Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

06 FdSc Bioscience - Metabolism and Enzymology > Week 4 - nucleic acids and macromolecules > Flashcards

Week 4 - nucleic acids and macromolecules Flashcards

1
Q

Give a brief introduction to the double helix of DNA

A
  • Double helix of DNA is composed of nucleic acids, of which there are four key possibilities:
  1. Adenine
  2. Guanine
  3. Cytosine
  4. Thymine
  • Swapping of amino acids can have an impact on downstream events
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Give a one sentance introduction into nucleic acids

A
  • Nucleic acids are the macromolecules involved in the storage, transmission and expression of genetic information
  • Nucleic acid polymers are made of monomers called nucleotides
  • There are two types of nucleic acid: DNA and RNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the difference in function between DNA and RNA?

A
  • Deoxyribonucleic acid stores genetic information
  • Ribonucleic acid expresses the information
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is a nucleotide composed of?

A
  • A 5C sugar (D-ribose in RNA and D-deoxyribose in DNA)
  • Nitrogenous base (adenine, guanine and cytosine and either thymine in DNA or uracil in RNA)
  • A phosphate group
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Describe the structural organisation of nucleotides

A
  • 5C sugar either D-ribose with -OH on 2’C or D-deoxyribose with -H on 2’C
  • Nitrogenous base attached to 1’C of sugar in condensation reaction
  • Phosphate group (PO4) joined by phosphodiester bond to the 5’C in condensation reaction
    • There may be more than one PO4 present attached to the first PO4 phosphoanhydride bonds which form by condensation reaction
    • Can be mono, di or tri phosphate e.g. ATP but can also be in nucleic acid
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the difference between a nucleotide and a nucleoside?

A
  • A nucleotide has a nitrogenous base and a phosphate group attached to the sugar
  • A nucleoside does not have the phosphate group attached to the sugar
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the different groups of nitrogenous base?

A
  • Purines - adenine and guanine
  • Pyrimidines - thymine, cytosine and uracil
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

List the different nitrogenous bases and the nucleosides and nucleotides that they form respectively

A
  • Adenine
    • Deoxyadenosine
    • Deoxyadenosine mono/di/triphosphate (dAMP/dADP/dATP)
  • Thymine
    • Deoxythymidine
    • Deoxythymidine monophosphate (dTMP)
  • Cytosine
    • Deoxycytidine
    • Deoxycytidine monophosphate (dCMP)
  • Guanine
    • Deoxyguanosine
    • Deuxyguanosine monophosphate (dGMP)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Describe the formation of nucleic acids from DNA / RNA

A
  • Linear polymers of nucleotides with a phosphate-sugar backbone and the nitrogenous base projecting from this
  • Backbone forms from the condensation reaction between PO4 of one nucleotide and the 3’C of the adjacent nucleotide forming a 3’,5’ phosphodiester bond
    • -H comes from sugar and -OH from the 5’ PO4
  • Free 5’ group and one end and free 3’ group at the other, nucleotide sequences are always written 5’->3’
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What does the formation of a nucleic acid polymer rely on?

A
  • Energy is required for the sythesis and is provided in the form dATP, dCTP, dGTP and dTTP in DNA or ATP, CTP, GTP and UTP in RNA
  • Relies on the presence of a template which is usually the DNA, order of nucleotides is determined by this template
    • Specific base pairing means that only particular pairs are allowed to form meaning new strand is directed by the base pairing with the existing template strand
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the specific base pairing in nucleic acids?

A
  • A-T, C-G in DNA
  • Three hydrogen bonds form between C-G and two form between A-T
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the structure of DNA?

A
  • DNA helix is composed of two complementary chains of DNA held together by base pairing hydrogen bonds which are twisted around a central axis to form a right-handed helix
    • Known as double helix
  • Chains are directed in different direction, 1 runs 3’->5’ and the other 5’->3’
  • Sugar-phosphate backbone is polar and charged so is on the outside of the molecule, nitrogenous bases are reasonably non-polar and are orinetated inwards where they hold the chain together
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is an important feature of DNA?

A
  • DNA molecule can unzip and the two strands are used as templates to produce 2x molecules of identical double helix DNA by complimentary base pairing - this is known as DNA replication
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the specific pairing in RNA molecules?

A
  • The specific pairing is always A-U and C-G
  • Three H bonds form between C-G and two H bonds form between A-U
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is RNA and how is it formed?

A
  • RNA is a single stranded chain of nucleotides formed by complimentary base pairing with a DNA template before the RNA chain is released
  • Plays a number of roles in cells related to the transmission and expression of genetic information
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the different types of RNA that are produced from a DNA template?

A
  • mRNA - messenger RNA copies the DNA code then acts as a template for protein synthesis on the ribosome
  • tRNA - transfer RNA picks up amino acids and directs them to the correct mRNA codon allowing the formation of a polypeptide chain
  • rRNA - ribosomal RNA is a constituent of ribosomes which acts as the site of polypeptide/protein synthesis
    • Ribosome allows amino acids bought by tRNA to align correctly against mRNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Give a brief overview of transcription and translation

A
  • Information on DNA template is used to form mRNA which converts the information into a sequence of amino acids (polypeptide chain)
  • Process is referred to as transcription and translation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is transcription?

A
  • It is the copying of a DNA strand to produce a complimentary RNA strand
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is translation?

A
  • The process by which mRNA directs the synthesis of specific proteins
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are proteins? By mass, how much do they make up of the cell?

A
  • Proteins are large, complex macromolecules that carry out structural and metabolic functions
  • They account for more than 50% of the dry weight of a cell
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What are the main types of proteins?

A
  • Structural proteins - provide cellular and tissue support
  • Storage proteins - store amino acids
  • Transport proteins - transport substances into and out of cells in the body
  • Hormonal proteins - coordinate bodily activities
  • Contractile proteins - responsible for movement
  • Enzymes - regulate chemical reactions
  • Antibodies - defend against foreign substances
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What do all proteins have in common?

What is the size range for proteins?

A
  • Whilst they are structurally sophisticated and diverse due to their structure and 3D shape
  • They are all made of 20 amino acid monomers arranged into polymers
  • Smallest is 3-10 amino acids, largest is 50,000 amino acids
  • Most are between 50-1000 amino acid
  • This results in a great variety of combinations of a.a. resulting in the diversity of functional proteins
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Compare and contrast some of the key differences between DNA and RNA

A
  • DNA deoxyribonucleic acid containing 5C sugar D-deoxyribose and RNA contains 5C sugar D-ribose
  • DNA is double stranded and RNA is single stranded
  • DNA & RNA are composed of nucleotides
  • Nucleotide has 3 subunits: 5C sugar, PO4 and a nitrogenous base
  • Phosphodiester bonds form between PO4 and sugar
  • RNA can be mRNA, tRNA or rRNA
  • Amino acid coded for by three bases (codon)
  • Series of three bases on DNA is a triplet but on RNA it is called a codon and on tRNA it is an anticodon
  • DNA undergoes self replication but RNA can’t
  • Base pairing in DNA is A-T & C-G, in RNA it’s A-U & C-G
  • DNA is ds and too large to pass through nuclear pores but mRNA can pass through to the ribosomes on the RER
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Describe the structure of amino acids

A
  • Central carbon with four valency sites
  • Attached to these sites are: -COOH, -NH3, H and an R group
  • -COOH and -NH3 are ionised to form -COO- and -NH4+
  • R group gives amino acid its distinct chemical characteristics
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

How can amino acids be grouped?

A
  • Although ever amino acid has unique R group they are grouped by chemical characteristics
    • Non-polar
    • Polar noncharged
    • Polar charged positive
    • Polar charged negative
  • (The types of chemical characteristics are covered separately on other cards)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What are non-polar amino acids?

A
  • Side chain doesn’t have a group capable of forming H bonds
  • They are relatively inert
  • Amino acids are:
    • Glycine
    • Alinine
    • Valine
    • Leucine
    • Isoleucine
    • Proline
    • Methionine
    • Cysteine
    • Phenylalanine
    • Tryptophan
27
Q

What are polar noncharged amino acids?

A
  • The side chains can form hydrogen bonds but are uncharged
  • Amino acids include:
    • Serine
    • Threonine
    • Tyrosine
    • Asparagine
    • Glutamine
28
Q

What are polar charged positive amino acids?

A
  • Side chain can be ionised and is polar
  • Also known as polar acidic amino acids
  • Amino acids include:
    • Aspartic acids
    • Glutamic acid
29
Q

What are polar charged negative amino acids?

A
  • Side chain can be ionised and is polar
  • Also known as polar basic amino acids
  • Amino acids include:
    • Histidine
    • Lysine
    • Arginine
30
Q

What is important about the amino acid cysteine?

A
  • It contains an -SH functional group which is important in protein structure where it can form disulphide linkages with adjacent -SH groups to stabilise protein structure
31
Q

What is the amino acid that doesn’t follow the general structure of amino acids?

A
  • Proline forms a ring structure with the amino group attached to the end of the R chain to form a ring
  • It is non polar
32
Q

Describe the stereochemistry of amino acids

A
  • The α carbon of the amino acid is asymmtric so two optical isomers can form
  • L-amino acids the amino group points to the left
  • D-amino acids the amino group points to the right
  • In nature only L-amino acids are found in naturally produced protein
    • D-amino acids can be synthetically produced
33
Q

Describe the formation of a polypeptide chain

A
  • Amino acids link by condensation reactions to form polypeptide chains (linear sequence of amino acids)
  • NH2 of one amino acid forms peptide bond with -COOH of another amino acid by condensation (this is -CONH- linkage)
  • Polypeptide chain backbone is -CN-αC-CN-αC-CN-αC- sequence
  • Variable R groups project from the chain
  • Chain can be hydrolysed
34
Q

What is meant by the term “protein native conformation”?

What does protein native conformation affect?

A
  • Protein can consist of one or more polypeptide chains twisted, wound and folded into a unique 3D macromolecule
  • Function and activity of protein depend on native conformation and in turn the sequence of amino acids in the polypeptide chain
35
Q

Generally, what does the function of proteins relate to?

What can proteins be classed as?

A
  • Function of protein relies on binding or recognising or interacting with another molecule
    • Enzyme-substrate
    • Antibody-foreign material
    • Hormone-receptor
  • The unique 3D conformation of the protein results in the specificity of function
  • The general form of the protein can be classified as either fibrous or globular
36
Q

How does the native conformation of a protein form?

A
  • Once a polypeptide is synthesized by a cell the chain folds spontaneously into its native conformation
  • R groups orientate in the 3D structure based on their chemical characteristics and that of the environment with the formation of distinct polar/charged areas in the structure
  • Native conformation of a protein can be described by looking at the protein structural levels
37
Q

What is the 1o protein structure?

A
  • Linear sequence of amino acids in the polypeptide chain
  • Sequence is recorded beginning at the free (-NH2) end and working to the free -COOH end
  • 1o sequence reads as a list of amino acids
    • Lys-Arg-Tyr-Val-Ala
  • Sequencers can analyse a polypeptide chan and list the sequence of amino acids
38
Q

What is 2o protein structure?

A
  • This is the intitial folding and stabilisation of the polypeptide chain
  • There are three mechanisms accounting for the initial folding to form coiled or folded patterns in the protein
  • Stabilisation of these structures is due to the formation of H bonds between sections of the polypeptide chain
  • R chain is not involved in bonding or stabilisation in 2o structure
39
Q

Why do hydrogen bonds form in the 2o structure?

A
  • Electropositive H+ and electronegative O- charged in the -CONH- linkage have affinity for each other
  • H bonds are relatively weak but are repeated over a long chain and can support the 3D shape of the protein
  • Folding is related to the α Carbon (αC) area of the backbone, since the -CONH- linkage is very rigid
40
Q

Describe the α helix of 2o structure

A
  • Coil held together by H bonds which occur at every 4th amino acid
  • H bonding stabilised the helix
  • The turns in the coil are generally around the α-carbon and generally the chain coils to the right
  • Proteins which are long fibres generally have one or more α helices
    • Keratin is entirely an α helix
  • Globular proteins often have several segments of α helices running in different directions
41
Q

Describe the β Sheet of 2o structure

A
  • Polypeptide chain turns back on itself and parallel regions of the chain may be linked by H bond
  • Chains run in different directions
  • When -NH and -CO groups of parallel chains are aligned they form a H bond which stabilised the 3D structure
  • the sheet forms a corrugated or pleated sheet with peaks and troughs formed by the α carbon with the -CONH- section forming the rigid backbone
  • Corrugated sheets may wind to form a cylinder with further H bonds
  • They occur in many natural products alng with α helices
  • Often form the dense core of globular proteins
  • Can forms regions in enymes and in fibrous proteins such as silk
  • Also found in the protein coat of some viruses
42
Q

Outline 3o structure

A
  • Further stabilisation of the conformation by bonding between R groups
  • Involves H bonding, ionic bond and hydrophobic interactions to maintain conformation
  • Disulphide bridges for between adjacent -SH of cysteine
  • Some or all of these bonds may be in a protein
43
Q

When do disulphise bridges form in 3o structure?

Where are they common?

A
  • form when adjacent cysteine monomers are brought close together in the 3D shape
  • Common in secreted proteins such as insulin but are rare in proteins that remain inside cells
44
Q

How can proteins have a 3o structure that makes them appear modular?

A
  • Many amino acids folded in distinct regions are called domains
  • Domains are connected by a flexible region of polypeptide chain and there is normally a gap between domains called a cleft or crevice
  • In many enzymes the active area may be in a cleft which has a unique environment that is polar/nonpolar/charged/bonding which may promote the reaction
  • Proteins that perform multiple functions may have eah function associated with a different domain
45
Q

What is 4o protein structure?

A
  • Formation of proteins from multiple polypeptide chains or subunits
  • Some proteins consist of 2 or more polypeptide chains
  • Each polypeptide chain is a subunit and the 4o structure is the relationship between subunits
  • Subunits are held together by:
    • H bonds
    • Ionic bonds
    • Hydrophobic interactions
    • Disulphide bridges
46
Q

Name some different examples of proteins with 4o structure

A
  • Collagen
  • Haemoglobin
  • Lactate dehydrogenase
  • Immunoglobulins / antibodies
  • These will all be covered separately in other flashcards
47
Q

Describe the 4o structure of collagen

A
  • Collagen is a fibrous protein composed of three subunits intertwined into a triple helix
  • Each subunit is in a helix form and the subunits are supercoiled
  • This gives great strength in tissues where collagen is found
48
Q

Describe the 4o structure of haemoglobin

A
  • Two types of polypeptide chain which occur twice
  • 2x α chains and 2 x β chains
  • Each subunit contains a haem prosthetic group which contains Fe for binding to oxygen
49
Q

Describe the 4o structure of lactate dehydrogenase

A
  • Enzyme converts pyruvate to lactate during fermentation
  • LDH is composed of four polypeptide chains of type A or B or combinations of both
    • Arrangements can be A0B4, A1B3, A2B2, A3B1, A4B0
  • LDH occurs in heart and muscle cells
    • Heart LDH1 = A0B4, Muscle LDH 5 = A4B0
  • LDH 5 functions better in low oxygen concentrations where lactic acid is accumulating
50
Q

Describe the 4o structure of immunoglobulins / antibodies

A
  • Glycoproteins which contain four polypeptdie chains, two heavy & two light
  • Heavy chains are linked by disulphide bonds and each of heavy chains is attached to a light chain by a disulphide bridge
  • Globular structure which has Y shape and 3 distinct domains
    • 2x Fab domains (two sections of heavy-light chains which bind and recognise antigens)
  • Specific fab sites for antigens where variation in specificity releates to a.a. content of polypep chain
  • Fc consists of 2x heavy which recognise and bind phagocytes which digest the foreign material attached to the fab domain
51
Q

When is a protein stable and when may it be denatured?

A
  • Whilst the protein is in its natural physical and chemical environment the conformational state is stable and the protein can carry out its function
  • If pH, [salt], temperature or other aspect of environment are altered the protein many lose its conformational state and become denatured (unable to function)
52
Q

Describe how we can denature proteins

A
  • Proteins transferred from aqueous to organic slvents will turn inside out to meet polar/nonpolr conditions
  • Chemical agents disrupt H bonding, ionic bonds and disulphide bridges resulting in ionisation and denaturation
  • Heat causes energy input into the bonds which break and result in loss of conformation
53
Q

What may happen to a proteins solubility during denaturation and what does this suggest?

A
  • Protein may become insoluble as the polypeptide chain is broken meaning it’ll precipitate out of solution
    • i.e. heat treatment of albumin in eggs causes white precipitate
  • if it doesn’t precipitate the native confomation may be reformed if the protein is put in its natural environment
    • Implies native conformation is determined by the 1o structure (a.a. sequence)
54
Q

What enables proteins to interact with a variety of different substances?

A
  • Chemical characteristics of R groups of amino acids allows them to form interactions with a wide range of other substances
55
Q

Outline glycoproteins

A
  • Covalent binding of proteins to carbohydrate units
  • have varied functions including enzymes, antibodies, receptors and recognition systems
  • Formation of H bonds between protein and carbohydrate may lead to increased conformational stability and allows uptake of water which may aid in cushioning and lubrication of tissues
  • Carbohydrate group may also prevent enzyme from attack
56
Q

Outline lipoproteins

A
  • Covalentyl linked lipids and proteins
  • Found in eukaryotic and prokaryotic cells where they act as an anchor mechanism for the protein molecule in the cell membrane
  • Protein is linked to lipid (phospholipids or fatty acids) through the N or C terminus of protein
  • Lipids, carbohydrates and proteins may also form linkages
57
Q

Outline cofactors

A
  • Proteins form interactions with inorganic and organic molecules which contribute to the functioning of the protein
  • Organic compounds linked to proteins are called coenzymes or prosthetic groups
  • Inorganic ions such as Na, K, Zn, Cu, Fe, I, Mg and Ca are often linked to proteins by electrostatic interactions with charged amino acids
  • Functional activity may be related to the presence of the inorganic ions particularly enzyme activity
  • R group may bind to other groups both organic and inorganic
58
Q

Describe the structure of enzymes

A
  • Most are glboular proteins (some are RNA enzymes)
  • have 3D conformation which must be intact for enzyme function
  • If 3D structure is altered or destroyed enzyme is denatured and won’t function
    *
59
Q

How may an enzyme, in the ES complex, catalyse the reaction?

A
  • Provide specific conditions (ionic, pH) or it may stress bonds in substrate or put susbtrates together in the correct orientation
  • All those lower the activation energy
  • Product is released and the active site returns to its unflexed state
  • Factors such as temp, pH [S] affect activity
  • Lowering activation energy means that reactions happen faster at physiological conditions
60
Q

How can enzymes catalyse biological reactions?

A
  • Increase rate of reaction by lowering EA
  • Create order amongst molecules to facilitate ore collisions and more reactions
  • Change rate at which equilibrium is acheived
61
Q

Describe the protein structure of enzymes

A
  • Have unique 3D native conformation
  • Active site is often a groove or cleft in the native conformation which has unique chemical and structural properties
  • Active site isnt necessarily a sequence of amino acids, may be amino acids bought together by movement of enzyme during the induced fit hypothesis
62
Q

Describe what happens to an enyme protein conformation according to the induced fit hypothesis

A
  • Process by which active site flexes to allow the causing conformational change to allow the entry of the substrate into the active site
  • When product releaed the active site returns to native conformation
  • During conformational change amino acids may be brought together from different areas of the protein to form the active site
    • These a.a. confer unique chemical and structural properties on the active site
  • Induced fit may bring R groups into active site conferring acidic or basic conditions
63
Q

How can different amino acids play different roles in the active site of an enzyme?

A
  1. Enabling substrate binding - associated with a.a. cysteine, histidine, serine, aspartate, glutamate and lysine
  2. Act as H+ acceptor and donor - associated with histidine, aspartate, and glutamate
  3. May also have one or more polypeptide chain or attached prosthetic groups which provide unique conditions at the active site

06 FdSc Bioscience - Metabolism and Enzymology (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions