Exam 1 Review Flashcards
1
Q
How large is a typical mammalian cell?
A
20um in diameter
2
Q
How many microns are in 1 millimeter?
A
1000
3
Q
How many nanometers are in 1 micron?
A
1000
4
Q
What is a model system?
A
A non-human species that is extensively studied to understand particular biological phenomena
5
Q
What is special about a model organism?
A
All genomes are sequenced
6
Q
What are some examples of model organisms?
A
E. coli Brewer's Yeast Fission Yeast Arabidopsis Thailand Drosophila melanogaster C elegans Zebrafish Mice
7
Q
How are E. coli used as model organisms?
A
They rapidly reproduce. Used to explore transcription/translation machinery
8
Q
How is Brewer’s Yeast used as a model organism?
A
Used to explore development of cell polarity, responses to environment
9
Q
How is Fission Yeast used as a model organism?
A
Used to identify cell cycle proteins, can do RNA interference (Brewer’s cannot)
10
Q
How is Arabidopsis Thaliana used as a model organism?
A
Important for world nutrition, disease resistance, used to study plant development
11
Q
How is Drosophila melanogaster used as a model organism?
A
To study development, genetic control of body patterning
12
Q
How is C elegans used as a model organism?
A
All 959 cells are identified and “fate mapped,” meaning their origins are known. Used to study cell differentiation
13
Q
How are zebrafish used as model organisms?
A
Transparent embryos useful for studying development, develop outside of mother, rapid development
14
Q
How are mice used as model organisms?
A
Closer to human physiology, many genes are almost identical
15
Q
What is the definition of resolution?
A
Visualizing 2 points of light as separate entities
16
Q
What kind of microscopy allows for higher resolution?
A
Superresolution
- Structured Illumination microscopy
- Stimulated Emission Depletion (STED) microscopy
17
Q
Describe the concept of resolution in the context of a high resolution microscope
A
A high resolution microscope distinguishes 2 points of light that are close together as 2 separate entities. The higher the resolution, the closer the points of light can be to one another
18
Q
Which has a higher resolution: an electron microscope or a light microscope?
A
Electron microscope
19
Q
What is the main difference between prokaryotic and eukaryotic cells?
A
Prokaryotes do not compartmentalize components into membrane-bounded organelles
20
Q
Where is most of the cell’s DNA contained?
A
The nucleus
21
Q
What is the genetic material?
A
DNA
22
Q
The nucleus is enclosed by (single, double) membrane
A
Double. Nuclear envelope
23
Q
What is the component of the cell that encloses the cell and separates the inside of the cell from the outside of the cell?
A
Plasma membrane
24
Q
What does the plasma membrane consist of ?
A
A lipid bilayer, which contains sterols and proteins
25
T/F: The plasma membrane is inflexible
False. The plasma membrane can be very flexible
26
What is the difference between cytoplasm and cytosol?
Cytoplasm: Contents of a cell that are contained within its plasma membrane but outside of the nucleus
Cytosol: Contents of the main compartment of the cytoplasm, excluding the membrane-bounded organelles
27
What is the function of the endoplasmic reticulum?
Produces materials for export. Involved in synthesis and modification of proteins and lipids – rough and smooth forms.
28
What is the function of rough endoplasmic reticulum?
Synthesis of proteins
29
What is the function of smooth endoplasmic reticulum?
Membrane synthesis
30
What is the purpose of the Golgi apparatus?
Receives molecules from the ER (cis side), modifies them, then directs them to exterior of the cell (plasma membrane) or other cellular compartments (trans side)
31
________ of proteins also occurs in the Golgi apparatus.
Glycosylation
32
What is the function of the mitochondria?
Generate chemical energy for the cell by oxidizing food molecules such as sugars to produce ATP
33
Mitochondria consume _____ and release _____.
Oxygen, carbon dioxide (cellular respiration)
34
The mitochondria is enclosed by (1,2,3,etc.) membranes.
2. An inner and outer. The inner is highly folded.
35
What is a chloroplast?
A large, green organelle that contains chlorophyll. Performs photosynthesis
36
What happens to the sugars created by a chloroplast?
They are oxidized by the mitochondria to produce ATP
37
How many membranes are chloroplasts surrounded by?
2.
38
T/F. Chloroplasts contain their own DNA, and reproduce themselves by dividing.
True.
39
What is the Endosymbiotic Theory?
The theory that mitochondria and chloroplasts are derived from bacteria that were engulfed by ancestral eukaryotic cells
40
What is a lysosome?
A small organelle that contains hydrolases for the breakdown of materials
41
What is a peroxisome?
An important catabolic and detoxification organelle. Provide a contained environment for the generation and degradation of hydrogen peroxide.
42
What is the cytoskeleton?
Molecules within the cytoplasm that give a cell structure. These molecules are polymers that can undergo polymerization or depolymerization
43
What is actin?
The thinner filaments are made of actin (microfilaments)
44
What is a covalent bond?
A bond in which electrons are shared between 2 atoms
45
When electrons are shared unequally, the bond is said to be a _______.
Polar covalent bond
46
What is an ionic bond?
A bond in which one atom steals electrons from another. Atoms are held together by ionic bonds are called salts rather than molecules
47
Which kinds of bonds are affected by water?
Ionic bonding and hydrogen bonding (really any non covalent bond)
48
What kind of bond is the strongest?
Covalent bond
49
If Cl steals electrons from Na, Cl becomes the _____ and Na becomes the _____. Both are ______.
Anion, cation, ions
50
How are atoms held together by ionic bonds held together?
By electrostatic forces. The charges are thus balanced
51
How can you measure the strength of the bond?
Measure the amount of energy that must be supplied to break the bond (kcal/mol)
52
What is an activated carrier molecule?
Molecules that can be split (C → A + B) to release free energy, but only if there is an excess of C relative to its equilibrium concentration.
53
What are some key activated carrier molecules?
ATP, GTP, NADH, FADH2, and NADPH
54
What is a catabolic reaction?
A reaction typically used to release energy to drive a chemical reaction. Think breakdown. Hydrolysis reactions are catabolic.
55
What is an anabolic reaction?
Usually requires energy. Anabolic reactions build new molecules and/or store energy. Think building. Condensation reactions are anabolic
56
All reactions that make or break covalent bonds require _______.
Catalysts (enzymes)
57
What are the 2 major kinds of pathways in a cell?
Catabolic and anabolic.
58
According to the 2nd Law of Thermodynamics, what kind of events generate an increase in disorder?
Spontaneous
59
A measure of a systems disorder is called its _____
Entropy
60
Spontaneous reactions are energetically (favorable/unfavorable)
Favorable
61
In a spontaneous reaction, the reactants have (more/less) energy than products
More energy. More order. Negative ΔG
62
In a spontaneous reaction, energy is (released/absorbed) by the system, and disorder (increases, decreases) in the system
Released, Increases
63
Non-spontaneous reactions are energetically (favorable/unfavorable)
Unfavorable
64
In a non-spontaneous reaction, the reactants have (more/less) energy than products
Less energy. Less order.
| Positive ΔG.
65
In a non-spontaneous reaction, energy is (released/absorbed) and disorder (increases, decreases)
Absorbed, decreases (against the 2nd Law)
66
How can an energetically unfavorable reaction occur?
If it is coupled to a spontaneous reaction. The overall ΔG must be negative for the combined reactions
67
How are chemical reactions coupled?
Using high-energy intermediates called activated carrier molecules (ATP carries a high energy phosphate group, NADH and NADPH carry high energy electrons)
68
What is a phosphate group?
-PO3 2-
69
What is an amino group?
NH2
70
Give a description for the primary level of protein structure.
Protein shape is specified by the sequence of amino acids because of their R groups. Each polypeptide folds in a characteristic way
71
Give a description for the secondary level of protein structure.
Alpha helices and beta sheets
72
What is significant about an alpha helix?
It is a good structure for crossing through a membrane
73
What is significant about a beta sheet?
R groups alternately project above or below the sheet. This gives the 2 surfaces different characteristics
74
Give a description of the tertiary level of protein structure
The 3-D structure
75
Give a description of the quaternary level of protein structure
Proteins formed by interactions between more than 1 polypeptide
76
What is an example of a tertiary structure?
A coiled-coil: intertwined alpha helices that form a stable structure
77
Define protein denaturation.
A process in which proteins unfold
78
In what situations can proteins renature?
After the denaturing "agent" is removed
79
Some proteins require helpers to fold – these are called ______.
Chaperones
80
What kind of proteins protect other proteins from heat denaturation?
Heat shock proteins
81
How can an alpha helix cross a membrane?
The helical structure can satisfy all backbone hydrogen-bonds internally, leaving no polar groups exposed to the membrane if the sidechains are hydrophobic
82
What is a protein domain?
Another level of protein organization. A distinct functional or structural unit in a protein that is responsible for a particular interaction
83
Individual domains are often associated with?
A particular function
84
T/F: Different proteins must have different domains.
False. Proteins can have similar domains
85
What are the subunits of proteins?
Amino acids.
86
What is the name of the bond between amino acids?
Peptide bonds
87
What is the monomer of nucleic acid (DNA, RNA, etc)?
Nucleic acids
88
What is the name of the bond between nucleotides?
Phosphodiester bond
89
What are the 3 amino acids that are most frequently phosphorylated?
Serine, Threonine, Tyrosine
90
Proteins work by binding to other molecules – these are called ______.
Ligands
91
What is a ligand?
A substance that binds to a protein, especially if it regulates the protein
92
Ligands fit (loosely, precisely) into a binding site so that many (covalent, non-covalent) bonds can form
Precisely, non-covalent
93
What creates a ligand binding "pocket" in the protein surface?
Polypeptide folding
94
A protein often has ______ which can bind different _____.
Domains, ligands
95
What are the 2 kinds of ligand interaction kinetics?
Long-lived (high affinity)
Ex) Ligand-receptor interactions
Transient (low affinity)
Ex) Ligand-enzyme interactions
96
Ligands can also be ______ of protein activity.
Inhibitors
97
Describe how ligands are used in feedback inhibition.
The final product of a pathway inhibits "upstream" allosteric enzyme. Ligand binding changes the enzymes's shape, which inactivates it to stop the reaction
98
Which nucleotide is the most widely used energy carrier?
ATP
99
How is ATP generated?
Generated from ADP by an energetically unfavorable reaction. A phosphate group is added to ADP, catalyzed by a kinase or another enzyme called ATP synthase
100
What is ATP synthase?
A giant complex in the mitochondria that converts ADP to ATP. Potential energy of proton gradient that drives the motor → mechanical energy of rotation/friction → chemical bond energy
101
How does ATP synthase convert ADP to ATP?
Using a proton gradient to drive a mechanical turbine
102
Where do protons get pumped to make the gradient which drives ATP synthase?
Between the inner and outer membrane
103
Where is ATP synthase located?
On the inner mitochondrial membrane
104
Where is the electron transport chain located?
Inside the outer mitochondrial membrane
105
How can you identify where the R group is on an amino acid?
All amino acids have an amine group (NH2) and a carboxyl group (COOH). The other part is the R group (not usually the hydrogen though)
106
How can you identify a peptide bond?
Occurs between amino acids (monomer of protein). Occurs between amine group and carboxyl group.
107
Nucleotides are covalently linked by __________ bonds creating a _________.
Phosphodiester, sugar-phosphate backbone
108
Each DNA strand has what?
Polarity
109
Phosphate at one end attached to the (5', 3') carbon of the sugar.
5'
110
OH group at the other end attached to the (5',3') carbon of the sugar
3'
