Chapter 1: An Introduction to Biochemistry Flashcards
Learn the basics?
1
Q
1.1 What is life? -List the five important insights pertaining to life!
A
- Life is complex and dynamic 2. Life is organized and self sustaining 3. Life is cellular 4. Life is information based 5. Life adapts and evolves
2
Q
1.1 What is life? 1. Life is complex and dynamic: -All organisms are composed of the same set of what? L> mainly = what 6 things?
A
- chemical elements - carbon, nitrogen, oxygen, hydrogen, sulfer and phosphorus
3
Q
1.1 What is life? - What are biomolecules?
A
-molecules synthesized via living organisms (they are organic -carbon- based)
4
Q
1.1 What is life? 2. Life is organized and self sustaining: - Living organisms are hierarchically meaning what?
A
- they consist of patterns of organization from smallest (atom) to largest (organism)
5
Q
1.1 What is life? 2. Life is organized and self sustaining: - Explain biological systems pertaining to above umbrella phrase.
A
- functional capacities of each level of organization are derived from the structural and chemical properties of the level under it.
6
Q
1.1 What is life? 2. Life is organized and self sustaining: - what are biomolecules made up of?
A
- atoms (formed from subatomic particles)
7
Q
1.1 What is life? 2. Life is organized and self sustaining: - When biomolecules become linked forming polymers they are called what?
A
- macromolecules
8
Q
Give three examples of macromolecules and their corresponding constituent biomolecules.
A
- Nucleic Acids (DNA and RNA) L> nucleotides 2. Proteins L> amino acids 3. Polysaccharides L> sugars
9
Q
1.1 What is life? 2. Life is organized and self sustaining: - what two things are cells made up of which help form complex super molecular structures?
A
- biomolecules and macromolecules
10
Q
1.1 What is life? 2. Life is organized and self sustaining: - Chemical Level: L> Sets of in depend molecules create efficient chemical pathways that do what?
A
- convert an entering molecule to a terminal product
11
Q
1.1 What is life? 2. Life is organized and self sustaining: - Chemical level: L> What is a pathway?
A
- a series of sequential chemical reactions
12
Q
1.1 What is life? 2. Life is organized and self sustaining: - Organization and ordered functioning of living organisms require the continuous acquisition of what two things? (third ?)
A
- energy 2. matter 3.and the removal of waste molecules!
13
Q
1.1 What is life? 2. Life is organized and self sustaining: - The sum of all reactions in a living organism is called what?
A
- metabolism
14
Q
1.1 What is life? 2. Life is organized and self sustaining: - What is homeostasis?
A
- capacity of a living organism to regulate metabolic processes despite variability in their internal and external environments
15
Q
1.1 What is life? 2. Life is organized and self sustaining: -what is the hierarchal organization of a multicellular organism?
A
- Organ system> Organs> Tissues> Cells> Organelles>Molecules> Atoms.
16
Q
1.1 What is life? 3. Life is cellular: -Cells vary in ___ and ___. L> however each is surrounded by a ____ that controls the transport of chemical substances into/out of the cell and it also mediates the cells responses to parts of the extracellular environment.
A
- size and function - membrane
17
Q
1.1 What is life? 3. Life is cellular: - If a cell was divided into it’s separate components what would occur?
A
- it would cease toto function in a life sustaining way….Cells only arise from division of exciting cells!
18
Q
1.1 What is life? 4. Life is information based: -biological information is expressed as what?
A
- coded messages….which are inherent in biomolecules…..genetic info is stored in genes.
19
Q
1.1 What is life? 4. Life is information based: -genes?
A
- linear arrangement of nucleotides in DNA….in turn specifies the linear sequence of aa in proteins and how they are synthesized.
20
Q
1.1 What is life? 5. Life adapts and evolves: - All life has a ___.
A
- common origin
21
Q
1.1 What is life? 5. Life adapts and evolves: - mutations?
A
- individual organism reproduces itself, stress induced DNA rep result in mutations or sequence changes.
22
Q
Extremoenzymes?
A
- enzymes that work under noxious conditions.
23
Q
Living organisms are made up of what two types of molecules?
A
- organic and inorganic
24
Q
List the percent of composition of the following elements in an organism: - Na+ - K+ - Mg 2+ - Calcium - H2O - Carbon
A
- Na, K, Mg, Calcium =approx 1% - H20= inorganic= 50-95% of a cell content by weight - everything else is carbon… ~50-5% of each cell
25
Everything is principally composed of what? L\> these principal atoms can readily form what?
- Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus and Sulfer - covalent bonds which allow the formation of important molecules like proteins
26
List some general features of carbon!
- can form four strong single covalent bonds with other carbon atoms or other atoms - makes the structural complexity and diversity of organic molecules possible - can form straight chains, branched chains or rings
27
Most biomolecules are derived from\_\_\_\_.
- hydrocarbons, the simplest type of organic molecules
28
What are hydrocarbons?
- carbon + hydrogen containing molecules which are hydrophobic aka insoluble in water
29
Examples of hydrocarbons? (4)
1. Alkane: c2H6 (all single bonds)....un-reactive, polar molecules...saturated 2. Alkene: C4H8 ....a double bond is present...reactive and unsaturated 3. Alkyne: C2H2, triple bond is present.... reactive and unsaturated 4. Aromatics: cyclic structure, conjugted alkene structure, more stable than the alkenes, have a smell to them.
30
All organic molecules are formed by attaching other molecule or groups of molecules to the _______ of a hydrocarbon.
- carbon backbone
31
Chemical properties of an organic molecule are determined by what?
- functional groups .....(specific arrangement of these)
32
List the nine possible functional groups.
33
What is the group structure of the functional group, Group name and its significance:
- Alcohol
- Hydroxyl
- Polar (H20 soluble), forms hydrogen bonds
34
What is the group structure of the functional group, Group name and its significance:
-Aldehyde
- Carbonyl
- Polar, Sugars
35
What is the group structure of the functional group, Group name and its significance:
- Ketone
- carbonyl
- polar, some sugars
36
What is the group structure of the followng family name functional group, Group name and its significance:
- Acids
- Carbonxyl
- weakly acidic, - charge when it donates a proton
37
What is the group structure of the followng family name functional group, Group name and its significance:
- Amine
- Amino
- weakly basic, positive charge when it accepts a proton
38
What is the group structure of the followng family name functional group, Group name and its significance:
- Amide
- Amido
- polar but does not bear a charge
39
What is the group structure of the followng family name functional group, Group name and its significance:
- Thiol
- Thiol
- easily oxidized; can = -S-S- (disulfide bonds) readily
40
What is the group structure of the followng family name functional group, Group name and its significance:
- Ester
- Ester
- in some lipids
41
What is the group structure of the followng family name functional group, Group name and its significance:
- Alkene
- double bond
- important structural component of many biomolecules
42
What are the four major classesl of small biomolecules?
- Amino acids
- Sugars
- Fatty acids
- Nucleotides
43
What is the main general function of the four small biomolecule classes?
- they are used in the synthesis of larger molecules, many of which are polymeres
- polymeres= proteins (made up of aa), carbohydrates( made up of sugars), nucleic acids ( made up of nucleotide) and lipids ( ade up of fatty acids).
44
Going by the four major classes of small biomoleucles: Amino acids (aa), Sugars, Fatty acids and Nucleotides. Give examples of a polymer made of each and its general function.
1. AA: proteins: catalysts and structural elements
2. Sugars: Carbohydrates: energy sources and structural elements
3. Fatty acids: Lipis: energy sources and strucural compont of complex lipids
4. Nucleotides: DNA and RNA: genetic info, protein synthesis
45
Amino acids contain what two types of functional groups?
-amino and carboxyl group!
46
- Amino acids are classified as \_\_\_, ____ or ___ depending on the location of the amino group in reference to the carboxyl group.
- alpha, beta and Y
47
Describe an alpha amino acid!
- most common type of aa
- amino group is attached to the carbon atom adjacent to the carboxyl group
Ex: H3N(positive)-CH-COOH
The R group comes off of the CH
48
What is the general structure of an alpha amino acid?
49
The R in the alpha amino acid structure can denote what?
- hydrogen atom (ex: glycine), a hydrocarbon group (ex: isopropyl) or a hydrocarbon derivative ( hydroxymethyl group in serine)
50
What is a B(beta)-amino acid?
- amino group is attached to the second carbon from the carboxyl group!
51
What is a Y-amino acid?
- amno group is attached to the 3rd carbon from the carboxyl group!
Image is y-aminobutryic acid (GABA)
52
What is special about alpha amino acids?
- they possess an additional r group attacehd to them....the chem property of each aa is determined largely by the properties of this r group
53
How many standard amino acids are there that occur in proteins?
- 20
54
What are non standard amino acids?
amino aicds that are modified versions of the standard aa..... which are in proteins as well
- structure and function of a protein molceule is modified by the conversion of certain aa residues into derivatives via phosphorylation, hydroxylation and other chemical modificaitons
55
What is a residue?
- a small molecule that is added to a macromolecule
56
Amino acids are largely used in the synthesis of long, comlex polymers called what two things?
- peptides(oligopeptide) = 50 or less amino acids
- polypeptides = more than 50
57
Individual aa's are joined via what?
- peptide bond.....which are amide linkages that form in a type of nucleophilic substituion reaction where the amino group nitrogen of one amino acid attacks the carbon of another.
58
When looking at a chain of amino acids, can you identify the peptide bond?
59
What functional groups are in a sugar?
- alcohol and a carbonyl
L\> described in terms of #of carbons and the type of carbonyl they contain!
60
Sugars with an aldehyde are called what?
L\>with a ketose?
- aldose
- ketose
61
Glucose contains six carbons and contains an aldehyde, what would you name it as?
-aldohexose
62
Fructose contains 6 carbons and contains a ketose, what would you name it?
ketohexose
63
Sugars are the basic units of ____ which are the most abundant oranic molecules found in nature.
- carbohydrates
64
The simplest carbohydrates are called? ex? More complex ones?ex?
- monosaccharides (glucose and fructose
- polysaccharides= polymers that contain thousans of sugar units ex: cellulose, glycogen
65
Carbs serve as a variety of functions in living organisms such as? (2)
- structural sources and ENERGY SOURCES
- glucose and sucrose - energy
- cellulose and chitin = structural
66
Some biomolecules contain carb parts such as?
- Nucleotides
L\> building blocks of nucleic acids...they contain either ribose or deoxyribose
- Proteins and lipids
L\> glycoproteins and glycolipids= on external surface of cell membrane where they play roles in cell to cell interactions
67
Ex: of Monosaccarides?
- Glucose ( aldohexose)
- Fructose ( ketohexose)
- Ribose ( aldopentose)
- 2-deoxyribose ( aldopentose)
68
Explain what a fatty acid is?
- monocarboxylic acids that usually contain an even number of carbon atoms
L\> in some organisms they are an energy source
- formula = R-COOH
L\> R= alkyl group that contains carbon and hydrogen atoms
69
What are the two types of Fatty acids?
1. Saturated Fatty Acids: contain no carbon-carbon double bonds...saturated with hdyrogen
2. Unsaturated Fatty Acids: contain one or more double bonds...therefore not fully saturated with hydrogens
70
Under physiological conditions how is the carboxyl group of fatty acids present?
R-COO minus
- its in ionized state
- the charged carboxyl group has an affinity for H2O but the long nonpolar hydrocarbon chain renders most fatty acids insoluble in water.
71
Lipids are?
- fatty acids help make up these.....most commonly how fatty acids are present vs being free.
- they are soluble in organic solvents such as chloroform or acetone but not in water
72
Phosphoglycerides?
- lipid molecules that resemble triacylglycerols containing only two fatty acids. The third hydroxyl gorup of glycerol is coupled with phosphate which attaches to small polar compounds...this is important in structural components of cell membranes.
73
What are triacylglycerols?
- fats and oils
- esters containing glycerol ( 3 carbon alcohol with three OH groups) and three fatty acids
74
Nucleotide contains what three components?
- a 5 carbon sugar
- nitrogenous base
- one or more phosphate groups
75
The nitrogenous bases of nucleotides are heterocyclic aromatic rings with a variety of substituents. What are the two types of bases?
- Bicyclic Purines( A, G)
- Monocyclic pyrimidines ( T, C, U)
76
Nucleotides are involved in many ____ and ___ reactions.
- biosynthetic
- energy generating
77
What is the general structure of a nucleotide?
78
Nucleotides are the building blocks of what?
- nucleic acids
79
What links nucleotides together when forming nucleic acids?
- phosphodiester linkages
80
Two types of nucleic acids?
- RNA
- DNA
81
Describe DNA
- genetic info
- two antiparallel polynucleotide strands wound around each other to form a right handed double helix.
L\> helix forms due to complementary base pairing
- genes specifiy aa seq in proteins....
82
Hydrogen bonding and relevence to DNA?
- a force of attraction between a polarized hydrogen of one molecula group and the electronegative ocygen or nitrogen atoms of a nearby molecule group together.
83
Describe RNA
- contains ribose not deoxyribose
- contains the base U instead of T
- single stranded
- complementary base pairing allows for complex structures
84
Metabolismis due to what?
- constant flow of energy and nutrients through an organism and the functional properties of thousands of catalytic biomolecules claled enzymes make it possible
85
What are the four main functions of metabolism?
1. acquistion and utilization of energy
2. synthesis of molecules needed for cell structure and functioning (proteins, carbs, lipids and nucleic acids)
3. growth and development
4. removal of waste products
86
What are the five common types of biochemical processes?
1. Nucleophilic substitution
2. Elimination
3. Addition
4. Isomerization
5. Oxidation- reduction
87
Explain a nucleophilic substitution
A: + B-X-------\> A-B + X:
- A: --\> attacking species aka nucleophile (nucleus lover)...they are anions (- charged) or netural species possessing nonbonding pairs
- B = electrophile....electron lover.....they are defficient in electron density and are therefore easily attacked by a nucleophile.
- as the bond between A and B forms the one between B-X breaks.
- X: = the leaving group aka the outgoing nucleophile
88
Can you tell if something is a nucleophilc substituion?
89
Is hydrolysis a nucleophilic substitution reactions?
- yes
- oxygen of water = nucleophile and the electrophile is usually the carbonyl carbon of an ester, amide or anyhydride ( a molecule containing 2 carbonyl groups linked via O atom)
90
Explain what an elimination reaction is!
- a double bond is formed when atoms in a molecule are removed
C2H4AB -----\> C2H4 + A+ + B-
- the removal of H2O from biomolecules containing OH is a commonly encountered example
91
Explain addition reactions!
- two molecule combine to form a single product
- Hydration is the most common example...H2O is added to an alkene an alcohol results
92
-Explain Isomerixation reactions
- atoms or gorups undergo intramolecular shifts
ex: interconversion between aldose and ketose sugar
93
Explain oxidation-reduction reactions!
- transfer of e- from a donor (reducing agent) to an e- acceptor (oxidizing agent)
- when reducing agents donate an e- they become oxidized
- as an oxidizing agent accepts an e- they become reduced.
L\> the two occur simultaneously usually
94
What are the two rules to be certain weather a carbon in a molecule has been oxidized or reduced?
1. oxidation has occured if a carbon atom gains oxygen or loses hydrogen
2. reduction has occured if a carbon atom loses oxygen or gains hydrogen
95
Examles in biological redox reactions of electron acceptors (oxidizing agents)
- NAD+/NADH
96
# Define energy
L\> how do cells generate most of this?
- capacity to do work....move matter
- via redox reactions.........the more reduced the molecule is ( the more H it has) = the more energy it contains
97
What are the three classes of biochemical pathways?
1. Metabolic
2. Energy Transfer
3. Signal transduction
98
What are the two types of metabolic pathways?
1. Anabolic
2. Catabolic
99
Explain Anabolic pathways
- large comlex molecules are synthesized from smaller precursors....
aa+aa+aa+aa+aa= peptide
100
Explain Catabolic pathways!
- large complex molecules are degraded into smaller, simpler products...some catabolic pathways release eenrgy.....and a fraction of this energy is captured and used to drive anabolic reactions.
101
Explain Transfer pathways!
- capture energy and turn it into something an organism can use to fuel biomolecular pathways.
ex: chlorophyll....capture enrgy....redox changes it to chemical bond energy in a sugar
102
Explain signal transduction pathways!
L\> three phases?
- allows cells to receive and respond to signals from their surroundings
- three phases : reception, transduction and response.
103
Explain the three phases of signle transduction!
1. Reception Phase
2. Transduction Phase
3. Response Phase
1. a signal molecule binds to a receptor protein
2. a cascade of intercellular reactions that triggers the cells
3. response to the orginal signal
104
What are te four living processes classifications?
1. Synthesis and degredation of biomolecules
2. Transport of ions and molecules across cell membranes
3. production of force and movement
4. removal of metabolic waste products and other toxic substances
