Topic 1: DNA and Proteins Flashcards
(40 cards)
What are the basic units of nucleic acids.
A nucleotide is the basic unit of a nucleic acid. It has three components:
A phosphate group
A sugar (two types are possible)
A base (four types are possible)
What are the nucleotide bases
There are five bases found in nucleic acid: Adenine Thymine Cytosine Guanine.
In RNA, thymine nucleotide base is replaced with uracil. The other three nucleotides remain unchanged.
What are the types of RNA
Ribonucleic acid (RNA) consist of a single strand of polynucleotides. It is found in: Transfer RNA (tRNA) Messenger RNA (mRNA) Ribosomal RNA (rRNA) Micro RNA (miRNA)
Whats the deal with chromosomes
Chromosomes in eukaryotic cells are made of chromatin, a mixture of DNA and proteins. DNA is coiled around proteins called histones.
Describe the process of DNA replication
DNA replication is semiconservative as each new strain contains one original and one new polynucleotide strand. Enzymes involved:
DNA Helicase -breaks the weak bonds joining the strains
DNA polymerase enzyme- joins the free bases to the sugar phosphate backbone. Works in the 5’ to 3’ direction.
RNA primer- provides the starting point for DNA synthesis
Ligase- connects Okazaki fragments
What are the three types of models
Conservative model is when the original double-stranded DNA molecule serves as the complete template for a DNA molecule made from two new strands.
Semi-conservative model is when the two strands of the original DNA molecule separate, and each strand serves as a template for a new DNA strand.
Dispersive model is when the original DNA molecule breaks into fragments that serve as templates for new DNA fragments
How does DNA bond together?
Purines join with pyrimidines in the DNA molecule by way of breaking relatively weak hydrogen bonds with the bases forming cross-linkages. This leads to the formation of a double stranded molecule of two opposing chains of nucleotides:
What is the DNA structure?
DNA Structure is that of phosphates linking neighbouring nucleotides together to form one half of a double-stranded DNA molecule.
What are genes?
Genes are segments of DNA that code for proteins or RNA. Genes consist of exons, which are segments that code for the synthesis of proteins, and introns, which are segments that do not code for proteins. 249 bases per chromosome.
Describe the process of transcription & Translation
Transcription is the genetic code copied from the DNA to mRNA (Messenger RNA). It occurs in the nucleus, uracil replaces thymine. Introns and exons are transcribe into a molecule called pre-mRNA.
- Weak hydrogen bonds are broken by helicase or RNA polymerase
- Free RNA nucleotides attached to exposed complementary bases.
- RNA polymerase joins sugar phosphate backbone. mRNA strand detaches.
RNA splicing happens before translation the pre-RNA has introns removed by spliceosome, resulting in mature mRNA.
Codons
Every 3 nucleotides make a codon, they code for an amino acid.
There are 64 possible codons (43 ) as there are 4 bases and 3 positions on a codon. Resulting in 2o possible amino acids.
Codons are degenerate, some amino acids have multiple codons.
Codons are non-overlapping and don’t share codons.
Translation rRNA
Mature mRNA passes through nuclear pores into the cytoplasm
mRNA meets ribosomes in cytoplasm and the rough endoplasmic reticulum
Ribosomes (40% protein, 60% rRNA) made of small ribosomal subunit, which reads the mRNA, and a large ribosomal subunit.
rRNA catalyses proteins from amino acids
Translation tRNA
Transfer RNA (tRNA) transfer the amino acids to ribosome.
tRNA’s have a specific attachment site for the corresponding mRNA binding region called an anticodon.
Anticodon is a complementary sequence to the codon, which codes for an amino acid.
Translation
- Mature mRNA attaches to small ribosomal unit.
- tRNA transfer RNA to ribosome, hydrogen bonds form between tRNA anticodon and mRNA codon.
- mRNA moves through, second tRNA transfers corresponding amino acids.
- Large ribosomal subunit catalyses chemical reaction, forming peptide bonds between amino acids
- Stage 3 and 4 are repeated until a stop codon is reached, Synthesised proteins moves to rough endoplasmic reticulum for modification.
Whats the deal with amino acids
There are approximately 20 different amino acids found in proteins.
All amino acids have a common structure:
.The ‘R’ group is variable, which means that it is different in each amino acid.
Ten must be obtained from our diet. These are called essential amino acids.
What is a polypeptide chain and how are they formed
A polypeptide chain is formed when amino acids are linked together via peptides bonds to form long chains.
The process of joining amino acids of called condensation.
A polypeptide chain may contain several hundred amino acids.
A polypeptide chain may be functional by itself but may also need to be joined to other polypeptide chains to be functional.
What are proteins
Proteins are macromolecules, consisting of many amino acids joined together as polypeptide chains. Each cell contains several hundred to several thousand proteins.
Elaborate on protein structures
Protein structure:
The conformation (or shape) a protein takes in dependent on the protein’s amino acid sequence. The ‘R’ groups of each amino acids each and interact with each other. These interactions determine the final confirmation of the protein.
A proteins conformation is central to its function, if the shape is altered then the protein may not be able to perform its biological function.
Proteins: Primary Structure
The primary (1) protein structure is the amino acid sequence.
Hundreds of amino acids link together to form polypeptide chains.
The chemical interaction (attraction and repulsion) of the individual amino acids helps define the final protein shape.
Proteins: Secondary Structure
The secondary (2) structure is the chain shape of the polypeptides chain.
There are two common types of secondary structure:
alpha-helix coil
beta-pleated sheets
Most proteins, e.g. lysozyme, contain a mixture of the two secondary structures, but the levels of each vary.
Secondary structure is result of hydrogen bond interaction between neighbouring CO and NH groups of the polypeptide backbone.
Proteins: Tertiary Structure
The tertiary (3) structure of a protein is the way in which it is folded (called its fold).
The protein folds because of interactions between the ‘R’ groups, or side chains on the amino acids. Several interactions may be involved:
. Disulfide bonding (reactions between two cysteine amino acids). These form the strongest links
. Weak bonding (ionic and hydrogen)
. Hydrophobic interactions.
Proteins: Quaternary Structure
Some proteins contain more than one polypeptide chain. The polypeptide chains, or subunits, aggregate together to become a functional unit. The aggregation of subunits is called the quaternary (4) structure of protein.
IN ESSENCE: There are four levels of protein structure. Primary structure (1): The sequence of amino acids in a polypeptide chain
Secondary structure (2): The shape of the polypeptide chain (e.g. alpha-helix). Tertiary structure (3): The overall conformation (shape) of the polypeptide caused by folding.
Quaternary Structure (4): The association of multiple subunits of polypeptides chains.
What is the deal with protein denaturation
Protein Denaturation refers to the loss of a protein’s three-dimensional structure.
It occurs because the bonds responsible for maintaining protein structure are altered
It usually results in loss of function
It is often irreversible.
Examples of protein are seen in many everyday circumstances:
Cooking food denatures protein and makes it easier to digest.
Alcohols disinfect by denaturing bacterial and viral proteins.
Examples of agents that cause protein denaturation are:
Strong acids and alkalis
Heat and radiation
Heavy Metals
Detergents and solvents
Whats the deal with globular proteins
Globular Proteins are very diverse in their structure.
They can exist as single chains or comprise several chains, as occurs in haemoglobin and insulin.
Properties of globular proteins:
Easily soluble in water
Tertiary structure is critical to function
Polypeptide chains are folded into spherical shape.
Functions of globular proteins: Catalytic e.g. enzymes Regulatory, e.g. hormones Transport, e.g. haemoglobin Protective, e.g. antibodies
Whats the deal with fibrous proteins
Fibrous Proteins form long shapes and are only found in animals.
Properties of fibrous proteins:
Water insoluble
Very tough physically; they may be supple or stretchy
Parallel polypeptide chains in long fibres or sheets
Functions of fibrous proteins:
Structural role in cells and organisms, e.g. collagen in connective tissue, bones, tendons
Contractile, e.g. myosin, actin
Whats the deal with enzymes
The complexity of the active site is what makes each enzyme so specific. Enzymes have a specific region where the substrate binds and where catalysis occurs. This is called the active site. The active site is usually a cleft or pocket at the surface of the enzymes. Substrate modification occurs at the active site.
Enzymes are substrate specific, although specificity varies from enzyme to enzyme due to its structure:
High specificity: The enzyme will only bind with a single type of substrate
Low specificity: The enzyme will bind a range of related substrates, e.g. lipase hydrolyse any free fatty acid chain.
When a substrate binds to an enzyme’s active site, an enzyme-substrate complex is formed.
Outline what substrate molecules are
Substrate molecules are the chemicals that an enzyme acts on. They are drawn into the cleft of the enzyme.
Explain how active sites function
The active site contains both binding and catalytic regions. The substrate is drawn to the enzyme’s surface and the substrate molecule(s) are positioned in a way to promote a reaction: either joining two molecules together or splitting up a large one. The complexity of the active site is what makes each enzyme so specific
Describe the lock and key model mechanism for enzymes.
The lock and key model of enzyme action, proposed earlier this century, proposed that that substrate was simply drawn into a closely matching cleft on the enzyme molecule.
Induced Fit Model
More recent studies have revealed that the process is much more likely to involve an induced fit.
- A substrate approaches the active site of the enzyme.
- The substrate induces a complementary change in the active site of the enzyme. The shape of the active site is complementary to the shape of the substrate. The enzyme binds with the substrate forming an enzyme substrate complex.
The enzyme catalyses the reaction of its substrate forming one or more products. The products form a different shape to its substrate and diffuse away. The active site then reverts to its original shape.
Explain the significance of biological catalysts
Catalysts speed up reactions by influencing the stability of bonds in the reactants. They may also provide an alternative reaction pathway, thus lowering the activation energy needed for a reaction to take place
Outline the difference between catabolic and catabolic reactions
Catabolic Reactions involve the breakdown of a larger molecules into smaller components, with the release energy (they are exergonic).
Enzymes involved in catabolic reactions can cause a single substrate molecule to be drawn into active site.
Chemical bonds are broken, causing the substrate molecule to break apart to become two separate molecules.
Catabolic reactions include:
- Digestion: breakdown of large food molecules.
- Cellular respiration: Oxidative breakdown of fuel molecules such as glucose.
Anabolic reactions, smaller molecules are joined to form larger ones. These reactions are endergonic; they require the input of energy.
Enzymes involved in anabolic reactions can cause two substrate molecules to be drawn into the active site.
New chemical bonds are formed resulting in the formation of a single molecules.
Examples include: Protein synthesis: build-up of polypeptides from peptide units. Cellular respiration: Oxidation of fuel molecules such as glucose.
