1 DNA AND PROTEINS Flashcards
(78 cards)
1
Q
What is meant by anti-parallel?
A
- The two strands of a DNA molecule are in opposite directions.
- Coding strand: 5’ to 3’
- Template strand: 3’ to 5’
2
Q
Describe the structure of a DNA molecule.
A
- Double helical structure formed from two anti-parallel, polynucleotide strands.
- Strands are composed of repeating nucleotides (sugar-phosphate backbone).
- Strands are held together by weak hydrogen bonds between the nitrogenous bases.
3
Q
What happens to chromatin when it is not dividing vs. when it is dividing?
A
Not dividing:
- Relaxed chromatin
- Chromosomes are spread out
Dividing:
- Condensed chromatin
- Chromosomes become a thick mass
4
Q
Describe the steps of DNA replication.
A
- Helicase
- Helicase separates two strands by breaking the weak hydrogen bonds between the complementary bases.
- Two strands are unwinded into a replication fork. - DNA polymerase
- DNA polymerase binds to template strand (3’ to 5’).
- Makes a new strand by adding bases from 5’ to 3’.
- 5’ to 3’ strand (lagging strand) is copied in a series of small chunks (Okazaki fragments).
- Each fragment starts with an RNA primer, then DNA pol adds a short row of DNA bases in the 5’ to 3’ direction. - Ligase
- DNA pol (ligase) joins the sugar and phosphate groups, forming two daughter DNA molecules.
5
Q
What is a semi-conservative process?
A
When a double helix replicates, each daughter molecules has one old strand from the parent molecules and one newly synthesised strand from DNA replication.
6
Q
What does DNA replication need to occur?
A
- Chromosomes
- Helicase
- Free nucleotides
- DNA polymerase
- Ligase
7
Q
Why is DNA replication important?
A
- Allows genetic information to be inherited from a parent cell to daughter cells.
- Ensures that daughter cells have a complete set of chromosomes containing the genetic information that programs a cell’s activities, ensuring daughter cells can survive and reproduce.
8
Q
What is a gene?
A
- A unique sequence of nucleotides that codes for a functional protein or an RNA molecule.
- Genetic information that codes for inherited traits.
9
Q
What is RNA?
A
- A nucleic acid.
- Composed of repeating nucleotides, each composed of a sugar, phosphate, and one of four nitrogenous bases.
- Single-stranded.
- Contains a ribose sugar.
- Fourth base in RNA is uracil (U) rather than thymine (T).
- Different types: mRNA, tRNA, and rRNA.
10
Q
Compare DNA and RNA.
A
- DNA is double stranded, while RNA is single stranded.
- DNA has a thymine, while RNA has a uracil.
- DNA has a deoxyribose sugar, while RNA has a ribose sugar.
- RNA have shorter strands.
11
Q
What is a protein?
A
A macromolecule composed of long chains of amino acids folded into a unique shape that gives cells their structure and function.
12
Q
What is a genotype and a phenotype?
A
Genotype: DNA inherited by a living thing.
Phenotype: Physical and behavioural traits.
13
Q
What is transciption?
A
- DNA nucleotide sequence of a gene rewritten into a complementary RNA nucleotide sequence.
- Resulting RNA molecule is a reliable transcript of the gene’s protein synthesising instructions.
- The RNA molecule that is synthesised is called a messenger RNA (mRNA), as it carries the genetic message from genes to the cell’s protein-synthesising machinery.
14
Q
What is translation?
A
- Nucleotide sequence on mRNA is translated into an amino acid sequence.
- Forms a polypeptide that is folded onto a functional protein.
- Site of translation are ribosomes, which link the amino acids to form a polypeptide that folds into a functional protein.
15
Q
How come translation and transcription can occur simultaneously in bacterial cells.
A
- Bacteria lack nuclei, so nuclear membrane do not separate bacterial DNA and mRNA from ribosomes.
- Causes a lack in compartmentalisation, allowing translation to begin while transcription occurs, resulting in rapid protein synthesis.
16
Q
Where does transcription and translation occur?
A
Transcription occurs in the nucleus, while mRNA must be transported to the cytoplasm for translation.
17
Q
What is pre-mRNA?
A
- An RNA molecule with a complementary nucleotide sequence to its gene.
- Contains exons (coding sequences) and introns (non-coding sequences).
18
Q
How is a pre-mRNA modified into a mature mRNA?
A
- Ends are modified by adding chemical groups that facilitate the export of mature mRNA from nucleus to cytoplasm while preventing degradation.
- Spliceosome binds to several short nucleotide sequences along an intron, and is rapidly degraded, and the spliceosome joins the two exons on either side of the intron.
- Forms an mRNA molecule with a continuous coding sequence.
19
Q
What is alternative RNA splicing?
A
- A single gene containing many exons can be spliced in different ways to from a variety of polypeptides with different functions.
- Causes the number of different protein products of a living thing to be greater than its number of genes.
20
Q
What is the product of transcription?
A
- An RNA molecule complementary to its DNA template and indentical to the non-coding template (coding strand).
- RNA nucleotides are assembled on the template, except U pairs with A.
21
Q
Describe the 3 steps of Transcription.
A
- Initiation
- RNA pol binds to target gene at a specific nucleotide sequence called the promoter.
- DNA strands unwind. - Elongation
- RNA pol unwinds the DNA.
- Joins RNA nucleotides complementary to the DNA template strand, elogating the RNA polynucleotide strand.
- DNA rewinds. - Termination
- Newly synthesised RNA molecule detaches from the DNA template strand.
- mRNA transcript is released.
22
Q
How does a cell make proteins in large amounts?
A
- Many pol molecules simultaneously transcribe a single gene.
- Increases amount of mRNA transcribed, therefore increases amount of protein synthesised.
23
Q
How is an mRNA strand read?
A
- Read in triplets of nucleotide bases (codon).
- Each codon specifies an amino acid to be added to the growing polypeptide chain.
24
Q
What is the start codon?
A
- AUG = Methionine (Met or M.
- Initiates translation at that location.
25
What are the stop codons?
UGA, UAA, and UAG
26
What is the function of a tRNA during translation?
Acts a translator which reads a codon and transfer a corresponding amino acid from the cytoplasm to a growing polypeptide in a ribosome.
27
Describe the structure of a tRNA.
- Specific amino acid binding site at one end.
- Nucleotide triplet (anticodon) that base-pairs with the complementary codon on mRNA at the other end.
28
What is the structure of a ribosome and its relevance to translation?
- Binding site of mRNA.
- Three binding sites for tRNAs.
- Central site holds the tRNA carrying the growing polypeptide chain.
- Right side holds the tRNA carrying the next amino acid to be added to the chain.
- Catalyses the formation of a peptide bond between amino acids.
29
Describe the 3 steps of Translation.
1. Initiation
- Brings together an mRNA, a tRNA bearing the first amino acid of the polypeptide, and two ribosomal subunits.
- Small ribosomal unit binds to mRNA.
- Specific initiator tRNA carries the amino acid (Met) to the start codon site.
- Large ribosomal unit attaches, completing the translation initiation complex.
2. Elongation
- Amino acids are added to the growing polypeptide chain one at a time.
- Anticodon of incoming tRNA base-pairs with its complementary mRNA codon.
- rRNA molecule in large ribosomal unit catalyses peptide bond between two amino acids.
- Ribosome translocates the mRNA and bound tRNAs along as translation progresses. Some tRNAs are removed and others added.
- tRNAs released from the ribosome's exit return to the cytoplasm, reloading them with the appropriate amino acid.
- Continues until a stop codon on mRNA is reached.
3. Termination
- One of the three stop codons enters the ribosome's right hand site.
- Codes for release factors.
- Release factors bind to tRNA site and break the bond between the polypeptide and the tRNA, releasing the completed polypeptide.
30
What is a polyribosome?
- A string of ribosomes that enable a cell to rapidly synthesise many copied of a polypeptide.
- Once a ribosome is far enough past the start codon, a second ribosome can attach to the mRNA, resulting in several ribosomes trailing along the mRNA.
31
State examples of proteins in living things.
- Enzymatic proteins: increases reaction rate.
- Transport proteins: transports solutes across membranes or around the body.
- Receptor proteins: responds to chemical stimuli.
32
Describe the structure of amino acids.
- Amino group
- Carboxylic acid group bonded to a carbon atom containing a variable group (R group or side chains).
33
What are the different properties of the side chains in amino acids that affect the structure and function of proteins?
- Hydrophilic side chains
- Hydrophobic side chains
- Acidic side chains
- Basic side chains
34
What happens when two amino acids are positioned where the amino group of one is adjacent to the carboxylic group of the other?
- Two groups can become bonded by a chemical reaction.
- Products are water and a dipeptide.
- A small molecule composed of the two amino acids linked by a covalent chemical bond (peptide bond).
35
What are the types of proteins?
Globular proteins (roughly spherical):
- water-soluble
- amino acids w/ hydrophilic side chains covering their surface.
Fibrous proteins (long fibres):
- insoluble
- amino acids w/ hydrophobic side chains covering their surface.
36
Describe the 4 levels of protein structure.
1. Primary
- Sequence of amino acids
2. Secondary
- Segments of the polypeptide chains repeatedly coiled or folded that result from hydrogen bonds.
- Creates beta-sheets and alpha-helices.
3. Tertiery
- Three-dimensional shape of a protein resulting from attractive forces between side chains of the various amino acids.
- Hydrogen bonds, hydrophobic interactions, covalent bonds, and ionic bonds.
4. Quaternary
- Overall protein structure resulting from the interactions of these polypeptide molecules.
- Two or more polypeptide chains.
37
What is denaturation and renaturation?
Denaturation:
- Protein quickly unravels and loses its shape.
- Lost part or all of its three-dimensional structure.
- Biologically inactive.
Renaturation:
- Polypeptide chain refolds into its native shape.
- Restores its function.
38
What causes denaturation?
Denaturation agents:
- High temperatures
- pH
- Salt concentration
- Other chemical substances
- React with amino side chains.
- Disrupts weak hydrogen bonds, ionic bonds, and covalent bonds.
39
What are enzymes?
Macromolecules that catalyse a specific chemical reaction without being consumed in the reaction.
40
What is activation energy?
- The initial energy investment required to break the bonds in molecules.
- Supplied by heat absorbed from the surroundings.
- Absorbed heat accelerates the collision between reactant molecules.
41
What is an enzyme-substrate complex?
The binding of an enzyme to its substrate to form an enzyme-substrate complex.
42
What is an active site?
A pocket or groove on the enzyme's surface where catalysis.
43
What is the induced fit?
- Active site is not rigid.
- When substrate enters, enzyme changes shape slightly due to interactions between the substrate's chemical groups and the side chains of the amino acid.
- Shape changes makes the active site fit more tightly around the substrate.
44
How does the induced-fit model catalyse chemical reactions?
Brings chemical groups of the active site into positions that enhance their ability to catalyse chemical reactions.
45
What are enzyme inhibitors and how do they function?
- Chemical substances that selectively inhibit the function of an enzyme.
- Attached to the enzyme by covalent bonds, in which case the inhibition is usually irreversible.
46
What are competitive and non-competitive inhibitors?
Competitive:
- Inhibitors that resemble the shape of the normal substrate and compete for admission into the active site.
- Reduces enzyme activity by blocking substrates from entering active sites.
Non-competitive:
- Do not directly compete with the substrate to bind to active site.
- Causes enzyme to change shape by binding to the allosteric site of the enzyme.
- Regulates enzyme activity and prevents over-accumulation of unnecessary products.
47
What does the rate of an enzyme-controlled reaction depend on?
- Concentration of enzymes and its substrates.
- The rate of an enzyme-controlled reaction increases with substrate concentration as more substrate molecules are available to access the vacant sites of available enzymes.
48
What are saturated enzymes?
When all enzyme molecules have their active sites occupied such that as soon as the product exits an active site, another substrate molecule enters.
49
What is controlled gene expression and what is its purpose?
- When some genes are acivated and expressed while others are deactivated and silenced.
- Determines phenotypes.
50
What is differential gene expression and what is its effect?
- Expression of different genes by cells with the same genome.
- Produces unique gene expression patterns that allows cells to synthesise some proteins and not others.
- Results in a unique set of proteins that carry out specific functions.
51
What are transcription factors?
Transcription factors (TFs) are regulatory proteins that control the rate of transcription
52
What needs to occur for a gene to be activated and its protein expressed?
Transcription factors must bind to the gene and facilitate the attachment of RNA polymerase.
53
What causes gene expression to stop?
External and internal factors from the surrounding environment.
54
Compare how gene expression is controlled in eukaryotes and prokaryotes.
Eukaryotes: Controlled by modifying DNA and chromatin and degrading mRNA and proteins.
Prokaryotes: Controlled at transcription and often occurs in response to signals from outside of the cell (e.g. hormones).
55
What are the 3 different forms of chromatin?
- Chromatin: Normal form
- Heterochromatin: Dense arrangement where DNA is tightly bound to histones, inaccessible for transcription.
- Euchromatin: Less dense arrangement, where DNA is loosely bound to histones, exposing genes for transcription.
56
What drives chromatin remodelling?
- Driven by enzymes that catalyse the addition and removal of chemical groups such as acetyl and methyl groups.
57
How does the addition of acetyl groups to histones affect chromatin remodelling?
Addition of acetyl groups to histones cause chromatin to become less condensed (euchromatin), exposing genes for transcription.
58
How does the addition of methyl groups to histones affect chromatin remodelling?
Addition of methyl groups to histones cause chromatin to condense (heterochromatin), therefore DNA cannot be transcribed.
59
Explain DNA methylation?
- The process of cells switching genes on and off by adding and removing methyl groups from cytosine nucleotides.
- Facilitated by enzymes called DNA methyltransferases (DMNTs).
- Adding methyl groups to cytosine (hypermethylation) causes genes to switch off and be silenced due to chromatin condensing, hence RNA pol cannot bind and transcribe.
- Removing methyl groups from cytosine (hypomethylation) causes chromatin to be less condensed, allowing RNA pol to bind and transcribe.
60
What is epigenetic control and what is its effect?
- Changes in gene expression that occur without altering the DNA nucleotide sequence of genes.
- Influences whether genes are turned on or off, impacting protein production and cell function.
- Affects how genes are read and utilized by the cell.
61
What is chromatin modification and DNA methylation responsible for?
Inherited human diseases
62
What regulates cell division and what effect does chromatin modification and DNA methylation have on it?
- Regulated by proto-oncogenes: codes growth factors, receptors and enzymes.
- Tumour suppressor genes: code DNA-repar proteins, cell-adhesion proteins, and enzymes that inhibit cell division.
- Chromatin modification and DNA methylation can silence or over-express these genes, leading to uncontrolled cell division (cancer).
63
State and explain post-transcriptional epigenetic factors that affect gene expression.
- Non-coding RNAs: large and divers population of small non-protein coding RNA molecules that regulate the number of mRNA transcripts and whether they are translated.
- miRNAs: Small, single-stranded RNA molecules capable of binding any mRNA molecule with at least 7/8 nucleotides of complementary sequence.
- siRNAs: Small, double-stranded RNA molecules capable of only binding a smaller number of target mRNAs.
- miRNAs and siRNAs associate with 1 or more enzymes to form an RNA-induced silencing complex (RISC).
- Degrades target mRNA or blocks its translation.
64
What are mutations?
- Changes to an organisms DNA nucleotide sequence.
- Alters genotypes and phenotypes and cause genetic diseases in living things.
- Leads to an altered mRNA strand.
65
What are large-scale and small-scale mutations?
Large-scale: Affects long segments of DNA that typically occur during cell division.
Small-scale: Changes to one nucleotide pair (point mutation).
66
What are the two types of point mutation?
Substitutions involving single nucleotide-pair changes and frameshift mutations involving the insertion or deletion of one or more nucleotide pairs.
67
What are silent mutations?
- Substitution of a single nucleotide pair which does not change the amino acid sequence of the polypeptide.
- No effect on phenotype.
68
What are missense mutations?
- Substitution of a single nucleotide pair that change 1 amino acid to another.
- May have little effect on protein as the new amino acid may have properties similar to those of the amino acid it replaces.
- May have large effect by altering tertiery structure and changing the protein's structure and function.
- Leads to a useless or inactive protein that impairs cellular function.
- Sometimes it leads to an improved protein.
69
What are nonsense mutations?
- Substitution of a single nucleotide pair that change a codon for an amino acid into a stop codon.
- Terminated translation prematurely.
- Results in a shorter polypeptide.
- Leads to non-functional proteins.
70
What are frameshift mutations?
- Occurs whenever the number of nucleotide pairs inserted or deleted is not a multiple of 3.
- Causes downstream nucleotides to be improperly grouped into codons.
- Leads to extensive missense and nonsense mutations that led to premature termination of protein synthesis.
71
Where does the most impactful frameshift mutation occur?
- During mitotic or meiotic cell division.
- Large sections of chromosomes are duplicated, translated, deleted, or inverted.
- Alters large nucleotide sequences causing frameshifts that produces a non-functioning protein.
72
What are mutagens?
Physical and chemical agents that interact with DNA in ways that cause mutations.
Examples:
- UV radiation induces disruptive thymine dimers that cause frameshift mutations further along the DNA molecule.
- Ionising radiation induces deletion mutations directly by causing single or double-stranded breaks in the sugar-phosphate backbone of DNA.
- X-rays
- Gamma rays
- Neutrons
- Protons
- Electrons
- Alpha particles
73
What are chemical mutagens and how do they mutate DNA?
- First type has chemical structures similar to DNA nucleotides and initiates mutations by pairing incorrectly during DNA replication.
- Second type induces mutations by reacting with nucleotides and altering the chemical structures of bases in a way that makes them pair incorrectly.
- Third type inserts itself into the double helix and distorts its shape, increasing the likelihood of mutation during DNA replication.
74
What are germ cell and somatic cells?
Germ cells: Reproductive cells that develop into sperm and egg through differentiation.
Somatic cells: Other body cells.
75
Describe germ cell mutations.
- Present in the DNA of sperm and egg cells during fertilisation and are passed on to offspring.
- If the mutation is present in the DNA of the fertilised egg cell (zygote), it develops into every cells in the adult body.
- Example: A mutation in a human sperm is present in all somatic cells in the offspring's body and half of its gametes.
76
Why are germ cell mutations an important source of genetic variation?
- Introduces new phenotypes into a population.
-Inherited characteristics may confer an advantage to the offspring in their environment.
77
Describe somatic cell mutations.
- Localised to a single tissue or organ as the mutated cell can only pass its genes on to cells of the same type through cell division.
78
Describe cancer.
- Changes in gene expression that cause cells to escape the control mechanisms that usually limit their growth and division.
- Caused by mutations that modify the expression of proto-oncogenes that stimulate cell division and tumour suppressor genes that inhibit cell division.
