Class Notes of DNA and Proteins Flashcards
What are the large molecules in living organisms called?
macromolecules
What is the main role of DNA in cell?
It is the long term storage of information
What is the function of DNA?
It contains the instruction to construct other components of the cell such as proteins and RNA molecules.
What is genes?
DNA segments that carry genetic information
Where is the DNA stored in eukaryotes (animals and plants)?
Inside the cell nucleus
Where is the DNA stored in the prokaryotes(bacteria)?
In the cells’ cytoplasm
What is the structure of DNA?
- Double helix structure consisting of two strands coiled like a spring
- DNA is composed of repeating units called nucleotides
- A nucleotides consists of sugar molecule, a phosphate group and a nitrogenous base
- Chains of nucleotides form the sugar-phosphate backbone
- there are 4 bases (adenine (A), thymine(T), guanine(G) and cytosine (C)
- adenine always form weak hydrogen bonds with thymine on the adjacent DNA strand of the double helix(A-T).
- Guanine always form weak hydrogen bonds with cytosine(G-C)
- hydrogen bonds are weak so they can break and reform easily when DNA is replicated
- There is always the same amount of thymine and adenine as there they are pairs.
What is X-ray crystallography?
- a piece of evidence that was useful in deducing the double-helical structure of DNA
- used to determine the atomic and molecular structure of a crystal.
- crystalline atoms cause a beam of incident X-rays to diffract onto many specific directions.
- by measuring the angles and intensities of these diffracted beams, produce the picture of a three-dimensional picture of the density of electrons within the crystal form which the average position of the atoms in the crystal can be determined as well as their chemical bonds.
What are genes?
a segment of the DNA molecule (i.e a sequence of bases ) that code for the production of protein molecules, a part of protein molecules (a polypeptide) or an RNA molecule
What does genes determine?
determine what proteins are made within cell therefore determine the structure and function of the cell.
What is a chromosome?
single DNA molecule and its associated histone proteins
Does each organism have the same number of chromosomes in each somatic cell (non-sex cells)
yes
Is the number and type of chromosomes in the somatic cells of an organism unique for each species
Is the number and type of chromosomes in the somatic cells of an organism unique for each species
What is needed for the cell to multiply?
for cells to multiply, the DNA has to be replicated so that each cell receives a complete copy of all chromosomes
When is a chromosome visible?
only visible just after the DNA has been copied and the 2 copies ( called sister chromatids) are still attached. the DNA is highly condensed and so becomes visible. it appears as an X-shaped joined at the centromere.
What is a karyogram?
Karyogram is photograph taken when the DNA is condensed and visible. these photos can be cut out and arranged in order of size, numbered and pasted.
Why is the karayotype of each specie unique?
it is unique as chromosmes vary in sizes and numbers between species . female xx and male xy.
Where are genes located on a chromosome?
they are located in specific positions on a chromosome. these positions are called the gene’s locus or gene loci.
How do the gene locus vary?
- gene present
- length
- banding pattern
How does prokaryotic cell differ from a eukaryotic cell
prokaryotic cells are much smaller and have no nucleus and lack membrane bound organelles.
What is the shape of the chromosome in a prokaryotic cell
It is a single circular chromosome. may also have smaller pieces of circular DNA called plasmids.
Describe the chromosome in eukaryotic cells?
Multiple rod-shaped chromosomes and two copies of their genetic material( on homologous chromosomes).
Where is the chromosome in a prokaryotic cell found?
found in a part of the cytoplasm called a nucleoid. the chromosome is surrounded by a semi-liquid fluid called cytosol mainly consisting of water, but also some organic and inorganic molecules.
What are the similarities between the DNA of mitochondria and chloroplasts and the DNA of bacteria?
They provide evidence supporting the theory of endosymbiosis . this theory suggests that mitochondria and chloroplasts originated as free living prokaryotic cells
What is DNA replication?
DNA is the process of copying chromosomes.
What is genetic code and where is it stored?
it is a sequence of bases on DNA that make up a code of instructions. it is stored in the nucleus of cells.
What does the genetic code provide
provides the information needed to instruct the cell to carry out its functions.
What are the steps involved in DNA replication
- the complementary strands of the double helix are unwounded by helicase. helicase breaks the hydrogen bonds between complementary bases. The bases are exposed.
- Free nucleotides pair with the exposed bases in a complementary way i.e A-T and G-C
- DNA polymerase join the nucleotides together to form 2 new strands of nucleotides which are complementary to the original strands.
- DNA polymerase checks that the new sequence is complementary to the original sequence. it removes and replaces misplaced nucleotides.
- the complementary strands of DNA then wind into 2 double helices.
What is the process of DNA replication known as
Semi-conservative replication
What does it mean by semi-conservative replication
Each double helix consists of one ‘new’ or newly synthesised and one ‘old’ or original strand of DNA. the ensures accuracy in the process of reproducing the gene.
What are the two types of sequences in a gene
introns and exons
What are exons
Part of DNA that are converted into mature messenger RNA(mRNA).
What is the process by which DNA is used as template to create mRNA called
Transcription
What are introns
Introns are part of genes that do not directly code for proteins
What are the two stages involved in protein synthesis called
transcription and translation
What happens during the process of transcription
- a section of DNA unwinds. exposes the bases of a gene
- Free RNA nucleotides complementary bind to the exposed bases on the DNA template, i.e A-U, G-C
- RNA polymerase checks the sequence of bases and join the RNA nucleotides together to make mRNA
- mRNA detaches from the DNA strand
- this RNA contains introns and exons. the introns are cut out and the exons are spliced together to make a shorter piece of mRNA that carries the code for a polypeptide
Why is uracil used instead of thymine
uracil is energetically less expensive to produce than thymine so is used in RNA
What is a codon
triplet of bases in mRNA
What happens during the process of translation
- mRNA leaves the nuclear pores and attaches to a ribosome in the cytoplasm of the cell
- tRNA molecules are found in the cytoplasm are responsible for carrying one specific amino acid to the ribosome
- tRNA’s are positioned correctly by complementary base-pairing between the anticodon on the tRNA and the codon on the mRNA.
- peptide bonds then forms between the first two amino acids and the first tRNA is released
- the ribosome moves along the mRNA allowing another tRNA to base-pair and position the next amino acid for a peptide bond to form
- more peptide bonds form as more amino acids are carried to the ribosome by other tRNA’s
- when the stop codon is reached the polypeptide chain is released.
What are ribosomes
small particles that are present in large numbers in all living cells and are the site of protein synthesis
What are amino acids
amino acids are the building blocks of proteins. the amino acid carried is specified by the anticodon on the tRNA molecule
What does the sequence of codon on the mRNA determine
it determines the sequence of amino acids in the polypeptide chain
What is the link between amino acids called?
peptide bond
What are the two main type of proteins
- fibrous or structural
- globular
What determines the specific function of each protein
the sequence and number of amino acid
What does the sequence and number of amino acid determine
it determines how the polypeptide will fold which determines it unique shape and function
What is the shape of proteins that is crucial to its function
3D shape
What are some type of proteins
enzymes, hormones, cell membrane receptors
What are the four levels of structure of proteins
- primary
- secondary
- tertiary
- quaternary
What is the primary structure of proteins
Primary structure is the linear sequence of the number and type of amino acids joined together in each polypeptide chain
What is the secondary structure of proteins and what is bonding called
The coiling or folding of localised sections of the polypeptide chain. hydrogen bonds form between some of the amino acids to cause this folding. the main folds produced are alpha helix or a beta-sheet and these result from an extremely regular sequence of amino acids
What is the tertiary structure of proteins
- the overall three-dimensional shape of the entire polypeptide is called the tertiary structure. further folding occurs to the secondary structure which makes the tertiary structure.
- the tertiary structure forms spontaneously as a result of interactions between different kinds of amino acids( attraction and repulsion) and the condition present in the cellular environment in which the protein will be used (e.g the pH)
What is the quaternary structure
If the protein consists of 2 or more polypeptide chains then the quaternary structure is the complex structure composed of all polypeptide chains bonding together. (e.g insulin and hemoglobin)
Explain why when an amino acid is deleted or substituted with another amino acid, the protein may be non-functional
the primary structure (linear sequence of amino acids) determines the tertiary structure. the folding of the polypeptide to form a unique 3D- shape hence a binding site for it. its function will not occur without amino acids of correct polarity, resulting in a non-functional protein
Explain why when an amino acid is deleted or substituted with another amino acid, the protein may continue to function normally
the primary structure (linear sequence of amino acids) determines the tertiary structure. if the folding of the polypeptide is unchanged in the functional region it still forms normal binding site then it is able to bind and function normally.
What are structural proteins
- they provide structural support within the organism (e.g keratin in hair, silk and collagen in skin and bone
- tend to have an elongated shape
- tend to have a regular sequence of amino acids and regular secondary structure such as alpha-helix and beta-sheet or a collagen helix (3 stranded helix)
- often have primary or secondary structure
What are globular proteins
- have non repeating amino acid sequence
- have irregular and unique shape that are compact and roughly spherical
- usually soluble
- haemoglobin , insulin
- always at least have primary, secondary and tertiary structure
Describe proteins and its binding
- proteins have specific binding sites
- these result from the unique structure of each proteins
- binding with molecules involve complementary shapes and weak chemical interactions like hydrogen bonds between amino acids on different proteins. binding is specific and unique
What are some examples of proteins with its unique binding sites
- enzymes - there is an active site that binds to a specific substrate
- antibodies- binding occurs between a specific antibody and a particular antigen. This allows the antibody to destroy foregin materials (e.g bacteria)
- cell membrane receptors and hormones- the binding between a hormone and its receptors on a target cell allows for communication in an organism
What is the denaturation of proteins
When the tertiary and/ or secondary structure of a protein is disrupted (ie the polypeptide chains unwind) a protein cannot function. this is called the denaturation of proteins.
What happens when a protein denatures?
it loses it normal shape and activity
What are some causes of protein denaturation ?
- high temperature
- pH
- chemicals
Give an review on enzymes
- enzymes are proteins
- they are tertiary structure proteins and have a 3-D shape
- globular proteins
- the shape of the active site of each enzyme is specific to the complementary shape of the material it works on called the substrate
- the shaped surface where it binds to the substrate is called the active site.
- an organic catalyst which speeds up a chemical reaction without it self being changed or destroyed
Describe the induced fit model of enzyme-substrate binding
- the enzyme active site is the region on the surface of an enzyme molecule with a particular shape into which only specific substrate molecules with the complementary shape will fit.
- enzyme-substrate binding is reversible
- the enzyme returns to the original shape
What happens when a enzyme and substrate binds
- weak bonds cause slight changes in the shape of the enzyme and substrate
- binding stresses the chemical bond in the substrate molecule so they break more easily, thus the requires chemical reaction proceeds more quickly
- catalase breaks down hydrogen peroxide in cells
How does enzymes increase the rate of reaction
- chemical reactions involve the breaking of chemical bonds in the molecule of the reactant and the formation of bonds in the product
- all reactant molecules require energy for their bonds to be broken and the energy needed to do this known as activation energy.
- enzymes lower the activation energy thus more quickly the reaction occurs because less energy is needed to break reactant bonds to initiate the reaction.
What factor affect enzymes
- physical- temperature
- chemical- pH, co-factors, inhibitors
How does temperature affect enzymes
- at high temperature, the tertiary structure of the protein is denatured as chemical bonds are broken
- at low temperature, the enzyme is still intact but there are fewer collisions and less energy is present so less reaction occurs
How does the pH affect enzyme
- enzyme has an optimum pH that will produce the shape required for its actions
- chemical interactions between atoms and side chains are affected by pH
- if an enzyme is exposed to a pH that is either side of its optimum pH the reaction rate will be lowered until the enzyme is denatured.
How does the co-factors affect enzyme
- some enzymes need other chemicals to be present to function effectively
- co-factors may bind to complete the active site of bind to the enzyme to alter the shape of the active site
How does inhibitors affect enzyme
- they are chemicals that inhibit/ reduce enzyme activity
- competitive inhibitors resemble the shape of the substrate molecule and compete with the enzyme for enzyme active site. it blocks the active site to prevent the substrate from binding
- non-competitive inhibitors bind elsewhere to the enzyme (allosteric site) causing the active site to change shape( also called allosteric inhibitors)
What is gene expression
- is the process by which the genetic code in the DNA is used to direct protein synthesis
- some cells, certain genes are turned off while in others they are expressed when exons are transcribed and then translated into proteins
State one environmental factor that could change the base sequence of DNA
anyone of these
- mutagenic chemicals
- ionising radiation
- viruses
Explain the difference between the potential consequence of mutation in germ cells and the potential consequences of mutations in somatic cells
If mutation occurs in a germ cell, there is potential that this could be passed onto the offspring of that individual. If the mutation occurs in a somatic cell, it will only affect the individual, it will not be passed on to offspring.
State the effect of increased DNA methylation
State the effect of increased DNA methylation
Define an epigenetic modification in a gene
Epigenetic change is a change in gene expression without altering DNA sequence(e.g methylation)
Explain one way in which the methylation of tumour suppressor genes can lead to cancer
Tumour suppressor genes control the cell cycle. when tumour suppressing gene expression is silenced by methylation, it can lead to uncontrolled cell division
State what is meant by the activation energy of a biological reaction
energy needed to break bonds in the reactants
Describe one way in which the active site of an enzyme is involved in increasing the rate of a biological reaction
increases chance of a reaction occurring by ensuring molecules have correct orientation to react thus lowers activation energy by placing stress on bonds within substrate.
