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Flashcards in Chapter 1: An Introduction to Biochemistry Deck (104):
1

1.1 What is life? -List the five important insights pertaining to life!

1. 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

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?

- chemical elements - carbon, nitrogen, oxygen, hydrogen, sulfer and phosphorus

3

1.1 What is life? - What are biomolecules?

-molecules synthesized via living organisms (they are organic -carbon- based)

4

1.1 What is life? 2. Life is organized and self sustaining: - Living organisms are hierarchically meaning what?

- they consist of patterns of organization from smallest (atom) to largest (organism)

5

1.1 What is life? 2. Life is organized and self sustaining: - Explain biological systems pertaining to above umbrella phrase.

- functional capacities of each level of organization are derived from the structural and chemical properties of the level under it.

6

1.1 What is life? 2. Life is organized and self sustaining: - what are biomolecules made up of?

- atoms (formed from subatomic particles)

7

1.1 What is life? 2. Life is organized and self sustaining: - When biomolecules become linked forming polymers they are called what?

- macromolecules

8

Give three examples of macromolecules and their corresponding constituent biomolecules.

1. Nucleic Acids (DNA and RNA) L> nucleotides 2. Proteins L> amino acids 3. Polysaccharides L> sugars

9

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?

- biomolecules and macromolecules

10

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?

- convert an entering molecule to a terminal product

11

1.1 What is life? 2. Life is organized and self sustaining: - Chemical level: L> What is a pathway?

- a series of sequential chemical reactions

12

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 ?)

1. energy 2. matter 3.and the removal of waste molecules!

13

1.1 What is life? 2. Life is organized and self sustaining: - The sum of all reactions in a living organism is called what?

- metabolism

14

1.1 What is life? 2. Life is organized and self sustaining: - What is homeostasis?

- capacity of a living organism to regulate metabolic processes despite variability in their internal and external environments

15

1.1 What is life? 2. Life is organized and self sustaining: -what is the hierarchal organization of a multicellular organism?

- Organ system> Organs> Tissues> Cells> Organelles>Molecules> Atoms.

16

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.

- size and function - membrane

17

1.1 What is life? 3. Life is cellular: - If a cell was divided into it's separate components what would occur?

- it would cease toto function in a life sustaining way....Cells only arise from division of exciting cells!

18

1.1 What is life? 4. Life is information based: -biological information is expressed as what?

- coded messages....which are inherent in biomolecules.....genetic info is stored in genes.

19

1.1 What is life? 4. Life is information based: -genes?

- linear arrangement of nucleotides in DNA....in turn specifies the linear sequence of aa in proteins and how they are synthesized.

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1.1 What is life? 5. Life adapts and evolves: - All life has a ___.

- common origin

21

1.1 What is life? 5. Life adapts and evolves: - mutations?

- individual organism reproduces itself, stress induced DNA rep result in mutations or sequence changes.

22

Extremoenzymes?

- enzymes that work under noxious conditions.

23

Living organisms are made up of what two types of molecules?

- organic and inorganic

24

List the percent of composition of the following elements in an organism: - Na+ - K+ - Mg 2+ - Calcium - H2O - Carbon

- 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