Biology U1

3 characteristics of DNA

1. information for creating life in the next generation

2. form of a code, language

3. can change through natural selection

Virus are not ____ but has ___ or ___

Virus are not organisms but has DNA or RNA

DNA and RNA stands for

Deoxyribonucleic Acid,

Ribonucleic Acid

Draw and label 3 components of DNA

label the bonds involved with the C numbered

1. Phosphate [PO₄]^3-

2. Pentose deoxyribose sugar

3. Nitrogenous base

Sugar-phophate backbone with a covalant bond

bases bonded in weak hydrogen bonds

The complementary base pairs are (FULL NAME)

Adenine - Thymine or Uracil (double bond)

Cytosine - Guanine (tripple bond)

Draw the deoxyribose VS ribose structure

DNA differs in ___ and ___ for all organisms

length, sequence

DNA is efficient becuase it is… (length and base paris)

• 2 meters long (human) and 3 billion base pairs.

• very storage efficient.

Make a table of DNA v.s. RNA with three of their differences

Which are purines and pyrimidines? How do they bond?

Purines: Adenine, guanine

Pyrimidines: Thymine, Uracil, Cytosine

purines and pyrimidines bond in hydrogen bonds (weaker than covalent bonds)

In what two processes are base sequence is critically maintained?

1. Mitosis

2. Gene expression

cbp are critcally maintained by accurately manipulating the active site of cbp

L.U.C.A

Last Universal Common Ancestor

• genetic ancestor fo all domains of life

• discovered by following the genes of trees, plants, fungi

what direction is DNA constructed in?

Attaches 5’ of a DNA nucleotide to the 3’ end of a strand.

Of the 3’ end of the parent strand to the 5’ end.

Why are purines and pyrimidines the only combination?

1. width of 3 rings (2 nm)is just enough for it to be stable

2. it has to be a constant width across the DNA to be stable

Draw the structure of nucleosomes

• octamer of histones in the core

• DNA strand coils around the histones

• H1 linker histone secures the DNA strand, attched in the linker DNA

What do Nucleosomes coil into?

Chromatin Fibre and then to a chromosome

What type of cell are nucleosomes found in?

Eukaryotic (animal) cells

Hershey and Chase’s Experiment 1952 (purpose, method and results)

• To discover what the heridetary material was

• radioactive phosphate labeled on DNA

• radioactive sulfur labeled on protein

1. two samples of bacteriophate with two different labels infects baceria

2. blend the mixture in a blender

3. centrifuge the sample so that:

   bacteriophate at the top (low density)

   bacteria at the bottom (high density)

• Sulfur remained on bacteriophage or extracellular

• Phosphate found in the bacetria

• proved the Avery-Macload-McCarty suspections

Watson and Crick discovery

DNA double helix structure and heridetery in 1953

Radtioisotopes’ definition and use

• Atom with an unstable nucleus that emits radiation as it changes to become more stable

• Trace location and movement of a labelled molecule

• A significant tech. breakthrough

Chargaff’s falsification (method and results)

• Examine base pairs of DNA in various species

• organise them into tables and percentages

• %A=%T

• %C=%G

• Falsified the tetranucleotide theory that A=T=C=G

4 reasons why DNA is replicated

• to repair when there is a need to

• to grow an organism

• to reproduce a new generation

• to regulate functions

Describe how a new strand of DNA is semi-conservative

half is a parental strand

half is a synthesised pair of the parental strand made from free nucleotides

How is genetic integrity maintained?

Active site of cbp is accurately manipulated to allow for genetic continuity and accuracy.

3 steps of polymerase chain reaction at 3 temepartures

after all nessecary things are collected in a test tube, it is put in the thermal cycler

1. 98C: DNA is denatured and base pairs are exposed and broken

2. 55C: lab primers anneal to base pairs as a start before nucleotides

3. 72C: Taq polymerase pairs free nucleotides to the remaining exposed bases and bonds the sugar-phosphate backbone

After 30 cycles, how many copies are made?

After 30 cycles, 2 billion copies are made

The purpose of PCR

to amplify samll amounts of DNA quickly

Why are taq enzymes speical?

• they are heat resistant and therefore can sustain its function through all the cycles of PCR without denaturing

• they were eenzymes found in hot springs

Gel Electrophoresis 6 steps

1. PCR to amplify the sample

2. Restriction DNA cut bonds of fragments of sequences excluding junk DNA. (there are distinct length and sequence of DNA to each person

3. Samples from different people in a test tube is loaded into wells of a gel slab

4. Voltage travels through the - and + enode of the gel slab

5. DNA moves towards the + enode opposite to the wells. Shorter fragments move faster, longer fragments move slower

6. After a certain amount of time, the fragments of DNA are suspended in the gel and is dyed to make visible.

Two uses of gel elctropheresis

DNA profiling in 2 categories

1. Forsenic investigations:

Compare for 100% between one sample with several others.

2. Paternity investigations

Compare for 50% match from a child to a mother or father’s DNA

Role of DNA Helicase

1. unwind DNA double helix structure

2. break hydrogen bonds of cdp to expose bases for a new pairing

Role of primase

1. attaches a primer (short fragment of RNA) to the parental strand that acts as a starting point for polymerase III

2. There are numerous primers on the lagging strand, but only one on the leading stand

Role of DNA polymerase III

1. Use the CBP adding of 5’ end of a nucleotide to the 3’ end of a parental nucleotide to build covalent sugar-phosphate backbones

2. Proofread and corrects DNA errors with a new nucleotide from the 3’ terminal using exonuclease activity

Role of DNA polymerase I

1. Removes primers and repalces it with DNA Nucleotides

Role of DNA ligase

1. Bonds Okazaki fragments together with phosphodiester bonds (covalent)

Describe the leading and lagging strand

Leading strand: 3’ end is away from the replication fork, therefore DNA replication can be continuously done as the replication fork expands

Lagging strand: 3’ end is at the replication fork, therefore DNA replication can only be discontinuously done because the polymerase III has to return to the replication fork as soon as it hits the primer.

4 Advantages of compartmentalisation

1. Carry out specialised functions in a seperate area

2. Increased efficiency and effectiveness as all metabolites and enzymes needed for a function is already concentrated in an area

3. Prevent interference of other enzymes

4. Prevent harming unrealted and healthy organelles

1 possible disadvantage of compartmentalisation

Delays communication signal to the speicalised area

How do Lysosomes and phagocytic vacuoles work together?

in what pH do lysosomes work in?

1. A vacuole engulfs a foreign particle in the cell (e.g. pathogens)

2. Lysosome in the vacuole breaks down the foreign particle

lysosome is optimal in a acidic pH of 4.5-5.5, which is not the same as the cell environment

lysosome is also a digestive enzyme, and could cuase harm to healthy parts of the cell if not compartmentalised

How does compartmentalisation allow modification of mRNA before DNA translation?

Because DNA transcription is compartmentalised, mRNA can stll be modified because it is still in the nucleus and not the cytoplasm where translation occurs.

This is not possible for prokaryotic cells

Give four examples of proteins and a one word description of its role

1. Collagen - structural

2. Hemeglobin - transports oxygen in RBCS

3. Insulin - signals blood to be taken into cells in the blood

4. Trypsin - digestive enzymes for breaking down protein macromolecules

Describe the roles of RNA polymerase

• Unwinds DNA double helix

• Break cbp hydrogen bonds of bases

• Build sugar-phosphate backbones of the mRNA strand using cbp of the mRNA strand and DNA strand

Describe gene expression and factors that could affect it.

• Refers to how much genetic information is used to produce functional products like proteins through activity of transcription, translation, etc.

• transcription is highl controlled beause it is the first step of gene expression.

• Factors: type of cell, external esignals, time, age.

11 of a eukaryotic animal cell (draw and label function)

1. Plasma Membrane

2. Cytoplasm

3. Cytoskeleton

4. Nucleus

5. Rough Endoplasmic Reticulum

6. Smooth Endoplasmic Reticulum

7. Mitochondria

8. Golgi Apparatus

9. Vesicles

10. 80S ribosomes

11. Lysosomes

13 of a eukaryotic plant cell (draw and label function)

1. Cell wall

2. Plasma Membrane

3. Cytoplasm

4. Cytoskeleton

5. Nucleus

6. Rough Endoplasmic Reticulum

7. Smooth Endoplasmic Reticulum

8. Mitochondria

9. Chloroplasts

10. Golgi Apparatus

11. Vesicles

12. 80S ribosomes

13. Sap Vacuole

5 of a prokaryotic cell (draw and label function)

1. Cell wall

2. Plasma membrane

3. Naked DNA

4. Cytoplasm

5. 70S ribosomes

Explain steps of DNA replication with a labeled diagram

directionality: 5’ to 3’

Explain steps of DNA transcription with a labeled diagram

What is the effect of DNA transcription on the DNA

None. there is no effect on it and it stays stable.

What is DNA translation? (location, required molecules & organelles, product)

• takes place in the cytoplasm

• requires mRNA, tRNA, ribosomes, amino acids (AA)

• produces a polypeptide chain

Draw a labeled diagram of a chain of polypeptide

monomers of amino acids, joined by peptide bonds, forming a chain of polypeptide/ protein

Different combinations of AA bonded makes various structures

3 types of RNA and there function

mRNA (messenger): contains the code for building the protein

tRNA (transfer): brings the amino acid that corresponds to the mRNA codon, to the ribosome

rRNA (ribosomes)

Explain steps of DNA translation using a labeled diagram

Definition for mRNA codon and tRNA anticodon

mRNA codon: 3 nucleotide sequence that corresponds to a tRNA and an AA

tRNA anticodon: 3 nulceotide sequence that base pairs with an mRNA codon

triplets ensure reliability of the process, making no wrong amino acids

Draw a diagram of a ribosome’s strucutre

Small subunit: binds to the mRNA molecule

Large subunit: location of the poplypeptide chain and tRNA entrance and exit. Has space for 3 tRNAs but only really has 2 at a time.

• make of ribosomal RNA (rRNA) and other proteins

How many possible codons and amino acids are there?

64 codons

20 amino acids

• Many codons can code for the same amino acid —> degenracy

• The same codons, code for the same amino acids in every organism on Earth with very few exceptions, evidence for LUCA

What is the functionality of the porous nuclear membrane?

Allows for diffusion fo mRNA and proteins

What are the advantages of a double layered nuclear membrane?

• made of lipid bilayers, that are interspersed with proteins

• Comparmentalise the nucleus in the cytoplasm (reason for the possibility of post-transcription modification)

• Further control of diffusion

What are the advantages of a continuity of the nuclear membrane and rER?

• Close proximity —> mRNA can be translated quickly with the ribosomes attached on the rER and outer membrane —> high efficiency of protein synthesis

The changes of the nuclear membrane during mitosis or meiosis

1. prochase: nuclear membrane breaks down into small vesicles, allowing the chromosomes to be exposed in the cytoplasm

2. Metaphase, anaphase: vesicles are free floating in the cell

3. Telophase: vesicles attach on to chromosomes, vesciles fuse with each other to reform the ucelar membrane.

How do free v.s. bound ribosomes differ?

Free ribosomes: in the cytoplasm, produce proteins that are used within the cell

Bound ribosomes: on the rER, produce proteins that is to be secreted out of the cell.

Draw a labeled diagram of the golgi apparatus

• Cis face twoards the rER

• Cisternae labeled

• Trans face towards the plasma membrane

What is the function of a golgi apparatus?

Sort, modify, tag polypeptides for destinations as a final matured protein.

it has the same material (lipid bilayer) as othe rmembranes in the cell, so it can fuse to other organelles in processes such as endocytosis, exocytosis

4 types of vesicles and their functions

1. Secretory: transport out of the cell

2. Transport: transport within the cell

3. Vacuoles: store H2O for osmotic pressure (plant cells only)

4. Lysosomes and peroxisomes: enzymes that break down materials

Advantages of vesicles (2)

• Membrane bound: can concentrate materials, making it easier to keep track of during transport.

• Same material as other membranes: can fuse into another and form out of another

Draw a labled diagram of endocytosis and exocytosis

The chronological order of organelles passed through in endocytosis and exocytosis

1. plasma membrane —> vesicle —> destination

2. rER —> vesicle —> Golgi apparatus —> vesicle —> plasma membrane

What is Clathrin and how does it help in endocytosis?

• A 3 legged protein that has a hexagonal latice

• Aids in pulling, shaping and pinching of the plasma membrane

• Gives vesicles structure and protection during transportation

• Breaks off when the vesicle arrives at the deestination, reused at another vesicle

Describe Normal RBC v.s. Sickle cell

Normal RBC:

• A sac of hemoglobin

• Disk like shape

Sickle Cell:

• A sac of mutated hemoglobin

• Shape of a sickle

• Cannot carry oxygen well —> blood clots, slow circulation —> sickle cell disease

• BUT, reduces malaria infection symptoms

Define gene mutation

Structural changes in genes at the molecular level, meaning the the nucleotide sequence of DNA is changed affecting the structure and function of proteins

3 types of point mutation

Point mutation: a single nucleotide in the DNA is

1. inserted

2. deleted

3. substituded

Base substitution and their effects

aka single-nulceotide polymorphism (SNPS)

• Silent —> neutral, same AA

• Missense —> beneficial, neutral, harmful, different AA

• Nonsense —> harmful and shortens DNA , stop codon

Normal RBC v.s. Sickle RBC base substitution example

Normal RBC: CTC (DNA) —> GAG (mRNA) —> Glu (AA) —> a globular protein structure

Sickle RBC: CAC (DNA) —> GUG (mRNA) —> Val (AA) —> a fibrous protein structure

Frameshift mutations (insertions and deletions)

The triplets sequence changes, so the reading frame shifts, usually resulting in non-functioning proteins

2 Causes of Mutations

1. Mutagens

2. Error in DNA replication or repair

Examples of Mutagens

Chemical mutagens

1. Mustard Gas

2. Nitrous Acid

3. Dioxin

Radiation mutagens

1. X ray

2. UV

3. Radioactive isotopes

Randomness of gene mutation

• Can occur randomly anywhere on the genome

• Some bases are more prone to mutations

• Have no deliberate mechanisms for mutations

What are somatic/germ cells and what are the effects of mutation on them?

Somatic Cells:

• All cells but germ cells

• Cause disease like cnacer

• Not passed on to offspring

Germ cells:

• Cells that give rise to gamates (egg and sperm)

• Lead to mutations in gamates too

• Passed on to offspring but has various effects

Overall imapct of mutation in species

• Mostly harmful or neutral

• Beneficial ones: help survive and evolve in natural selection

Issue of commerical genetic tests

1. Providing info about potential future health issues and risk is problematic because…

   1. Anxiety

   2. Uninformed decisions

   3. Family impacts

   4. Misleading, misunderstandings

   5. Lack of counseling or comprehensive healthcare

Conserved sequences

Identical or similar DNA sequences across a species or group of species

Highly conserved sequences

Similar DNA sequences over long periods of evolution

3 hypotheses for highly conserved sequences

1. (Null hypothesis) it happened randomly

2. the gene’s proteins are fundamental to life that variations and mutations do not survive

3. There was a low mutation rate (low rate of transcription, translation, replication)

Draw an amino acid and label the groups

draw a dipeptide condensation reaction and label the bond

word equation of amino acid condensation

amino acid + amino acid —> dipeptide + water

Definition of condensation

joining of 2 molecules together to form one molecule, with water as a byproduct.

examples: dipeptide and nucleic acid formation

Definition of Non-essetial AA

AA that can be synthesized from other AAs or the human body

Definition of Essential AA

AA that cannot be syntehsized by the human body, and must be obtained through the diet (e.g. egg, meat)

Variety of polypeptide

Although only 20 AAs exist form the genetic code, the combination that it creates makes the polypeptide different in

• length of AA

• Order/ sequence of AA (not all have to be used)

INIFINITE combinations of AAs —> INFINITE variety of polypeptides

Name 3 examples of polypeptides and their functions

1. Lysozyme: enzyme

2. Myoglobin: oxygen storage and transport

3. Glucagon: hormone that raises blood glucose levels

Effect of pH and temperature on protein structure

Outside of optimal range —> decraesed enzyme activity

Denatured—> loss of structure —> inactive or dysfunctional protein that has altered solubility and charge.

Describe gene knockout

• A technique that makes a gene inoperative

• Learn what changed in the absence of it

• There is a library of knockout mice that are model organisms for research purposes.

Crispr-cas9 procedure outline and examples

• Precisely cut DNA at desired sequence

• Creates a mutation in the species OR substitute in a new sequence

• Natural repair process takes over

• Mutate that specific gene as a result

Examples:

• Decaf coffee

• Take HIV virus out of DNA to clear infections

• Modify wheat to remove gluten

the usage of crispr still raises ehtical concerns. a solution could be international regulation systems.

Directionality of DNA transcription

mRNA is synthesised from 5’ to 3’

Directionality of DNA translation

Ribosomes move 5’ to 3’ along the mRNA

Outline of the initiation of transcription

• Transcription factors guide RNA polymerase to the promotor region (a non coding region before the gene), where RNA polymerase binds to and begin transcription

Steps of post-transcriptional modification before translation

1. 5’ menthyl cap and 3’ Poly-A tail is added at the beginning and end of the gene, including the leader and trailor. This is to stabalise against the degredation of mRNA

2. RNA is processed: introns are spliced from the mRNA

Definition of an Intron

non-coding sequence of DNA transcribed into RNA, but is removed in splicing of post transcriptional modifications.

Definition of an extron

coidng sequences of DNA or RNA within transcripted genes.