DNA & Proteins Flashcards

Question

What are enzymes?

Answer 1

Enzymes are proteins which help catalyse chemical reactions in a cell which could potentially occur on their own. Enzymes are catalysts for organic chemical reactions because they can be re-used after producing products.

Answer 2

1. The substrate binds to the active site of the enzyme in a complementary manner to form the enzyme-substrate complex 2. The active site changes slightly to produce a tighter fit around the substrates. This puts stress on the substrate chemical bonds, weakening them and lowering the activation energy for the reaction. 3. The reaction occurs and the product(s) of the reaction are released from the enzyme and the enzyme returns to its original form

Answer 3

When catalysing a reaction, enzymes will either join separate substrates or split them.

Answer 4

Activation energy. Catalysts help reduce it (e.g. enzymes)

Answer 5

They reduce the activation energy allowing more reactions to happen within an amount of time.

Answer 6

At low temperatures, molecules move slower. This results in fewer successful collisions between the enzyme and substrate(s) over time, hence lowering the rate of reaction.

Answer 7

At a higher temperature, molecules move faster, increasing reaction rate. However, temperatures can be too high. At these temperatures, enzymes are denatured. This is because high thermal energy may disrupt chemical bonds in the enzyme, altering the shape of the active site irreversibly. This results in the enzyme and substrate(s) no longer being complementary in shape, resulting in a loss of function; lowering the rate of reaction.

Answer 8

Most human enzymes are most effective at 37C. The normal human body temperature is 37C because of this. But this can differ between species (e.g. the enzymes for certain algae that live in hot springs have an optimum temperature of 60C - 80C)

Answer 9

Low pH (acidic) or high pH (alkaline) environments can denature enzymes, causing them to lose their specific shape and function. Some enzymes are most effective at a neutral pH (7), while others may be effective at different pH levels (e.g. pepsin in the stomach which works best at an acidic pH (2)).

Answer 10

An inhibitor is a molecule which binds to an enzyme that is NOT its substrate (It could be similar in shape to its substrate). This prevents enzyme-substrate reaction.

Answer 11

Competitive inhibitors permanently bind and block the active site of the enzyme and render it completely ineffective. Non-competitive inhibitors may bind to parts of the enzyme other than the active site which distorts the active site region, rendering substrates unable to attach.

Answer 12

Increasing reactant (substrate) concentration increases the rate of enzyme-controlled reaction until the point of saturation, where there is too much substrate and all active sites of all enzymes are occupied. The graph of rate of reaction plateaus at this point.

Answer 13

Increasing the concentration of enzyme allows for more active sites which allows for more substrate-enzyme reactions at once. However, this relationship assumes there is ample substrate at all times. More enzyme molecules allow for more successful substrate-enzyme collisions, however this rate of collision & reaction will plateau once the amount of substrate (reactant) becomes limited. This results in there being too many active sites for the number of substrate molecules to react, hence plateauing the increase in reaction rate.

Answer 14

- Catalysing reactions (enzymes) - Structural (e.g. hair, nails, tendons, ligaments, skin) - Movement (muscle fibres) - Transport (haemoglobin carrying O2 to deoxygenated regions, membrane transport proteins) - Defence (antibodies produced by white blood cells) - Communication (hormones, DNA replication)

Answer 15

By binding to molecules in a complementary manner. E.g., enzymes recognise and bind to their substrate E.g., Cell membranes receptors recognise and bind to specific hormones

Answer 16

Polypeptide chains of amino acids. They use any of the 20 amino acids with different chemical properties in a sequence.

Answer 17

The specific amino acid sequence that determines where it will fold or coil.

Answer 18

1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quaternary structure

Answer 19

Primary structure is the order/sequence of varying amino acids in a linear polypeptide chain. Basically, it is the 'list' of amino acids in a polypeptide.

Answer 20

It is determined by the base sequence on mRNA which is transcribed by genes from DNA. Remember that protein chains are synthesised by translating mRNA base code, so the sequence is given by the mRNA translated for the protein.

Answer 21

Secondary structure is the folding of sections of the polypeptide chain into helices and sheets. It only considers the secondary features (folding and coiling).

Answer 22

Specific amino acid sequences will determine where a protein folds and coils. Folds are known as beta sheets and coils are known as alpha helixes.

Answer 23

Tertiary structure is the overall 3D shape of a single polypeptide chain.

Answer 24

It is determined by where the secondary structure is folded and coiled, contributing to the overall shape.

Answer 25

Quaternary structure is the overall 3D shape of 2 or more polypeptides (tertiary + tertiary). It occurs when multiple polypeptides interact and create chemical bonds between each other.

Answer 26

DNA → transcription → RNA → translation → PROTEIN

Answer 27

The part of DNA to be copied unwinds, separating the two strands. The enzyme RNA polymerase assembles the mRNA molecule at the template strand with surrounding RNA nucleotides. mRNA carries the genetic information from the DNA in the nucleus to the ribosomes in the cytoplasm for protein synthesis.

Answer 28

In eukaryotic cells, transcription occurs in the nucleus and the mRNA travels out the nucleus through nuclear pores to the site of translation (ribosome in the cytoplasm). In prokaryotic cells, transcription and translation occur in the cytosol.

Answer 29

In eukaryotes, before the mRNA leaves the nucleus, it is spliced, meaning that sections of RNA are removed. Both exons (coding DNA) and introns (non-coding DNA) are transcribed to form pre-mRNA. Introns (non-coding sequences) are removed and exons (coding sequences) are spliced together (joined). mRNA then leaves the nucleus to be translated and expressed.

Answer 30

1. The mRNA attaches to the ribosome 2. A tRNA molecule carrying a specific amino acid attaches to a 3-base codon on the mRNA through complementary base pairing with the tRNA molecule’s anti-codon (complementary codon). 3. The ribosome (containing rRNA) joins amino acids together with peptide bonds (using tRNA molecules with various codons and amino acids) to form the polypeptide. 4. The polypeptide folds and coils into a unique 3D shape to create the functional protein.

Answer 31

A ribosome is found in ALL cells of ALL living things. It is located in the cytosol either freely floating or attached to the rough endoplasmic reticulum. Ribosomes are the site of protein synthesis where translation occurs. They are made up of 40% protein and 60% rRNA (ribosomal RNA).

Answer 32

rRNA is produced in the nucleolus of cells. The nucleolus is a site within the nucleus specifically for producing and assembling ribosomes and rRNA. The function of rRNA is to catalyse the formation of peptide bonds between amino acids during translation.

Answer 33

NO. There is nothing that ‘reads’ mRNA code. It is translated naturally with complementary tRNA molecules that have respective amino acids. The ribosome is purely a site for protein synthesis.

Answer 34

Yes, each base triplet (codon) codes for only one of the 20 amino acids, but there is more than one codon for each amino acid.

Answer 35

As an undifferentiated cell. E.g. the zygote (a type of stem cell) will divide by mitosis and then differentiate (specialise). Meaning it gains a unique role as a cell. A zygote is the resultant cell of the unison between a male gamete (sperm) and female gamete (egg).

Answer 36

All cells have identical DNA and are initially stem cells with a similar structure and function. Differentiation is the process where these cells specialise and gain a unique structure and function, BUT THE DNA REMAINS IDENTICAL. Examples of differentiated (specialised) cells: - Nerve cells - Muscle cells (many types) - Red blood cells - White blood cells - Fat (adipose) cells

Answer 37

Cellular differentiation is CONTROLLED by gene expression. Gene expression considers WHICH genes are expressed and synthesised into proteins, hence it will control cellular differentiation by altering the properties of the cell with various proteins.

Answer 38

The phenotypes of an individual refer to the observable (and biochemical) traits resulting from the genotype. The genotype is the specific set of genes (alleles) that an organism is able to express for a trait. Consider Punnett squares.

Answer 39

Protein synthesis IS gene expression. An expressed gene is synthesised into a protein. RNA and proteins are both products of genes and gene expression.

Answer 40

1. Environmental factors 2. Products of other genes (RNA & proteins) 3. DNA methylation 4. Histone modification

Answer 41

Various temperatures can cause the expression of different genes. Low oxygen can stimulate the gene expression of the gene which codes for the protein ‘Erythropoietin’ which increases the production of red blood cells.

Answer 42

Gene expression can be controlled at the point of transcription as a form of long-term regulation of gene expression. (Preventing a protein from ever being transcribed) It can also be controlled at the point of translation as a short-term regulation of gene expression. (Reducing the production of a specific protein temporarily)

Answer 43

Transcription factors are regulatory proteins that CONTROL gene expression which in turn controls the production of proteins like hormones and RNA Activator proteins will switch genes on by binding to DNA promoter region, activating transcription Repressor proteins will switch genes off by blocking the attachment of RNA polymerase, preventing transcription

Answer 44

Some gene products (miRNA) can prevent translation by binding to mRNA, forcing it to be unable to bind to the ribosome.

Answer 45

mRNA can also be degraded (cut up) by the gene product small-interfering RNA (siRNA), preventing it from being translated.

Answer 46

- At the point of transcription (transcription factors) - At the point of translation (miRNA, siRNA)

Answer 47

A protein. It is based on information from an expressed gene.

Answer 48

Epigenetics refers to long-term inheritable changes in gene expression that do not involve changes in the DNA sequence. Epigenetics is what CONTROLS which genes are expressed and which are not. Epigenetic changes can be passed onto daughter cells. Epigenetics can be inherited. This the reason identical twins can be different.

Answer 49

Genetics is the base sequence - can’t change. Epigenetics is the layer above that which considers what genes are expressed and all the factors that influence it.

Answer 50

DNA methylation is an epigenetic change where the addition of a methyl group (CH3) to a cytosine nucleotide can deactivate genes (other forms of epigenetics can activate genes). Increased DNA methylation of a gene can prevent RNA polymerase from binding and thus transcribing the gene which reduces gene expression (protein synthesis)

Answer 51

Histones are the proteins that package DNA into chromatin. By modifying these, cells can regulate which genes are turned on or off. DNA that is loosely wrapped around histones is easily accessible and therefore easily transcribed, whereas tightly wrapped DNA is not accessible and prevents transcription.

Answer 52

Epigenetic markers (e.g. methyl group or markers which cause histone modification) are like bookmarks, they make it easier to find and read certain parts of the text. This analogy is only partly correct because epigenetics can also deactivate genes. So they stick pages together too.

Answer 53

Yes. Epigenetic changes can lead to cancer by deactivating tumour suppressor genes (genes that prevent cell division) or activating oncogenes (genes that promote cell division), increasing the rate of cell division

Answer 54

Mutations are a random and permanent change in the sequence of nucleotides in DNA Spontaneous mutations generally occur during DNA replication (mistakes the cell doesn't notice) and cell division (mitosis or meiosis)

Answer 55

- Ionising radiation (e.g. x-rays, UV, gamma rays) - Mutagenetic chemicals - Some viruses

Answer 56

- DNA polymerase mismatches DNA base pairs - Leading to the insertion of incorrect bases (this can sometimes be repaired) - Upon futher replication the mismatched base is permanently changed in the DNA base sequence on both stands due to the semiconservative nature of DNA replication and how the sequence change is passed on

Answer 57

- Errors occur during cell division (mitosis or meiosis) - Chromosomes do not separate correctly - Cells can receive extra or missing chromosomes when chromosomes do not separate evenly - Example: Down syndrome (trisomy 21)

Answer 58

Mutagens are physical or chemical factors that increase the rate of mutation in DNA Examples of mutagens: - Ionising radiation - Mutagenic chemicals (chemicals, cigarette smoke) - Viruses (mutations can occur if some of the viral DNA becomes involved in the host cell’s DNA)

Answer 59

- Substitutions - Deletions - Insertions

Answer 60

Substitution is the replacement of bases on DNA. Substitutions can have a range of effects, depending on the amino acid and the location in the polypeptide

Answer 61

A deletion is the removal of a DNA base. This causes a frameshift (causing every amino acid to shift back by one, making EVERY codon different. Deletions are very significant changes) resulting in an extensive change to the amino acid sequence

Answer 62

An insertion is the addition of a DNA base to the sequence. An insertion could change every codon on mRNA from the point of insertion/deletion because it causes a frameshift.

Answer 63

Frameshifts will alter every single codon on a DNA strand. A mutation in DNA sequence may cause change to DNA and then the mRNA codons, thus the amino acid sequence Changing the way the protein folds and coils and hence its function

Answer 64

It is possible that a single DNA base mutation does not change the amino acid produced.

Answer 65

Mutations in germ-line cells (reproductive) are more serious. If a mutation occurs in a germ cell the mutation will be present in every cell of the resultant organism and can be passed on to the future generations (the offspring) which results in absent or altered proteins in the offspring and potential diseases. In somatic cells if a mutation occurs it will be confined to a part of the organism because the mutation will only be present in the cell and any new cells produced via mitosis

Answer 66

Germ-line cells are gametes or cells that divide by meiosis to produce gametes (reproductive cells) Somatic cells are cells that do not lead to gametes (body/non-reproductive cells)

Answer 67

Cell membrane is breached to release cell contents. Enzymes are used to remove proteins (like histones) from the DNA and isolate it. The DNA is then amplified using other methods like PCR to produce a greater yield.

Answer 68

Polymerase Chain Reaction: 1. Heat DNA sample to 95C to break weak hydrogen bonds between base pairs and separate the strands. 2. Place RNA primers and cool sample to 55C. Primers bind to the single strands preventing them from re-joining and providing a starting point for the DNA synthesis by DNA polymerase. 3. Heat sample to 72C, and add free nucleotides and heat-tolerant DNA polymerase to join free nucleotides to the separated strands. This will double the quantity of DNA. Repeat for more.

Answer 69

1. Collect cells (sample) 2. Extract DNA a. PCR if more DNA samples are needed 3. Cut the DNA in fragments using the same restriction enzyme 4. Separate the fragments using gel electrophoresis. Load them into the wells of the porous gel. 5. Pass an electric current through the chamber. Since DNA is negatively charged (bc of its phosphate group), the fragments will move from the negative end at the wells towards the positive end. 6. The smaller fragments will end up closer to the positive end than the larger ones. This produces a unique fingerprint for each sample.

Answer 70

Basically, restriction enzymes are used to cut DNA at specific locations. There are thousands of restriction enzymes all purposed for a specific cut-recognition site (usually only 4 - 8 bases long).

Answer 71

A marking in the child’s DNA fingerprint will either come from the genetic information of the mother or one of the dads. This makes it possible to figure out who the father is. If comparing DNA samples to the same person (e.g. comparing crime scene sample and suspect or victim), the sample would display matching DNA banding patterns to the person of interest. If interpreting a paternity gel electrophoresis (e.g. comparing the fathers DNA bands to a child’s), the sample would display SOME matching DNA banding patterns to the parent.

Answer 72

An electropherogram is a GRAPHICAL/DIGITAL representation of the results of electrophoresis. It is not the DNA fingerprint produced by an image of fragment separation in the electrophoresis gel. The x-axis has fragment length and there are peaks throughout which represent different loci. If there are two alleles at a locus it is heterozygous, and homozygous if there is only one.

Answer 73

Long stretches of DNA made up of repeating elements called short tandem repeats (STRs) which are repeated nucleotide sequences of 2-8 bases The number of repeats of an STR is a unique identifier for an individual, which generate unique DNA profiles.

Answer 74

STRs or tandem repeats can be cut using restriction enzymes and then separated with gel electrophoresis for comparison. As individuals will likely have different numbers of repeats at a given satellite DNA site, they will generate unique DNA profiles for every individual.

Answer 75

If the alleles from a specific DNA marker produce a single band in electrophoresis, then the fragments are the same length and that individual is homozygous for the allele. On the contrary, if the bands are separated they are different lengths, meaning that the individual is heterozygous for that allele.

Answer 76

1. Extract DNA sample and multiply using PCR *The primers involved in starting PCR usually target STRs/satellite DNA sites since they are unique to individuals.* 2. DNA sample is cut using restriction enzymes which will produce unique DNA fragments 3. The fragments are analysed using gel electrophoresis 4. Electrophoresis bands of known size are used to create DNA profile displayed as an electropherogram

Answer 77

Genetic engineering is the process of combining DNA from two separate origins to create ‘recombinant DNA.’ This creates a genetically modified organism (GMO), also known as a transgenic organism.

Answer 78

1. Extract DNA from cells 2. Select gene (probes) 3. Remove gene (restriction enzymes) 4. Transfer DNA to a different organism

Answer 79

Cell is broken apart with heat and detergent to release its contents. The DNA is separated from the other contents of the cell like histones (using various processes).

Answer 80

Probes (similar to primers) are single strands of DNA or RNA that are designed to be complementary and bind to a specific segment of DNA (using known bases in a sequence). This is how specific parts are located. They are labelled with radioactive or fluorescent markers.

Answer 81

When cutting DNA, some restriction enzymes will make a clean cut (blunt ends), or leave single-stranded overhangs (sticky ends) which can be used to form recombinant DNA.

Answer 82

- Microinjection - Viral vectors - Bacterial plasmids (for plants) - Yeast - Electroporation - CRISPR

Answer 83

Microinjection is a physical method of gene transfer where DNA from a donor is injected directly into the cell. This is often used in animals. It is very inefficient because the host DNA and donor DNA may not always integrate.

Answer 84

The DNA from a donor is inserted into a virus (the pathogenic viral DNA is removed with the restriction enzyme used to extract donor DNA) The virus integrates the DNA into the host cell as it naturally would when it infects a host. Viruses work by injecting their genetic information into cells and causing replication of themselves. We can use this system for genetic modifications.

Answer 85

Gene of interest is removed from cell using specific restriction enzyme Bacterial plasmid is cut using the same restriction enzyme to produce complementary sticky ends. The gene and plasmid are combined and join due to complementary base pairing. Enzyme DNA ligase seals the breaks in DNA The plasmid is inserted back into bacteria Bacteria can be used to infect the plant, which will directly incorporate its own DNA (including the gene of interest) into the DNA of the plant cells

Answer 86

A plasmid is a circular DNA molecule found in bacteria, separate from the chromosomal DNA. It’s used as a vector (a ‘vehicle’) to transfer genes between species.

Answer 87

A bacterial transformation is the process where DNA (like a gene) is incorporated into bacterial DNA (usually bacterial plasmids). The process is the same as using bacterial plasmids for gene editing without the part where it's added to a plant cell, instead allowing it to multiply with the gene of interest included.

Answer 88

Yeasts are single-celled eukaryotic organisms They have plasmids which can be modified like bacterial plasmids Since it is a eukaryote, both introns and exons can be inserted, as it has the splicing machinery to remove introns It can also produce proteins.

Answer 89

An electrical pulse is used to deliver DNA directly into cells. The pulse induces temporary pores in the cell membrane Cell membrane reseals and is left unharmed

Answer 90

Bacteria have an adaptive immune system called CRISPR. When a virus attacks a bacteria, the bacteria stores a copy of the virus DNA This can be transcribed to RNA, loading into an enzyme called Cas9, and used to cut the virus

Answer 91

The Cas9 enzyme is programmable and can be ‘equipped’ with a specific sequence of bases called guide RNA (instead of the viral DNA which occurs naturally). This is manufactured by scientists to be complementary to the target DNA base sequence to be cut. It can then cut the specific site on the DNA which was located by guide RNA.

Answer 92

Disrupt: Making a single cut to deactivate the gene. The gene can also be repaired with the inclusion or exclusion of additional bases (non-homologous end joining). Delete: Guide RNA can be used to target two locations. Cas9 will cut the DNA in two places and remove a portion of the gene. The two remaining ends will join and that cut section will have been removed (non-homologous end joining). Insert: Adding a DNA template along with the guide RNA allows Cas9 to also insert a new gene after a deletion (homology directed repair). Disruptions and deletions cause frameshifts.

Answer 93

Proteins may be designed from scratch or from modifications to existing proteins. 1. Design the shape of the protein 2. Determine the correct amino acid sequence to achieve that 3. Construct a gene (DNA sequence) to code for the desired amino acid sequence. 4. Gene is then transferred to bacteria or yeast to produce the new protein. 5. Cells are lysed (killed, breached) and protein is isolated (released).

Answer 94

If there are mutations in the target sequence Cas9 will not be effective (guide RNA no longer complementary) Repair enzymes may fix Cas9 cuts Cas9 may make cuts in multiple spots due to short guide RNA targets (4-8 bases) potentially reoccurring at other points in the DNA sequence.

Answer 95

Most concerns are related to possible impacts on environment or human health. - May outcompete native plants if released - May result in ‘superweeds’ that cannot easily be controlled - Interbreeding between GMO and non-GMO of a species - Unknown side effects to human health - e.g. possible allergies from new substances

Answer 96

Application: Industrial enzymes - catalysing specific chemical reactions efficiently Limitation: Side effects (e.g. immune responses that threaten human health)

DNA & Proteins Flashcards

Become smart