Topic 1: DNA and Proteins Flashcards
What are the most common elements found in the human body?
Carbon, hydrogen, nitrogen, oxygen, phosphorous, sulfur (CHNOPS).
What are three criteria of organic compounds?
All organic compounds:
Contain carbon
Are complex
Are produced by or associated with living things
What are the four major types of organic compounds?
Nucleic acids (DNA and RNA)
Proteins
Carbohydrates
Lipids (fats)
1.1 DNA stores and transmits genetic information: it functions the same way in all living things.
How does it function?
DNA functions the same way in all living things - it uses a 3 base system (codons) to direct protein synthesis.
What do DNA and RNA stand for?
Deoxyribonucleic acid and ribonucleic acid.
What does DNA do?
DNA stores and transmits the genetic information of all living things.
What is a polymer? How is it related to DNA and RNA?
Polymers are long molecules made up of smaller subunits. DNA is a polymer.
What subunits make up the polymer DNA and RNA?
Nucleotides, the building blocks of all DNA and RNA.
What are polynucleotides?
Multiple nucleotides joined together.
What are the main components of a DNA nucleotide?
A 5-carbon sugar, deoxyribose
A phosphate group
One of four nitrogenous bases, A (adenine), T (thymine), G (guanine), and C (cytosine)
Where is the specific genetic coding of DNA found?
The specific genetic coding of DNA is found in the combination/order of the four nitrogenous bases.
What forms the main support of a DNA molecule?
The sugars and phosphates of nucleotides join together to form a sugar-phosphate backbone, forming two, running along each side of the double helix.
1.2 DNA is a helical double-stranded molecule.
What does this mean?
DNA does not exist as a single polynucleotide molecule, but rather a pair of molecules that spiral together to form a double helix.
How are the two strands of a double helix bound together?
The two DNA strands that make up a double helix of DNA are bound together via weak hydrogen bonds.
Explain complementary base pairs
The nitrogenous bases of each DNA nucleotide can only bond with their counterparts, A-T and G-C. This are known as complementary base pairing, and those are the base pairs.
Why are the two strands of a DNA molecule said to be complementary?
The two strands of a DNA molecule are said to be complementary as their bases correspond with each other.
What is similar between DNA and RNA?
DNA and RNA are both nucleic acids with sugar-phosphate backbones and nitrogenous bases.
What are the three major differences between DNA and RNA?
RNA is a single stranded molecule, compared to DNA which is a double-stranded molecule.
RNA has ribose for a sugar, another a 5-carbon sugar, but it has one more oxygen compared to deoxyribose.
RNA has the base uracil instead of thymine, which adenine bonds to instead.
(RNA is also usually a lot shorter than DNA).
What are some differences between eukaryotic and prokaryotic cells?
Eukaryotic cells - complex cells, DNA contained in the nucleus
Prokaryotic cells - simple cells, have free-floating DNA and do not have membrane-bound organelles (just ribosomes)
What is it meant by linear DNA, and what cells have linear DNA?
Linear DNA refers to the fact that it is a straight line, each molecule having a start and a finish. Eukaryotic cells have linear DNA.
What does linear DNA do to minimise its length?
Linear DNA molecules are very long, they are compacted by winding themselves around special proteins called histones, forming nucleosomes which can further condense into chromatin.
What doe nucleosomes coil up into?
Nucleosomes can further be compacted by coiling into chromatin.
What does the term homologous pairs mean?
Homologous pairs refers to the matching pairs of chromosomes found in a cell. Every chromosome has a matching chromosome in the same cell, and they contain the same genes in the same locations.
What is a gene?
A gene is a segment of DNA on a chromosome that contains the information to manufacture a polypeptide chain or an RNA molecule.
Describe the nature of DNA in prokaryotic cells.
In prokaryotic cells, DNA is free-floating, drifting around the cytosol of the cell. It is also circular.
Aside from prokaryotic cells, where else can unbound and circular DNA be found?
DNA is also unbound and circular in the chloroplasts and mitochondria of eukaryotic cells.
What is a karyotype?
A karyotype is a picture made up of images of a cell’s chromosomes, the photos are taken during cell division and are ordered in their homologous pairs and in size order.
1.5 Replication of DNA allows for genetic information to be inherited
How is DNA passed on from parent cells to daughter cells? How is it passed on in sexual reproduction?
When a cell divides, it copies its DNA before dividing, allowing each daughter cell to receive a copy.
In sexual reproduction, each individual receives half of a parent’s genetic material.
1.6 The structural properties of the DNA molecule, including the nucleotide composition and pairing, and the weak bonds between strands of DNA allow for replication.
How is this so?
Weak hydrogen bonds so they can be easily broken for new strands to be synthesised along the exposed bases.
Complementary base pairing allows for new strands to be synthesised that are perfectly accurate complementary strands.
1.7 Base pairing rules and the method of DNA replication are ___?
Universal. The complementary base pairing system and method of DNA replication applies to all life on earth.
Why is DNA replication described as a semi-conservative process?
DNA replication is described as a semi-conservative process as it produces two daughter DNA molecules from one parent DNA molecule, and each daughter DNA molecule inherits one strand of DNA from the parent molecule and has one newly synthesised strand, conserving some of the parent DNA molecule in each daughter DNA molecule.
What unzips the double helix of the DNA molecule in DNA replication?
DNA helicase enzyme.
Why is the DNA molecule unzipped in DNA replication?
DNA is unzipped in DNA replication to expose the bases of the two DNA strands, allowing for new strands to be formed by attaching to them, following the complementary base pairing system.
In DNA replication, what joins free-floating nucleotides to the exposed bases of the DNA strands? What end does it start from?
DNA polymerase enzyme, starting from the 3’ direction.
All cells are made up of many chemical compounds. Where do most of these chemical compounds come from?
Most of the chemical compounds that make up a cell are manufactured by the cell itself.
The manufacturing processes that cells go through to produce the chemical compounds they need require many chemical reactions, each step being ___ by a ___
Each manufacturing process in producing chemical compounds for a cell requires many chemical reactions, each step being catalysed (caused or accelerated) by a specific enzyme.
What is an enzyme?
Enzymes are protein molecules made from one or more polypeptide chains
Are all proteins functional?
No. There are many protein molecules in cells that are not functiona (i.e., enzymes), but are instead structural, such as keratin (found in hair, nails) and collagen (found in tendons, ligaments).
3.1 Protein synthesis involves transcription of a gene into messenger RNA (mRNA), and translation of mRNA into an amino acid sequence at the ribosomes. In eukaryotic cells transcription occurs in the nucleus.
Why does DNA have to make a copy of itself in the form of an mRNA molecule?
DNA is unable to leave the nucleus, however, protein synthesis requires the help of ribosomes, which are located in the cytoplasm. So, DNA transcribes a copy of its information, making an mRNA strand, so that the genetic code can be taken out of the nucleus for protein synthesis.
What codes for enzymes, and what do they (enzymes) do?
The genetic code of DNA codes for enzymes, which direct the metabolism of the cell (the chemical reactions that take place)
What is transcription (general) and where does it occur?
Transcription is the process by which a working copy of DNA is produced (an mRNA strand) and occurs in the nucleus.
Describe the process of transcription in detail
First, the enzyme RNA polymerase unzips the relevant region of the DNA molecule.
The enzyme then attaches free-floating RNA nucleotides to the exposed bases of one of the DNA strands, the template strand (also called the non-coding strand), to produce a single strand of messenger RNA (mRNA).
Whilst following complementary base pair rules when joining free-floating nucleotides, the base thymine is replaced with uracil, which bonds to adenine instead.
After being produced, the mRNA stand then peels off and enters the cytoplasm via a nuclear pore, carrying the code outside the nucleus.
The DNA then zips up again.
What is the difference between DNA polymerase and RNA polymerase?
DNA polymerase is an enzyme used to attach free-floating nucleotides to exposed DNA strands during DNA replication to produce a strand of DNA. RNA polymerase has the same function but also unzips part of the DNA molecule and is used during transcription To produce an mRNA strand. RNA polymerase also attaches the nucleotide base uracil instead of thymine to the exposed bases.
What indicates the beginning of a gene on a DNA molecule?
The start codon (TAC) indicates the beginning of a gene on a DNA molecule.
What is the mRNA strand produced in transcription identical to?
The mRNA strand produced in transcription is identical to the strand of DNA that did not act as the template strand, the non-template strand, which is called the coding strand. (Identical except the mRNA replaces thymine with uracil and ribose sugar).
Describe the process of translation in detail
Translation is the process that occurs when the mRNA strand from transcription moves outside of the nucleus and into the cytoplasm. In the cytoplasm, the mRNA strand attaches to a ribosome on the rough endoplasmic reticulum.
tRNA molecules then begin to bring in specific enzymes to the ribosome, matching up their anti-codons (exposed base triplets on one end of the molecule) with their corresponding complementary codons on the mRNA strand with the help of the ribosome which acts as a site where the tRNA and mRNA are brought together.
As more tRNA molecules bring in more amino acids, the amino acids join with a peptide link, forming a polypeptide chain, and then the tRNA molecules are released, having completed their function, delivering their amino acids.
When the ribosome reaches the end of the mRNA strand and the polypeptide chain of amino acids has been completed, it breaks away from the ribosome and folds into its final protein shape, ready to carry out its function.
What is translation (general) and where does it occur?
Translation is the process where a protein (polypeptide chain made up of a chain of amino acids) is produced. It occurs in the cytoplasm, specifically in ribosomes, which the mRNA strand attaches to. It is located on the rough endoplasmic reticulum.
What are ribosomes made up of?
Ribosomes themselves are made up of RNA and proteins. The RNA in ribosomes is a special type produced in the nucleolus, a region in the nucleus. It is called ribosomal RNA (rRNA)
What arethe sections of an mRNA strand called? What do they do?
Base triplets called codons, each one coding for a specific amino acid. There are also codons for ‘start’ and ‘stop’, indicating the beginning and end of the instruction for the synthesis of a protein.
Describe the structure of a tRNA molecule and explain what it is.
Transfer RNA (tRNA) is another type of RNA that is about 80 nucleotides long and is folded into a t shape. At one end there is an exposed triplet of bases, an anticodon, and at the other end a specific amino acid is attached.
What does tRNA do in translation?
tRNA molecules bring their specific amino acids to the ribosome in translation, matching up with the complementary codon on the mRNA with the help of the ribosome, which acts as the site where the tRNA and mRNA are brought together.
What happens as more tRNA molecules attach to mRNA to deliver their amino acids?
As more tRNA molecules bring in more amino acids, the amino acids join with a peptide link, forming a polypeptide chain, and then the tRNA molecules are released.
What happens when the ribosome reaches the end of the mRNA strand and the polypeptide chain has been completed?
When the ribosome reaches the end of the mRNA strand and the polypeptide chain has been completed, it breaks away from the ribosome and folds into its final protein shape, ready to carry out its function.
The process of translation can be summarised in three stages, what are they? What do all three stages require?
- Initiation - the use of the start codon AUG.
- Chain elongation - the building of the amino acid sequence (polypeptide chain) from the codons.
- Termination - the completion of the mRNA sequence with one of the step codons, UAG, UAA, or UGA. The polypeptide chain is completed and released.
All three stages require energy and enzymes.
Why are codons made up of three nucleotide bases?
Having one nucleotide base (A,U,C,G) code for one type of amino acid would mean only four different amino acids could be designated out of the 20 amino acids that make up proteins.
Having triplets of nucleotide bases code for an amino acid allows for 64 combinations, more than enough to code for each amino acid, even allowing for some ‘punctuation marks’ and some amino acids being coded for by more than one codon.
What are exons and introns and how are they different?
An exon is a DNA sequence that is translated (‘expressed’) into proteins, called a coding sequence.
An intron is a sequence that is transcribed but then edited or spliced out of the mRNA before translation, called a non-coding sequence.
Their key difference is that the exons contain genetic code used in translation to form a polypeptide chain, while introns are only transcribed and spliced shortly after as they do not contain any genetic information for protein synthesis.
Where are introns found vs where they are uncommon?
Introns are common in more complex eukaryotic cells, which have many introns.
They are more uncommon in more simple eukaryotic cells, which have hardly any introns in their DNA, and they are even rarer in prokaryotic cells.
What are macromolecules and how do they relate to proteins?
Macromolecules are big molecules. Proteins are macromolecules made up of one or more polypeptide chains.
What is a polypeptide chain?
Polypeptide chains are polymers made up of amino acids joined by peptide bonds.
What are the elements found in proteins?
Carbon, hydrogen, nitrogen, oxygen, and some sulfur (CHNO and some S)
Why do only some proteins contain sulfur?
Only 2 of the 20 amino acids contain sulfur, and not every amino acid sequence must have these amino acids, so not every protein may have sulfur.
Why is the number for different possible proteins almost limitless?
The number of amino acids ranges from 20-1000s, each ordered with a unique sequence of amino acids. The possible combinations of proteins with these two criteria is seen as almost limitless.
What do the sequence of amino acids of a polypeptide chain determine?
The sequence of amino acids of a polypeptide chain determine the way the polypeptide chain will fold up after it is made, giving it a specific 3D shape. This shape determines how the protein functions. This folding must be very precise to achieve specific shapes.
List the four different levels of that the structure of a protein can be broken up into.
Primary, secondary, tertiary, and quaternary.
What is the first level of structure of a protein? What is its structure determined by?
The first level of the structure of a protein is the primary structure, the sequence of amino acids in the polypeptide chain/s.
Its structure is determined by the sequence of bases on the mRNA strand that codes for its amino acid sequence. The mRNA base sequence is determined by the sequence of bases on the DNA that was transcribed.
What is the second level of the structure of a protein? What is its structure determined by?
The second level of the structure of a protein is the secondary structure, the coiling or folding of sections of the polypeptide chain. These sections are alpha-helices and beta-pleated sheets.
Its structure is determined by its primary structure, which determines the positions of the hydrogen bonds that produce the coils and folds.
What is the third level of the structure of a protein?
What is its structure determined by?
The third level of the structure of a protein is the tertiary structure, the 3D shape of the entire polypeptide chain.
Its structure is determined by its primary and secondary structures. Disulfide bonds and hydrogen bonds play an important role.
What is the fourth level of the structure of a protein?
The fourth level of the structure of a protein is the quaternary structure and consists of two or more polypeptide chains. Not all proteins have a quaternary structure, as many are made up of one polypeptide chain.
What are the two main classes of protein structure?
Fibrous proteins - long and narrow strands - have a structural role, they ARE something.
Globular proteins - more compact and round shape - have a functional role, they DO something.
5.1 Proteins are essential to cell structure and function, what are five functions of proteins in organisms and examples of them?
Structural - in hair and nails (keratin), ligaments (collagen).
Catalyse reactions - enzymes (e.g., polymerase).
Transport - carrying oxygen (haemoglobin).
Defence - antibodies produced by white blood cells (immunoglobulins).
Coordination - hormones (e.g., insulin)
List some examples of types of proteins and what causes proteins to have specific roles.
Some types of proteins are enzymes, some hormones, receptor proteins and antibodies.
The specific structure of proteins allow for them to all have different functions.
What are hormones? Are they all proteins? What is an example?
Some, but not all, hormones are made of protein.
Hormones are chemical messengers that are secreted into the blood and transported around the body; however, a particular hormone will only produce an effect in cells, tissues, or organs that are ‘tuned in’ to that hormone by having receptors (signal-receiving molecules) with shapes complementary to part of the hormone molecule
These structures are called target cells, target tissues, and target organs
An example of a protein hormone is insulin, which regulates blood sugar levels
What are receptor molecules/cell receptors?
Cell receptors are special protein molecules that send and receive signals.
Protein receptor molecules are found in cells and allow for hormones to bind to them.
The region of the receptor molecule that has a shape complementary to that of a specific hormone is called the binding site.
What are antibodies?
Antibodies, called immunoglobulins, are protein molecules that bind to antigens (cells that the body does not recognise), stopping them from functioning in order to protect the body.
A 3D region on the antibody called the antigen site allows for this to occur.
5.3 Explain why the 3-dimensional structure of a protein is critical to its function. Provide examples.
Proteins work because of their 3D shape, examples including enzymes, some hormones, receptor proteins, and antibodies, all of which require a specific structure to carry out their functions.
Many genetic diseases are due to the person’s cells producing proteins which have an abnormal 3D structure, such as sickle-cell anaemia, Tay-Sachs diseases and cystic fibrosis.
