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Module 2- Foundations in Biology > 2.3- nucleic acids > Flashcards

2.3- nucleic acids Flashcards

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1
Q

What is a double helix

A

The shape of a DNA molecule, due to the coiling of the two sugar-phosphate backbone strands into a right-handed spiral configuration

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2
Q

What is a monomer

A

A molecule that when repeated, makes up a polymer- nucleotides are the monomer of nucleic acids

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3
Q

What is a nucleotide

A

A molecule consisting of a 5 carbon sugar, a phosphate group, and a nitrogenous base

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4
Q

What is a polynucleotide

A

a large molecule containing many nucleotides

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5
Q

Describe nucleotides

A
  • Biological molecules that participate in nearly all biological processes
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6
Q

Describe the general structure of nucleotides

A
  • Phosphate esters of pentose sugars- where a nitrogenous base is linked to the C1 of the sugar residue
  • a phosphate group is linked to either the C3 or the C5 of the sugar residue, by covalent bonds formed by condensation reactions
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7
Q

What do nucleotides form

A
  • The monomers of nucleic acids- DNA and RNA
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8
Q

What is the pentose sugar in DNA and RNA

A
  • DNA= Deoxyribose

- RNA= Ribose

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9
Q

What do nucleotides become when they contain more than one phosphate group- give 3 named examples

A
  • Phosphorylated nucleotides
  • Adenosine- ribose and adenine
  • Adenosine monophosphate- ribose, adenine and 1 phosphate (AMP)
  • Adenosine diphosphate- ribose, adenine and 2 phosphates (ADP)
  • Adenosine triphosphate- ribose, adenine and 3 phosphates (ATP)
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10
Q

What is ATP

A

An energy-rich end-product of most energy-releasing biochemical pathways- used to drive most energy-requiring metabolic processes in cells

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11
Q

What do nucleotides help regulate

A

-Many metabolic pathways, for example by ATP, ADP, and AMP

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12
Q

What coenzymes are adenine nucleotides part of, and what are these involved in

A

NADP- nicotinamide adenine dinucleotide phosphate- used in photosynthesis

NAD- nicotinamide adenine dinucleotide- used in respiration

FAD- flavine adenine dinucleotide and coenzyme A- both used in respiration

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13
Q

List 4 general functions of nucleotides

A
  • Form monomers of nucleic acids
  • become phosphorylated nucleotides when they contain more than one phosphate group
  • help regulate many metabolic pathways
  • May be components of co-enzymes
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14
Q

What is a nucleoside

A

Consist of a sugar and base- no phosphate group

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15
Q

Where is DNA found

A

In the nuclei of all eukaryotic cells, within the cytoplasm of prokaryotic cells and in some types of viruses

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16
Q

What is DNA

A
  • the hereditary material and carries coded instructions used in the development and functioning of all living organisms
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17
Q

What is DNA an example of, and what are the others

A
  • Macromolecules (large numbers of atoms) that make up the structure of living organisms
  • proteins
  • carbohydrates
  • lipids
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18
Q

What type of structure is DNA and why

A
  • a polymer

- it is made up of many repeating monomeric units- nucleotides

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19
Q

What does a molecule of DNA consist of

A

Two polynucleotide strands running in opposite directions- antiparallel

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20
Q

What does each DNA nucleotide consist of

A
  • phosphate group
  • 5-carbon sugar- deoxyribose
  • one of 4 nitrogenous bases- adenine, guanine, thymine or cytosine
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21
Q

What does DNA stand for

A

Deoxyribonucleic acid

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22
Q

Name and explain the covalent bonds in nucleotides

A
  • between sugar residue and phosphate group is phosphodiester
  • between sugar and base is glycosidic
  • broken when polynucleotides break down, formed when synthesised
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23
Q

Describe the length of DNA molecules and what this means

A

-long- can carry a lot of encoded genetic information

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24
Q

What type of reaction is used to form a nucleotide- describe it

A

Condensation- 2 x OH from deoxyribose, 1x H (from OH) from phosphate, and 1x H from base forms 2 water molecules

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25
Q

What are the 2 types of bases, what is the difference, an which of the 4 bases does each include

A

Purines- 2 hexagonal rings- adenine or guanine

Pyrimidines- 1 hexagonal ring- thymine or cytosine

26
Q

Describe base pairing

A

Complimentary- one purine with one pyrimidine- equal sized ‘rungs’ on DNA ladder- can then twist into double helix- gives molecule stability

Adenine with thymine- 2 x hydrogen bonds

Guanine with Cytosine- 3 x hydrogen bonds

27
Q

What is the upright part of the large DNA molecule formed by

A
  • sugar-phosphate backbones of the antiparallel polynucleotide strands
28
Q

What does the ‘opposite direction’ of the 2 strands refer to

A

The direction that the 3rd and 5th carbon molecules on the 5 carbon sugar are facing

29
Q

Where do you count from to identify carbon numbers on the sugar, and where is the 5th carbon

A

clockwise from oxygen

attached upwards from the fourth

30
Q

What us the 5’ and the 3’ end of the molecule

A

5’- where the phosphate group is attached to the 5th carbon atom of the deoxyribose sugar

3’- where the phosphate group is attached to the 3rd carbon atom of the deoxyribose sugar

31
Q

How is the structure of DNA suited to its function

A

Strong covalent bonds between sugar and base- the integrity of coded info from bases protected

Hydrogen bonds weak- easy to break in replication

Covalent bonds in backbone strong- stable

Complimentary bases- stability

32
Q

How is DNA organised in eukaryotic cells

A
  • majority of DNA content (the genome) in nucleus
  • each large molecule of DNA tightly wound around special histone proteins into chromosomes
  • each chromosome is therefore one molecule of DNA
  • also a loop of DNA without the histone proteins inside mitochondria and chloroplasts
33
Q

What is a gene

A

a section of DNA that codes for a polypeptide or for a length of RNA that is involved in regulating gene expression

34
Q

How is DNA organised in prokaryotic cells, and what is this similar to

A
  • DNA in a loop within cytoplasm- not enclosed in a nucleus

- not wound around histone proteins- described as naked- same as viruses

35
Q

Describe the process of DNA replication

A
  • Gyrase unwinds the DNA
  • Helicase unzips the 2 strands- the replication fork moves along the molecule
  • Primase makes primers (RNA) to signal where the nucleotides need to be added
  • DNA polymerase adds the nucleotides on the leading strand continuously (as it’s in the 5’-3’ direction) - using each single strand as a template
  • The lagging strand travels in a 3’-5’ direction, so DNA polymerase works discontinuously
  • This means nucleotides are added as Okazaki fragments, which are stuck together by DNA Ligase- which takes longer
  • The strands are held apart by SSB proteins
36
Q

What is meant by semiconservative replication

A

One parent DNA strand, and one new daughter strand

When 2 original strands separate and each acts as a template for a new, complementary strand

37
Q

Why does DNA need to be replicated

A

So that when a cell divides, each new daughter cell receives a full set of genetic instructions

38
Q

When does DNA replication occur

A

during interphase, before the cell divides

39
Q

What does cell division result in eukaryotes

A
  • each chromosome having an identical copy of itself
  • At first they are joined together, at the centromere, forming 2 sister chromatids
  • The DNA within mitochondria and chloroplasts also replicates each time these organelles divide- just before the cell divides
40
Q

What is added to the unzipped strand during DNA replication

A

Free phosphorylated nucleotides- present in the nucleoplasm within the nucleus are bonded to exposed bases, following complementary base pairing rules

41
Q

What specific thing requires energy in DNA replication, and what provides this

A

-hydrolysis of the activated nucleotides, to release extra phosphate groups, supplies the energy to make phosphodiester bonds between the sugar residue of one nucleotide and the phosphate group of the next

42
Q

What is the end result of DNA replication

A
  • 2 DNA molecules- identical to each other and the parent molecule
  • each of these molecules contains one new and one old strand- it is semi-conservative replication
43
Q

Describe DNA replication in prokaryotes

A
  • The loops of DNA in prokaryotes, and inside mitochondria and chloroplasts, also replicate semi conservatively
  • a bubble sprouts from the loop and this unwinds and unzips, and then complementary nucleotides join to the exposed nucleotides
  • eventually, the whole loop is copied
44
Q

What are mutations, and how often do they occur

A
  • When errors are made during replication and the wrong nucleotide is inserted
  • 1 in 10’8 base pairs
45
Q

What is it called when a mutation changes the genetic code

A

a point mutation

46
Q

What reduces mutation risk

A

Enzymes that can proofread and edit out incorrect nucleotides

47
Q

What are different versions of particular genes called

A

Alleles

48
Q

What can mutations be

A
  • harmful
  • neither advantage nor disadvantage
  • advantageous
49
Q

In which ways is RNA different to DNA

A
  • the sugar molecule in each nucleotide is ribose- not deoxyribose- has no O on 2nd carbon
  • The nitrogenous base uracil (a pyrimidine) replaces thymine
  • the polynucleotide chain is usually single-stranded and shorter
  • 3 forms mRNA, tRNA, rRNA
50
Q

What is a polypeptide

A

A polymer made of many amino acid units joined together by peptide bonds

51
Q

What does each gene contain

A

A code that determines the sequence of amino acids in a particular polypeptide or protein

52
Q

What percentage of an organisms dry mass do proteins account for

A

75%

53
Q

Give examples of proteins

A
  • Structural- cytoskeleton threads

- enzymes

54
Q

What determines the primary structure of a polypeptide

A

DNA base triplets

55
Q

How is a polypeptides tertiary structure created

A

The folding of a polypeptide chain

56
Q

What are examples of how the tertiary structure of a polypeptide determines its function

A
  • Shape of the active site on an enzyme must be complementary to the shape of the substrate molecule
  • Part of an antibody molecule must have a complementary shape to antigens
  • Receptor on the cell membrane must have a complementary shape to the cell signalling molecule to detect
  • Ion-channel protein must have hydrophilic amino acids lining inside and lipophilic amino acids on the outside that will be next to lipid bilayer of plasma membrane
57
Q

Describe the nature of the genetic code

A
  • near universal- almost all living organisms have the same triplet of the base to code for amino acid
  • Degenerate- other than methionine and tryptophan, there is more than one base triplet for the amino acid- reduces effect of point mutations, as the change in one base of triplet could produce another base triplet that still codes for same AA
  • Non-overlapping- still read starting from a fixed point in groups of 3 bases- if bases are added or deleted it causes a frameshift- as every base triplet after that, and hence every amino acid coded for is changed
58
Q

What are the 2 stages of protein synthesis

A

Transcription and translation

59
Q

Describe transcription

A
  • gene unwinds and unzips
  • Hydrogen bonds between complementary nucleotide vases break
  • RNA polymerase catalyses the formation of temporary H bonds between RNA nucleotides and their complementary, unpaired DNA bases
  • A with U (not T)
  • T with A
  • C with G
  • molecule being paired with is called the template strand
  • Complementary length of RNA produced is the same as the coding strand other than T
  • mRNA passes out of the nucleus through the nuclear envelope and attaches to a ribosome
60
Q

Describe how ribosomes are formed

A
  • made in the nucleolus in 2 smaller subunits
  • pass separately out of the nucleus through pores in the envelope and come together to form a ribosome
  • Magnesium ions help to bind 2 subunits together
  • made of ribosomal RNA and protein in roughly equal parts
61
Q

Describe tRNA

A
  • tRNA molecules are made in the nucleolus and pass out to the cytoplasm. They are single-stranded polynucleotides but can twist into a hairpin shape
  • at the end is a trio of nucleotide bases that recognises and attaches to a specific amino acid
  • at the loop of the hairpin there is a triple of bases called an anticodon that is complementary to a specific codon of bases on the mRNA
62
Q

Describe translation

A
  • tRNA molecules bring the amino acids to find their place when the anticodon binds by temporary H bonds to the complementary codon on the mRNA molecule
  • as the ribosome moves along the length of mRNA, it reads the code, and when 2 amino acids are adjacent to each other peptide bonds form between them
  • Energy (in form of ATP) is needed
  • The amino acid sequence for the polypeptide is therefore ultimately determined by the sequence of triplets of nucleotide bases on the length of DNA- the gene
  • After the polypeptide has been assembled, the mRNA breaks down- its component molecules can be recycled into new lengths of mRNA, with different codon sequences
  • The newly synthesised polypeptide is helped, by chaperone proteins in the cell to fold correctly into its 3D shape ( tertiary structure) in order to carry out its function

Module 2- Foundations in Biology (7 decks)

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