midterm 1 Flashcards
1
Q
Valence electrons are those in the outermost shell, or valence shell
A
The chemical behavior of an atom is mostly determined by the valence electrons
Elements with a full valence shell are chemically inert
2
Q
carbon
A
- Living organisms consist mostly of carbon-based compounds
* Carbon is unparalleled in its ability to form large, complex, and varied molecules
3
Q
Organisms consist mostly of carbon-based compounds (i.e. organic compounds)
A
Carbon can bond to four other atoms or groups of atoms, making a large variety of molecules possible.
4
Q
hydroxyl
A
-OH
5
Q
carbonyl
A
=C=O
6
Q
carboxyl
A
-COOH
7
Q
amino group
A
-NH2
8
Q
sulfhydryl group
A
-SH
9
Q
Phosphate group
A
—OPO3 2−
10
Q
methyl group
A
ch3
11
Q
methyl group
A
CH3
12
Q
Dehydration reaction: synthesizing a polymer
A
Dehydration removes a water molecule, forming a new bond.
13
Q
Hydrolysis: breaking down a polymer
A
Hydrolysis adds a water molecule, breaking a bond.
14
Q
Carbohydrates (sugars)
A
functions: energy storage, structure
15
Q
Covalent bonds between monosaccharides (5 or 6 carbon sugars) produce disaccharides
A
glucose + fructose = sucrose
16
Q
Sugar is stored in the form of long polymers of glucose (starch and glycogen)
A
starch (plants)
glycogen (animals)
17
Q
cellulose is a polymer of glucose
A
due to orientation of glucose in starch, humans can’t break down as sugar w b-amylase, but can w gut bacteria
18
Q
Galactomannans are another type of polysaccharide
A
Guar Gum and Locust Bean Gum
long chain saccharides not based on glucose
19
Q
Sources of polysaccharides used as thickening agents
A
Acacia gum (gum arabic), Carrageenan, Guar gum, Tara gum, Carob bean
20
Q
why is melted ice cream sticky?
A
added polysaccharides, add body and mouth feel bc ABSORB WATER which is why its in beans
21
Q
lipids (fats and oils)
A
function: energy storage, membrane structure
22
Q
Fats consist of glycerol linked to 3 fatty acids (triglyceride)
A
hallmark of lipids is hydrophobic. Hydrocarbon = Hydrogen and Carbon
23
Q
the presence of double bonds determines the melting temperature of a fat
A
unsaturated fats have double bond kinks
24
Q
saturated fat - no room to take up hydrogens, already full of carbons.
A
solid at room t - animals
25
unsaturated fat has kinks (double bonds) in chain so cant get close together until very cold
liquid at room t - plants
26
if you add hydrogens to unsaturated to remove double bonds, makes solid at room t
trans fats
27
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Unsaturated lipids (i.e. oils) are transformed into saturated lipid by the addition of hydrogen, which reduces double
bounds. Partial hydrogenation often leads to “trans-fats”.
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can cause heart disease
28
phospholipids have
hydrophillic heads and hydrophobic fatty acid tails
29
Proteins
Function: control most cellular activities (enzymatic reactions) and are important for cell and tissue structure.
30
proteins based on amino acids
amino group, carboxyl group, and R group
31
20 amino acids
20 amino acids
32
nonpolar amino acids
only C and H, no O. hydrophobic - protein structure
33
polar amino acids
contain O, hydrophyllic
34
electrically charged amino acids
interact w water bc water has partial charges
35
Humans can synthesize 12 of the 20 amino acids.
| The remaining 8 (“essential”) must be obtained from food.
vary in prevalence - corn vs beans
36
proteins are long chains
assembled by ribosome, peptide bond. You end up w amino end and carboxyl end
37
after protein synthesis, long chain w amino end and carboxyl end
assembles into 3d molecule, mediated by characteristics of proteins (polar/nonpolar/ionic/covlent bonds)
38
Proteins are polymers of amino acids, which fold into specific shapes as covalent, hydrogen, an ionic bonds form between their different amino acids.
the shape of a protein determines its function
39
Protein structure depends on pH
Protein structure depends on pH
40
Nucleic acids (DNA and RNA)
Function: information storage and protein production
41
sugar-phosphate backbone
DNA consists of two strands, in opposite orientation, held together by weak (hydrogen) bonds which can be dissociated easily
42
DNA different from RNA because
deoxyribose vs ribose sugar, uracil in RNA
43
Bacterial cell (prokaryote)
Ribosomes
Plasma membrane Cell wall Capsule
Flagella
circular Bacterial chromosome
44
eukaryotic cell size varies over several orders of magnitude
eukaryotic organelles are about the same size as bacteria
45
how prokaryotic cell turn into eukaryotic cell
internal membrane systems came from invagination and evolution of plasma membrane
46
mitochondria and chloroplasts come from
engulfment of other prokaryotes and evolution
47
Membrane-bound compartments of a eukaryotic cell
1. Information storage and processing
- nucleus
2. Protein production and processing
- endoplasmic reticulum - golgi apparatus and associated vesicles
3. Energy capture and utilization
- mitochondria - chloroplasts
4. Waste storage and removal
- vacuole (plants) - lysosome (animals)
48
photosynthesis happens in
chloroplasts
49
cell respiration happens in
mitochondria
50
difference between plant and animal cell
cell wall, chloroplasts, vacuole
51
Nucleus
DNA, RNA production, processing, and export
52
nuclear membrane (why exist?)
regulatory opportunities, protein production
53
for RNA to be made:
proteins have to be transported through nuclear envelope through pore complexes
54
ribosomes either free in cytoplasm or on rough ER.
ER is large vesicle, proteins in ER can either stay or be transported into Golgi via vesicles
55
The Golgi apparatus modifies proteins and ships them to various places in the cell
(blebs off packaged proteins for shipment anywhere)
56
mitochondria and chloroplasts are similar organelles due to 2 membranes - derived from same process of engulfment
Mitochondria have highly organized intermal membranes (involved in respiration), as well as their own DNA an protein synthesis machinery
57
mitochondria have own DNA as remnant of engulfment of prokaryote
not all of the proteins necessary for mitochondrial function are in mitochondrial genome, instructions/information must come from nuclear DNA. How? migrated.
58
Chloroplasts have highly organized internal membranes where are involved in photosynthesis
Electron Transport Chain?
59
why do tomatoes turn from green to red?
chloroplasts --> chromoplast
| chlorophylls -> lycopene
60
Carotenoids are plastids like chloroplast
amyloplast (starch), elaioplast (oi), proteinoplast (protein)
61
Cyanogenic glucosides in plants
Cassava (roots) Sorghum (roots) Almond (seeds) Cherry (seeds) Apple (seeds) Plums (seeds) Peaches (seeds) Apricots (seeds)
62
Cytoskeleton
Cytoplasmic architecture, intracellular transport, chromosome movement
• Microtubules • Microfilaments • Cell wall
63
Cell wall
• Controls cell shape, plant rigidity • Regulates water uptake/loss • Regulates interactions of plants with other organisms
64
plasma membrane
Compartment • Concentrates materials • Regulates entry and exit of substances • Regulates responses to external signals (receptionist)
65
cholesterol
one end hydrophilic, one end hydrophobic
66
Two major classes of proteins in milk
Casein –micelles (curds) Lacalbumin –soluble (whey)
67
1 calorie (cal) =
amount of heat necessary to raise 1 ml of water, 1o C
68
1 Calorie (Cal) =
1000 cal = 1 kcal
69
LaVoisier 18th century father of chemistry
Measured heat production in a guinea pig by enclosing it in ice and measuring the amount that melted
70
3 stages of respiration
3 stages of respiration
–Glycolysis (breaks down glucose into two molecules of pyruvate)
–Citric acid cycle (completes the breakdown of pyruvate)
–Oxidative phosphorylation (uses electrons from glycolysis and the citric acid cycle to transform O2 into water)
71
Molecules you need to remember (photosynthesis)
•ATP •NADH, FADH2 •Pyruvate (oxyloacetate, citrate) •Acetyl CoA •Carbon dioxide •Water •Oxygen
72
Alcohol fermentation
pyruvate → ethanol carbon dioxide + ATP
73
Lactic acid fermentation
pyruvate → lactic acid + ATP
74
photosynthetic organisms
```
Plants
Unicellular protist
Cyanobacteria
Purple sulfur bacteria
Multicellular alga
animal - e. chlororitca
```
75
The stages of the Calvin cycle
The stages of the Calvin cycle
1. Carbon fixation: CO2 is added to a 5 carbon sugar (ribulose bis-phosphate), which is immediately transformed into two 3-
carbon sugars.
2. Reduction: High energy electrons are added to these 3-carbon
sugars, resulting in the production of glyceraldehyde 3-phosphate.
3. Regeneration of ribulose bis-phosphate.
76
The structure of chlorophyll
Light absorbing “head”
Tail attaches molecule to membrane.
77
Dry conditions create problems
Photosynthesis needs CO2.
• Allowing CO2 to enter a leaf, also makes it possible for water to escape.
• How does a plant photosynthesize in hot, dry conditions?
78
Some C4 plants have specialized bundle sheath cells
Some plants initially fix carbon into a 4-carbon organic acid and then transfer it to the Calvin cycle
79
Gross Primary Productivity (GPP)
Total amount of CO2 that is fixed by plants through photosynthesis = energy captured
80
Net Primary Productivity (NPP)
Gross primary productivity minus the energy used by plants for their own growth and development (respiration)
81
NPP = GPP - R
Units: biomass = g/m2/yr
| energy = calories/m2/yr
82
human appropriation of Net Primary Productivity (HANPP)
Food: plants, animal products Fiber: construction, paper, clothing Fuel: wood, oil, gas
83
Alternatives to fossil fuels
• Hydroelectric • Nuclear • Geothermal • Solar • Wind • Biofuels
84
The motivation for biofuels
• Energy security (only a few places in the world produce oil)
• “Peak oil”, i.e. long term availability of fossil fuels • Environmental degradation • Economics (the cost of importing oil is a large
fraction of the budget of many countries)
85
Types of biofuels
Alcohol • Biodiesel (oils) • Gas (methane)
86
The ethanol fuel energy balance
| energy output/energy input
Corn (U.S.A.) 1.3
Sugar cane (Brazil) 8
87
sources of plant oils
canola, algae
88
• Plant and animal oils are too viscous to be used as vehicle fuel.
• They must be “trans-esterified”
89
Methane (natural gas) production
Anaerobic fermentation by methanogenic bacteria
| C6H12O6 → 3CO2 + 3CH4
90
DNA replication
parent molecule -- separation of strands -- daughter DNA molecules each consisting of one parental strand and one new strand
91
The chromosome number problem:
organisms that reproduce sexually must find a way to reduce the chromosome number in their gametes by half, to prevent an exponential increase in chromosome number.
92
Meiosis produces genetic novelty
1. Independent assortment
| 2. Crossing over
93
Independent assortment
Two equally probable arrangements of chromosomes at metaphase I
94
Original definition of “gene”
“special conditions, foundations and determiners which are present [in the gametes] in unique, separate and thereby independent ways [by which] many characteristics of the organism are specified”
95
New definition gene:
The gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products.
96
Gene
The DNA sequence required to synthesize a product (protein or RNA) important for the function of a cell.
97
Some important RNAs
Ribosomal RNA Transfer RNA
| microRNA
98
DNA sequences can be broadly classified as:
1. Coding sequence (i.e. sequence that actually produces something)
2. Transcribed, non-coding sequences 1.Regulatory sequences
99
The value of punctuation
• The “punctuation marks”in DNA are sequences that are recognized by proteins that regulate the transcription or the processing of the RNA produced by that DNA sequence.
A gene encompasses both the sequence that produces the final product, and the regulatory sequences required to produce that product.
• A change in the sequence of the coding region or the regulatory elements of a gene can have significant effects on its function.
