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Unit 3 – How Do Cells Maintain Life?

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Version 2.1

Semester 1 - 2018



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Name:



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VCE BIOLOGY UNIT 3 HOW DO CELLS MAINTAIN LIFE?

CONTENTS

Biology cross study specifications (key science skills) Scientific practical investigation VCAA Study design – Unit 3 Biology VCAA Assessment tasks Unit 3 course outline Key action words in tests and examinations Tips for successful practical work

Area of Study 1 – How do cellular processes work?

Topic 1: Plasma membranes 1.1 Structure and function of plasma membranes 1.2 Movement of substances across the plasma membrane 1.3 The role of organelles in the production of proteins Key glossary terms and revision notes

Topic 2: Protein structure, functional diversity and the proteome 2.1 Protein structure 2.2 The functional diversity of proteins 2.3 The nature of the proteome Key glossary terms and revision notes

Topic 3: Nucleic acids, gene structure, expression and regulation 3.1 Nucleic acids – DNA and RNA 3.2 Gene structure and the genetic code 3.3 Gene expression 3.4 Gene regulation Key glossary terms and revision notes

Topic 4: Structure and regulation of biochemical pathways 4.1 Enzymes and biochemical pathways 4.2 Regulation of enzymes Key glossary terms and revision notes

Topic 5: Photosynthesis 5.1 Photosynthesis and chloroplasts 5.2 The stages of photosynthesis 5.3 Factors that affect the rate of photosynthesis Key glossary terms and revision notes

Topic 6: Cellular respiration 6.1 Cellular respiration 6.2 Aerobic respiration 6.3 Anaerobic respiration 6.4 Factors that affect the rate of cellular respiration Key glossary terms and revision notes



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Area of Study 2 – How do cells communicate?

Topic 7: Cellular signals 7.1 Signalling molecules 7.2 Signal transduction 7.3 Apoptosis Key glossary terms and revision notes

Topic 8: Responding to antigens 8.1 Antigens 8.2 Cellular and non-cellular pathogens 8.3 Innate immunity 8.4 The lymphatic system 8.5 Adaptive immunity Key glossary terms and revision notes

Topic 9: Immunity 9.1 Immunity and vaccinations 9.2 Deficiencies and malfunctions of the immune system 9.3 Monoclonal antibodies in treating cancer Key glossary terms and revision notes

Glossary Unit 3 Key glossary terms and definitions



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BIOLOGY CROSS-STUDY SPECIFICATIONS Units 1-4: Key Science Skills The development of a set of key science skills is a core component of the study of VCE Biology and applies across Units 1 to 4 in all areas of study. In designing teaching and learning programs and in assessing student learning for each unit, teachers should ensure that students are given the opportunity to develop, use and demonstrate these skills in a variety of contexts when undertaking their own investigations and when evaluating the research of others. As the complexity of key knowledge increases from Units 1 to 4 and as opportunities are provided to undertake investigations, students should aim to demonstrate the key science skills at a progressively higher level. The key science skills are common to all VCE science studies and have been contextualised in the following table for VCE Biology.

Key Science Skill VCE Biology Units 1-4

Develop aims and questions, formulate hypotheses and make predictions

- determine aims, hypotheses, questions and predictions that can be tested - identify independent, dependent and controlled variables

Plan and undertake investigations

- determine appropriate type of investigation: conduct experiments (including use of controls); solve a scientific or technological problem; use of databases; simulations; access secondary data, including data sourced through the internet that would otherwise be difficult to source as raw or primary data through fieldwork, a laboratory or a classroom

- select and use equipment, materials and procedures appropriate to the investigation, taking into account potential sources of error and uncertainty

Comply with safety and ethical guidelines

- apply ethical principles when undertaking and reporting investigations - apply relevant occupational health and safety guidelines while undertaking

practical investigations, including following relevant bioethical guidelines when handling live materials

Conduct investigations to collect and record data

- work independently and collaboratively as appropriate and within identified research constraints

- systematically generate, collect, record and summarise both qualitative and quantitative data

Analyse and evaluate data, methods and scientific models

- process quantitative data using appropriate mathematical relationships and units

- organise, present and interpret data using schematic diagrams and flow charts, tables, bar charts, line graphs, ratios, percentages and calculations of mean

- take a qualitative approach when identifying and analysing experimental data with reference to accuracy, precision, reliability, validity, uncertainty and errors (random and systematic)

- explain the merit of replicating procedures and the effects of sample sizes in obtaining reliable data

- evaluate investigative procedures and possible sources of bias, and suggest improvements

- explain how models are used to organise and understand observed phenomena and concepts related to biology, identifying limitations of the models



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BIOLOGY CROSS-STUDY SPECIFICATIONS (CONT.)

Key Science Skill VCE Biology Units 1-4

Draw evidence-based conclusions

- determine to what extent evidence from an investigation supports the purpose of the investigation, and make recommendations, as appropriate, for modifying or extending the investigation

- draw conclusions consistent with evidence and relevant to the question under investigation

- identify, describe and explain the limitations of conclusions, including identification of further evidence required

- critically evaluate various types of information related to biology from journal articles, mass media and opinions presented in the public domain

- discuss the implications of research findings and proposals

Communicate and explain scientific ideas

- use appropriate biological terminology, representations and conventions, including standard abbreviations, graphing conventions and units of measurement

- discuss relevant biological information, ideas, concepts, theories and models and the connections between them

- identify and explain formal biological terminology about investigations and concepts

- use clear, coherent and concise expression - acknowledge sources of information and use standard scientific referencing

conventions



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SCIENTIFIC INVESTIGATIONS PRACTICAL REPORT HEADINGS Students undertake scientific investigations across Units 1 to 4 of this study. Scientific investigations may be undertaken in groups, but all work for assessment must be completed individually. Students maintain a logbook of practical activities in each unit of this study for recording, authentication and assessment purposes. The following headings are to be used by students in the development of their reports for the practical investigations undertaken.

Section Content and activities

Title Title of investigation including names and dates

Introduction Explanation or reason for undertaking the investigation, including a clear aim, a hypothesis and/or prediction and relevant background biological concepts

Methodology Summary that outlines the materials and methodology used in the investigation including relevant annotated diagrams

Identification and management of relevant risks, including the relevant health, safety and ethical guidelines (if relevant) followed in the investigation

Results Presentation of collected data/evidence in appropriate format to illustrate trends, patterns and/or relationships

Discussion Analysis and evaluation of primary data

Identification of any outliers and their subsequent treatment

Linking of results to relevant biological concepts

Identification of limitations/errors in data and methods, and suggested improvements

Conclusion Conclusion that provides a response to the question and relationship to hypothesis

References and acknowledgements Referencing and acknowledgment of any sourced content that has been used throughout the investigation.



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VCE BIOLOGY UNIT 3 STUDY DESIGN 2017-2021 HOW DO CELLS MAINTAIN LIFE? The cell is a dynamic system of interacting molecules that define life. An understanding of the workings of the cell enables an appreciation of both the capabilities and the limitations of living organisms whether animal, plant, fungus or microorganism. The convergence of cytology, genetics and biochemistry makes cell biology one of the most rapidly evolving disciplines in contemporary biology. In this unit students investigate the workings of the cell from several perspectives. They explore the importance of the insolubility of the plasma membrane in water and its differential permeability to specific solutes in defining the cell, its internal spaces and the control of the movement of molecules and ions in and out of such spaces. Students consider base pairing specificity, the binding of enzymes and substrates, the response of receptors to signalling molecules and reactions between antigens and antibodies to highlight the importance of molecular interactions based on the complementary nature of specific molecules. Students study the synthesis, structure and function of nucleic acids and proteins as key molecules in cellular processes. They explore the chemistry of cells by examining the nature of biochemical pathways, their components and energy transformations. Cells communicate with each other using a variety of signalling molecules. Students consider the types of signals, the transduction of information within the cell and cellular responses. At this molecular level, students study the human immune system and the interactions between its components to provide immunity to a specific antigen. A student practical investigation related to cellular processes and/or biological change and continuity over time is undertaken in either Unit 3 or Unit 4, or across both Units 3 and 4, and is assessed in Unit 4, Outcome 3. The findings of the investigation are presented in a scientific poster format as outlined in the Scientific Practical Investigations section of this guide. Area of Study 1 - How do cellular processes work? In this area of study students focus on the cell as a complex chemical system. They examine the chemical nature of the plasma membrane to compare how hydrophilic and hydrophobic substances move across it. They model the formation of DNA and proteins from their respective subunits. The expression of the information encoded in a sequence of DNA to form a protein is explored and the nature of the genetic code outlined. Students use the lac operon to explain prokaryotic gene regulation in terms of the ‘switching on’ and ‘switching off’ of genes. Students learn why the chemistry of the cell usually takes place at relatively low, and within a narrow range of, temperatures. They examine how reactions, including photosynthesis and cellular respiration, are made up of many steps that are controlled by enzymes and assisted by coenzymes. Students explain the mode of action of enzymes and the role of coenzymes in the reactions of the cell and investigate the factors that affect the rate of cellular reactions. Outcome 1 On completion of this unit the student should be able to explain the dynamic nature of the cell in terms of key cellular processes including regulation, photosynthesis and cellular respiration, and analyse factors that affect the rate of biochemical reactions. To achieve this outcome, the student will draw on key knowledge outlined in Area of Study 1 and the related key science skills in the study design. Key knowledge Topic 1: Plasma membranes the fluid mosaic model of the structure of the plasma membrane and the movement of hydrophilic and hydrophobic

substances across it based on their size and polarity the role of different organelles including ribosomes, endoplasmic reticulum, Golgi apparatus and associated vesicles

in the export of a protein product from the cell through exocytosis cellular engulfment of material by endocytosis.



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Topic 2: Nucleic acids and proteins nucleic acids as information molecules that encode instructions for the synthesis of proteins in cells protein functional diversity and the nature of the proteome the functional importance of the four hierarchal levels of protein structure the synthesis of a polypeptide chain from amino acid monomers by condensation polymerisation the structure of DNA and the three forms of RNA including similarities and differences in their subunits, and their

synthesis by condensation polymerisation the genetic code as a degenerate triplet code and the steps in gene expression including transcription, RNA

processing in eukaryotic cells and translation. Topic 3: Gene structure and regulation

the functional distinction between structural genes and regulatory genes the structure of genes in eukaryotic cells including stop and start instructions, promoter regions, exons and introns use of the lac operon as a simple prokaryotic model that illustrates the switching off and on of genes by proteins

(transcriptional factors) expressed by regulatory genes. Topic 4: Structure and regulation of biochemical pathways the role of enzymes as protein catalysts in biochemical pathways the mode of action of enzymes including reversible and irreversible inhibition of their action due to chemical

competitors at the active site, and by factors including temperature, concentration and pH the cycling of coenzymes (ATP, NADH, and NADPH) as loaded and unloaded forms to move energy, protons and

electrons between reactions in the cell. Topic 5: Photosynthesis the purpose of photosynthesis chloroplasts as the site of photosynthesis, an overview of their structure and evidence of their bacterial origins inputs and outputs of the light dependent and light independent (Calvin cycle) stages of photosynthesis in C3 plants

(details of the biochemical pathway mechanisms are not required) factors that affect the rate of photosynthesis, including light, temperature and carbon dioxide concentration. Topic 6: Cellular respiration the purpose of cellular respiration the location of, and the inputs and outputs of, glycolysis including ATP yield (details of the biochemical pathway

mechanisms are not required) mitochondria as the site of aerobic cellular respiration, an overview of their structure and evidence of their bacterial

origins the main inputs and outputs of the Krebs (citric acid) cycle and electron transport chain including ATP yield (details

of the biochemical pathway mechanisms are not required) the location of anaerobic cellular respiration, its inputs and the difference in outputs between animals and yeasts

including ATP yield factors that affect the rate of cellular respiration, including temperature, glucose availability and oxygen

concentration.



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Area of Study 2 - How do cells communicate? In this area of study students focus on how cells receive specific signals that elicit a particular response. Students apply the stimulus-response model to the cell in terms of the types of signals, the position of receptors, and the transduction of the information across the cell to an effector that then initiates a response. Students examine unique molecules called antigens and how they elicit an immune response, the nature of immunity and the role of vaccinations in providing immunity. They explain how malfunctions in signalling pathways cause various disorders in the human population and how new technologies assist in managing such disorders. Outcome 2 On completion of this unit the student should be able to apply a stimulus-response model to explain how cells communicate with each other, outline human responses to invading pathogens, distinguish between the different ways that immunity may be acquired, and explain how malfunctions of the immune system cause disease. To achieve this outcome, the student will draw on key knowledge outlined in Area of Study 2 and the related key science skills in the study design. Key knowledge Topic 7: Cellular signals the sources and mode of transmission of various signalling molecules to their target cell, including plant and animal

hormones, neurotransmitters, cytokines and pheromones the stimulus-response model when applied to the cell in terms of signal transduction as a three-step process

involving reception, transduction and cellular response difference in signal transduction for hydrophilic and hydrophobic signals in terms of the position of receptors (on

the membrane and in the cytosol) and initiation of transduction (details of specific chemicals, names of second messengers, G protein pathways, reaction mechanisms or cascade reactions are not required)

apoptosis as a natural, regulatory process of programmed cell death, initiated after a cell receives a signal from inside (mitochondrial pathway) or from outside (death receptor pathway) the cell resulting in the removal of cells that are no longer needed or that may be a threat to an organism, mediated by enzymes (caspases) that cleave specific proteins in the cytoplasm or nucleus (details of specific cytoplasmic or nuclear proteins are not required)

malfunctions in apoptosis that result in deviant cell behaviour leading to diseases including cancer. Topic 8: Responding to antigens an antigen as a unique molecule or part of a molecule that initiates an immune response including the distinction

between non-self antigens, self-antigens and allergens invading cellular and non-cellular pathogens as a source of non-self antigens, and preventative strategies including

physical, chemical and microbiological barriers in animals and plants that keep them out the characteristics and roles of components (macrophages, neutrophils, mast cells, dendritic cells, complement

proteins) of the innate (non-specific) immune response to an antigen including the steps in the inflammatory response

the role of the lymphatic system in the immune response including the role of secondary lymphoid tissue (with reference to lymph nodes) as the site of antigen recognition by lymphocytes, and as a transport system for antigen presenting cells including dendritic cells

the characteristics and roles of components of the adaptive (specific) immune response including the actions of B lymphocytes and their antibodies (including antibody structure) in humoral immunity, and the actions of T helper and T cytotoxic cells in cell-mediated immunity.

Topic 9: Immunity the difference between natural and artificial immunity, and active and passive strategies for acquiring immunity vaccination programs and their role in maintaining herd immunity for a particular disease in the human population the deficiencies and malfunctions of the immune system as a cause of human diseases including autoimmune

diseases (illustrated by multiple sclerosis), immune deficiency diseases (illustrated by HIV) and allergic reactions (illustrated by reactions to pollen)

the use of monoclonal antibodies in treating cancer.



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Area of Study 3 – Practical investigation A student-designed or adapted investigation related to cellular processes and/or biological change and continuity over time is undertaken in either Unit 3 or Unit 4, or across both Units 3 and 4. The investigation is to relate to knowledge and skills developed across Units 3 and 4 and may be undertaken by the student through laboratory work and/or fieldwork. The investigation requires the student to identify an aim, develop a question, formulate a hypothesis and plan a course of action to answer the question and that complies with safety and ethical guidelines. The student then undertakes an experiment that involves the collection of primary qualitative and/or quantitative data, analyses and evaluates the data, identifies limitations of data and methods, links experimental results to science ideas, reaches a conclusion in response to the question and suggests further investigations which may be undertaken. The results of the investigation are presented in a scientific poster format according to the template provided in the Scientific Practical Investigations section of this guide. A practical logbook must be maintained by the student for record, authentication and assessment purposes Outcome 3 On the completion of this unit the student should be able to design and undertake an investigation related to cellular processes and/or biological change and continuity over time, and present methodologies, findings and conclusions in a scientific poster. To achieve this outcome, the student will draw on key knowledge outlined in Area of Study 3 and the related Key Science Skills in this study design. Key knowledge Topic 10: Practical investigation independent, dependent and controlled variables the biological concepts specific to the investigation and their significance, including definitions of key terms, and

biological representations the characteristics of scientific research methodologies and techniques of primary qualitative and quantitative data

collection relevant to the selected investigation, including laboratory work (biochemistry, cytology, immunology) and/or fieldwork (geomorphology); precision, accuracy, reliability and validity of data; and minimisation of experimental bias

ethics and issues of research including identification and application of relevant health, safety and bioethical guidelines

methods of organising, analysing and evaluating primary data to identify patterns and relationships including sources of error and limitations of data and methodologies

models, theories and classification keys, and their use in organising and explaining observed phenomena and biological concepts including their limitations

the nature of evidence that supports or refutes a hypothesis, model or theory the key findings of the selected investigation and their relationship to cytological, biochemical and/or evolutionary

concepts the conventions of scientific report writing and scientific poster presentation including biological terminology and

representations, standard abbreviations, units of measurement and acknowledgment of reference.



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SCHOOL-BASED ASSESSMENT SATISFACTORY COMPLETION The award of satisfactory completion for a unit is based on whether the student has demonstrated the set of outcomes specified for the unit. Teachers should use a variety of assessment tasks to provide a range of opportunities for students to demonstrate the key knowledge and key skills in the outcomes. The areas of study and key knowledge and key skills listed for the outcomes should be used for course design and the development of learning activities and assessment tasks. Assessment of levels of achievement The student’s level of achievement in Unit 3 will be determined by School-assessed Coursework. School-assessed Coursework tasks must be a part of the regular teaching and learning program and must not unduly add to the workload associated with that program. They must be completed mainly in class and within a limited timeframe. Where teachers provide a range of options for the same School-assessed Coursework task, they should ensure that the options are of comparable scope and demand. The types and range of forms of School-assessed Coursework for the outcomes are prescribed within the study design. The VCAA publishes Advice for teachers for this study, which includes advice on the design of assessment tasks and the assessment of student work for a level of achievement. Teachers will provide to the VCAA a numerical score representing an assessment of the student’s level of achievement. The score must be based on the teacher’s assessment of the performance of each student on the tasks set out in the following table. Contribution to final assessment *School-assessed Coursework for Unit 3 will contribute 16 per cent to the study score (8% per outcome)

Outcomes Marks* Assessment tasks

Outcome 1 Explain the dynamic nature of the cell in terms of key cellular processes including regulation, photosynthesis and cellular respiration, and analyse factors that affect the rate of biochemical reactions.

50 A report related to at least two practical activities from a practical logbook. The assessment task may be written or multimodal (approximately 50 minutes or not exceeding 1000 words).

Outcome 2 Apply a stimulus-response model to explain how cells communicate with each other, outline human responses to invading pathogens, distinguish between the different ways that immunity may be acquired, and explain how malfunctions of the immune system cause disease

50

At least one task selected from: a report of a practical activity annotations of activities or investigations from a

practical logbook a graphic organiser a bioinformatics exercise an evaluation of research media response data analysis a response to a set of structured questions problem solving involving biological concepts, skills

and/or issues a reflective learning journal/blog related to selected

activities or in response to an issue. The assessment task/s may be written or multimodal (approximately 50 minutes or not exceeding 1000 words for each task).

Practical work and assessment Practical work is a central component of learning and assessment. As a guide, between 3½ and 5 hours of class time should be devoted to student practical work and investigations for each of Areas of Study 1 and 2. External assessment The level of achievement for Units 3 and 4 is also assessed by an end-of-year examination, which will contribute 60 per cent to the study score.



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KEY ACTION WORDS IN BIOLOGY ASSESSMENT TASKS Every question in a test, examination or practical investigation report will contain an action word which gives context to the type of response required. Prior to answering each question, it is imperative that you understand what the action is asking you to do. This will ultimately direct the way you respond. account state reasons for, report on, give an

account of, narrate a series of events or transactions.

analyse identify components and the relationship between them; draw out and relate implications.

annotate add labels/notes or text to diagrams. apply put to use in a particular situation. assess make a judgement of value, quality,

outcomes, results or size. calculate find a numerical answer. clarify make clear or plain. classify arrange or include in classes, groups or

categories. compare show how things are similar or different

(if comparing data, make reference to the data)

conclude come to a judgement or result based on the reasoning or arguments that you present.

construct represent or develop in graphical form. contrast show how things are different or

opposite. create originate or bring into existence. define give the precise meaning or a word,

phrase or physical quantity. demonstrate show by example. describe provide characteristics and features. design provide steps for an experiment or

procedure. determine find the only possible answer. discuss identify issues and provide points for

and/or against. distinguish give differences between two or more

different items. draw represent by means of pencil lines. evaluate assess the implications and limitations. examine inquire into. explain make the relationships between things

evident and provide why and/or how.

extrapolate infer from what is known. identify recognise and name. infer explain a possible reason for something

observed. interpret draw meaning from. investigate plan, inquire into and draw conclusions

about. justify support an argument or conclusion. label add labels to a diagram. list write down items without explanation. measure find the value of. modify change in form or amount in some way. name present remembered concepts or facts. outline sketch in general terms; indicate the

main features of. plan use strategies to develop a series of

steps or processes. predict suggest what may happen based on

available information. propose put forward a plan or suggestion for

consideration or action. recall present remembered ideas, facts or

experiences. recommend provide reasons in favour. record store data/information and observations

for later. select choose one or more items, features,

objects. sequence arrange in order. show give the steps in a calculation. sketch make a quick, rough drawing of

something. solve work out the answer to a problem. state give a specific name, value or other brief

answer. suggest put forward an idea for consideration. summarise give a brief statement of the main points

of something. synthesise combine various elements to make a

whole.



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TIPS FOR SUCCESSFUL PRACTICAL WORK FOUNDATION BIOLOGY

Writing an experimental aim When writing an aim, it should relate to the direct variables (IV ad DV) in the hypothesis, describing how each will

be studied or measured. The aim does not need to include the details of the method.

Example 1 Hypothesis: If the temperature is increased, then the rate of transpiration in plants will also increase. Aim: To investigate the rate of transpiration of corn seedlings in different air temperatures over 24 hours. Variables: temperature (IV) and transpiration rate (DV).

Example 2 Hypothesis: Red flowers attract more bees than blue flowers. Aim: To compare the number of visits by bees to red flowers with the number of visits by bees to blue flowers over a set period of time. Variables: number of visits by bees (DV) and level of contrast of the colour of flowers with their background (IV).

Formulating a hypothesis A hypothesis is a suggested explanation for past observations that can be tested in an experiment. When

formulating a hypothesis is easy to use the cause-and-effect (‘if…., then…’) statement. A hypothesis should make mention of both your independent and dependent variables.

Example: ‘If plants are exposed to low light levels, then the rate of photosynthesis will decrease’.

Independent (IV) = light levels Dependent (DV) = rate of photosynthesis

Identifying the variables Make sure to understand the variables throughout the experiment:

Independent (experimental) – the variable being tested and therefore deliberately changed. Dependant – The variable you are measuring against the independent variable. Controlled – Multiple variables you keep consistent (the same) throughout the experiment. Uncontrolled – Variables out of your control that may have impacted on the overall results.

OH&S Identifying the possible OH&S risks within an investigation is important for the health and safety of yourself and

others. What is equally as important, is identifying the possible precautions to take to minimise the risks. An OH&S table should be developed that identify both of these.

Example:

Risk Precaution Sharp Knife (cuts) Plenty of space around you to cut without being knocked

Always cut well away from fingers Place sharp objects in middle of bench when not in use and knives in their sheaths

Glass breakages and spillages Place beakers in middle of bench to avoid falling off bench Always clean up any spilt liquids safely if spillages occur

Hot Plate (burns) Place hot plate in middle of bench with warning sign next to it Wear heat proof gloves when using the hot plate Turn hot plate off when not in use



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Following the Method Make sure to read through the method very carefully, highlighting key instructions and taking note of equipment,

measurements and time. Always ask for clarification if uncertain about a specific instruction. Mark each instruction when completed. This helps finding where you are up to in the method.

Collecting and Presenting Data Data Tables What columns and rows will you need in your data table? Always use a ruler and pencil to draw your data table. Make sure all row and column lines are drawn. Collect accurate data and present it neatly. Any mistakes should be erased. Unreadable data will lead to a loss of

marks.

Graphs When graphing your data, make sure to present the data using the correct type of graph (line of column). Only connect data points if a trend is obvious. If not, and appropriate, a line of best fit should be used (straight or

curved). Make sure both of your x and y axis are uniformly scaled (even distribution of measurements along axis) Make sure you label each axis with units of measurements, an appropriate title, and a key if needed. Any mistakes should be rubbed out (always use pencil).



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Types of Data Quantitative data Data collected about numeric variables is quantitative data. Like categorical variables, numeric variables can be

counted. Unlike categorical variables, numeric variables can also be measured, because they have a measurable quantity, like length, mass or time. Numeric variables can be discrete or continuous:

o Discrete (how many?) are values that can be counted or measured, but which can only have certain values. Examples are number of fish in a pond, number of red blood cells on a slide, number of times a lever is pulled.

o Continuous (how much?) may be any number value within a given range that can be measured. Examples are age, temperature, length, mass and wavelength.

Qualitative data Data collected about categorical variables is known as qualitative data. Categorical variables can be counted but

not measured, and relate to a type or category such colour or gender, or states such as on/off or wet/dry. Categorical variables can be nominal or ordinal:

o Ordinal (ordered) (what type?) variables are categorical variables in which there is an inherent order. They have a ranking or level, so they can be counted and also ordered. Examples are age group, position in a sequence, and trophic level.

o Nominal (unordered) (which category?) variables are categorical variables in which there is no inherent order; they can be counted but not ordered. Examples are flower colour, gender, number of children, and dog breed.

Analysing Patterns in Data If asked to compare results:

Make mention of any trends or patterns that are obvious (linear, exponential or inverse or none) Quote actual data collected when comparing and highlight major differences or similarities. If you collected inaccurate data (due to errors), or outliers, make mention of this.



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Identifying and Reducing Errors When an instrument is used to measure a physical quantity and obtain a numerical value, the aim is to determine

the true value. However, for a number of reasons the measured value is often not the true value. The difference between the true value and the measured value is called the error.

This error in the measured value is the result of errors in the experiment. The two types of experimental errors are: o systematic errors o random errors

Systematic errors Systematic errors are errors that affect the accuracy of the investigation and generally

caused by o faulty calibration of equipment o poorly maintained instruments, or o faulty reading of the instrument by the user (e.g. parallax error)

Systematic errors can be reduced by:

o using equipment which is best suited to the data you need to collect o use your equipment properly, ensuring you have been trained to use the equipment o making sure your instruments or measuring devices are properly calibrated and functioning correctly o use alternative equipment that could give a more accurate reading (e.g. digital equipment over analogue)

Random errors Random errors are unpredictable variations that affect the precision of a measurement and are always present.

Common sources of random errors include: estimating a value that lies between two measurements inability to read a measurement due to fluctuations in the measurement

Random errors can be reduced by:

making more or repeated measurements increasing the sample

Improving accuracy and precision and handling outliers Accuracy A measurement is considered to be accurate if it is judged to be close to the true value if it could be measured

perfectly. If an experiment is performed and it is determined that a given substance had a mass of 2.70 g, but the true value

was 3.20 g, then the measurement is not accurate since it is not close to the true value. Accuracy can be improved by reducing systematic errors. Precision Experimental precision refers to how closely two or more measurement values agree with each other. A set of precise measurements will have very little spread about their mean value. If the same experiment was conducted (as above) five times, and each time the substance was measured at 2.70 g,

then the experimental data was precise. A measured mass of 2.7 g ± 0.1 g is less precise than 2.7 g ± 0.001 g. Precision can be improved by reducing random errors. Outliers Readings that lie a long way from other results are sometimes called outliers. Outliers must be further analysed and accounted for (if possible). Sometimes an outlier may be dismissed if it was caused by a random error. Extra readings may be useful in further

examining an outlier.



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Reliability Reliability (sometimes called repeatability) is the ability to obtain the same results if an experiment is repeated.

Because a single measurement or experimental result could be affected by errors, replication and repeat trials are key components of reliability. To improve reliability, you should:

specify the materials and methods in detail include replicate (several) samples within each experiment take repeat readings of each sample run the experiment or trial more than once.

Validity Validity refers to whether your results are real results and whether they apply to all situations. Results are invalid,

for example, if you think you have measured a variable but have actually measured something else. Factors influencing validity include:

whether your experiment measures what it claims to measure. In other words, your experiment should test your hypothesis.

the certainty that something observed in your experiment was the result of your experimental conditions and not some other cause that you did not consider. In other words, whether the independent variable influenced the dependent variable in the way you have concluded.

the degree to which your findings can be generalised to the wider population your sample is taken from, or to a different population, place or time.

Drawing and Labelling When labelling biological drawings, follow

the guidance below: Use a sharp pencil. Label all relevant structures,

including all tissues in the case of microscopy.

Use a ruler for label lines and scale bars.

Label lines should start exactly at the structure being labelled; don’t use arrowheads.

Arrange label lines neatly and make sure they don’t cross over each other. It is visually attractive, though not essential, if the length of the label lines is adjusted so that the actual labels are right or left justified, i.e. line up vertically above each other on either side of the drawing.

Labels should be written horizontally, as in a textbook, not written at the same angle as the label line. As previously mentioned, a title, stating what the specimen is, should be added at the top or bottom of the

drawing.



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Responding to Discussion Questions Write neatly and write clearly. Read the whole question carefully. Make sure to respond to the action word in the stem of the question. Don’t repeat the question in your answer. Just answer the question! Quality of answer is better than quantity. Space provided is usually an estimate of length of response required (accounting for different sizes in handwriting) Use dot point to set out your answers if desired. Objective writing Scientific reports should be written in an objective (unbiased) style.

Concise writing To be concise use short sentences with a simple structure. The opposite of being concise is being verbose (wordy).

When editing your writing consider how you could say the same thing using fewer words

Writing a Conclusion Your conclusion should be one or two paragraphs that link your evidence to your hypothesis. It should provide a carefully considered response to your aim based on your results and discussion. You should clearly state whether your hypothesis was supported or not supported. Draw your conclusions by identifying trends, patterns and relationships in the data. Do not provide irrelevant information or introduce new information in your conclusion.



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VCE BIOLOGY UNIT 3 Area of study 1 Topic 2: Protein structure, functional diversity and the proteome

Key Knowledge protein functional diversity and the nature of the proteome the functional importance of the four hierarchal levels of protein structure the synthesis of a polypeptide chain from amino acid monomers by condensation polymerisation



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TOPIC 2 PROTEIN STRUCTURE, FUNCTIONAL DIVERSITY AND THE PROTEOME 2.1 – PROTEIN STRUCTURE Building a protein Proteins are _______________________ molecules that vary in ________,

___________ and ______________ The building blocks (monomers) of proteins are ____________________ All amino acids have the same basic structure:

o a central __________ atom o an __________ group (NH2) on one side o a _____________ group (COOH) on another side o a single ______________ atom on another o a _________________________ (side chain) on the other side

Types of amino acids There are well over 100 amino acids in our cells, however, only

_______ of these are used to ________________________ in the human body

Cells can make _______ of these, but the other _____ (essential amino acids) must be obtained from __________

It is the ___________________________ that differs between each amino acid The R-group determines the chemical nature of the amino acid in regards to it being:

o ___________ or ________________ (hydrophobic or hydrophilic) o _______________ or __________________

The chemical nature of amino acids determines how they ______________ with each other to form the proteins overall unique three-dimensional shape



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Condensation polymerisation Amino acids are joined by in a process known as

_____________________________________ In this reaction, the ________ from one amino acid’s carboxyl

group reacts with a _______ from another amino acid’s amino group, releasing a ____________ molecule

A _____________ bond is formed between the N and C Two amino acids joined by a peptide bond is a

_________________ A chain of amino acids joined by peptide bonds is known as

a ____________________ chain Protein structure Proteins are large ______________________ that can contain thousands of amino acids and may contain _______ or

_______________ polypeptide chains These polypeptide chains are _____________ and organised into specific shapes that are vital to the correct functioning

of the protein A single _______________ to one amino acid can alter its _____________, and consequently the _____________ of the protein There are four different levels of organisation when describing protein structure:

1. _________________ structure 2. _________________ structure 3. _________________ structure 4. _________________ structure

Primary structure What is primary structure?

It is ____________ to each protein Linear sequences of 2 to 9 amino acids are known as peptides The linear sequence of amino acids:

o provides information on how proteins will ___________ o can be compared to identify what changes to the sequence render the protein

_________________________ o can be compared between proteins to determine the ______________________ history of a protein



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Secondary structure The next step in the formation of a functional protein is the

______________ or _____________ of the polypeptide chain This results in the formation of _________________ structures There are three types of secondary structures:

o _______________________ – hydrogen bonds form to make tight coils producing a helical shape

o _________________________________ - hydrogen bonds form to make flattened sheets causing the chains to fold back on each other

o ______________________ – other parts of the polypeptide chain that do not fold into defined arrangements

Tertiary structure Polypeptide chains continue to fold further, forming more stable ______________ or ______________ three-dimensional

shapes This is known as the tertiary structure The tertiary structure occurs due to

different types of bonds between the _________________:

o ________________ bonding (hydrogen bridge)

o ________________ bonding o __________________ bonding

(disulfide bridge) o _____________________ interactions

The three-dimensional structure of a protein is critical to its function

The tertiary structure is the final structure for some proteins

Quaternary structure A quaternary structure is formed when ______ or more polypeptide chains

join to create a single functional protein The polypeptides may be identical or different Some proteins will not become ___________ until they achieve their quaternary

structure Haemoglobin and antibodies are examples of a proteins with a quaternary

structure



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Protein classification Proteins can be classified as one of two types based on their shape:

Fibrous Globular

Shape Long and _______________ Spherical or ________________ Role ________________ (strength and support) ___________________ (catalytic, transport

etc.) Solubility Generally _______________ in water Generally ______________ in water Structure __________________ amino acid sequence __________________ amino acid sequence Stability _________ sensitive to heat, pH etc. ____________ sensitive to heat, pH etc. Examples

Collagen, keratin, actin, myosin, fibrin, elastin

Enzymes, hormones, antibodies, haemoglobin

Factors affecting protein function The environment surrounding proteins plays an important role in maintaining the ________________ and ______________

of the protein Usually the loss of function of the protein is due to __________________ (unfolding) of the protein The factors in the environment affecting protein structure and function include:

o ________________________ o _______ o concentration of ions or molecules that act as _________________

Denaturation and renaturation A protein is said to have denatured when the hydrogen bonds, disulfide bridges,

hydrophobic interactions that create the tertiary structure of the protein are __________ and the __________ of the protein is _____________

If a protein becomes ___________ denatured, the reaction is non-reversible and the protein remains non-functional

However, a protein that is _______________ denatured may be able to fold again (renature) when the appropriate conditions are present

The effect of temperature and pH on proteins Proteins can be denatured at ________ temperatures due to the breaking of bonds Hydrogen bond can break at temperatures above ___________ The optimal temperature for proteins varies with the organism and its environment Most proteins have a specific _______ range in which their function is optimal, but this range can be quite different

for each specific protein If the pH reaches too far ___________ or falls too far ____________ the optimal pH, then the tertiary structure is affected



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The effect of cofactors on protein function Some proteins require ______________________ chemical compounds known as cofactors for their biological function The presence and concentration of cofactors such as salts, specific elements such as iron, magnesium and calcium

ions, or organic molecules such as vitamins can play a significant role in the _____________ and _________________ of proteins

o E.g. magnesium is essential for chlorophyll function in plants and a lack of magnesium ions causes the yellowing of leaves due to the plant’s inability to synthesise chlorophyll.



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2.2 – FUNCTIONAL DIVERSITY OF PROTEINS

Various protein functions Virtually every _______________ of a living organism depends on proteins Each protein has a different function, which play a vital role in the regulation, functioning and maintenance of both

individual cells and entire organisms The specific _____________________________________ of each protein enables it to carry out its function This diversity can be explained by the numerous ways amino acids can be put together to form various polypeptide

chains



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Structural Transport Hormones Function: Provides support, strength and protection

Function: Carry molecules from one location to another or across cell membranes

Function: Signalling between cells; stimulation or inhibition

Examples: Collagen and elastin is used to

make tendons and ligaments Keratin forms hair and nails

Examples: Haemoglobin transports oxygen

around the body Transport proteins move

substances across membranes

Examples: Insulin and glucagon regulate

blood sugar levels Adrenaline acts on specific target

tissues in response to ‘fight or flight’

Cell surface receptors Neurotransmitters Motility Function: Receiving signals such as hormones and growth factors, transmission of nerve impulse

Function: Signalling between nerve cells

Function: Allows movement of cells and their organelles

Examples: Thyroxin receptors bind thyroxin

to trigger an increase in metabolism

Receptors allow for the binding of neurotransmitters to transmit nerve impulses

Examples: Endorphins reduce pain and

stress by binding to nerve cell receptors

Acetylcholine triggers muscles to contract

Examples: Contractile proteins are

responsible for the motion of cilia and flagella

Actin and myosin work together to move muscles

Defensive Enzyme Toxins Function: Combating against foreign agents such as bacteria or viruses

Function: Catalyse biochemical reactions

Function: Chemical for defence and to aid the capture of food

Examples: Antibodies produced by

lymphocytes combat bacteria and viruses

Complement proteins attack bacteria punching holes in them

Examples: Amylase breaks down

carbohydrates in food ATPase produces ATP required

for cellular energetics

Examples: Snake venom contains many

proteins that can paralyse and digest prey

The castor oil plant produces ricin, a deadly toxin



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2.3 – THE NATURE OF THE PROTEOME

The proteome What is the proteome?

The proteome is a direct result of a cell or organism’s _____________ (complete set of

genetic instructions) It is estimated that there are over _______________ different proteins in the human

proteome The proteome varies between cell __________, ____________________ stage and

_______________________ conditions Although a cell may contain the entire genome, only specific genes will be

_______________ (switched on) at any given time which ensures a cell produces ________ the proteins required for the specific functions it carries out

o E.g. all cells contain the gene for producing insulin, however, only in a pancreatic cell is this gene expressed Proteomics What is proteomics?

This is performed by using mathematical calculations and X-ray

analysis of proteins to help determine their different levels of structure Understanding proteomics is essential as it is proteins that carry out

most of the activities of the cell By knowing __________ and ____________ proteins are produced in an

organism, as well as how proteins ______________, we can better understand the functioning of cells and organisms One of the ways to determine changes in the proteome is by comparing the proteomes of cells under different

_____________________ o E.g. by comparing the protein expression of a diseased cell and a healthy cell, the proteins affected by the

disease can be determined Applications of proteomics When the final structure of the protein is understood, this information can be

applied in a variety of ways: o ___________________ can be made to stop pathogenic microorganisms

causing disease o Insect proteins can be identified as targets for new ________________ o Development of new _________________ which protect against allergens o Development of ___________________________ which target specific

proteins involved the prevention of disease and the growth of cancers o Analysis of changes in blood proteins as a tool in early diagnosis of

_________________



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Topic 2 Key Glossary Terms Define each of the following terms in a glossary in your workbook. Also available on quizlet.com

alpha helixes globular protein proteomics amino acids monomer quaternary structure beta-pleated sheets peptide bond random coils cofactor peptides rational drugs condensation polymerisation polymer renature denature polypeptide chain R-group dipeptide primary structure secondary structure disulfide bridge protein tertiary structure fibrous protein proteome

Topic 2 Notes

Key Questions Revision Notes:



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Unit 3 Key Glossary Terms and Definitions A abscisic acid: A plant hormone that inhibits cell growth, helps close stomata and promote dormancy. acetyl coenzyme A: The coenzyme formed when pyruvate first enters into the mitochondria. activation energy: The energy that is required to start a biochemical reaction. active artificial immunity: The type of immunity that involves the activation of B and T lymphocytes through exposure to a vaccine; long lived immunity. active natural immunity: The type of immunity that involves the activation of B and T lymphocytes through direct exposure to a foreign antigen; long lived immunity. active site: The specific site of the enzyme that binds the substrate and where catalysis occurs active transport: The movement of particles against a concentration gradient from an area of high concentration to an area of low concentration; this process requires energy. adaptive immunity: An immune response that is specific to a particular antigen. adenine: The purine nitrogenous base that pairs with thymine in DNA and uracil in RNA. adenosine diphosphate (ADP): The low-energy molecule that can be converted to ATP; contains two phosphates. adenosine triphosphate (ATP): An energy-carrying biological molecule, which, when broken down by donating a phosphate, drives energy-requiring cellular activities. aerobic respiration: The breakdown of glucose in the cell using oxygen, the energy from which is used to synthesise 30-32 ATP; comprised of glycolysis, the Krebs cycle and electron transport chain; AIDS (acquired immune deficiency syndrome): A syndrome in which helper T lymphocytes are destroyed and are in sufficiently low numbers that the immune response to infection is impaired; can result from HIV. allergen: An antigen that elicits an allergic reaction. allergic reaction: The rapid and vigorous overreaction of the immune system to antigens called allergens; involves the production of IgE by B lymphocytes and the release of histamines by mast cells; also referred to as an allergy. allergy: The rapid and vigorous overreaction of the immune system to antigens called allergens; involves the production of IgE by B lymphocytes and the release of histamines by mast cells; also referred to as an allergy. alpha helixes: A coiled secondary protein structure within a polypeptide chain; stabilised by hydrogen bonds between adjacent amino acids. amino acid derived hormone: Small signalling molecules derived from the amino acids tyrosine and tryptophan; e.g. thyroxine and dopamine.

amino acids: The monomer of polypeptides; contain an amine group and a carboxyl group at either ends. amphipathic: A type of molecule that has both hydrophilic and hydrophobic regions; e.g. a phospholipid, aquaporin. anabolic reaction: biochemical reaction in which larger molecules are made from smaller molecules; requires input of energy to build new bonds anaerobic respiration: Respiration in the absence of oxygen; comprised of glycolysis and fermentation; produces 2 ATP, lactic acid in animals and ethanol and carbon dioxide in plants and fungi. antibody: Proteins produced by plasma B lymphocytes that are highly selective for, and bind to, specific antigen molecules; also known as immunoglobulin. antibody-mediated immunity: The specific line of immunity (third line of defence) that involves the production of B lymphocytes and antibody; also known as humoral immunity. anticodon: The three nucleotides on a transfer RNA (tRNA) molecule that join to the codons on mRNA by complementary base pairing during the process of translation. antigen: A molecular substance capable of triggering an immune response; can be labelled as self or non-self. antigen binding site: The site on an antibody or T cell receptor molecule that binds specific antigen. antigenic variation: The mechanism of changing surface antigen, usually to avoid detection or an immune attack. antigen presenting cell (APC): A cell that uses MHC-II (HLA-II) on its surface to present foreign antigens to helper T lymphocytes to elicit an adaptive immune response; includes macrophages, dendritic cells and B lymphocytes. antihistamine: A drug that blocks the effects of histamines released by the body during allergic reactions; binds to target cells histamine receptors. antiparallel: Running in opposite directions, with one strand in the 5' to 3' direction and the other in the 3' to 5' direction (referring to the two strands in DNA molecules). antiretroviral drug: A drug that specifically inhibits replication of retroviruses. apoptosis: Regulated and programmed cell death. apoptotic bodies: Cell fragments produced as a result of apoptosis. aquaporin: A transport protein in the plasma membrane of plant and animal cells that specifically moves water across the membrane. ATP synthase: The enzyme responsible for synthesising ATP from ADP and Pi. autocrine signalling: A type of chemical signalling in which the signalling molecule is received by the same cell or cell type that secretes it.



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