally from phospholipids?
Sphingolipids lack glycerol and are built around a sphingosine molecule.
100
What is cholesterol and why is it important?
A steroid lipid that regulates membrane fluidity and serves as a precursor for hormones.
101
What common structural feature do steroids share?
A four-ring carbon structure.
102
How do glycolipids differ from phospholipids?
Glycolipids have carbohydrate groups attached, instead of a phosphate group. This aids in cell recognition.
103
What is the significance of essential fatty acids?
They are fatty acids that must be obtained through diet because cells cannot synthesize them.
104
How do unsaturated fatty acids affect membrane fluidity?
They introduce kinks that prevent tight packing, increasing fluidity.
105
What role do fatty acids play in energy storage?
They are a dense form of energy stored in adipose tissue as triglycerides.
106
How is the ester bond in triglycerides formed?
Through a dehydration reaction between the carboxyl group of fatty acids and the hydroxyl groups of glycerol.
107
What effect do trans fats have on health?
Trans fats are associated with negative health effects, including increased risk of heart disease.
108
How can hydrogenation affect fatty acids?
It can convert unsaturated fats to trans fats, changing their physical and biological properties.
109
What are glycoconjugates?
Molecules that consist of carbohydrates covalently attached to proteins or lipids.
110
What is a glycoprotein?
A protein with one or more covalently attached carbohydrate groups.
111
Where are glycoproteins commonly found?
On the extracellular surface of cell membranes, where they participate in cell recognition.
112
What are proteoglycans?
Proteins that are heavily glycosylated with long chains of sugars, often found in the extracellular matrix.
113
What function do proteoglycans serve in tissues?
They help retain water and provide structural support in the extracellular matrix.
114
What is peptidoglycan?
A polymer consisting of sugars and amino acids that forms the bacterial cell wall.
115
What distinguishes peptidoglycan from other glycoconjugates?
It forms a mesh-like structure that provides mechanical strength to bacterial cell walls.
116
What is a glycolipid?
A lipid with a carbohydrate attached, important in cell recognition and membrane stability.
117
What is lipopolysaccharide (LPS) and where is it found?
LPS is found in the outer membrane of Gram-negative bacteria and can trigger immune responses.
118
What is a gram negative bacteria?
A type of bacteria that possesses two cellular membranes. Between these two membranes, there is a cell wall.
119
How do vitamins differ from other biomolecules?
Vitamins are organic compounds that are essential for life but cannot be synthesized in sufficient amounts by the organism.
120
What is an a biologically active toxin?
An antigenic poison or venom of plant or animal origin, especially one produced by or derived from microorganisms and causing disease when present at low concentration in the body.
121
What is the fluid mosaic model?
A model describing the plasma membrane as a dynamic, fluid structure with a mosaic of lipids, proteins, and carbohydrates.
122
What is lateral diffusion in membranes?
The movement of lipids and proteins within the same layer of the membrane.
123
What is flip-flop in membrane dynamics?
The rare movement of a lipid from one leaflet of the bilayer to the other. (this can be forced by flipase.)
124
What is the role of integral membrane proteins?
They span the bilayer and participate in functions such as transport, signaling, and enzymatic activity.
125
How do peripheral membrane proteins differ from integral proteins?
They associate loosely with the membrane surface and do not span the bilayer.
126
What is the significance of glycoproteins on the cell surface?
They are involved in cell-cell recognition, signaling, and immune responses.
127
Why is membrane fluidity important?
Membrane fluidity is important because it controls how easily compounds can diffuse through the membrane.
128
How do cholesterol molecules affect membrane fluidity?
They stabilize membranes by preventing them from becoming too fluid at high temperatures or too rigid at low temperatures.
129
What is the role of membrane asymmetry?
Different lipid compositions in each leaflet allow specialized functions and signaling events.
130
How do lipids and proteins contribute to the selective permeability of membranes?
Their specific interactions and structures create barriers that control the passage of substances
131
What experimental technique provided evidence for the fluid mosaic model?
Freeze-fracture electron microscopy.
132
How do membrane proteins become glycosylated?
Through the covalent attachment of carbohydrate groups, usually in the endoplasmic reticulum and Golgi apparatus
133
What is the function of lipid rafts?
They are microdomains enriched in cholesterol and sphingolipids that organize signaling molecules.
134
How is the membrane involved in cell signaling?
Through receptor proteins that bind ligands and initiate intracellular signaling cascades.
135
What is an example of a membrane protein function?
Transporting ions or molecules across the cell membrane via channels or carriers.
136
Why are some membrane proteins described as “transmembrane”? What characteristic must they have to be transmembrane?
Because they extend through the entire lipid bilayer.
They must be amphipathic
137
What does “selective permeability” mean?
The ability of the cell membrane to allow only certain molecules to cross.
138
Which amino acids are basic?
Lysine, Histidine and arginine
139
Which amino acids are acidic?
Aspartic acid and glutamic acid
140
What is the only amino acid that can form sulfur bridges?
Cysteine
141
Are Eicosanoids molecules that persist in the body?
No they degrade rapidly
142
What are some characteristics of sphingolipids?
They have a pair of of non-polar hydrocarbon chains
and a polar “head” region
They also consist of a core molecule of sphingosine (which itself has a polar region and a single
hydrocarbon chain) bonded to a fatty acid (providing a second hydrophobic chain) and another
molecular that is often polar
143
What are some steroids?
Bile acid, testosterone estrogen and vitamin D
144
What are the two main systems used for signalling in the human body?
The endocrine system (slow signalling)
The nervous system (quick response)
145
145
Who presented the sandwich model? Why was it wrong?
Gortner & Grendel.
The sandwich model proposed that proteins formed continuous layers on the outer surfaces of a lipid bilayer. However, this model was ultimately disproven because it couldn't explain how membranes could be both a barrier and dynamically involved in transport and signaling.
146
What are the two main categories of transport?
Passive transport (no energy required) and active transport (energy required)
147
What is a catabolic reaction?
Catabolic reactions are those that involve breaking apart a molecule to release
energy.
148
What are anabolic reactions?
Anabolic reactions involve using energy to bring molecules together
149
What is a reaction that is said to be endergonic
Endergonic reactions require energy, which is absorbed by the reaction, and ∆G (Gibbs free energy) is positive in such cases.
150
What do enzymes do to favour reactions?
They catalyse the reaction
151
How can an enzyme lower activation energy
Enzymes bring reactants in close proximity
Enzymes can align reactants in the best orientation to allow them to react
Enzymes strain certain bonds to favour bond-breaking
Enzymes provide an optimal microenvironment for the reaction to proceed
152
What is a substrate?
The reactant of a reaction.
153
What distinguishes simple diffusion from facilitated diffusion in membrane transport?
Simple diffusion allows small, nonpolar or small uncharged polar molecules to cross directly through the lipid bilayer, while facilitated diffusion requires specific protein channels or carrier proteins to help larger or charged molecules move down their concentration gradient.
154
Which types of molecules typically cross the plasma membrane via simple diffusion?
Gases (e.g., CO₂, N₂, O₂), nonpolar molecules (e.g., benzene), and small, uncharged polar molecules (e.g., ethanol, water, urea).
155
How does the concentration gradient influence the rate of simple diffusion?
The greater the difference in concentration across the membrane, the faster the diffusion of particles occurs.
156
What role do aquaporins play in water movement across the plasma membrane?
Aquaporins are specialized pores that facilitate the rapid transport of water molecules across the membrane, supplementing the limited diffusion of water through the lipid bilayer.
157
Define osmosis and explain how osmotic pressure can affect cell volume.
Osmosis is the diffusion of water across a selectively permeable membrane; osmotic pressure is the force driving water to flow from areas of low solute concentration to high solute concentration, which can cause cells to swell (in hypotonic solutions) or shrink (in hypertonic solutions).
158
How do plant cells utilize osmosis to maintain turgor pressure?
In a hypotonic environment, water enters plant cells, generating turgor pressure against the rigid cell wall, which is necessary for structural rigidity.
159
How do contractile vacuoles help paramecia regulate osmotic pressure?
Contractile vacuoles pump excess water out of the cell, preventing the paramecium from bursting in hypotonic freshwater environments.
160
What is the primary difference between facilitated diffusion and simple diffusion regarding protein involvement?
Facilitated diffusion relies on protein channels or carrier proteins to assist in transporting molecules, whereas simple diffusion occurs directly through the lipid bilayer without protein aid.
161
How does the Na⁺-K⁺ pump create a membrane potential?
By actively pumping 3 Na⁺ ions out of the cell and 2 K⁺ ions into the cell per ATP consumed, it generates an electrochemical gradient with a net positive charge outside the cell.
162
What is co-transport, and how does it relate to active transport?
Co-transport harnesses the energy stored in an existing concentration gradient to move another molecule against its gradient, utilizing the gradient generated by active transport.
163
What are the main types of bulk transport, and what does each process accomplish?
Phagocytosis: Engulfing large solid particles (cell “eating”).
Pinocytosis: Internalizing extracellular fluid and dissolved solutes (cell “drinking”).
Receptor-mediated endocytosis: Selectively internalizing specific molecules when sufficient binding occurs at surface receptors.
164
What are some factors that affect enzyme activity?
Temperature, pH, substrate concentration, enzyme concentration.
165
What are hypertonic and hypotonic environments?
Hypertonic solutions are ones that have a higher solute concentration than that of the cell
Hypotonic = opposite
165
What are inhibitors and activators?
Inhibitors decrease enzyme activity by binding to enzymes, while activators enhance enzyme activity by promoting proper function.
166
What are the three types of inhibitors?
Competitive inhibitors, non-competitive inhibitors and uncompetitive inhibitors.
167
How do competitive inhibitors function?
They are inhibitors that bind to the free enzyme before the substrate can bind, and prevents the substrate from binding.
168
How do non-competitive inhibitors function?
They are inhibitors that do not preferentially bind E alone or ES – their effect is to prevent the = conversion of ES to E + P. This is why they are considered “non-competitive” – they are indifferent to whether the substrate binds the enzyme or not.
169
What are uncompetitive inhibitors?
Inhibitors will only bind to the ES complex (and not free enzyme), and will
actually have an effect on both KM and Vmax.
170
Which factors of the Michaelis-Menten curve are affected by each inhibitor?
Competitive inhibitor= km
Noncompetitive inhibitors= vmax
uncompetitive inhibitors=km_vmax
171
What is feedback inhibition?
It is when the last product of a metabolic pathway inhibits the first enzyme. This serves as an “off switch” to the pathway when enough product has been produced.
172
What are the oxidoreductases?
Enzymes that catalyse oxidation/reduction reactions
173
What are transferases?
Enzymes that move a chemical group from one substrate to another
174
What are hydrolyses?
Enzymes that hydrolyse a bond
175
What are lyases?
Enzymes that break a covalent bond without hydrolysis
176
What are isomerases?
Enzymes that rearrange isomers
177
What are ligases?
Enzymes that bring two molecules together
181
182
What is an easy way to recognize thymine?
It is a pyrimidine, has an oxygen on its first carbon and an extra methyl group.
183
What is an easy way to recognize guanine?
It is the only purine with an oxygen instead of an amine in its right ring.
184
What is an easy way to recognize cytosine?
It is the only pyrimidine with an amine.
185
