7. Nucleic acids and proteins

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1

phosphate and deoxyribose molecules are held together by a covalent bond called...

phosphodiester bond or linkage (arranged like: phosphate-oxygen-carbon)

2

reaction between the phosphate group on the 5' carbon and the hydroxyl group on the 3' carbon is...

condensation reaction with a molecule of water released

3

pyramidines

cytosine and thymine

4

purines

adenine and guanine

5

role of histones

DNA packaging

6

why is DNA packaging essential?

the nucleus is microscopic but a single human molecule of DNA in a chromosome may be 4 cm long

7

histones and DNA together form...

nucleosomes

8

nucleosome

- consists of two molecules of each of four different histones
- DNA wraps twice around these eight protein molecules
- DNA is negatively charged and histones positively charged
- often a fifth type of histone attached to the linking string of DNA near each nucleosome

9

types of DNA sequence: highly repetitive sequences

- account for between 5% and 45% of the total genome
- composed of 5-300 base pairs
- can move from one genome location to another

10

the centromere of chromosomes is largely made of highly repetitive sequences called...

satellite DNA

11

introns and exons

- introns: non-coding fragments
- extrons: coding fragments

12

types of DNA sequence: single copy genes that have coding functions

provide the base sequences essential to produce proteins at the cell ribosomes

13

types of DNA sequence: structural DNA

- highly coiled DNA that does not have a coding function
- occurs around the centromere and near the ends of chromosomes at the telomeres

14

frequency of various types of DNA sequence

- protein-encoding genes (exons): 1-2%
- introns: 24%
- highly repetitive sequences: 45%
- structural DNA: 20%
- inactive genes (psuedogenes): 2%
- other: 7-8%

15

models of DNA replication

conservative model and dispersive model

16

origins of DNA

- eukaryotic: thousands
- prokaryotic: one

17

elongation of a new DNA strand 1

- a primer is produced under the direction of primase at the replication fork
- this primer is a short sequence of RNA, usually only 5-10 nucleotides
- primase allows joining of RNA nucleotides that match the exposed DNA bases at the point of replication

18

elongation of a new DNA strand 2

the enzyme DNA polymerase III then allows the addition of DNA nucleotides in a 5' to 3' direction to produce the growing DNA strand

19

elongation of a new DNA strand 3

- DNA polymerase I also participates in the process
- it removes the primer from the 5' end and replaces it with DNA nucleotides

20

leading strand

- 5' to 3' direction
- primer, primase, and DNA polymerase required
- formed continuously, so it required primase and primer only once

21

lagging strand

- 5' to 3' direction
- assembled in fragments, so primer, primase, and DNA polymerase required for the formation of each fragment
- fragments are called Okazaki fragments
- once Okazaki fragments are assembled, an enzyme called DNA ligase attaches the sugar-phosphate backbones of the gragments to form a single DNA strand

22

role of helicase

unwinds the double helix at replication forks

23

role of primase

synthesize RNA primer

24

role of DNA polymerase III

synthesizes new strand by adding nucleotides onto the primer (5' to 3' direction)

25

role of DNA polymerase I

removes the primer and replaces it with DNA

26

role of DNA ligase

joins the ends of DNA segments and Okazaki fragments

27

central dogma

states that information passes from genes on the DNA to an RNA copy, which then directs the production of proteins at the ribosome by controlling the sequence of amino acids

28

transcription: DNA --> RNA

- helicase not involved
- RNA polymerase separates the two DNA strands and also allows polymerization of RNA nucelotides as base-pairing occurs along the DNA template
- to provide these functions, the RNA polymerase first combines with a region of the DNA strand called a promoter
- process begins once RNA polymerase has attached tot he promoter region for a particular gene

29

sense and antisense strand

- sense: DNA strand that carries the genetic code (has same sequence as the newly transcribed RNA except with thymine in place of uracil)
- antisense: the strand that is copied during transcription

30

promoter region

- short sequence of bases that is not transcribed
- determines which DNA strand is the antisense strand

31

sections of DNA involved in transcription

promoter --> transcription unit --> terminator

32

terminator

a sequence of nucleotides that, when transcribed, causes the RNA polymerase to detach from the DNA ; when this happens, transcription stops

33

composition of ribosomes

- can be seen with an electron microscope
- large and small subunit - are composed of ribosomal RNA (rRNA) molecules and many distinct proteins
- roughly 2/3 of the ribosome mass is rRNA
- molecules of the ribosomes are constructed in the nucleolus of eukaryotic cells
- decoding of a strand of mRNA to produce a polypeptide occurs in the space between the two subunits

34

sites in ribosome

- A site: holds the tRNA carrying the next amino acid to be added to the polypeptide chain
- P site: holds the tRNA carrying the growing polypeptide chain
- E site: site from which tRNA that has lost its amino acid is discharged

35

translation process

- RNA --> protein
- initiation, elongation, translocation, termination

36

initiation phase

- start codon (AUG) is on 5' end of all mRNA's
- each codon (not stop codons) attaches to a particular tRNA (5' to 3')
- the 3' end of tRNA is free and has the base sequence CCA (site of amino attachment)
- 20 amino acids bind to appropriate tRNA (now called an activated amino acid)
- an activated amino acid - methionine attached to a tRNA with the anticodon UAC - combines with an mRNA strand and a small ribosomal subnit
- the small subunit moves down the mRNA until it contact the start codon (AUG)
- hydrogen bonds form between the initiator tRNA and the start codon
- a large ribosomal subunit combines with these parts to form the translation initiation complex
- joining the initiation complex are proteins called initiation factors that require energy from guanosine triphosphate (GTP) for attachment

37

elongation phase

- involves tRNA's bringing amino acids to the mRNA-ribosomal complex
- elongation factors assist in binding the tRNA's to the exposed mRNA codons at the A site
- initiator trNA then moves to the P site
- ribosomes catalyze the formation of peptide bonds between adjacent amino acids brought to the polypeptide assembling area

38

translocation phase

- involves the movement of the tRNAs from one site of the mRNA to another
- a tRNA binds with the A site
- its amino acid is then added to the growing polypeptide chain by a peptide bond - this causes the polypeptide chain to be attached to the new tRNA that moves into the now exposed A site
- the now empty tRNA is transferred to the E site where it's released (occurs in the 5' to 3' direction)
- therefore the ribosomal complex is movin along the mRNA toward the 3' end

39

termination phase

- occurs when one of three stop codons appears at the open A site
- a release factor fills the A site (does not carry an amino acid)
- it catalyses hydrolysis of the bond linking the tRNA in the P site with the polypeptide chain (this frees the polypeptide, releasing it from the ribosome)
- the ribosome then separates from the mRNA and splits into its two subunits

40

haemoglobin function

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

41

actin and myosin function

proteins that interact to bring about muscle movement (contraction) in animals

42

insulin function

a hormone secreted by the pancreas that aids in maintaining blood glucose level in vertebrates

43

immunoglobins

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

44

amylase

digestive enzyme that catalyses the hydrolysis of starch

45

primary organization

- the unique sequence of amino acids held together by peptide bonds in each protein
- order or sequence in which amino acids are arranged is determined by the nucleotide base sequence in the DNA of an organism
- primary structure determines the next three levels of protein organization

46

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 the side chains, R groups
- two most common configurations of secondary structure are the a-helix and the b-pleated sheet

47

tertiary organization

- polypeptide chain bends and golds over itself because of interactions among R-groups and the peptide backbone - results in three-dimensional conformation
- interactions that cause tertiary organization include: covalent bonds between sulfur atoms to create disulfide bonds, hydrogen bonds between polar side chains, Van der Waals interactions among hydrophobic side chains are forced inwards when the hydrophillic side chains interact with water towards the outside of the molecule, ionic bonds between positively and negatively charged side chains
- important in determining the specificity of the proteins known as enzymes

48

quaternary organization

- involves multiple polypeptide chains which combine to form a single structure
- conjugated proteins

49

fibrous proteins

- composed of many polypeptide chains in a long, narrow shape
- insoluble in water (example: collagen, actin)

50

globular proteins

- more three-dimensional in shape and mostly water soluble
- example: haemoglobin , insulin

51

amino acids with non-polar side chains

- hydrophobic
- found in regions of proteins that are linked to the hydrophobic area of the cell membrane
- no electrical charge
- important in determining the specificity of an enzyme

52

amino acids with polar side chains

- hydrophilic
- found in regions of proteins that are exposed to water
- electrical charge
- important in determining the specificity of an enzyme

53

metabolism

sum of all the chemical reactions that occur in you as a living organism

54

anabolism

the type of reaction that uses energy to build complex organic molecules from simpler ones

55

catabolism

the type of reaction that breaks down complex organic molecules with the release of energy

56

anabolic reactions

- build complex molecules
- are endergonic
- are biosynthetic
- example: photosynthesis

57

catabolic reactions

- break down complex molecules
- are exergonic
- are deradative
- example: cellular respiration

58

mechanism of enzyme action

- the surface of the substrate contacts the active site
- enzyme changes shape to accommodate substrate
- enzyme-substrate complex forms
- activation energy is lowered and substrate is altered by rearrangement of existing atoms
- the transformed substrate is released from the active site
- the unchanged enzyme is free to combine with other substrate molecules
- E + S <--> ES <--> E + P

59

competitive inhibition

- competitive inhibitor competes directly for the active site of an enzyme
- result is that the substrate has fewer encounters with the active site and the chemical reaction rate is decreased
- reversible (may be overcome by increasing substrate concentration) or irreversible

60

non-competitive inhibition

- involves an inhibitor that does not compete for the enzyme's active site
- the inhibitor interacts with another site on the enzyme (allosteric site)
- also called allosteric inhibition
- causes a change in the shape of active site, making it non-functional
- reversible or irreversible

61

end-product inhibition

- prevents the cell from wasting chemical resources and energy by making more of a substance than it needs
- when present in sufficient quantity, the assembly line is shut down (done by inhibiting the action of the enzyme in the first step of the pathway)