Topic 7: Nucleic Acids and Proteins - Assessment Statements and Outline

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1

Describe the structure of DNA, including the antiparallel strands, 3'-5' linkages and hydrogen bonding between purines and pyrimidines

DNA is composed of 2 antiparallel strands (they run in opposite directions). Each strand is composed of nucleotides which contain a phosphate group and deoxyribose sugar and a nitrogenous base. Each deoxyribose molecule contains 5 carbons. The fifth carbon always bonds with a phosphate group through a phosphodiester bond. The third carbon also bonds with a phosphate group contained in another nucleotide. At one end of each strand there is a free 5th carbon bonded with a phosphate group and and the other end there is a free 3rd carbon. The nitrogenous bases contained in the nucleotides form base pairs. These being A and T and G and C. A and G are double ring purines and C and T are single ring pyrimidines. A purine always pairs with a pyrimidine. The base pairs are connected by hydrogen bonds. A and T form 2 hydrogen bonds and C and G form 3 hydrogen bonds

2

Outline the structure of nucleosomes

Nucleosomes are composed of 2 molecules of 4 histone proteins each, which form the core. DNA then wraps around the 8 histone proteins twice. The DNA and Histones are attracted by opposite charges. DNA-negative, histone- positive. The nucleosome is held together by a H1 Histone. Once part of the nucleosome DNA cannot be transcribed

3

State that nucleosomes help supercoil chromosomes and help to regulate transcription

Nucleosomes form the smallest component of a supercoiled DNA other than the DNA itself. Nucleosomes hold the DNA in place. Many nucleosomes will hold a single string of DNA. A group of nucleosomes containing a single strand of DNA are further supercoiled to form chromosomes. With the DNA wrapped so tightly around the histones, the DNA is inaccessible to transcription enzymes. This inaccessibility helps regulate transcription of the DNA molecule.

4

Distinguish between unique or single-copy genes and highly repetitive sequences in nuclear DNA

DNA contains repetitive sequences and single copy genes. Repetitive sequences comprise 5-45% of the total genome and contain 5-300 base pairs per sequence. Could be up to 100,000 replicates of a certain type per genome. Repetitive DNA is usually dispersed throughout the genome and does not apear to have any coding function. They are considered to be transposable elements that can be moved from one location to another. Single copy genes on the other hand have coding functions, and provide the base sequences needed to produce proteins. Less than 2% of a chromosome contains coding genes.

5

State that eukaryotic genes can contain exons and introns

Eukaryotic genes are made up of numerous fragments of protein encoding information called exons and numerous fragments of non-coding fragments called intorns. Introns and exons and mixed together within the gene.

6

DNA

nucleic acid composed of nucleotides, one of the larges biomolecules known, large amount of covalent and hydrogen bonds, negatively charged

7

Phosphodiester Bond

Covalent bond that connects the phosphate and deoxyribose molecules

8

Purines

A and G
Double-ring structures

9

Pyrimidines

T and C
single-ring structures

10

Exons

coding fragments of genes

11

Introns

non-coding fragments of genes

12

Genomics

Research into genomes (whole sets of genes)

13

Satellite DNA

clustered sections of repetitive DNA

14

Genes

comprised of numerous fragments of protein-encoding information mixed with non-coding fragments

15

Structural DNA

Highly coiled, does not have a coding function. Located around centromere and near telomeres.

16

Pseudogens

non-functional copies of genes, rendered non-functional by mutations (have internal "stop" codons)

17

mRNA

carries base sequences from nucleus to ribosome. the transcript that carries the code of DNA

18

State that DNA replication occurs in a 5' to 3' direction

DNA replication occurs in a 5' to 3' direction due to the fact that DNA polymerase III adds new nucleotides to the new strand of DNA in a 5' to 3' direction

19

Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates

Prokaryotes have circular DNA and therefore have a single origin of replication. Replication is bidirectional starting at this point. At the origin of replication helicase separated the DNA molecule into two strands. There are helicase enzymes or replication forks at either end of the origin. The enzyme primase forms a primer that bonds to the strand that runs 3' to 5'. The DNA Polymerase III adds nucleotides to the primer in the same direction. The DNA Polymerase I then removes the primer and replaces it with DNA. The new DNA strand formed with the old strand that runs 5' to 3' forms slightly different. instead of forming continuously it uses the same enzymes to form fragments moving away from the helicase enzyme. these fragments are called okazaki fragments. The okazaki fragments are then joined by DNA ligase which completes the backbone by adding a phosphate group. The nucleotides that are joined to the old strand are called deoxynucleoside triphosphates. This is due to the fact that they have 2 extra phosphate groups that a lost and used as energy when they are bonded to the old strand.

20

State that DNA replication is initiated at many points in eukaryotic chromosomes

Eukaryotic chromosomes having extremely long and linear DNA molecules need multiple origins of replication in order to be efficient. These multiple origins of replication allow replication to be faster and more efficient

21

Semiconservative model

One strand is from the old molecule and one strand is new nucleotides

22

Origins of Replication

Sites where the replication of a DNA molecule begins.

23

Anti-parallel strands

The two strands run in opposite directions: One strand goes from 5' to 3', the other goes from 3' to 5'

24

Helicase

an enzyme that untwists the double helix at the replication forks, separating the two parental strands and making them available as template strands

25

RNA Primase

An enzyme that adds nucleoside triphosphates on the lagging strand to forms an RNA primer using the parental DNA strand as a template.

26

DNA Polymerase III

An enzyme that synthesizes new strands by adding nucleotides onto the primer

27

DNA Polymerase I

An Enzyme that removes RNA primers and replaces them with the appropriate nucleotides during DNA replication.

28

DNA Ligase

an enzyme that eventually joins the sugar-phosphate backbones of the Okazaki fragments

29

Leading Strand

the new strand of DNA that is synthesized in the same direction as the unzipping

30

Lagging Strand

the new strand of DNA that is synthesized in the opposite direction to the unzipping. It is made by joining the Okazaki fragments together.

31

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

32

Deoxynucleoside Triphosphate

Free nucleotides in the nucleus, contain a deoxyribose, a nitrogenous base, and 3 phosphate groups. 2 phosphate groups are lost when bonded and used as energy for the bonding

33

Transcription

process in which part of the nucleotide sequence of DNA is copied into a complementary sequence in RNA

34

RNA Polymerase

Enzyme that adds nucleoside triphosphates using base pairing to the DNA template

35

State that Transcription is carried out in a 5' to 3' direction

Just like in replication when nucleotides are added during transcription the 5' end of the RNA nucleotides is bonded to the 3' end of the new RNA molecule

36

Distinguish between the sense and antisense strands of DNA

Sense strand carries the genetic code and has the same base sequence as the new RNA molecule except it has thymine and the RNA molecule has Uracil. the antisense strand is the stand being transcribed and contains the complementary base pairs of the sense strand.

37

Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator

During transcription the enzyme RNA polymerase attaches to the promoter regions and begins to unwind the DNA molecule. A transcription bubble forms where the RNA polymerase is. This bubble contains the antisense strand, the RNA polymerase, and the new RNA molecule which has begun to form. the RNA molecule forms because the RNA polymerase helps bind nucleoside triphosphates that are in the nucleoplasm to the growing strand. At the end of the anti

38

State that eukaryotic RNA needs the removal of introns to form mature mRNA

In eukaryotic RNA there are sections of bases that are non-coding. These sequences are called introns and need to be removed fro the RNA molecule in order for the molecule to become functional mRNA.

39

Sense Strand

DNA strand that carries the genetic code, has the same base sequence as the new RNA molecule, but the RNA molecule has uracil instead of thymine

40

Antisense Strand

DNA strand being copied during transcription, is complementary to the RNA stand

41

Promoter Region

determines which DNA strand is the antisense strand, short sequence of bases that is not transcribed. A specific sequence of DNA bases at the start of a gene to which RNA polymerase binds

42

Terminator Region

A sequence of bases that when translated cause the RNA polymerase to detach from the DNA molecule. Transcription stops. A Specific sequence of DNA bases marking the end of the transcription process

43

Nucleoside Triphosphate

contins 3 phosphate groups, ribose, and nitrogenous base

44

Explain that each tRNA molecule is recognized by a tRNA-activating enzyme that binds a specific amino to the tRNA, using ATP for energy

Each tRNA bonds to only one specific amino acid. The amino acid and tRNA molecule are bond by a specific enzyme. There is a specific enzyme for each of the 20 amino acid-tRNA molecule pairs. The bond between the tRNA molecule and the enzyme requires energy and this energy is supplied by ATP. The bonded amino acid and tRNA molecule form a structure called an activated amino acid.

45

Outline the structure of ribosomes, including protein and RNA composition, large and small subunits, three tRNA binding sites and mRNA binding sites

Ribosomes are composed of ribosomal RNA molecules (rRNA) and many distinct proteins. Molecules of the ribosomes are constructed in the nucleus. Ribosomes contains two subunits, one large and one small. Both are composed of rRNA and proteins. The ribosome contains 3 different tRNA binding sites held between the two subunits. The A site holds the tRNA carrying the next amino acid to be added to the polypeptide chain. The P site holds the tRNA carrying the growing polypeptide chain. The E site is the site from which the tRNA molecule that has lost its amino acid is discharged. The mRNA binding site is also located between the two subunits.

46

State that translation consists of initiation, elongation, translocation and termination

The process of translation consists of four phases which are initiation, elongation, translocation and termination.

47

State that translation occurs in a 5' to 3' direction

The start codon of all mRNA molecules is located on the 5' end and the stop codon is located at the 3' end. This means that translation takes place in a 5' to 3' direction from the stat codon to the stop codon.

48

Draw and label the structure of a peptide bond between two amino acids

...

49

Explain the process of translation, including ribosomes, polysomes, start codons and stop codons

Translation takes place within a ribosome. First the start codon (AUG) of the mRNA molecule binds to the ribosomes. Next the tRNA molecule with the anticodon UAC is bonded to the enzyme methionine by way of the tRNA activating enzyme and ATP. The tRNA with the activated amino acid bonds to the start codon of the mRNA molecule located in the ribosome. More tRNA molecules containing activated amino acids bond to the mRNA molecule in order of the codons. Once a tRNA molecule has bonded to the mRNA and the amino acid has by bonded to the polypeptide chain the tRNA molecule is released from the E site. When the stop codon reaches the A site a release factor fills the A site and frees the tRNA molecule and polypeptide chain from the ribosome.

50

State that free ribosomes synthesize proteins for use primarily within the cell and that bound ribosomes synthesize proteins primarily for secretion of for lysosomes

Polypeptides synthesized by free ribosomes are primarily used within the cell and polypeptides synthesized by ribosomes connected to the rough endoplasmic reticulum are secreted out of the cell or are used in lysosomes.

51

Translation

change in language from DNA to the language of protein

52

Ribosomes

Contains 2 subunits both containing rRNA molecules and many distinct proteins

53

A site

holds the next amino acid to be added to the polypeptide chain

54

P site

holds the tRNA carrying the growing polypeptide chain

55

E site

site from which tRNA that has lost its amino acid is discharged

56

Phases of Translation

Initiation, elongation, translocation, termination

57

Start codon

AUG, codes for the amino acid methionine

58

CCA

sequence at open end of tRNA molecules

59

GTP (Guanosine triphosphate)

energy- rich compound, joins the two subunits of the ribosome

60

Elongation factors

bind the tRNA to the exposed mRNA codons at the A site

61

Release factor

protein that catalysis hydrolysis of the bond linking the tRNA in the P site with the polypeptide chain

62

Explain the four levels of protein structure, indicating the significance of each lavel

The four levels of protein structure are primary, secondary, tertiary, and quaternary. Primary structure is the unique chain or sequence of amino acids held together by polypeptide bonds. Secondary structure is created by hydrogen bonds between the oxygen of a carboxyl group and the hydrogen of an amine group which produce either an alpha-helix or beta-pleated structure. Tertiary organization refers to the 3 Dimensional structure created by different bonds and forces between the R-groups of the amino acids. Tertiary structure is important in determining the specificity of enzymes. Quaternary organization involves multiple polypeptide chains which combine to form a single structure.

63

Outline the difference between fibrous and globular proteins, with reference to two examples of each protein type

Fibrous proteins are composed of many polypeptide chains in a long, narrow shape and are insoluble in water. Examples of fibrous proteins are collagen and actin. Globular proteins are more 3 dimensional and are mostly water soluble. Examples of globular proteins are haemoglobin and insulin.

64

Explain the significance of polar and non-polar amino acids

Non-polar amino acids are usually found in hydrophobic areas. Polar amino acids are usually found in hydrophilic areas that are exposed to water. Both polar and non-polar amino acids are found in the membrane which give it its unique structure.The polarity of amino acids are also important in determining the specificity of an enzyme.

65

State four functions of proteins, giving a named example of each

haemoglobin-protein containing iron that transports oxygen from the lungs to all parts of the body in vertebrates
insulin- hormone secreted by pancreas that aids in maintaining blood glucose level
immunoglobulins-group of proteins that act as antibodies to fight bacteria and viruses
amylase- digestive enzyme that catalyses the hydrolysis of starch

66

Haemoglobin

protein containing iron that transports oxygen from the lungs to all parts of the body in vertebrates

67

Actin and myosin

proteins that interact to bring about muscle movement in animals

68

Insulin

hormone secreted by pancreas that aids in maintaining blood glucose level

69

immunoglobulins

group of proteins that act as antibodies to fight bacteria and viruses

70

amylase

digestive enzyme that catalyses the hydrolysis of starch

71

Collagen

a fibrous protein that plays a structural role in the connective tissue in humans

72

Proteins

Contains carbon, hydrogen, oxyge, and nitrogen. source of energy. Needed by tissue for repair and growth. Made up of 20 amino acids.

73

Primary organization

the unique sequence of amino acids held together by peptide bonds in each protein

74

Secondary organization

created by the formation of hydrogen bonds between the oxygen from the carboxyl group of one amino acid and the hydrogen from the amino group of another; does not involve side chains, R groups. Common structures are alpha-helix and beta-pleated.

75

Tertiary organization

polypeptide bends and folds over itself due to interactions among R-group and the peptide backbone.
Causes:
1. H bonds between polar side chains.
2. ionic bonds between +/- side chains
3. Van der Waals reaction among Hydrophobic side chains of the amino acid
4. Disulfide bonds (covalent) or bridges between sulfur atoms

76

Quaternary organization

involves multiple polypeptide chains which combine to form a single structure. Not all proteins are quaternary.

77

Conjugated protein

A compound, such as hemoglobin, made up of a protein molecule and a nonprotein prosthetic group.

78

Haem

The iron-containing prosthetic group (non-polypeptide group) found in haemoglobin.

79

Alpha-helix

A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure.

80

Beta-pleated sheet

One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.

81

Prosthetic group

A non-protein, but organic, molecule (such as vitamin) that is covalently bound to an enzyme as part of the active site.

82

Fibrous proteins

long and narrow in shape and are mostly insoluble

83

Globular proteins

rounded 3-D shape and are mostly soluble in water

84

Functions of proteins

Structural, transport, Movement, Defense

85

State that metabolic pathways consist of chains and cycles of enzyme-catalyzed reactions

Metabolic reactions are catalyzed by enzymes and occur in a specific sequence. Metabolic reactions often take place in either chains, cycles or both. In all sequences of reactions a substance is changed by a reaction with an enzyme, and then another, and so on until it forms the final product.

86

Describe the induced-fit model

In the induced-fit model enzymes change shape to conform to the specific substance that it is binding to. Results from a change in the R-groups of the amino acids.

87

Explain that enzymes lower the activation energy of the chemical reactions that they catalyze

Enzymes lower the amount of energy required for a specific reaction. This causes a decrease in the amount of time necessary to carry out a reaction. They do not alter the proportion of the reactants to products.

88

Explain the difference between competitive and non-competitive inhibition, with reference to one example of each

Competitive inhibition takes place when an inhibitor competes directly fro the active site of an enzyme. Sulfanilamide competes with PABA and blocks the enzyme in bacteria. Non-competitive inhibition takes place when an inhibitor interacts with another site on the enzyme and changes. Mercury is a non-competitive inhibitor that binds to sulfur groups. Both can be reversible or irreversible.

89

Explain the control of metabolic pathways by end-product inhibition, including the role of allosteric sites

End-product inhibition prevents the cell from wasting chemical resources and energy by making more of a substance than it needs. Once the desired amount of product is produced a allosteric enzyme is used to prevent the creation of excess product.

90

Metabolism

sum of all chemical reactions that occur within a living organism

91

Anabolism

reaction that uses energy to build complex organic molecules from simpler ones, endergonic, biosynthetic
Example: Photosynthesis

92

Catabolic

reaction that breaks down complex organic molecules with release of energy, exergonic, degradative
Example: Cellular Resperation

93

Enzyme

specialized proteins that speed up chemical reactions

94

Substrate

reactant of an enzyme-catalyzed reaction

95

Active site

The specific portion of an enzyme that attaches to the substrate by means of weak chemical bonds.

96

Enzyme-substrate complex

an enzyme molecule together with the molecule on which it act, correctly arranged at the active site of the enzyme

97

Mechanism of Enzyme action

1. Substance contacts the active site of the enzyme
2. Enzyme changes
3. Enzyme complex forms temporarily
4. Activation energy is lowered
5. transformed substance is released
6. unchanged enzyme is freed

E + S <-> ES <-> E + P

98

Activation Energy AE

the minimum amount of energy required to start a chemical reaction

99

Inhibitors

ph, temperature, substance concentration. Affect the active site. The activity of the enzyme may be altered because of them

100

Allosteric inhibition

two active sites, one for a substrate and one for an inhibitor

101

Factors that Affect Enzymatic Activity

PH, Temperature, Substrate concentration, Inhibation

102

Lock-and-key model

The model of the enzyme that shows the substrate fitting perfectly into the active site

103

Induced-fit model

change in the shape of an enzyme's active site that enhances the fit between the active site and its substrate(s)

104

Competitive inhibition

The process of a substance reducing the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics.

105

Non-competitive inhibition

No competition (ALLOSTERIC INHIBITION) binds to a site other than the binding site causing a change in the shape making in non-functional

106

End-product inhibition

is a negative feedback process which regulates the reaction rate. If it gets too much it begins to produce less if it becomes scarce or doesn't produce enough it begins to produce more

107

Allosteric enzyme

an enzyme which contains a region to which small regulatory molecules may bind in addition to and separate from the substrate binding site, thereby affecting catalytic activity