bio task 2 study notes

what is HCG?

• Human chorionic gonadotropin (HCG) is a hormone produced by some of the cells in the blastocyst/embryo when it implants in the endometrium

• HCG maintains the corpus luteum

what is the corpus luteum?

oxytocin

•  stimulates the production of milk and

• causes the uterine muscles to contract and cervix to soften i.e causes female to go into labour and give birth

• after birth, oxytocin secretions continue, causing uterus to contract and expel placenta

what is the role of relaxin?

loosens uterine muscles during pregnancy and prepare the body for birth

what is the role of lutenising hormone?

• promotes final maturation of the ovarian follicle, ovulation and development of the corpus luteum in females.

• also stimulates the secretion of testosterone.

what is the role of follicle stimulating hormone (FSH)?

stimulates maturation of follicles in the ovaries of females

what are the two types of proteins?

1. fibrous proteins: form structural components of cells and tissues. They are long and insoluble in water eg. collagen in skin and keratin in hair

2. Globular proteins: usually spheircal in shape, compact and soluble in water

   • Eg. haemoglobin, antibodies, hormones and enzymes

what is internal fertilsation?

• Sperm is released inside female’s body in copulation.

• union of male and female gametes (sperm and egg) inside the body of the female

• isnt restricted to terrestial organisms but is favourble 

• eg. humans, tortoise, most mammals

what is external fertilisation?

• External fertilisation occurs in an outside environment

• Has to occur in a body of water otherwise the male and female sex cells dry out.

• Are exposed to external elements and can contract diseases, be eaten or die out

•  Generally is only done by animals that can be in a body of water eg.
              ■ Fish such as salmon
              ■ Amphibians such as frogs

advantages of external fertilisation

• little energy required to mate

• larger numbers of offspring produced

• large numbers of gametes released: more zygotes, higher chance of survival and more offspring produced

• less competition 

disadvantages of external fertilisation

• fertilised is not nurtured by parent, which leaves it susceptible to predation and disease. the likelihod of it surviving until birth is low

• Droughts and dry seasons tarnish the quality of the deposited gametes, so it is favourable for it to occur in aquatic environments

what are nonsense mutations?

a type of point mutation. 

Occurs when the DNA change creates a premature STOP codon which truncates the polypeptide. Cystic fibrosis is an example

what are the 3 types of substitution point mutation?

1. non sense

2. mis sense

3. silent

what are the advantages  of internal fertilisation?

advantage:

• fetus is nurtured inside the body of parent, protecting it from predation and disease

  - This means genetically varied offspring survive to continue to sexually reproduce, which increases genetic diversity. This it increases likelihood of a population being able to survive a selective pressure, enabling it to continue to adapt to changing environments and reproduce, as a result, contributing to the continuity of the species.

• close proximity: increased likelihood of fertilisation

what are the advantages and disadvantages of sexual reproduction?

advantages:

• variation in the population

• species are able to adapt better to their environment and any environmental changes

• disease events less likely to affect the population

disadvantages

• time consuming 

• requires mating partner

• large energy expenditure

• fewer offspring produced

what are the advantages and disadvantages of asexual reproduction?

advantage:

• populations can increase rapidly when conditions are favourable

• only one parent needed

• able to be enacted under external pressures (i.e quick and not energy intensive)

• no requirement for investment in care of offpspring

disadvantage:

• lack of genetic diversity

• reduced ability to adapt to external pressures- which can result in large extinction events (eg. the brie mould going extinct)

what are the steps of PCR?

1. denaturation- DNA sample is heated ~95ºC to separate the two strands of DNA

2. annealing- DNA sample is cooled to ~50ºC to allow primers to anneal to the start of the single strand of DNA

3. extension- sample is heated to the optimal temperature (~72ºC) for a heat tolerant polymerase (Taq) to function

   
   

what is a frameshift mutation?

when a single base is inserted or deleted, every single codon after the mutation is affected, altering the reading frame of the gene

• They have a huge effect on the DNA as it can change the amino acid sequence, ultimately impacting the protein it will produce.

what is a mutagen?

• A mutagen is an agent that increases the rate of genetic mutation by interfering with the function of nucleic acids. 

• They can be spontaneous (caused by copying errors during DNA replication) or induced by exposure to external elements

• they can be physical (radiation), chemical or biological.

what is PCR?

polymearase chain reaction

• a technique used to amplify DNA, in vitro

• each PCR reaction doubles the amount of DNA

• The reaction occurs in a thermal cycler and uses variation in temperature to control the replication process

what is the difference between point and chromosomal mutations?

• point: a change in one nucleotide in the DNA

• chromosomal: changes to segments of a chromosome, leading to large scale changes in the DNA

what processes can be involved in a point mutation?

• Insertion (extra nitrogenous base added)

• Deletion (nitrogenous base not include)

• Substitution (wrong nitrogenous base added)

how can the physical structure of proteins be described?

• The structure of proteins can be described as primary, secondary, tertiary or quaternary

  
  

primary structure of proteins

•  a polymer of amino acids arranged in a linear chain (polypeptides)

secondary structure of proteins

• The polypeptide chain then folds up in various ways.

• forms as a result of the amino acid chain becoming linked by hydrogen bonds, either

  twisting the polypeptide into a spiral (alpha helix) or folding it into a pleated sheet (beta pleated sheet)

tertiary structure of proteins

• Certain forces of attraction between alpha helices and pleated sheets (such as disulfide bonds) cause the polypeptide to fold into a more complex three-dimensional shape

• results from further folding of secondary proteins, can form globular proteins

quaternary structure of proteins

•  some complex proteins consist of more than one amino acid chain

• Each polypeptide chain is referred to as a subunit.

what is a structural protein?

• protein function

• Structural proteins are often fibrous and stringy (such as collagen and elastin), and found in connective tissues such as skin, cartilage, bone, tendons and ligaments

what are enzymes?

• Protein molecules are involved in all biochemical aspects of cellular metabolism

• Important in gene functioning, replicating, repairing and transcribing DNA

• catalyse bio chemical reactions

what are sensory proteins?

• proteins that change their shape or biochemical activity in response to stimuli (changes in the environment).

• eg: opsins are proteins in the retina (innermost layer) of the eye that detect light.

Transport and storage proteins

• Bind, store or carry other molecules in cells

• Eg. histones package DNA, ferritin stores iron in haemoglobin

hormonal proteins

• coordinate an organism's activities by triggering responses
  Examples: insulin, glucagon

immunological proteins (antibodies)

• protect against disease by recognising foreign bodies and microbes; activate immune cells

• Eg: immunoglobulins (antibodies), complement, major histocompatibility complex proteins

fungi (asexual reproduction)

• reproduce asexually when conditions are good/ favourable

• spores: mitosis produces genetically identical cells which are distributed into the environment by wind or vectors

  • eg. dust clouds when mushrooms are stepped on

• budding: nucleus divides and a bulge is formed on the side of the cell which is then split off by cytokinesis and bud detaches itself from the mother cell

  • After a bud develops to a certain point and even before it is severed from the parent cell, it is itself capable of budding by the same process. (a chain of cells may be produced.)

fungi (sexual reproduction)

• occurs when conditions are bad via meiosis. this increases genetic variation

what is binary fission?

• a single cell divides into two daughter cells

• begins with DNA replication where the genetic information is copied and divided into two

• the cell elongates and splits into two in cytokinesis, producing daughter cells with identical genetic information as the parent

• asexual reproduction

• occurs in bacteria and protists

protist reproduction

can reproduce both asexual or sexual

Binary fission: the division of the parent body into two identical daughter cells. eg. amoeba, paramecium

Budding: A small outgrowth develops from the cell of the parent body which separates and develops into a new individual. Example: Arcella

Interphase (Before mitosis)

• DNA is present as uncondensed chromatin (not visible under microscope)

• DNA is contained within a clearly defined nucleus

• Centrosomes and other organelles have been duplicated

• Cell is enlarged in preparation for division

• DNA replication occurs as cell prepares for divison

Prophase (mitosis)

• DNA supercoils and chromosomes condense (becoming visible under microscope)

• Chromosomes are comprised of genetically identical sister chromatids (joined at a centromere)

• Paired centrosomes move to the opposite poles of the cell and form microtubule spindle fibres

• The nuclear membrane breaks down and the nucleus dissolves

metaphase (mitosis)

• Microtubule spindle fibres from both centrosomes connect to the centromere of each chromosome

• Microtubule depolymerisation causes spindle fibres to shorten in length and contract

• This causes chromosomes to align along the centre of the cell (equatorial plane or metaphase plate)

anaphase (mitosis)

• Continued contraction of the spindle fibres causes genetically identical sister chromatids to separate

• Once the chromatids separate, they are each considered an individual chromosome in their own right

• The genetically identical chromosomes move to the opposite poles of the cell

telophase (mitosis)

• Once the two chromosome sets arrive at the poles, spindle fibres dissolve

• Chromosomes decondense (no longer visible under light microscope)

• Nuclear membranes reform around each chromosome set

• Cytokinesis occurs concurrently, splitting the cell into two

Meiosis 1

Meiosis 1:

P-I: Chromosomes condense, nuclear membrane dissolves, homologous chromosomes form bivalents, crossing over occurs

M-I: Spindle fibres from opposing centrosomes connect to bivalents (at centromeres) and align them along the middle of the cell

A-I: Spindle fibres contract and split the bivalent, homologous chromosomes move to opposite poles of the cell

T-I: Chromosomes decondense, nuclear membrane may reform, cell divides (cytokinesis) to form two haploid daughter cells

Meiosis II

The second division separates sister chromatids

P-II: Chromosomes condense, nuclear membrane dissolves, centrosomes move to opposite poles (perpendicular to before)

M-II: Spindle fibres from opposing centrosomes attach to chromosomes (at centromere) and align them along the cell equator

A-II: Spindle fibres contract and separate the sister chromatids, chromatids (now called chromosomes) move to opposite poles

T-II: Chromosomes decondense, nuclear membrane reforms, cells divide (cytokinesis) to form four haploid daughter cells 

what is the difference between mitosis and meiosis?

mitosis:

• produce 2 identical daughter cells

• diploid cells

• PMAT 1x

• occurs in somatic (body) cells

meiosis:

• procue 4 different daughter cells

• haploid cells

• PMAT 2x

• occurs in germ line cells (gametes)

Incomplete dominance

The phenotype of heterozygous individuals appears as a blend of the phenotypes of either type of the homozygote

Co dominance

• Occurs when pairs of alleles are expressed equally in the phenotype of a heterozygous individual

• superscripts used to indicate different co dominant alleles

autosomal recessive inheritance

• recessive allele is only expressed when no dominant allele is present

• have to be homozygous recessive for it to be expressed

• not sex linked

  eg. cystic fibrosis

autosomal dominant

• dominant allele is always expressed

• only need one allele for dominant trait to be expressed (hetero or homo)

• eg. Achondroplasty dwarfism

x linked dominant

• affect both genders equally since it only needs one x chromosome for the trait to be expressed

x linked recessive

• affect men more than women

• higher chance of a male to inherit one faulty x chromosome

• if a woman has dominant allele, it will mask the recessive one

• eg. haemophilia, red-green colour blindness

what are the steps in transcription?

1. RNA polymerase binds to a sequence of DNA called the promotor found near the beginning of a gene.

2. RNA polymerase moves along the DNA strand, unwinding a small section of DNA and breaking its hydrogen bonds

3. RNA polymerase reads the template strand, matching complementary free floating nucleotides to create a chain containg the same coding info

4. A mRNA molecule is sequentially snythesised by RNA polymearase as it continues to move along the DNA strand

5. terminator sequences end the transcription of DNA and the mRNA molecule moves from the nucleus to the cytoplasm

what are the steps in translation

1. mRNA attaches to a ribosome at a particular start codon

2. Ribosomes move along mRNA temporarily pairing the bases of transfer RNA (tRNA) anticodons with their complementary codons on the mRNA

3.  A second tRNA molecule attaches to the next codon on the mRNA strand

4. The ribosome catalyses the formation of a peptide bond between two amino acids

5. The first tRNA molecule moves away from the ribosomes leaving its amino acid

6. The ribosome continues to move along the mRNA until it reaches a stop codon

7. The polypeptide chain and mRNA strand are released from the ribosome

what is transcription and translation?

transcription: the process of making an mRNA copy of a gene’s DNA sequence

translation: the process in which ribosomes decode the genetic information in mRNA to form a polypeptide chain

what is DNA and why important

• DNA (deoxyribonucleic acid) is a type of nucleic acid that is responsible for storing genetic information in cells

• It acts as an instruction manual containing information needed for the growth, survival and replication of an organism

eukaryotic vs prokaryotic DNA

DNA structure?

• DNA is a long chain and double stranded molecule, in the shape of a ‘double helix’ (similar to a twisted ladder)

  • It is made up of two strands that have an antiparallel arrangement- they are parallel but run in opposite directions

• The vertical sides of the ladder are made of alternating sugar and phosphate molecules (sugar-phosphate backbone)

• Consists of building blocks called nucleotides which are composed of a deoxyribose sugar, a phosphate group and a nitrogenous base

• There are 4 nitrogenous bases: adenine, thymine, cytosine and guanine (all tigers can growl)

what are nucleotides

• Consists of building blocks called nucleotides which are composed of a deoxyribose sugar, a phosphate group and a nitrogenous base

• There are 4 nitrogenous bases: adenine, thymine, cytosine and guanine (all tigers can growl)

  • The nitrogenous bases bond to each other through weak hydrogen bonds

  • A and T have a double bond and G and C have a triple bond

  • Each base has a complementary base pairing (Adenine and thymine), (Cytosine and Guanine)

  • Ensure the proportions of bases are maintained (A:T and G:C is alway 1:1)

RNA structure

RNA structure

• Consists of nucleotides, which contain a ribose sugar, phosphate and nitrogenous bases

• Unlike DNA, RNA is single stranded

• Has the same bases as DNA except for thymine which is replaced with uracil

  • Therefore, adenine pairs with uracil while cytosine pairs with guanine

FOLLICLE STIMULAATING HORMONE (FSH)

important for stimulating maturation of follicles in the ovaries of females

•  luteinising hormone (LH)

• promotes final maturation of the ovarian follicle, ovulation and

  development of the corpus luteum in females. It also stimulates the secretion of testosterone.

Duplications chromosomal mutation

• part of chromosome is copied, resulting in duplicate sections (potentially increases gene

  expression)

• Changes amount of proteins produced

translocation chromosomal mutation

Translocation (crossing over/ recombination): segments of two chromosomes are exchanged (may interrupt gene sequences)

Deletions

• a portion of the chromosome is removed (along with any genes contained within this segment)

Inversions

– a segment of a

chromosome is removed and then

replaced within the chromosome in

reverse order

what is a chromosomal mutation

Changes to segments of a chromosome, leading to large-scale changes to the DNA of an organism

• They occur due to spontaneous errors in cell division 

• Crossing over during meiosis increases the probability of error

Part of chromosome: inversion, deletion, translocation, duplication

whole chromosome: aneuploidy/ non disjunction

aneuploidy

aneuploidy/ non disjunction

• Non-disjunction refers to the chromosomes failing to separate correctly, resulting in gametes with one extra, or one missing, chromosome.

• causes chromosomal abnormalities

• eg. Down syndrome (trisomy 21, 3 copies of chromosome 21)

steps in DNA replication

1. enzyme helicase unwinds and unzips DNA

2. Single-stranded binding proteins bind and stabilise the separated strands

3. DNA primase creates primers on DNA strands (primers signal beginning of replication)

4. DNA polymerase III reads and adds complementary nucleotides after the primer

5. DNA replication occurs in the 5’-3’ direction

6. DNA polymerase I will proofread and edit the strand to check for errors

7. Two new strands sealed together by ligase

which direction is DNA replication done

5’ to 3’

• DNA replication is continous for leading strand (5’-3’) and discontinius for lagging strand (3’-5’)

• lagging strand is replicated in sections (okazaki fragments)

• DNA is anti parallel and dna replication is semi conservative

what are SNPs?

• single nucleotide polymorphism

• a nucleotide is substituited for another

• Not classified as a mutation because it occurs in at least 1% of the population

• mostly occur in non coding regions (introns)

Why are SNPs useful in genetic studies?

• Determine differences between individuals and populations (similar to fingerprinting)

• Track human migration routes throughout history

• Study human evolution

• Help increase genetic diversity and prevent species from going extinct

• Genetic screening for the presence of diseases eg.sickle cell anaemia

DNA profiling vs DNA sequencing

• DNA sequencing determines the precise order of nucleotides

• DNA profiling is used to identify and compare individuals by characteristics in their DNA

sexual reproduction in plants

Through the use of pollinators eg. bees, the pollen is transferred to each flower. The pollen is transferred to the female reproductive organs where the pollen attaches to the stigma and then transports the sperm cells inside to the ovary where fertilisation occurs

sex organs in flowers

female: Carpel: ovary( fertilisation) , style, stigma (sticky part where pollen germinates/ collects)

male: stamen: anther (produces pollen) , filament

asexual plants

vegetative propagation

○ parts of the parent plant detach and will grow into new individuals

■ only one parent and specialised plant tissues in the parent plant can grow into offspring which are clones of the parent

population genetics in conservation

Its aim is to avoid extinction of species by applying conservation methods that ensure the maintenance of biodiversity

used to

• investigate speciation

• monitor inbreeding

• measure extinction risk

Population genetics in disease inheritance

• Identifying the regions of DNA associated with a disease can show

  • How to treat it

  • Who is more likely to be affected

  • What goes wrong in the cell to cause it

Applications of DNA profiling

• Determining parentage- a person’s DNA profile consists of a combination of their parent’s alleles

  • All of the STRs in a person’s DNA profile should also be present in their mother’s and/or father’s DNA profile

• Identification-

  • Used to determine the identity of a suspect of a crime or unrecognisable victims in forensic investigations

  • Natural disaster- determine the identity of people killed in natural disaster
    
    

applications of DNA sequencing

• genetic testing (determine likelihood of someone getting a genetic disease or diagnose it)

• Molecular biology research:

• study Human evolution and migration routes

• identification