Exam 1: Lectures 1-6 Flashcards
1
Q
Cell theory
A
All organisms are made of cells that come from preexisting cells (Virchow, 1859)
2
Q
Theory of evolution by natural selection
A
When individuals within a population have varying traits that can be passed on to offspring, and when certain versions of those traits allow those individuals to survive and reproduce better than those with other versions (Darwin and Wallace, 1858)
3
Q
Classification of organisms (general to specific)
A
Domain (general)
Kingdom
Phylum
Class
Order
Family
Genus
Species (specific)
4
Q
Binomial nomenclature
A
The unique two-name name given to each organism; written as genus-species where genus is capitalized and species is not (Linnaeus, 1735)
5
Q
Three domains
A
- Bacteria
- Archaea
- Eukarya
(Woese, 1970)
6
Q
Scientific Method
A
- Make an observation
- Ask a question
- Generate a hypothesis
- Make predictions
- Experiment to test the hypothesis
- Results: do they support the hypothesis?
7
Q
Hypothesis
A
A falsifiable question/claim to explain a set of observations
8
Q
Hypothesis testing
A
A hypothesis may be tested through experimental design
9
Q
Components of experimental design
A
- Control group that doesn’t receive treatment
- All treatments handles identically to eliminate variance
- Repeatability; large sample size and replication
10
Q
Chromosome theory of inheritance
A
Hereditary/genetic info is encoded in genes which are located on chromosomes inside the cells; includes the central dogma that DNA can be translated to RNA and transcribed into proteins (Sutton, Boveri, and Crick, 1902)
11
Q
Atom
A
The smallest unit of a chemical element that retains the characteristics of that element; composed of electrons (negative), protons (positive), and neutrons (neutral)
12
Q
Chemical bonds
A
Performed by electrons; covalent or ionic bonds
13
Q
Ionic bonds
A
Chemical bonds between ions where no electron sharing occurs; rather, electrons are completely transferred from one atom to another
14
Q
Covalent bonds
A
Chemical bonds where atoms share electrons; can be polar or nonpolar depending on how strongly the atom attracts the electrons
- polar: when electrons are shared unequally (electrons spend more time orbiting one atom than the other)
- nonpolar: when electrons are shared equally
15
Q
Moles and molarity
A
Mole: the number of molecules present in a sample (Avogadro’s number)
Molarity: the number of moles in one liter of solution
16
Q
Chemical reactions
A
Occur when a molecule is combined with another molecule or is broken down into another substance
Reactant + Reactant –> Product
17
Q
Endothermic
A
Reaction that absorbs heat and causes the immediate surrounding temperature to decrease
18
Q
Exothermic
A
Reaction that releases heat and causes the immediate surrounding temperature to rise
19
Q
1st Law of Thermodynamics
A
Energy is conserved; energy is never created or destroyed, just transferred or changed
20
Q
2nd Law of Thermodynamics
A
Entropy (disorder) increases and order decreases in the process of a reaction
21
Q
General properties of water
A
- Good solvent
- High specific heat
- High surface tension
- High heat of vaporization
- Denser as a liquid than as a solid
- Hydrogen bonds have a role in pH
22
Q
General properties of carbon
A
Carbon can make many covalent bonds because it is missing four electrons in its valence shell
Carbons bound together make carbon backbones which give either chain or ring shapes to molecules
23
Q
Amino acids
A
Monomers that bind together to make proteins; can be ionized or nonionized
24
Q
Amino acid structures
A
There are 20 types of amino acids, all of which have the same shape with varying R-groups
A nonionized amino acid is comprised of an amino group (H2N), carboxyl group (COOH), R-group, and hydrogen atom all bounded around a carbon atom
25
Protein formation & characteristics
Amino acids link with peptide bonds to form proteins
Proteins have three structural characteristics:
1. Directionality: amino groups are on one side and carboxyl groups are on the other
2. Flexibility: each amino acid can rotate around the carbon in the backbone
3. R-groups: they stick out and can interact with each other or water
26
Peptide bond formation
Covalent bonds between the COO- of one ionized amino acid and the H3N+ of another
27
Protein primary structure
Simple amino acid chain held together by peptide bonds (single shoelace)
28
Protein secondary structure
The polypeptide bends and folds and forms hydrogen bonds, allowing different parts of the same protein to interact; can take the form of an alpha-helix or a beta-pleated sheet (untied shoelace laced into a shoe)
29
Protein tertiary structure
Further folding and interactions between R-groups give the protein a more 3D shape; tertiary structure contains secondary structures (shoelace fully tied)
30
Protein quaternary structure
Several polypeptides in their tertiary structures bond to each other (tieing two shoes together by the laces)
31
General protein functions
- catalyze reaction
- antibodies
- motor proteins and movement
- cell-to-cell signaling
- cell structure
- substance transport
32
Enzymes
Proteins that catalyze reactions by lowering the activation energy
33
Enzyme-substrate interactions
Each enzyme is specific to a given substrate (aka reactants); the enzyme binds to substrates at an active site, which holds them in close together in a particular orientation which allows the reacting groups to more easily undergo reactions
34
Activation energy
Kinetic energy needed for a reaction to occur; less is needed when enzymes are active, therefore threshold is reached sooner
35
Effects of temperature and pH on enzymes
Higher temperatures, up to a point (until denaturation), increase kinetic energy and the rate of reaction
pH affects the charges in an active site since pH affects amino acids, and the enzyme cannot bind to the substrate
36
Nucleotides
A monomer made of a phosphate group, 5-carbon sugar, and nitrogenous base
37
Types of nucleotides
Differ in nitrogenous base
Pyrimidines (CUT the Py)
- cytosine
- uracil
- thymine
Purines (PURe As Gold)
- guanine
- adenine
38
DNA structure
Primary structure: nucleotides connected by phosphodiester linkages
Secondary structure: phosphodiester backbone on the outside and nitrogenous bases on the inside forming two antiparallel strands in a double helix
- cytosine-guanine
- adenine-thymine
Tertiary structure: supercoil!
39
RNA structure
Primary structure: nucleotides connected by phosphodiester linkages
Secondary structure: spontaneously-formed hairpin shape with complementary base pairings on the same strand
- adenine-uracil
- cytosine-guanine
Tertiary structure: diverse!
40
Nucleic acid formation
Polymer composed of nucleotides bound by phosphodiester linkages, which form a backbone with nitrogenous bases sticking out and 5' and 3' on opposite ends
41
Phosphodiester linkage formation
Link between the phosphate group of one nucleotide and the sugar of another nucleotide
42
DNA characteristics
- very stable
- template for its own synthesis: double helix separates into two strands, free bases pair with complementary bases on the original (template) strand, ending with two new identical DNA helixes
43
RNA characteristics
- template for its own synthesis
- can be catalysts (like enzymes)
44
What do DNA and RNA have in common?
- phosphodiester bonds
- sugar-phosphate backbone
- cytosine-guanine
- forms template for own synthesis
45
How do DNA and RNA differ?
DNA:
- deoxyribose sugar
- antiparallel strands
- double helix
- adenine-thymine
- less reactive
RNA:
- ribose sugar
- base pairings on same strand
- hairpin
- adenine-uracil
- more reactive
46
Carbohydrates
Macromolecule sugars; monosaccharides or polysaccharides
47
Carbohydrate structure
Carbonyl group (C-O), hydroxyl functional groups (-OH), and C-H bonds
Full formula: (CH2O)n
48
Monosaccharies
Monomer/simple sugar
49
Polysaccharides
Polymers made up of monosaccharides linked by glycosidic linkages; can be made up of the same or different monomers
50
Monosaccharide structure
Diverse structure:
- number of carbons in backbone can vary from 3-7 (backbone forms a ring structure if there are more than 5 carbons)
- spatial arrangement of atoms varies
- location of the carbonyl group varies (this changes monosaccharide classification)
51
Polysaccharides structure
Monosaccharides connected by glycosidic linkages between hydroxyl groups, where the location of the bond varies greatly
52
Glycosidic linkages
Covalent bonds between hydroxyl groups (-OH) that produces H2O due to excess leftover atoms from bond
53
Ring structures
Carbohydrates can be formed into ring structures when the oxygen atom from the 5-carbon bonds to the 1-carbon
For example: glucose can take the form of an alpha-glucose ring or a beta-glucose ring, where the only difference is the orientation of the 1-carbon and its hydroxyl group and C-H bond
54
Carbohydrates in energy storage
Starch (plants) and glycogen (humans)
55
Starch
Carbohydrate produced in chloroplasts of plants and stored in the roots and stem; composed of alpha-glucose monomers connected with glycosidic linkages to form helix-shaped polysaccharides
These polysaccharides take the form of either amylose (unbranched) or amylopectin (branched), which together make up starch
56
Glycogen
Carbohydrate in animals stored in the liver and muscles; composed of alpha-glucose monomers connected with glycosidic linkages to form helix-shaped polysaccharides
Glycogen is made up of only amylopectin (branched) polysaccharides, which are much more highly branched than in starch
57
Carbohydrates in cell structure
These carbohydrates are strong and elastic and resist cell decay; for example, cellulose in plants, chitin in animals, and peptidoglycan in bacteria
58
Cellulose
Found in plants
Composed of beta-glucose monomers that form long horizontal strands bonded by glycosidic linkages where every other beta-glucose is flipped (upside down)
Horizontal strands are connected with hydrogen bonds on each beta-glucose to the adjacent strands
59
Chitin
Found in animals; makes up exoskeletons
Organized in the same orientation as cellulose, but made up of N-acetyl-glucosamine monomers
Because of the N-acetyl groups, vertical bonds in chitin structure alternate between hydrogen bonds and N-acetyl bonding to adjacent monomer; horizontal bonds are still glycosidic linkages
60
Peptidoglycan
Found in bacteria
Composed of N-acetyl-glucosamine and N-acetyl-muramic acid monomers; monomers alternate with each other in horizontal strands bonded by glycosidic linkages
Parallel strands are vertically bonded by alternating peptide bonds and N-acetyl bonds
61
Carbohydrates in cell identification
Glycoproteins
62
Glycoproteins
Carbohydrate covalently bonds to a protein embedded within the plasma membrane of a cell and sticks out from the surface of the membrane; glycoproteins are unique to each type of cell
63
Lipids
Non-polar and hydrophobic molecules made up of carbon and hydrogen connected by covalent bonds
64
Types of lipids
Different types defined by solubility
- steroids
- phospholipids
- fats
65
Lipid structure
Lipids are only made up of hydrocarbons with structure varying very slightly between types
66
Cell (plasma) membranes
Layer of molecules that surrounds the cell, separates the internal and external environments, and selectively regulates the passage of molecules and ions
Main functions:
- helps to regulate cell volume and function
- keeps inside and outside of cell different
- keeps all cell components together
67
Membrane composition
Made up of lipids forming a bilayer
68
Bilayer formation
Phospholipids organize themselves into two stable rows with their hydrophilic heads interacting with water on the outside (inside cell and outside cell) and their hydrophobic fatty acid tails on the inside interacting with each other
69
Selective permeability
Some substances cross the plasma membrane more easily than others while some don't cross at all; impacted by hydrophobic tails and depends on size and charge of molecule
70
Membrane permeability per molecule
High permeability:
Hydrophobic molecules (O2, CO2, N2)
Small, uncharged, polar or nonpolar molecules (H2O, indole, glycerol)
Large, uncharged, polar molecules (glucose, sucrose)
Low permeability:
Ions (Cl-, K+, Na+)
71
How do lipids alter permeability?
The degree of saturation of the lipids affects how permeable the membrane is
72
Proteins in the bilayer
Proteins in the membrane can be peripheral (only on one side of the membrane) or integral (spans entire membrane; faces both internal and external fluids)
Can be ion channels, transporters, or pumps
73
Ion channels
Pores in plasma membrane that make the membrane permeable to ions; each channel is selective to a given ion
Perform facilitated diffusion; the ion follows the concentration gradient but is facilitated by the channel
74
Carrier proteins (transporters)
Another type of facilitated diffusion where the molecule is "carried" across the membrane by a transporter protein; involves a conformational change in the protein and is often a coupled transport (exchange)
75
Pumps
Pumps transport molecules against the concentration gradient, which is a form of active movement and requires energy
76
Fluid-mosaic model
Lipids and proteins in membrane are constantly in motion; dynamic, lateral movements
77
Hypertonic
Lower concentration of solutes inside cell than outside; water moves out of cell to even concentration
78
Hypotonic
Higher concentration of solutes inside cell than outside; water moves into cell to even concentration and potentially bursts the cell
79
Isotonic
The concentration of solutes inside and outside the cell is the same; no water moves in or out
80
Organism
A living entity made up of one or more cells
81
Five characteristics of an organism
1. Made up of cells
2. Can replicate itself
3. Product of evolution
4. Hereditary/genetic info is encoded in genes
5. Is able to acquire and use energy by a) acquiring chemical energy as ATP, and b) obtaining molecules from diet as building blocks
82
Cell
A highly organized compartment bounded by a thin, flexible membrane and containing chemicals in an aqueous solution
- the smallest unit of life
- the structural and functional unit of organisms
83
The three unifying theories of biology
1. Cell theory
2. Evolution by natural selection
3. Chromosome theory of inheritance (and the central dogma)
84
Tree of Life
A family tree of organisms, or phylogenetic tree, which depicts the evolutionary history and relationships between species
85
Prokaryotes
Lack a true nucleus; all of Domains Bacteria and Archaea
86
Eukaryotes
Have a true nucleus bound in a membrane; all of Domain Eukarya (plants, fungi, animals)
87
Roles of protons, neutrons, and electrons
Protons: form nucleus with neutrons, help determine charge of atom alongside electrons, define atomic number, add to amount of neutrons to determine mass number of atom
Neutrons: form nucleus with protons, differing amounts cause isotopes, add to amount of protons to determine mass number of atom
Electrons: help determine charge of atom alongside protons, orbit nucleus, form bonds
88
Electrons and orbitals
Electrons orbit the nucleus in paths called orbitals; atoms can have multiple orbitals where each orbital holds up to two electrons and are grouped into levels called electron shells
89
Valence shell
The outermost electron shell where the number of orbitals depends on the element; an atom is most stable when the valence shell is full, and attempts to form chemical bonds when valence shell is not full
90
Endergonic
Non-spontaneous chemical reactions that require energy input
91
Exergonic
Spontaneous chemical reactions where the reactants have more potential energy than the products
92
Why is water a good solvent?
Polarity of water molecules and their ability to create hydrogen bonds allow other charged or polar molecules to dissolve in water
93
Cohesion
When like molecules bond together; for example, hydrogen bonds
94
Hydrogen bonds
Weak interactions between H of one water molecule and O of another
95
Adhesion
When unlike molecules bond together; for example, hydrogen bonds formed between water molecules and other substances that allow molecules to dissolve
96
Hydrophilic molecules
"Water-loving" molecules that interact with water and easily dissolve; typically charged or polar
97
Hydrophobic molecules
"Water-fearing" molecules that don't dissolve in water; typically nonpolar and uncharged
98
High specific heat of water
The energy required to raise one gram of water temperature by one degree C is high
99
High surface tension of water
The surface of water forms an elastic membrane of tightly bound molecules due to high number of hydrogen bonds
100
High heat of vaporization of water
The energy required to change one gram of water from liquid form to gas form is high
101
Why is water denser as a liquid than as a solid?
Due to the latticed organization of water molecules in ice, there is more space and air between the molecules, causing the ice to float in water
102
pH
The measurement of the concentration of excess (not bonded to anything) H+ ions there are in a solution
pH = -log [H+]
103
How do hydrogen bonds play a role in pH?
H+ + OH- <--> H20
Water is unstable and is constantly dissociating and rebonding, resulting in unbonded H+ ions which indicate pH
104
Proteins
Large polymer molecules made up of amino acid monomers; sometimes called peptides or polypeptides when they are made up of over 50 amino acids
105
Ionized amino acid
In an ionized amino acid, the amino group is H3N+ and the carboxyl group is COO-
These charges contribute to chemical reactivity and bond forming, and help amino acids form hydrogen bonds and stay in solutions
106
How is protein folding regulated?
Folding is directed by amino acids in their primary structure and regulated by molecular chaperones that can fold proteins, recognize mistakes, and fix unfolded proteins
107
Steroids
Groups of 4-ringed hydrocarbons that differ based on which side groups are attached to the rings; for example, cholesterol
108
Phospholipids
Three parts:
- phosphate (hydrophilic head)
- glycerol
- two hydrocarbon chains (hydrophobic tails)
Phospholipids are amphipathic (have both hydrophobic and hydrophilic parts)
109
Fats
Two parts linked by ester linkage:
- glycerol
- hydrocarbon tails (can have three tails, making it a triglyceride)
110
Saturated vs. unsaturated lipids
Saturated lipids have only single C-C bonds
Unsaturated lipids have at least one double C=C bond
Unsaturated tails have a kink; when many lipids are unsaturated, the bilayer leaves more space for molecules to cross through
111
Cholesterol in the bilayer
Cholesterol is hydrophobic and interacts with the fatty acid tails in the bilayer; fills the spaces and increases the density and stiffness of the membrane, which decreases fluidity and permeability
112
Diffusion
When particles move from areas of high concentration to low concentration; is passive and spontaneous
113
Osmosis
When water moves from areas of low solute to high solute; is passive and spontaneous
